From plain110 at gmail.com Sat Nov 1 00:16:17 2008
From: plain110 at gmail.com (=?GB2312?B?xr3Utg==?=)
Date: Fri, 31 Oct 2008 16:16:17 -0700
Subject: [Pw_forum] problem of cutoff convergence
Message-ID: <2c39f6770810311616s2638923fp4f14e7eb4f2122b5@mail.gmail.com>
Hi,
I met a problem with cutoff convergence when I ran the Si nanowire self
consistent calculation to get the lda band gap.
I found a big jump 0.3-0.4ev of band gap at 45Ry. Before and after this
point, the band gap curve is flat.
(HOMO does not change much, but lumo had a big jump. )
And the position of this jump will shift with different structure (before
I relaxed the structure, this big jump was at 30Ry.)
I used Si.pz-vbc.UPF, H.pz-vbc.UPF, poseudopotential to run this
calculation.
I found similar thing when I calculate silane band gap. The jump of 0.4ev
happens at 60-65Ry. And I used the same poseudopotential to calculate.
So what can be the reason for this big jump in band gap with respect to
cutoff?
thank you very much!
yuan ping
university of california, Davis
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From plain110 at gmail.com Sat Nov 1 01:56:49 2008
From: plain110 at gmail.com (=?GB2312?B?xr3Utg==?=)
Date: Fri, 31 Oct 2008 17:56:49 -0700
Subject: [Pw_forum] problem of cutoff convergence
In-Reply-To: <2c39f6770810311616s2638923fp4f14e7eb4f2122b5@mail.gmail.com>
References: <2c39f6770810311616s2638923fp4f14e7eb4f2122b5@mail.gmail.com>
Message-ID: <2c39f6770810311756h21a68dectf244c4cb58621984@mail.gmail.com>
I forgot to attach the bandgap vs cutoff plot. We can see the big jump
clearly from this graph.
yuan ping
university of
california, Davis
2008/10/31 ?? <plain110 at gmail.com>
> Hi,
> I met a problem with cutoff convergence when I ran the Si nanowire self
> consistent calculation to get the lda band gap.
> I found a big jump 0.3-0.4ev of band gap at 45Ry. Before and after this
> point, the band gap curve is flat.
> (HOMO does not change much, but lumo had a big jump. )
> And the position of this jump will shift with different structure (before
> I relaxed the structure, this big jump was at 30Ry.)
> I used Si.pz-vbc.UPF, H.pz-vbc.UPF, poseudopotential to run this
> calculation.
> I found similar thing when I calculate silane band gap. The jump of 0.4ev
> happens at 60-65Ry. And I used the same poseudopotential to calculate.
> So what can be the reason for this big jump in band gap with respect to
> cutoff?
> thank you very much!
>
> yuan ping
>
> university of california, Davis
>
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From paulatto at sissa.it Sat Nov 1 02:42:06 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Sat, 1 Nov 2008 02:42:06 +0100 (CET)
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <490B39BC.2080306@cam.ac.uk>
References: <490B39BC.2080306@cam.ac.uk>
Message-ID: <28392.79.1.61.189.1225503726.squirrel@webmail.sissa.it>
On Ven, Ottobre 31, 2008 18:00, David Tompsett wrote:
> cut
If you're using xlf compiler it may be a problem with some dos-style line
terminators. Try to "cat -v" the input file which is causing troubles, if
you get some "^M" at the end of the lines, that's the cause.
cheers
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
----------------------------------------------------------------
SISSA Webmail https://webmail.sissa.it/
Powered by SquirrelMail http://www.squirrelmail.org/
From wangqj1 at 126.com Sat Nov 1 03:43:25 2008
From: wangqj1 at 126.com (wangqj1)
Date: Sat, 1 Nov 2008 10:43:25 +0800 (CST)
Subject: [Pw_forum] u caculate
Message-ID: <22323454.52281225507405619.JavaMail.coremail@bj126app81.126.com>
Dear Matteo
In the example of caculate the value of U,after I extract the occupatin numbers ,I execute the ucalc_sc1 file ,and gave these errors :
/tmp/ifortLWE1zB.o(.text+0x742e): In function `invmat_':
: undefined reference to `dgetrf_'
/tmp/ifortLWE1zB.o(.text+0x744e): In function `invmat_':
: undefined reference to `dgetri_'
ucalc_sc1.j: line 32: ./r.x: don't have that file or list
grep: Umat.out: don't have that file or list
.......................
I want to know what's wrong with it and how I should modify it .Thank you !
Beat Wishes
yours sincerely
Qianjin Wang
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From matteo at umn.edu Sat Nov 1 04:06:38 2008
From: matteo at umn.edu (Matteo Cococcioni)
Date: Fri, 31 Oct 2008 22:06:38 -0500
Subject: [Pw_forum] u caculate
In-Reply-To: <22323454.52281225507405619.JavaMail.coremail@bj126app81.126.com>
References: <22323454.52281225507405619.JavaMail.coremail@bj126app81.126.com>
Message-ID: <490BC7BE.2060907@umn.edu>
Dear Qianjin
you need to recompile the codes in that directory putting the correct
path to lapack libraries.
I think this information is contained inside a file called
comp_resp_mat.j. This was constructed to
compile on a specific machine and unfortunately is not general enough to
work on any machine.
Matteo
wangqj1 wrote:
> Dear Matteo
> In the example of caculate the value of U,after I extract the
> occupatin numbers ,I execute the ucalc_sc1 file ,and gave these errors :
> /tmp/ifortLWE1zB.o(.text+0x742e): In function `invmat_':
> : undefined reference to `dgetrf_'
> /tmp/ifortLWE1zB.o(.text+0x744e): In function `invmat_':
> : undefined reference to `dgetri_'
> ucalc_sc1.j: line 32: ./r.x: don't have that file or list
> grep: Umat.out: don't have that file or list
> .......................
> I want to know what's wrong with it and how I should modify it .Thank
> you !
> Beat Wishes
> yours sincerely
> Qianjin Wang
>
>
> ????????10????,???????????? <http://www.yeah.net>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
From sks.jnc at gmail.com Sat Nov 1 05:51:23 2008
From: sks.jnc at gmail.com (S. K. S.)
Date: Sat, 1 Nov 2008 10:21:23 +0530
Subject: [Pw_forum] problem of cutoff convergence
In-Reply-To: <2c39f6770810311616s2638923fp4f14e7eb4f2122b5@mail.gmail.com>
References: <2c39f6770810311616s2638923fp4f14e7eb4f2122b5@mail.gmail.com>
Message-ID: <d5eefb3d0810312151t6ed50a79r6192ef599d4d2b1e@mail.gmail.com>
Dear Yuan ping,
I met more surprising problem even in the case of
a bulk system. There for almost all the energy cut-offs used
(40 Ry to 120 Ry in steps of 10 Ry)
the values for the pressure is reasonably well converged, except just a
single point of energy cut-off (~70 Ry).
I think, it can be a problem associated with the particular
pseudopotential used.
It is really an interesting experience to check the convergence
of some physical properties as a function of energy cut-offs.
I guess, many others in this forum also might have already come across
similar kind of jump, what you have found. Expecting
comments from them.
regards,
SKS
R&D
JNCASR
Bangalore
From bipulrr at gmail.com Sat Nov 1 06:39:07 2008
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Sat, 1 Nov 2008 11:09:07 +0530
Subject: [Pw_forum] Projected density of states of phonon
Message-ID: <3a749910810312239g3594c34dl6b26b76ce7c30f7f@mail.gmail.com>
Hello Soyalp,
I am calculating phonon of ScAs and ScSb using PWSCF, I read a paper
Solid State Commun. 147 (2008) 198
There the author mentioned about projected density of states of
phonon. So can anybody tell me how to find that? Means what option we
have to set in input file to obtain the projected density of states of
phonon.
It will be helpful for me
thanks
--
Bipul Rakshit
PhD Student,
Barkatullah University,
Bhopal 462026,
MP, India
From bipulrr at gmail.com Sat Nov 1 10:19:34 2008
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Sat, 1 Nov 2008 14:49:34 +0530
Subject: [Pw_forum] Projected density of states of phonon
In-Reply-To: <3a749910810312239g3594c34dl6b26b76ce7c30f7f@mail.gmail.com>
References: <3a749910810312239g3594c34dl6b26b76ce7c30f7f@mail.gmail.com>
Message-ID: <3a749910811010219o26ca43f1nc7eb08fcf3665ea6@mail.gmail.com>
Hello Pwscf users,
I am calculating phonon of ScAs and ScSb using PWSCF, I read a paper
Solid State Commun. 147 (2008) 198
There the author mentioned about projected density of states of
phonon. So can anybody tell me how to find that? Means what option we
have to set in input file to obtain the projected density of states of
phonon.
It will be helpful for me
thanks
--
Bipul Rakshit
PhD Student,
Barkatullah University,
Bhopal 462026,
MP, India
From wangqj1 at 126.com Sat Nov 1 09:55:59 2008
From: wangqj1 at 126.com (wangqj1)
Date: Sat, 1 Nov 2008 16:55:59 +0800 (CST)
Subject: [Pw_forum] about u
Message-ID: <2682107.349061225529759561.JavaMail.coremail@bj126app28.126.com>
Dear Matteo
According to your advice I correct the path to lapack libraries in comp_resp_mat.j file .It as follows:
ifort -o r.x resp_mat.f90 -L/opt/intel/mkl/8.0.2 b/32 -lmkl_ia32 -lguide -lpthread
#
But it still turns up the same error .
In your examples the comp_resp_mat.j file as follows:
ifort -o r.x resp_mat.f90 -L/soft/local/intel/mkl72/lib/64/ -lmkl_lapack \
-lmkl_ipf -lguide -lpthread
# -lmkl_ia32 -lguide -lpthread
Can you give me some advice ? Thank you very much !
Best Wishes
yours sincerely
Qianjin Wang
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From dat36 at cam.ac.uk Sat Nov 1 12:56:55 2008
From: dat36 at cam.ac.uk (D.A. Tompsett)
Date: 01 Nov 2008 11:56:55 +0000
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <c92002fa0810311309u652cbcc2ob4ec433c35bae3e6@mail.gmail.com>
References: <490B39BC.2080306@cam.ac.uk>
<c92002fa0810311309u652cbcc2ob4ec433c35bae3e6@mail.gmail.com>
Message-ID: <Prayer.1.3.1.0811011156550.27996@hermes-1.csi.cam.ac.uk>
Dear Ian and All,
below is the input file. It is from directory example01 and every
calculation in it fails with the same message: read_namelists : error
Please let me know if you can see what is wrong.
Thanks,
David.
Input:
#!/bin/sh
# run from directory where this script is
cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
EXAMPLE_DIR=`pwd`
# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi
# function to test the exit status of a job
. ../check_failure.sh
$ECHO
$ECHO "$EXAMPLE_DIR : starting"
$ECHO
$ECHO "This example shows how to use pw.x to calculate the total energy and"
$ECHO "the band structure of four simple systems: Si, Al, Cu, Ni."
# set the needed environment variables
. ../environment_variables
# required executables and pseudopotentials
BIN_LIST="pw.x bands.x"
PSEUDO_LIST="Si.vbc.UPF Al.vbc.UPF Cu.pz-d-rrkjus.UPF NiUS.RRKJ3.UPF"
$ECHO
$ECHO " executables directory: $BIN_DIR"
$ECHO " pseudo directory: $PSEUDO_DIR"
$ECHO " temporary directory: $TMP_DIR"
$ECHO " checking that needed directories and files exist...\c"
# check for directories
for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
if test ! -d $DIR ; then
$ECHO
$ECHO "ERROR: $DIR not existent or not a directory"
$ECHO "Aborting"
exit 1
fi
done
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
if test ! -d $DIR ; then
mkdir $DIR
fi
done
cd $EXAMPLE_DIR/results
# check for executables
for FILE in $BIN_LIST ; do
if test ! -x $BIN_DIR/$FILE ; then
$ECHO
$ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
$ECHO "Aborting"
exit 1
fi
done
# check for pseudopotentials
for FILE in $PSEUDO_LIST ; do
if test ! -r $PSEUDO_DIR/$FILE ; then
$ECHO
$ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
$ECHO "Aborting"
exit 1
fi
done
$ECHO " done"
# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
BANDS_COMMAND="$PARA_PREFIX $BIN_DIR/bands.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO " running bands.x as: $BANDS_COMMAND"
$ECHO
for diago in david cg ; do
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
# self-consistent calculation
cat > si.scf.$diago.in << EOF
&control
calculation = 'scf'
restart_mode='from_scratch',
prefix='silicon',
tstress = .true.
tprnfor = .true.
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1,
ecutwfc =18.0,
/
&electrons
diagonalization='$diago'
mixing_mode = 'plain'
mixing_beta = 0.7
conv_thr = 1.0d-8
/
ATOMIC_SPECIES
Si 28.086 Si.vbc.UPF
ATOMIC_POSITIONS
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS
10
0.1250000 0.1250000 0.1250000 1.00
0.1250000 0.1250000 0.3750000 3.00
0.1250000 0.1250000 0.6250000 3.00
0.1250000 0.1250000 0.8750000 3.00
0.1250000 0.3750000 0.3750000 3.00
0.1250000 0.3750000 0.6250000 6.00
0.1250000 0.3750000 0.8750000 6.00
0.1250000 0.6250000 0.6250000 3.00
0.3750000 0.3750000 0.3750000 1.00
0.3750000 0.3750000 0.6250000 3.00
EOF
$ECHO " running the scf calculation for Si...\c"
$PW_COMMAND < si.scf.$diago.in > si.scf.$diago.out
check_failure $?
$ECHO " done"
# band structure calculation along delta, sigma and lambda lines
cat > si.band.$diago.in << EOF
&control
calculation='bands'
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
prefix='silicon'
/
&system
ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1,
ecutwfc =18.0, nbnd = 8,
/
&electrons
diagonalization='$diago'
/
ATOMIC_SPECIES
Si 28.086 Si.vbc.UPF
ATOMIC_POSITIONS
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS
28
0.0 0.0 0.0 1.0
0.0 0.0 0.1 1.0
0.0 0.0 0.2 1.0
0.0 0.0 0.3 1.0
0.0 0.0 0.4 1.0
0.0 0.0 0.5 1.0
0.0 0.0 0.6 1.0
0.0 0.0 0.7 1.0
0.0 0.0 0.8 1.0
0.0 0.0 0.9 1.0
0.0 0.0 1.0 1.0
0.0 0.0 0.0 1.0
0.0 0.1 0.1 1.0
0.0 0.2 0.2 1.0
0.0 0.3 0.3 1.0
0.0 0.4 0.4 1.0
0.0 0.5 0.5 1.0
0.0 0.6 0.6 1.0
0.0 0.7 0.7 1.0
0.0 0.8 0.8 1.0
0.0 0.9 0.9 1.0
0.0 1.0 1.0 1.0
0.0 0.0 0.0 1.0
0.1 0.1 0.1 1.0
0.2 0.2 0.2 1.0
0.3 0.3 0.3 1.0
0.4 0.4 0.4 1.0
0.5 0.5 0.5 1.0
EOF
$ECHO " running the band-structure calculation for Si...\c"
$PW_COMMAND < si.band.$diago.in > si.band.$diago.out
check_failure $?
$ECHO " done"
cat > si.bands.in << EOF
&inputpp
prefix='silicon',
outdir='$TMP_DIR'
filband='si.band'
lsym=.true.,
/
EOF
if test "`echo $diago`" = "david";
then
$ECHO " running the symmetry analysis for Si bands...\c"
$BANDS_COMMAND < si.bands.in > si.bands.out
$ECHO " done"
fi
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
# self-consistent calculation
cat > al.scf.$diago.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
prefix='al'
tprnfor = .true.
tstress = .true.
/
&system
ibrav= 2, celldm(1) =7.50, nat= 1, ntyp= 1, ecutwfc =15.0,
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05
/
&electrons
diagonalization='$diago'
mixing_beta = 0.7
/
ATOMIC_SPECIES
Al 26.98 Al.vbc.UPF
ATOMIC_POSITIONS
Al 0.00 0.00 0.00
K_POINTS
60
0.0625000 0.0625000 0.0625000 1.00
0.0625000 0.0625000 0.1875000 3.00
0.0625000 0.0625000 0.3125000 3.00
0.0625000 0.0625000 0.4375000 3.00
0.0625000 0.0625000 0.5625000 3.00
0.0625000 0.0625000 0.6875000 3.00
0.0625000 0.0625000 0.8125000 3.00
0.0625000 0.0625000 0.9375000 3.00
0.0625000 0.1875000 0.1875000 3.00
0.0625000 0.1875000 0.3125000 6.00
0.0625000 0.1875000 0.4375000 6.00
0.0625000 0.1875000 0.5625000 6.00
0.0625000 0.1875000 0.6875000 6.00
0.0625000 0.1875000 0.8125000 6.00
0.0625000 0.1875000 0.9375000 6.00
0.0625000 0.3125000 0.3125000 3.00
0.0625000 0.3125000 0.4375000 6.00
0.0625000 0.3125000 0.5625000 6.00
0.0625000 0.3125000 0.6875000 6.00
0.0625000 0.3125000 0.8125000 6.00
0.0625000 0.3125000 0.9375000 6.00
0.0625000 0.4375000 0.4375000 3.00
0.0625000 0.4375000 0.5625000 6.00
0.0625000 0.4375000 0.6875000 6.00
0.0625000 0.4375000 0.8125000 6.00
0.0625000 0.4375000 0.9375000 6.00
0.0625000 0.5625000 0.5625000 3.00
0.0625000 0.5625000 0.6875000 6.00
0.0625000 0.5625000 0.8125000 6.00
0.0625000 0.6875000 0.6875000 3.00
0.0625000 0.6875000 0.8125000 6.00
0.0625000 0.8125000 0.8125000 3.00
0.1875000 0.1875000 0.1875000 1.00
0.1875000 0.1875000 0.3125000 3.00
0.1875000 0.1875000 0.4375000 3.00
0.1875000 0.1875000 0.5625000 3.00
0.1875000 0.1875000 0.6875000 3.00
0.1875000 0.1875000 0.8125000 3.00
0.1875000 0.3125000 0.3125000 3.00
0.1875000 0.3125000 0.4375000 6.00
0.1875000 0.3125000 0.5625000 6.00
0.1875000 0.3125000 0.6875000 6.00
0.1875000 0.3125000 0.8125000 6.00
0.1875000 0.4375000 0.4375000 3.00
0.1875000 0.4375000 0.5625000 6.00
0.1875000 0.4375000 0.6875000 6.00
0.1875000 0.4375000 0.8125000 6.00
0.1875000 0.5625000 0.5625000 3.00
0.1875000 0.5625000 0.6875000 6.00
0.1875000 0.6875000 0.6875000 3.00
0.3125000 0.3125000 0.3125000 1.00
0.3125000 0.3125000 0.4375000 3.00
0.3125000 0.3125000 0.5625000 3.00
0.3125000 0.3125000 0.6875000 3.00
0.3125000 0.4375000 0.4375000 3.00
0.3125000 0.4375000 0.5625000 6.00
0.3125000 0.4375000 0.6875000 6.00
0.3125000 0.5625000 0.5625000 3.00
0.4375000 0.4375000 0.4375000 1.00
0.4375000 0.4375000 0.5625000 3.00
EOF
$ECHO " running the scf calculation for Al...\c"
$PW_COMMAND < al.scf.$diago.in > al.scf.$diago.out
check_failure $?
$ECHO " done"
# band structure calculation along delta, sigma and lambda lines
cat > al.band.$diago.in << EOF
&control
calculation='bands'
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
prefix='al'
/
&system
ibrav= 2, celldm(1) =7.50, nat= 1, ntyp= 1,
ecutwfc =15.0, nbnd = 8
/
&electrons
diagonalization='$diago'
/
ATOMIC_SPECIES
Al 26.98 Al.vbc.UPF
ATOMIC_POSITIONS
Al 0.00 0.00 0.00
K_POINTS
28
0.0 0.0 0.0 1.0
0.0 0.0 0.1 1.0
0.0 0.0 0.2 1.0
0.0 0.0 0.3 1.0
0.0 0.0 0.4 1.0
0.0 0.0 0.5 1.0
0.0 0.0 0.6 1.0
0.0 0.0 0.7 1.0
0.0 0.0 0.8 1.0
0.0 0.0 0.9 1.0
0.0 0.0 1.0 1.0
0.0 0.0 0.0 1.0
0.0 0.1 0.1 1.0
0.0 0.2 0.2 1.0
0.0 0.3 0.3 1.0
0.0 0.4 0.4 1.0
0.0 0.5 0.5 1.0
0.0 0.6 0.6 1.0
0.0 0.7 0.7 1.0
0.0 0.8 0.8 1.0
0.0 0.9 0.9 1.0
0.0 1.0 1.0 1.0
0.0 0.0 0.0 1.0
0.1 0.1 0.1 1.0
0.2 0.2 0.2 1.0
0.3 0.3 0.3 1.0
0.4 0.4 0.4 1.0
0.5 0.5 0.5 1.0
EOF
$ECHO " running the band-structure calculation for Al...\c"
$PW_COMMAND < al.band.$diago.in > al.band.$diago.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
# self-consistent calculation
cat > cu.scf.$diago.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
prefix='cu'
tstress = .true.
tprnfor = .true.
/
&system
ibrav = 2, celldm(1) =6.73, nat= 1, ntyp= 1,
ecutwfc = 25.0, ecutrho = 300.0
occupations='smearing', smearing='gaussian', degauss=0.02
/
&electrons
diagonalization='$diago'
conv_thr = 1.0e-8
mixing_beta = 0.7
/
ATOMIC_SPECIES
Cu 63.55 Cu.pz-d-rrkjus.UPF
ATOMIC_POSITIONS
Cu 0.0 0.0 0.0
K_POINTS (automatic)
8 8 8 0 0 0
EOF
$ECHO " running the scf calculation for Cu...\c"
$PW_COMMAND < cu.scf.$diago.in > cu.scf.$diago.out
check_failure $?
$ECHO " done"
# band structure calculation along delta, sigma and lambda lines
cat > cu.band.$diago.in << EOF
&control
calculation='bands'
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
prefix='cu'
/
&system
ibrav = 2, celldm(1) =6.73, nat= 1, ntyp= 1,
ecutwfc = 25.0, ecutrho = 300.0, nbnd = 8
/
&electrons
diagonalization='$diago'
/
ATOMIC_SPECIES
Cu 63.55 Cu.pz-d-rrkjus.UPF
ATOMIC_POSITIONS
Cu 0.0 0.0 0.0
K_POINTS
28
0.0 0.0 0.0 1.0
0.0 0.0 0.1 1.0
0.0 0.0 0.2 1.0
0.0 0.0 0.3 1.0
0.0 0.0 0.4 1.0
0.0 0.0 0.5 1.0
0.0 0.0 0.6 1.0
0.0 0.0 0.7 1.0
0.0 0.0 0.8 1.0
0.0 0.0 0.9 1.0
0.0 0.0 1.0 1.0
0.0 0.0 0.0 1.0
0.0 0.1 0.1 1.0
0.0 0.2 0.2 1.0
0.0 0.3 0.3 1.0
0.0 0.4 0.4 1.0
0.0 0.5 0.5 1.0
0.0 0.6 0.6 1.0
0.0 0.7 0.7 1.0
0.0 0.8 0.8 1.0
0.0 0.9 0.9 1.0
0.0 1.0 1.0 1.0
0.0 0.0 0.0 1.0
0.1 0.1 0.1 1.0
0.2 0.2 0.2 1.0
0.3 0.3 0.3 1.0
0.4 0.4 0.4 1.0
0.5 0.5 0.5 1.0
EOF
$ECHO " running the band-structure calculation for Cu...\c"
$PW_COMMAND < cu.band.$diago.in > cu.band.$diago.out
check_failure $?
$ECHO " done"
cat > cu.bands.in << EOF
&inputpp
prefix='cu',
outdir='$TMP_DIR'
filband='cu.band'
lsym=.true.,
/
EOF
if test "`echo $diago`" = "david";
then
$ECHO " running the symmetry analysis for Cu bands...\c"
$BANDS_COMMAND < cu.bands.in > cu.bands.out
$ECHO " done"
fi
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
# self-consistent calculation
cat > ni.scf.$diago.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
prefix='ni'
tprnfor = .true.,
tstress = .true.
/
&system
ibrav=2, celldm(1) =6.48, nat=1, ntyp=1,
nspin = 2, starting_magnetization(1)=0.7,
ecutwfc = 24.0, ecutrho = 288.0,
occupations='smearing', smearing='methfessel-paxton', degauss=0.02
/
&electrons
diagonalization='$diago'
conv_thr = 1.0e-8
mixing_beta = 0.7
/
ATOMIC_SPECIES
Ni 58.69 NiUS.RRKJ3.UPF
ATOMIC_POSITIONS
Ni 0.0 0.0 0.0
K_POINTS
60
0.0625000 0.0625000 0.0625000 1.00
0.0625000 0.0625000 0.1875000 3.00
0.0625000 0.0625000 0.3125000 3.00
0.0625000 0.0625000 0.4375000 3.00
0.0625000 0.0625000 0.5625000 3.00
0.0625000 0.0625000 0.6875000 3.00
0.0625000 0.0625000 0.8125000 3.00
0.0625000 0.0625000 0.9375000 3.00
0.0625000 0.1875000 0.1875000 3.00
0.0625000 0.1875000 0.3125000 6.00
0.0625000 0.1875000 0.4375000 6.00
0.0625000 0.1875000 0.5625000 6.00
0.0625000 0.1875000 0.6875000 6.00
0.0625000 0.1875000 0.8125000 6.00
0.0625000 0.1875000 0.9375000 6.00
0.0625000 0.3125000 0.3125000 3.00
0.0625000 0.3125000 0.4375000 6.00
0.0625000 0.3125000 0.5625000 6.00
0.0625000 0.3125000 0.6875000 6.00
0.0625000 0.3125000 0.8125000 6.00
0.0625000 0.3125000 0.9375000 6.00
0.0625000 0.4375000 0.4375000 3.00
0.0625000 0.4375000 0.5625000 6.00
0.0625000 0.4375000 0.6875000 6.00
0.0625000 0.4375000 0.8125000 6.00
0.0625000 0.4375000 0.9375000 6.00
0.0625000 0.5625000 0.5625000 3.00
0.0625000 0.5625000 0.6875000 6.00
0.0625000 0.5625000 0.8125000 6.00
0.0625000 0.6875000 0.6875000 3.00
0.0625000 0.6875000 0.8125000 6.00
0.0625000 0.8125000 0.8125000 3.00
0.1875000 0.1875000 0.1875000 1.00
0.1875000 0.1875000 0.3125000 3.00
0.1875000 0.1875000 0.4375000 3.00
0.1875000 0.1875000 0.5625000 3.00
0.1875000 0.1875000 0.6875000 3.00
0.1875000 0.1875000 0.8125000 3.00
0.1875000 0.3125000 0.3125000 3.00
0.1875000 0.3125000 0.4375000 6.00
0.1875000 0.3125000 0.5625000 6.00
0.1875000 0.3125000 0.6875000 6.00
0.1875000 0.3125000 0.8125000 6.00
0.1875000 0.4375000 0.4375000 3.00
0.1875000 0.4375000 0.5625000 6.00
0.1875000 0.4375000 0.6875000 6.00
0.1875000 0.4375000 0.8125000 6.00
0.1875000 0.5625000 0.5625000 3.00
0.1875000 0.5625000 0.6875000 6.00
0.1875000 0.6875000 0.6875000 3.00
0.3125000 0.3125000 0.3125000 1.00
0.3125000 0.3125000 0.4375000 3.00
0.3125000 0.3125000 0.5625000 3.00
0.3125000 0.3125000 0.6875000 3.00
0.3125000 0.4375000 0.4375000 3.00
0.3125000 0.4375000 0.5625000 6.00
0.3125000 0.4375000 0.6875000 6.00
0.3125000 0.5625000 0.5625000 3.00
0.4375000 0.4375000 0.4375000 1.00
0.4375000 0.4375000 0.5625000 3.00
EOF
$ECHO " running the scf calculation for Ni...\c"
$PW_COMMAND < ni.scf.$diago.in > ni.scf.$diago.out
check_failure $?
$ECHO " done"
# band structure calculation along delta, sigma and lambda lines
cat > ni.band.$diago.in << EOF
&control
calculation='bands'
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
prefix='ni'
/
&system
ibrav=2, celldm(1) =6.48, nat=1, ntyp=1,
nspin = 2, starting_magnetization(1)=0.7,
ecutwfc = 24.0, ecutrho = 288.0, nbnd = 8
/
&electrons
diagonalization='$diago'
/
ATOMIC_SPECIES
Ni 58.69 NiUS.RRKJ3.UPF
ATOMIC_POSITIONS
Ni 0.0 0.0 0.0
K_POINTS
28
0.0 0.0 0.0 1.0
0.0 0.0 0.1 1.0
0.0 0.0 0.2 1.0
0.0 0.0 0.3 1.0
0.0 0.0 0.4 1.0
0.0 0.0 0.5 1.0
0.0 0.0 0.6 1.0
0.0 0.0 0.7 1.0
0.0 0.0 0.8 1.0
0.0 0.0 0.9 1.0
0.0 0.0 1.0 1.0
0.0 0.0 0.0 1.0
0.0 0.1 0.1 1.0
0.0 0.2 0.2 1.0
0.0 0.3 0.3 1.0
0.0 0.4 0.4 1.0
0.0 0.5 0.5 1.0
0.0 0.6 0.6 1.0
0.0 0.7 0.7 1.0
0.0 0.8 0.8 1.0
0.0 0.9 0.9 1.0
0.0 1.0 1.0 1.0
0.0 0.0 0.0 1.0
0.1 0.1 0.1 1.0
0.2 0.2 0.2 1.0
0.3 0.3 0.3 1.0
0.4 0.4 0.4 1.0
0.5 0.5 0.5 1.0
EOF
$ECHO " running the band-structure calculation for Ni...\c"
$PW_COMMAND < ni.band.$diago.in > ni.band.$diago.out|
check_failure $?
$ECHO " done"
done
$ECHO
$ECHO "$EXAMPLE_DIR : done"
On Oct 31 2008, lan haiping wrote:
>Hi, David
>the error information has clearly shown that
>your input file has some wrong tag .
>please check it again ,or post to the forum with your
>input file
>
>On Sat, Nov 1, 2008 at 1:00 AM, David Tompsett <dat36 at cam.ac.uk> wrote:
>
>> Dear All,
>> I have recently compiled the parallel version of Quantum
>> Espresso without errors.
>>
>> But when I try to run some of the post-installation test examples I find
>> that each fails with:
>> Abort on node localhost due to MPI_Abort (Type 2)
>> So the program is calling abort.
>>
>> It looks like there is some error from: read_namelists : error
>> # 1
>> The output files have:
>>
>> Program PWSCF v.4.0.3 starts ...
>> Today is 31Oct2008 at 13:25:44
>>
>> Parallel version (MPI)
>>
>> Number of processors in use: 2
>> K-points division: npool = 2
>>
>> For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW
>>
>> Current dimensions of program pwscf are:
>> Max number of different atomic species (ntypx) = 10
>> Max number of k-points (npk) = 40000
>> Max angular momentum in pseudopotentials (lmaxx) = 3
>>
>> from read_namelists : error # 1
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from
>> read_namelists : error # 1
>> reading namelist control
>>
>>
>>
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> stopping ...
>> bindloe04:0.MPID_Abort: bindloe04:0.MPI Abort by user Aborting program !
>> bindloe04:0.MPID_CH_Abort: bindloe04:0.Aborting program!
>> bindloe04:1.MPID_Abort: bindloe04:1.MPI Abort by user Aborting program !
>> bindloe04:1.MPID_CH_Abort: bindloe04:1.Aborting program!
>>
>>
>>
>> What could cause this?
>>
>> Thanks for your help,
>> David Tompsett.
>>
>> --
>> David A. Tompsett
>> Quantum Matter Group
>> Cavendish Laboratory
>> J. J. Thomson Avenue
>> Cambridge CB3 0HE
>> U.K.
>> Tel: +44 7907 566351 (mobile)
>> Fax: +44 1223 337351
>> http://www-qm.phy.cam.ac.uk/
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
>
--
David A. Tompsett
Quantum Matter Group
Cavendish Laboratory
J. J. Thomson Avenue
Cambridge CB3 0HE
U.K.
Tel: +44 7907 566351 (mobile)
Fax: +44 1223 337351
http://www-qm.phy.cam.ac.uk/
From akohlmey at cmm.chem.upenn.edu Sat Nov 1 16:25:48 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 1 Nov 2008 11:25:48 -0400 (EDT)
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <Prayer.1.3.1.0811011156550.27996@hermes-1.csi.cam.ac.uk>
References: <490B39BC.2080306@cam.ac.uk>
<c92002fa0810311309u652cbcc2ob4ec433c35bae3e6@mail.gmail.com>
<Prayer.1.3.1.0811011156550.27996@hermes-1.csi.cam.ac.uk>
Message-ID: <Pine.LNX.4.64.0811011121570.2302@localhost.localdomain>
On Sat, 1 Nov 2008, D.A. Tompsett wrote:
DT> Dear Ian and All,
DT> below is the input file. It is from directory example01 and every
DT> calculation in it fails with the same message: read_namelists : error
david,
this looks like your compiler supports only a specific format
of namelists, that is different from what the more frequently
used compilers implement. what compiler/platform are you running on?
the example scripts are regularly tested on a significant number of
platforms.
a second possibility is that you have something that creates additional
output in the heredocs generated by the script. please have a look at
the *.in files in the results directory and see, if there is something
odd, e.g. where the original script had a variable.
cheers,
axel.
DT>
DT> Please let me know if you can see what is wrong.
DT>
DT> Thanks,
DT> David.
DT>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From jtmullen at ncsu.edu Sat Nov 1 17:25:35 2008
From: jtmullen at ncsu.edu (jtmullen at ncsu.edu)
Date: Sat, 1 Nov 2008 12:25:35 -0400 (EDT)
Subject: [Pw_forum] K point grid density in Electron-Phonon calculations
Message-ID: <60382.98.27.55.52.1225556735.squirrel@webmail.ncsu.edu>
Greetings,
Is there a way to define the K-point grid density in calculations
performed by ph.x ? I am defining the nq1, nq2, and nq3 for the phonon
density, but find that I would like to define, in some manner, the k
points which are used in the calculations.
Regards
Jeff Mullen
Physics
North Carolina State University
From dat36 at cam.ac.uk Sat Nov 1 17:33:19 2008
From: dat36 at cam.ac.uk (D.A. Tompsett)
Date: 01 Nov 2008 16:33:19 +0000
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <Pine.LNX.4.64.0811011121570.2302@localhost.localdomain>
References: <490B39BC.2080306@cam.ac.uk>
<c92002fa0810311309u652cbcc2ob4ec433c35bae3e6@mail.gmail.com>
<Prayer.1.3.1.0811011156550.27996@hermes-1.csi.cam.ac.uk>
<Pine.LNX.4.64.0811011121570.2302@localhost.localdomain>
Message-ID: <Prayer.1.3.1.0811011633190.20751@hermes-1.csi.cam.ac.uk>
Dear Alex and All,
thanks for the help. I understand better what the
"read_namelists : error" is now. I am using mpif90 for my compiler on a
unix platform.
I paste here one of the .in files (si.band.cg.in) which looks OK to me:
&control
calculation='bands'
pseudo_dir = '/home/dat36/Programs/Espresso/espresso-4.0.3/pseudo/',
outdir='/home/dat36/Programs/Espresso/espresso-4.0.3/TestJunk/',
prefix='silicon'
/
&system
ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1,
ecutwfc =18.0, nbnd = 8,
/
&electrons
diagonalization='cg'
/
ATOMIC_SPECIES
Si 28.086 Si.vbc.UPF
ATOMIC_POSITIONS
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS
28
0.0 0.0 0.0 1.0
0.0 0.0 0.1 1.0
0.0 0.0 0.2 1.0
0.0 0.0 0.3 1.0
0.0 0.0 0.4 1.0
0.0 0.0 0.5 1.0
0.0 0.0 0.6 1.0
0.0 0.0 0.7 1.0
0.0 0.0 0.8 1.0
0.0 0.0 0.9 1.0
0.0 0.0 1.0 1.0
0.0 0.0 0.0 1.0
0.0 0.1 0.1 1.0
0.0 0.2 0.2 1.0
0.0 0.3 0.3 1.0
0.0 0.4 0.4 1.0
0.0 0.5 0.5 1.0
0.0 0.6 0.6 1.0
0.0 0.7 0.7 1.0
0.0 0.8 0.8 1.0
0.0 0.9 0.9 1.0
0.0 1.0 1.0 1.0
0.0 0.0 0.0 1.0
0.1 0.1 0.1 1.0
0.2 0.2 0.2 1.0
0.3 0.3 0.3 1.0
0.4 0.4 0.4 1.0
0.5 0.5 0.5 1.0
I also paste below all of the warnings sent to stderr during the compile. I
am not sure if they are related to my problem:
fortcom: Warning: iotk_stream.spp, line 54: A dummy argument with an
explicit INTENT(OUT) declaration is not given an explicit value. [VAL]
subroutine
iotk_stream_read_LOGICAL1(unit,header,val,setpos,getpos,noval,ierr)
-------------------------------------------------^ fortcom: Warning:
iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
declaration is not given an explicit value. [VAL] subroutine
iotk_stream_read_INTEGER1(unit,header,val,setpos,getpos,noval,ierr)
-------------------------------------------------^ fortcom: Warning:
iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
declaration is not given an explicit value. [VAL] subroutine
iotk_stream_read_REAL1(unit,header,val,setpos,getpos,noval,ierr)
----------------------------------------------^ fortcom: Warning:
iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
declaration is not given an explicit value. [VAL] subroutine
iotk_stream_read_REAL2(unit,header,val,setpos,getpos,noval,ierr)
----------------------------------------------^ fortcom: Warning:
iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
declaration is not given an explicit value. [VAL] subroutine
iotk_stream_read_COMPLEX1(unit,header,val,setpos,getpos,noval,ierr)
-------------------------------------------------^ fortcom: Warning:
iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
declaration is not given an explicit value. [VAL] subroutine
iotk_stream_read_COMPLEX2(unit,header,val,setpos,getpos,noval,ierr)
-------------------------------------------------^ fortcom: Warning:
iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
declaration is not given an explicit value. [VAL] subroutine
iotk_stream_read_CHARACTER1(unit,header,val,setpos,getpos,noval,ierr)
---------------------------------------------------^ ar: creating libiotk.a
fftw.c(27449): warning #188: enumerated type mixed with another type
EXPECT_INT(dir);
^
fftw.c(27450): warning #188: enumerated type mixed with another type
EXPECT_INT(type);
Please let me know if you can see how I might fix this eg. by altering the
input file to make the namelist reader happy.
Thanks for any help,
David.
On Nov 1 2008, Axel Kohlmeyer wrote:
>On Sat, 1 Nov 2008, D.A. Tompsett wrote:
>
> DT> Dear Ian and All, DT> below is the input file. It is from directory
> example01 and every DT> calculation in it fails with the same message:
> read_namelists : error
>
>david,
>this looks like your compiler supports only a specific format
>of namelists, that is different from what the more frequently
>used compilers implement. what compiler/platform are you running on?
>
>the example scripts are regularly tested on a significant number of
>platforms.
>
>a second possibility is that you have something that creates additional
>output in the heredocs generated by the script. please have a look at
>the *.in files in the results directory and see, if there is something
>odd, e.g. where the original script had a variable.
>
>
>cheers,
> axel.
>
>DT>
>DT> Please let me know if you can see what is wrong.
>DT>
>DT> Thanks,
>DT> David.
>DT>
>
>
--
David A. Tompsett
Quantum Matter Group
Cavendish Laboratory
J. J. Thomson Avenue
Cambridge CB3 0HE
U.K.
Tel: +44 7907 566351 (mobile)
Fax: +44 1223 337351
http://www-qm.phy.cam.ac.uk/
From akohlmey at cmm.chem.upenn.edu Sat Nov 1 19:23:19 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 1 Nov 2008 14:23:19 -0400 (EDT)
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <Prayer.1.3.1.0811011633190.20751@hermes-1.csi.cam.ac.uk>
References: <490B39BC.2080306@cam.ac.uk>
<c92002fa0810311309u652cbcc2ob4ec433c35bae3e6@mail.gmail.com>
<Prayer.1.3.1.0811011156550.27996@hermes-1.csi.cam.ac.uk>
<Pine.LNX.4.64.0811011121570.2302@localhost.localdomain>
<Prayer.1.3.1.0811011633190.20751@hermes-1.csi.cam.ac.uk>
Message-ID: <Pine.LNX.4.64.0811011246540.2302@localhost.localdomain>
On Sat, 1 Nov 2008, D.A. Tompsett wrote:
DT> Dear Alex and All,
DT> thanks for the help. I understand better what the
DT> "read_namelists : error" is now. I am using mpif90 for my compiler on a unix
DT> platform.
sorry, but this is like answering "i have a red sedan car" when being
asked about model and make. what _kind_ of unix and what compiler vendor
and version do you have. mpif90 is usually a wrapper and can "contain"
any compiler.
try running "mpif90 -v" and/or "mpif90 -showme" to get some hints of
the compiler and send in the output.
and try running "uname -a" to get some info about the kind of unix.
thanks,
axel.
[...]
DT> I also paste below all of the warnings sent to stderr during the compile. I
DT> am not sure if they are related to my problem:
DT>
DT> fortcom: Warning: iotk_stream.spp, line 54: A dummy argument with an
DT> explicit INTENT(OUT) declaration is not given an explicit value. [VAL]
DT> subroutine
DT> iotk_stream_read_LOGICAL1(unit,header,val,setpos,getpos,noval,ierr)
DT> -------------------------------------------------^ fortcom: Warning:
DT> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> declaration is not given an explicit value. [VAL] subroutine
DT> iotk_stream_read_INTEGER1(unit,header,val,setpos,getpos,noval,ierr)
DT> -------------------------------------------------^ fortcom: Warning:
DT> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> declaration is not given an explicit value. [VAL] subroutine
DT> iotk_stream_read_REAL1(unit,header,val,setpos,getpos,noval,ierr)
DT> ----------------------------------------------^ fortcom: Warning:
DT> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> declaration is not given an explicit value. [VAL] subroutine
DT> iotk_stream_read_REAL2(unit,header,val,setpos,getpos,noval,ierr)
DT> ----------------------------------------------^ fortcom: Warning:
DT> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> declaration is not given an explicit value. [VAL] subroutine
DT> iotk_stream_read_COMPLEX1(unit,header,val,setpos,getpos,noval,ierr)
DT> -------------------------------------------------^ fortcom: Warning:
DT> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> declaration is not given an explicit value. [VAL] subroutine
DT> iotk_stream_read_COMPLEX2(unit,header,val,setpos,getpos,noval,ierr)
DT> -------------------------------------------------^ fortcom: Warning:
DT> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> declaration is not given an explicit value. [VAL] subroutine
DT> iotk_stream_read_CHARACTER1(unit,header,val,setpos,getpos,noval,ierr)
DT> ---------------------------------------------------^ ar: creating libiotk.a
DT> fftw.c(27449): warning #188: enumerated type mixed with another type
DT> EXPECT_INT(dir);
DT> ^
DT>
DT> fftw.c(27450): warning #188: enumerated type mixed with another type
DT> EXPECT_INT(type);
DT>
DT>
DT> Please let me know if you can see how I might fix this eg. by altering the
DT> input file to make the namelist reader happy.
DT>
DT> Thanks for any help,
DT> David.
DT>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From dat36 at cam.ac.uk Sat Nov 1 20:31:44 2008
From: dat36 at cam.ac.uk (D.A. Tompsett)
Date: 01 Nov 2008 19:31:44 +0000
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <Pine.LNX.4.64.0811011246540.2302@localhost.localdomain>
References: <490B39BC.2080306@cam.ac.uk>
<c92002fa0810311309u652cbcc2ob4ec433c35bae3e6@mail.gmail.com>
<Prayer.1.3.1.0811011156550.27996@hermes-1.csi.cam.ac.uk>
<Pine.LNX.4.64.0811011121570.2302@localhost.localdomain>
<Prayer.1.3.1.0811011633190.20751@hermes-1.csi.cam.ac.uk>
<Pine.LNX.4.64.0811011246540.2302@localhost.localdomain>
Message-ID: <Prayer.1.3.1.0811011931440.21596@hermes-1.csi.cam.ac.uk>
Dear Alex and All,
I have tried to get some more info on my compiler.
I did this by running "module list" in my login environment:
Currently Loaded Modulefiles:
1) dot 8) intel/fce/9.1.041
2) torque 9) infinipath/mpi/2.2
3) moab 10) infinipath/openfabrics/2.2
4) gold/2.1.6.0 11) infinipath/core/2.2
5) intel/mkl/9.0.018 12) mpiexec/0.82
6) intel/idbe/9.1.046 13) default-infinipath
7) intel/cce/9.1.046
I think this indicates that my compiler is intel fortran 9.1.041.
Also the output from "uname -a" is: Linux bindloe04
2.6.9-67.0.4.EL_lustre.1.6.4.3smp #1 SMP Sun Feb 17 08:05:22 EST 2008
x86_64 x86_64 x86_64 GNU/Linux
I hope that makes it clearer.
Thanks again,
David.
On Nov 1 2008, Axel Kohlmeyer wrote:
>On Sat, 1 Nov 2008, D.A. Tompsett wrote:
>
> DT> Dear Alex and All, DT> thanks for the help. I understand better what
> the DT> "read_namelists : error" is now. I am using mpif90 for my
> compiler on a unix DT> platform.
>
>sorry, but this is like answering "i have a red sedan car" when being
>asked about model and make. what _kind_ of unix and what compiler vendor
>and version do you have. mpif90 is usually a wrapper and can "contain"
>any compiler.
>
>try running "mpif90 -v" and/or "mpif90 -showme" to get some hints of
>the compiler and send in the output.
>and try running "uname -a" to get some info about the kind of unix.
>
>thanks,
> axel.
>
>
> [...] DT> I also paste below all of the warnings sent to stderr during
> the compile. I DT> am not sure if they are related to my problem: DT> DT>
> fortcom: Warning: iotk_stream.spp, line 54: A dummy argument with an DT>
> explicit INTENT(OUT) declaration is not given an explicit value. [VAL]
> DT> subroutine DT>
> iotk_stream_read_LOGICAL1(unit,header,val,setpos,getpos,noval,ierr) DT>
> -------------------------------------------------^ fortcom: Warning: DT>
> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> declaration is not given an explicit value. [VAL] subroutine DT>
> iotk_stream_read_INTEGER1(unit,header,val,setpos,getpos,noval,ierr) DT>
> -------------------------------------------------^ fortcom: Warning: DT>
> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> declaration is not given an explicit value. [VAL] subroutine DT>
> iotk_stream_read_REAL1(unit,header,val,setpos,getpos,noval,ierr) DT>
> ----------------------------------------------^ fortcom: Warning: DT>
> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> declaration is not given an explicit value. [VAL] subroutine DT>
> iotk_stream_read_REAL2(unit,header,val,setpos,getpos,noval,ierr) DT>
> ----------------------------------------------^ fortcom: Warning: DT>
> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> declaration is not given an explicit value. [VAL] subroutine DT>
> iotk_stream_read_COMPLEX1(unit,header,val,setpos,getpos,noval,ierr) DT>
> -------------------------------------------------^ fortcom: Warning: DT>
> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> declaration is not given an explicit value. [VAL] subroutine DT>
> iotk_stream_read_COMPLEX2(unit,header,val,setpos,getpos,noval,ierr) DT>
> -------------------------------------------------^ fortcom: Warning: DT>
> iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> declaration is not given an explicit value. [VAL] subroutine DT>
> iotk_stream_read_CHARACTER1(unit,header,val,setpos,getpos,noval,ierr) DT>
> ---------------------------------------------------^ ar: creating
> libiotk.a DT> fftw.c(27449): warning #188: enumerated type mixed with
> another type DT> EXPECT_INT(dir); DT> ^ DT> DT> fftw.c(27450): warning
> #188: enumerated type mixed with another type DT> EXPECT_INT(type); DT>
> DT> DT> Please let me know if you can see how I might fix this eg. by
> altering the DT> input file to make the namelist reader happy. DT> DT>
> Thanks for any help, DT> David. DT>
>
>
--
David A. Tompsett
Quantum Matter Group
Cavendish Laboratory
J. J. Thomson Avenue
Cambridge CB3 0HE
U.K.
Tel: +44 7907 566351 (mobile)
Fax: +44 1223 337351
http://www-qm.phy.cam.ac.uk/
From akohlmey at cmm.chem.upenn.edu Sun Nov 2 00:13:38 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 1 Nov 2008 19:13:38 -0400 (EDT)
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <Prayer.1.3.1.0811011931440.21596@hermes-1.csi.cam.ac.uk>
References: <490B39BC.2080306@cam.ac.uk>
<c92002fa0810311309u652cbcc2ob4ec433c35bae3e6@mail.gmail.com>
<Prayer.1.3.1.0811011156550.27996@hermes-1.csi.cam.ac.uk>
<Pine.LNX.4.64.0811011121570.2302@localhost.localdomain>
<Prayer.1.3.1.0811011633190.20751@hermes-1.csi.cam.ac.uk>
<Pine.LNX.4.64.0811011246540.2302@localhost.localdomain>
<Prayer.1.3.1.0811011931440.21596@hermes-1.csi.cam.ac.uk>
Message-ID: <Pine.LNX.4.64.0811011908330.2282@localhost.localdomain>
On Sat, 1 Nov 2008, D.A. Tompsett wrote:
DT> Dear Alex and All,
DT> I have tried to get some more info on my compiler.
DT> I did this by running "module list" in my login environment:
DT> Currently Loaded Modulefiles:
DT> 1) dot 8) intel/fce/9.1.041
DT> 2) torque 9) infinipath/mpi/2.2
DT> 3) moab 10) infinipath/openfabrics/2.2
DT> 4) gold/2.1.6.0 11) infinipath/core/2.2
DT> 5) intel/mkl/9.0.018 12) mpiexec/0.82
DT> 6) intel/idbe/9.1.046 13) default-infinipath
DT> 7) intel/cce/9.1.046
DT>
DT> I think this indicates that my compiler is intel fortran 9.1.041.
could be, but need not be. you still may have a different fortran
compiler (gfortran, g95) embedded in your mpif90. are you seeing
the same problems, when you compile a serial version?
what is the F90 definition in your make.sys gfortran or ifort?
DT>
DT> Also the output from "uname -a" is: Linux bindloe04
DT> 2.6.9-67.0.4.EL_lustre.1.6.4.3smp #1 SMP Sun Feb 17 08:05:22 EST 2008
DT> x86_64 x86_64 x86_64 GNU/Linux
DT>
DT> I hope that makes it clearer.
unfortunately, no. this makes both the compiler warnings and
the problems reading input files very mysterious. i have the
same compiler on my desktop - only one patchlevel old - and
i see neither of the two problems that you encounter.
you make sys is the one created from configure?
and you run 'make clean' after all new runs of configure
or changing of compiler options? right?
cheers,
axel.
DT>
DT> Thanks again,
DT> David.
DT>
DT> On Nov 1 2008, Axel Kohlmeyer wrote:
DT>
DT> >On Sat, 1 Nov 2008, D.A. Tompsett wrote:
DT> >
DT> > DT> Dear Alex and All, DT> thanks for the help. I understand better what
DT> > the DT> "read_namelists : error" is now. I am using mpif90 for my
DT> > compiler on a unix DT> platform.
DT> >
DT> >sorry, but this is like answering "i have a red sedan car" when being
DT> >asked about model and make. what _kind_ of unix and what compiler vendor
DT> >and version do you have. mpif90 is usually a wrapper and can "contain"
DT> >any compiler.
DT> >
DT> >try running "mpif90 -v" and/or "mpif90 -showme" to get some hints of
DT> >the compiler and send in the output.
DT> >and try running "uname -a" to get some info about the kind of unix.
DT> >
DT> >thanks,
DT> > axel.
DT> >
DT> >
DT> > [...] DT> I also paste below all of the warnings sent to stderr during
DT> > the compile. I DT> am not sure if they are related to my problem: DT> DT>
DT> > fortcom: Warning: iotk_stream.spp, line 54: A dummy argument with an DT>
DT> > explicit INTENT(OUT) declaration is not given an explicit value. [VAL]
DT> > DT> subroutine DT>
DT> > iotk_stream_read_LOGICAL1(unit,header,val,setpos,getpos,noval,ierr) DT>
DT> > -------------------------------------------------^ fortcom: Warning: DT>
DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
DT> > iotk_stream_read_INTEGER1(unit,header,val,setpos,getpos,noval,ierr) DT>
DT> > -------------------------------------------------^ fortcom: Warning: DT>
DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
DT> > iotk_stream_read_REAL1(unit,header,val,setpos,getpos,noval,ierr) DT>
DT> > ----------------------------------------------^ fortcom: Warning: DT>
DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
DT> > iotk_stream_read_REAL2(unit,header,val,setpos,getpos,noval,ierr) DT>
DT> > ----------------------------------------------^ fortcom: Warning: DT>
DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
DT> > iotk_stream_read_COMPLEX1(unit,header,val,setpos,getpos,noval,ierr) DT>
DT> > -------------------------------------------------^ fortcom: Warning: DT>
DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
DT> > iotk_stream_read_COMPLEX2(unit,header,val,setpos,getpos,noval,ierr) DT>
DT> > -------------------------------------------------^ fortcom: Warning: DT>
DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
DT> > iotk_stream_read_CHARACTER1(unit,header,val,setpos,getpos,noval,ierr) DT>
DT> > ---------------------------------------------------^ ar: creating
DT> > libiotk.a DT> fftw.c(27449): warning #188: enumerated type mixed with
DT> > another type DT> EXPECT_INT(dir); DT> ^ DT> DT> fftw.c(27450): warning
DT> > #188: enumerated type mixed with another type DT> EXPECT_INT(type); DT>
DT> > DT> DT> Please let me know if you can see how I might fix this eg. by
DT> > altering the DT> input file to make the namelist reader happy. DT> DT>
DT> > Thanks for any help, DT> David. DT>
DT> >
DT> >
DT>
DT>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From sporevoyager at gmail.com Sun Nov 2 12:12:56 2008
From: sporevoyager at gmail.com (shangy)
Date: Sun, 2 Nov 2008 19:12:56 +0800
Subject: [Pw_forum] help on "wrong total_weight"!
Message-ID: <94be399f0811020312t2bc72278gb389e2f4b1b6bae8@mail.gmail.com>
Dear all:
I encountered the error message "wrong total_weight" in my phdos
calculation with serial matdyn.x. The QE-4.0.2 was compiled with
ifort-10.1.015_intal64, lam-7.1.4(and also openmpi-1.2.7) and MKL-10.0.3.020
under RedHat Enterprise Linux Server 5.2 environment. The CPU is Quad-Core
AMD Opteron(tm) Processor 2356. The detail information of my calculation are
as follows:
I want to obtain the phonon-dos of silicon vacancy (ground state
configuration) with Si63 supercell at gamma point. The step-by-step
inputfiles are:
for scf calculation
-------------------
&CONTROL
calculation = 'scf'
verbosity = 'high'
restart_mode = 'from_scratch'
pseudo_dir = '/home/pub/pplib/'
outdir = '/tmp/'
prefix = 'Si-V1'
tprnfor = .true.
nstep = 200
/
&SYSTEM
ibrav = 1
celldm(1) = 20.70
nat = 63
ntyp = 1
occupations = 'smearing'
degauss = 0.002
smearing = 'mv'
ecutwfc = 34
/
&ELECTRONS
conv_thr = 1.0D-8
diagonalization='david'
mixing_mode = 'plain'
mixing_beta = 0.3
/
ATOMIC_SPECIES
Si 28.0855 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (crystal)
.
Si coordinates
.
etc
K_POINTS
1
0.0 0.0 0.0 1.0
-----------------
for phonon calcuation:
----------------------
&INPUTPH
amass(1) = 28.0855
outdir = '/tmp/'
prefix = 'Si-V1'
tr2_ph = 1.0d-12
alpha_mix(1) = 0.1
iverbosity = 0
reduce_io = .true.
! recover = .true.
fildyn = 'Si-V1.dynG'
! epsil = .true.
trans = .true.
/
0.0 0.0 0.0
--------------
for the IFC calculation:
-----------------------
&input
fildyn = 'Si-V1.dynG'
flfrc = 'Si-V1.fc'
zasr = 'crystal'
/
1 1 1
1
Si-V1.dynG
-----------------
All the above calcualtions finished well. However, the forenamed error
message appeared when I calculated the phonon dos with dense q-points.
for the phonon dos calculation:
-------------------------------
&input
flfrc = 'Si-V1.fc'
asr = 'crystal'
dos = .true.
nk1=10, nk2=10, nk3=10
deltaE = 0.1
fldos = 'Si-V1.phdos-10-0.1'
flfrq = 'Si-V1.freq-10-0.1'
flvec = 'Si-V1.modes-10-0.1'
ntyp = 1
amass(1) = 28.0855
/
--------------------
The matdyn.x stopped and complained that
--------the matdyn.x outfile-----
warning: symmetry operation # 34 not allowed. fractional translation:
-0.0000387 0.0000000 0.0000387 in crystal coordinates
Norm of the difference between old and new effective charges:
0.00000000000000000000
Norm of the difference between old and new force-constants:
0.01586035815826266834
0.833333333333333
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from frc_blk : error # 1
wrong total_weight
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
---------------------
So, what's wrong with it? code bug or miscompiled?Is something wrong with
the input-parameters in my inputfile? I searched the mailist and found
nothing could solve the problem. BTW, with the similar calculation, I got
optic frequency of 514.4 cm^-1 (expt. 518 cm^-1) at gamma point using the
perfect Si64 suprecell. If you would like to test the problem, the
Si-V1.dynG can be found at http://www.divshare.com/download/5725901-c73 due
to the froum file limits. Please be patient for 15 seconds adversting when
you download it :).
Any ideas are appreciated! Thanks a lot!
Best regards!
shany
Graduate School of Chinese Academy of Sciences
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From giannozz at democritos.it Sun Nov 2 19:33:07 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 2 Nov 2008 19:33:07 +0100
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <490B39BC.2080306@cam.ac.uk>
References: <490B39BC.2080306@cam.ac.uk>
Message-ID: <B4DE4FCB-DDBA-49FD-B451-8F4C1DEF0A40@democritos.it>
On Oct 31, 2008, at 18:00 , David Tompsett wrote:
> error # 1
> reading namelist control
> [...]
> What could cause this?
it is explained in the MIA (Most Ignored Answers: it used to be FAQ,
but since nobody ever reads them, the new name is closer to reality).
Either there is a misspell in namelist control, or there is a DOS ^M
that shouldn't be there, or (if it happens in parallel excution on more
than one processor only) your MPI library does not perform the correct
input redirection. Use "pw.x -in file-name" to read data from 'file-
name'
Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From lfhuang at theory.issp.ac.cn Mon Nov 3 03:13:50 2008
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Mon, 03 Nov 2008 10:13:50 +0800
Subject: [Pw_forum] =?utf-8?q?Projected_density_of_states_of_phonon?=
Message-ID: <20081103021350.15647.qmail@ms.hfcas.ac.cn>
Dear Rakshit:
I will send you the code for PVDOS that was written by prof. Kohlmeyer.
And please thank prof. Kohlmeyer for his kindness.
Best Wishes!
Yours Sincerely
L.F.Huang
> Date: Sat, 1 Nov 2008 14:49:34 +0530
> From: "Bipul Rakshit"
> Subject: Re: [Pw_forum] Projected density of states of phonon
> To: "PWSCF Forum"
> Message-ID:
>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello Pwscf users,
>
> I am calculating phonon of ScAs and ScSb using PWSCF, I read a paper
>
> Solid State Commun. 147 (2008) 198
>
> There the author mentioned about projected density of states of
> phonon. So can anybody tell me how to find that? Means what option we
> have to set in input file to obtain the projected density of states of
> phonon.
>
> It will be helpful for me
> thanks
>
> --
> Bipul Rakshit
> PhD Student,
> Barkatullah University,
> Bhopal 462026,
> MP, India
------
======================================================================
L.F.Huang(???) lfhuang at theory.issp.ac.cn
======================================================================
Add: Research Laboratory for Computational Materials Sciences,
Instutue of Solid State Physics,the Chinese Academy of Sciences,
P.O.Box 1129, Hefei 230031, P.R.China
Tel: 86-551-5591464-328(office)
Fax: 86-551-5591434
Web: http://theory.issp.ac.cn (website of our theory group)
http://www.issp.ac.cn (website of our institute)
======================================================================
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From asaaravindh at yahoo.co.in Mon Nov 3 14:29:42 2008
From: asaaravindh at yahoo.co.in (asa aravindh)
Date: Mon, 3 Nov 2008 18:59:42 +0530 (IST)
Subject: [Pw_forum] Mg and O pseudo potential
Message-ID: <320481.23653.qm@web7903.mail.in.yahoo.com>
Dear all...
I want to do calculations on Fe/MgO/Fe system.. and I found that the pseudo potential Fe.pbe-nd-rrkjus.UPF
is apropriate as far af Fe is concerned. But I couldnt find any similar pp for Mg and O.
Can anybody give me some information regarding this. Is there any such pp availale for Mg and O or any other common pp for Fe , Mg and O
any help would be greatly appreciated.
Thanks
Asa
Bollywood news, movie reviews, film trailers and more! Go to http://in.movies.yahoo.com/
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From yuminqian at gmail.com Tue Nov 4 08:25:16 2008
From: yuminqian at gmail.com (yumin qian)
Date: Tue, 4 Nov 2008 15:25:16 +0800
Subject: [Pw_forum] phonon mode and displace pattern
Message-ID: <aa128b2c0811032325g6edd0a4ar2d27d36821e6e85e@mail.gmail.com>
There are several things I don't know about the phonon dispersion
analysis
1 How to discern longitudinal and transverse mode ?
2 In the process of dynamic matrix construction , for a particular
mode how to displace atoms ,
I don't think I know the real meaning of "displacements along
irreps of decomposed 3N-dimensional representation ",
3 How to tell which mode does a dispersion curve belongs to ?
4 If I want to see a particular mode , how should I choose the
parameter of : nrapp
5 if I want to see a particular atom or a subset of atoms displace,
such as in p4/mmm SrCrO3 crystal ,fix Sr,Cr and let O displace ,how should
I choose the parameter: nat_todo, and so only part of the modes of this
crystal are caculated , ,how to tell which mode are they belong to.
ATOMIC_POSITIONS
Sr 0.500000000 0.000000000 0.412027344
Sr 0.000000000 0.500000000 0.412027344
Cr1 0.000000000 0.000000000 0.058596874
Cr2 0.500000000 0.500000000 0.058594869
O 0.000000000 0.000000000 0.412132248
O 0.500000000 0.500000000 0.412139067
O 0.250003893 0.250003893 0.058620564
O 0.250003893 0.749996107 0.058620564
O 0.749996107 0.250003893 0.058620564
O 0.749996107 0.749996107 0.058620564
Many thanks
--
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel: + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603 Beijing 100190
China
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From anna.ferrari at unito.it Tue Nov 4 10:26:06 2008
From: anna.ferrari at unito.it (Anna Maria Ferrari)
Date: Tue, 4 Nov 2008 10:26:06 +0100
Subject: [Pw_forum] (no subject)
Message-ID: <000001c93e5f$7b311800$2376c082@desdemona>
POST DOC position available
at the crystal group TORINO
starting from february 1st 2009
required
1) phd
2) 24 months experience abroad
skills: experience in ab initio calculations
two years grant
30000 euro brutto per year
title "Quantum-mechanic characterization of
the properties of crystalline materials from bulk to nanostructured
materials"
contact anna.ferrari at unito.it
***********************************
Anna Maria Ferrari
Dipartimento Chimica IFM
Universit? di Torino
via P. Giuria 5
10125 Torino ITALY
phone ++39 +11 6707563
fax ++39 +11 670 7855
***********************************
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From anna.ferrari at unito.it Tue Nov 4 10:27:55 2008
From: anna.ferrari at unito.it (Anna Maria Ferrari)
Date: Tue, 4 Nov 2008 10:27:55 +0100
Subject: [Pw_forum] (no subject)
Message-ID: <002501c93e5f$b02cc8b0$2376c082@desdemona>
POST DOC position available
at the crystal group TORINO
starting from february 1st 2009
required
1) phd
2) 24 months experience abroad
skills: experience in ab initio calculations
two years grant
30000 euro brutto per year
title "Quantum-mechanic characterization of
the properties of crystalline materials from bulk to nanostructured
materials"
contact anna.ferrari at unito.it
***********************************
Anna Maria Ferrari
Dipartimento Chimica IFM
Universit? di Torino
via P. Giuria 5
10125 Torino ITALY
phone ++39 +11 6707563
fax ++39 +11 670 7855
***********************************
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From forum.san at gmail.com Tue Nov 4 13:38:02 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Tue, 4 Nov 2008 18:08:02 +0530
Subject: [Pw_forum] Problem in execution of pw.x (qe-4.0.2)
Message-ID: <cb60cbc40811040438wbf74268hf6daeb7d7f8cf55e@mail.gmail.com>
Hello all,
The Quantum-Espresso - 4.0.2 is installed with pathscale-3.0
compiler, ACML-4.1.0 and fftw-3.1.2 libraries on a 16 node Rocks-4.2
cluster (Cent OS 4.3).
When pw.x is run, the following error appearied immediately after
the job submission.
$ mpiexec -machinefile ./host -np 8 /opt/apps/espresso-4.0.2_acml/bin/pw.x
-in input1.in
Program PWSCF v.4.0.2 starts ...
Today is 4Nov2008 at 16:59:40
Parallel version (MPI)
Number of processors in use: 8
R & G space division: proc/pool = 8
For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW
Current dimensions of program pwscf are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 40000
Max angular momentum in pseudopotentials (lmaxx) = 3
#############################################################################
###########################################
# FROM IOTK LIBRARY, VERSION 1.1.0development
# UNRECOVERABLE ERROR (ierr=-1)
# ERROR IN: iotk_scan_begin (iotk_scan.spp:155)
# CVS Revision: 1.7
# Tag not found
namel=HEADER
#############################################################################
###########################################
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0[cli_0]: aborting
job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
rank 0 in job 3 masternode_32841 caused collective abort of all
ranks
exit status of rank 0: killed by signal 9
I've tried to run this job with different number of processes. In
each run same error has appeared.
But the same input file works well with QE-3.1.1.
Will it be possible to know why its not working with QE-4.0.2?
Thanks,
Sangamesh
Consultant - HPC
Locuz Enterprise Solutions
Bangalore, India
From paulatto at sissa.it Tue Nov 4 14:05:11 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 04 Nov 2008 14:05:11 +0100
Subject: [Pw_forum] Problem in execution of pw.x (qe-4.0.2)
In-Reply-To: <cb60cbc40811040438wbf74268hf6daeb7d7f8cf55e@mail.gmail.com>
References: <cb60cbc40811040438wbf74268hf6daeb7d7f8cf55e@mail.gmail.com>
Message-ID: <49104887.2000800@sissa.it>
Sangamesh B ha scritto:
> ###########################################
> # FROM IOTK LIBRARY, VERSION 1.1.0development
> # UNRECOVERABLE ERROR (ierr=-1)
> # ERROR IN: iotk_scan_begin (iotk_scan.spp:155)
> # CVS Revision: 1.7
> # Tag not found
> namel=HEADER
> #############################################################################
>
Dear Sangamesh,
since you are not providing us your input file I can only guess. You
error can be caused by changing some input options and parameters. If I
remember correctly, you have to clean the temporary files and directory
for the job if you change the number of pools.
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
From michele.amato at unimore.it Tue Nov 4 17:50:53 2008
From: michele.amato at unimore.it (Michele Amato)
Date: Tue, 4 Nov 2008 17:50:53 +0100 (CET)
Subject: [Pw_forum] from read_namelist : error # 1 reading namelist system
Message-ID: <62798.155.185.12.237.1225817453.squirrel@webmail2.unimore.it>
Dear all,
I'm trying to do a relaxation of a silicon-germanium nanowires; when I
start the calculation I get always the following error:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from read_namelists : error # 1
reading namelist system
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
What kind of error is? Where can I look to understand something?
Thank you very much
Michele
From degironc at sissa.it Tue Nov 4 18:01:57 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 04 Nov 2008 18:01:57 +0100
Subject: [Pw_forum] from read_namelist : error # 1 reading namelist
system
In-Reply-To: <62798.155.185.12.237.1225817453.squirrel@webmail2.unimore.it>
References: <62798.155.185.12.237.1225817453.squirrel@webmail2.unimore.it>
Message-ID: <49108005.7070002@sissa.it>
tipically a mispelled or misplaced variable in SYSTEM namelist ...
stefano
Michele Amato wrote:
> Dear all,
>
> I'm trying to do a relaxation of a silicon-germanium nanowires; when I
> start the calculation I get always the following error:
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> from read_namelists : error # 1
> reading namelist system
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> stopping ...
>
> What kind of error is? Where can I look to understand something?
>
> Thank you very much
>
> Michele
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
From Giovanni.Cantele at na.infn.it Tue Nov 4 18:13:58 2008
From: Giovanni.Cantele at na.infn.it (Giovanni Cantele)
Date: Tue, 04 Nov 2008 18:13:58 +0100
Subject: [Pw_forum] from read_namelist : error # 1 reading namelist
system
In-Reply-To: <62798.155.185.12.237.1225817453.squirrel@webmail2.unimore.it>
References: <62798.155.185.12.237.1225817453.squirrel@webmail2.unimore.it>
Message-ID: <491082D6.5090701@na.infn.it>
Michele Amato wrote:
> Dear all,
>
> I'm trying to do a relaxation of a silicon-germanium nanowires; when I
> start the calculation I get always the following error:
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> from read_namelists : error # 1
> reading namelist system
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> stopping ...
>
> What kind of error is? Where can I look to understand something?
>
> Thank you very much
>
> Michele
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
Dear Michele,
usually a good point to start with is the QE user guide, at
http://www.quantum-espresso.org/wiki/index.php/User_Guide
In the "Troubleshooting (PWscf)
<http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_%28PWscf%29>"
section you can find:
pw.x stops with error in reading
There is an error in the input data. Usually it is a misspelled namelist
variable, or an empty input file. Note that out-of-bound indices in
dimensioned variables read in the namelist may cause the code to crash
with really mysterious error messages. Also note that input data files
containing ^M (Control-M) characters at the end of lines (typically,
files coming from Windows PC) may yield error in reading. If none of the
above applies and the code stops at the first namelist (?control?) and
you are running in parallel: your MPI libraries might not be properly
configured to allow input redirection, so that what you are effectively
reading is an empty file. See above.
The other way is try to browse the PWSCF forum, where many questions
have been answered several times. One example in your case:
http://www.democritos.it/pipermail/pw_forum/2006-January/003544.html
Ciao,
Giovanni
--
Dr. Giovanni Cantele
Coherentia CNR-INFM and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario di Monte S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Fax: +39 081 676346
E-mail: giovanni.cantele at cnr.it
giovanni.cantele at na.infn.it
Web: http://people.na.infn.it/~cantele
Research Group: http://www.nanomat.unina.it
From n.benedek at imperial.ac.uk Tue Nov 4 18:31:55 2008
From: n.benedek at imperial.ac.uk (Benedek, Nicole A)
Date: Tue, 4 Nov 2008 17:31:55 -0000
Subject: [Pw_forum] Phonons at generic q-point
Message-ID: <9C7B922DE2C5F646A82FC35DF4DEE76B0289655B@icex2.ic.ac.uk>
Dear All,
I have been trying to run a parallel phonon calculation at generic q-point for a SrTiO3 multilayer (16 atoms) using espresso 4.0.3. I run an initial scf calculation with wf_collect=true and then a ph.x calculation with lnscf=true. The calculation always crashes with the following error (full input pasted below):
! ... rest of modes
Representation 47 1 modes - To be done
Representation 48 1 modes - To be done
from openfilq : error # 1
file sto_mag.wfc not found
stopping ...
The wfc files are present and written to the same directory from which the calculation is running and this is not a 'recovered' calculation.
So far I have tried the following tests:
* The examples for Si at http://people.sissa.it/~degironc/QE-Tutorial/ (all run successfully);
* Phonon dispersion and q=0 calculations for bulk SrTiO3 (all run successfully);
* Phonon calculation at M for bulk SrTiO3, with lnscf=true (run successfully);
* Phonon calculation at q=0 for SrTiO3 multilayer (run successfully).
I also noticed the message 'Found additional translation' printed at the top of the output. I had a look through the source code (sgam_at.f90 and sgam_at_mag.f90), so I know this message is printed if the identity is found to have fractional translations. I found one previous post about this message in the archive (http://tinyurl.com/5k926j) but it seemed to concern how parallel jobs were re-started before the wf_collect keyword existed (I run all my calculations with wf_collect=true and my phonon calculation uses the same number of processors as the initial scf run). Is this message the source of my problems or is there something else going on? Any hints would be appreciated.
Cheers,
Nicole
Nicole Benedek
Research Associate
Department of Materials
Imperial College London
! INPUT FILE FOR PHONON CALC
Phonons of SrTiO3 multilayer at X
&inputph
tr2_ph=1.0d-14,
amass(1)=87.62,
amass(2)=47.88,
amass(3)=15.9994,
prefix='sto_mag',
outdir='./'
fildyn='sto_mag.dynX',
lnscf=.true.
/
0.0 0.5 0.0 ! X point in BZ for orthorhombic primitive systems
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From dalcorso at sissa.it Tue Nov 4 18:45:08 2008
From: dalcorso at sissa.it (Dal Corso Andrea)
Date: Tue, 04 Nov 2008 18:45:08 +0100
Subject: [Pw_forum] Phonons at generic q-point
In-Reply-To: <9C7B922DE2C5F646A82FC35DF4DEE76B0289655B@icex2.ic.ac.uk>
References: <9C7B922DE2C5F646A82FC35DF4DEE76B0289655B@icex2.ic.ac.uk>
Message-ID: <1225820708.3320.32.camel@dhpc-5-53.sissa.it>
This bug has been fixed in the cvs version but not yet in the 4.0.3
version.
Please add the line:
twfcollect=.false.
at line 285 of PH/phonon.f90
284 CALL electrons()
285 !
286 CALL close_files()
Between CALL electrons and CALL close_files.
And change also line 20 of phonon.f90 with:
USE control_flags, ONLY : gamma_only, twfcollect
Then recompile and try again.
The alternative is not to use wf_collect=.true. in the pw calculation.
Andrea
On Tue, 2008-11-04 at 17:31 +0000, Benedek, Nicole A wrote:
> Dear All,
>
> I have been trying to run a parallel phonon calculation at generic
> q-point for a SrTiO3 multilayer (16 atoms) using espresso 4.0.3. I run
> an initial scf calculation with wf_collect=true and then a ph.x
> calculation with lnscf=true. The calculation always crashes with the
> following error (full input pasted below):
>
> ! ... rest of modes
>
> Representation 47 1 modes - To be done
>
> Representation 48 1 modes - To be done
>
> from openfilq : error # 1
> file sto_mag.wfc not found
> stopping ...
>
> The wfc files are present and written to the same directory from which
> the calculation is running and this is not a 'recovered' calculation.
>
> So far I have tried the following tests:
>
> * The examples for Si at http://people.sissa.it/~degironc/QE-Tutorial/
> (all run successfully);
> * Phonon dispersion and q=0 calculations for bulk SrTiO3 (all run
> successfully);
> * Phonon calculation at M for bulk SrTiO3, with lnscf=true (run
> successfully);
> * Phonon calculation at q=0 for SrTiO3 multilayer (run successfully).
>
> I also noticed the message 'Found additional translation' printed at
> the top of the output. I had a look through the source code
> (sgam_at.f90 and sgam_at_mag.f90), so I know this message is printed
> if the identity is found to have fractional translations. I found one
> previous post about this message in the archive
> (http://tinyurl.com/5k926j) but it seemed to concern how parallel jobs
> were re-started before the wf_collect keyword existed (I run all my
> calculations with wf_collect=true and my phonon calculation uses the
> same number of processors as the initial scf run). Is this message the
> source of my problems or is there something else going on? Any hints
> would be appreciated.
>
> Cheers,
>
> Nicole
>
> Nicole Benedek
> Research Associate
> Department of Materials
> Imperial College London
>
> ! INPUT FILE FOR PHONON CALC
>
> Phonons of SrTiO3 multilayer at X
> &inputph
> tr2_ph=1.0d-14,
> amass(1)=87.62,
> amass(2)=47.88,
> amass(3)=15.9994,
> prefix='sto_mag',
> outdir='./'
> fildyn='sto_mag.dynX',
> lnscf=.true.
> /
> 0.0 0.5 0.0 ! X point in BZ for orthorhombic primitive systems
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
--
Andrea Dal Corso Tel. 0039-040-3787428
SISSA, Via Beirut 2/4 Fax. 0039-040-3787528
34014 Trieste (Italy) e-mail: dalcorso at sissa.it
From prasenjit.jnc at gmail.com Tue Nov 4 23:32:27 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Tue, 4 Nov 2008 23:32:27 +0100
Subject: [Pw_forum] memory problem
Message-ID: <627e0ffa0811041432i1faff684xec92d7b293f49afc@mail.gmail.com>
Hi everybody,
While doing a relaxation calculation using pw.x (v.4.0) and 80 processors
the dynamical memory required by the code keeps on increasing. If I grep the
lines of the output file which contains the information about memory usage,
I get the following output:
per-process dynamical memory: 334.6 Mb
per-process dynamical memory: 498.3 Mb
per-process dynamical memory: 498.3 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 507.1 Mb
per-process dynamical memory: 1867.8 Mb
per-process dynamical memory: 1867.8 Mb
per-process dynamical memory: 1867.8 Mb
per-process dynamical memory: 1867.8 Mb
After this the job is getting killed with the following error message:
Oct 31 13:49:45 2008 13128 4 7.02 handleTSRegisterTerm(): TS reports task
<0> pid <30753> on host<node0833> killed or core dumped
My system consists of a cluster of 147 atoms (516 electrons) in a
47.3x47.3x51.6 (in bohr) box. I'm using a wavefn. cut off of 25 Ry & a
charge density cut off of 210 Ry. For ion_dynamics I'm using bfgs and for
electrons, I'm using the davidson diagonalization scheme.
The machine details are:
Model: IBM BCX/5120
Architecture: eServer e326 Cluster Opteron
Processor Type: Opteron Dual Core 2.6 GHz
Number of Nodes: 1280 (4 cores per node)
Number of Processors/cores: 2560/5120
Memory: 8 GB/node
Internal Network: Infiniband (5Gb/s)
Disk Space: 100 TB + SAN
Operating System: Red Hat RHEL4
The code has been complied using openmpi--1.2.5--intel--10.1
Can any one please let me know why the job is getting killed? Is it due to
some memory problem?
For the same job why does the memory requirement go on increasing?
Also, can you please let me know how the code calculates the memory
requirement? I tried to look into the clib/memstat.c file but could't make
much of it because I'm not familiar of C programming language.
With regards,
Prasenjit
--
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
+39 3807528672 (M)
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From ravitri2k at gmail.com Wed Nov 5 01:55:33 2008
From: ravitri2k at gmail.com (Ravi Maranganti)
Date: Tue, 4 Nov 2008 18:55:33 -0600
Subject: [Pw_forum] LO-TO splitting in insulators
Message-ID: <59b3d4f30811041655h4e99a792k8076ec2750ef42e0@mail.gmail.com>
Hello pwscf users
I want to find the real space interatomic force constants in an insulator
excluding the contribution from the macroscopic electric field. So i am
calculating the phonon dispersions by specifying .epsil.='false'. And then i
am using q2r.x to find out the real space force constants. Then when i use
matdyn.x with zasr='simple' to calculate the phonon dispersions , i can see
LO-TO splitting at the gamma point. What am i missing? Thanks !
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From nakhmanson at anl.gov Wed Nov 5 02:05:56 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Tue, 04 Nov 2008 19:05:56 -0600
Subject: [Pw_forum] Is maxirr=N working in phonon calculations?
Message-ID: <4910F174.10508@anl.gov>
Dear All,
I run a small test with a 5-atom PbTiO3 cell in P4/mmm
symmetry, where it is supposed to have 10 irreps (i.e.,
each 3d irrep in Pm-3m symmetry splits into a 1d+2d)
and I asked the program to compute only 5 of these
as shown below:
> node02 {1003} > more PbTiO3.tp-relaxed-STO-t.ph.G.inp
> 'tp-STO-t-PbTiO3, phonons at G'
> &inputph
> prefix = 'tp-STO-t-PbTiO3'
> amass(1) = 207.20000
> amass(2) = 47.86700
> amass(3) = 16.00000
> tr2_ph = 1e-20
> niter_ph = 100
> alpha_mix = 0.5
> maxirr = 5
> trans = .true.
> epsil = .true.
> fildyn = 'PbTiO3.tp-relaxed-STO-t.G.dyn'
> iverbosity = 1
> outdir='./'
> /
> 0.0 0.0 0.0
> node02 {1004} >
Still the code blasted through all 10 irreps. I grep-ped
out "maxirr" in /PH/*.f90 and saw that it is being set and reset
in multiple places (I cannot trace it without my head spinning),
so I decided to ask a question about this instead. Of course,
there is always a chance that I made a stupid error in my input,
so PLZ be kind to me :))
Also, is there any system to which irreps are computed first and
which later? Or is this process completely random, i.e. it would
be futile to cover a certain frequency window by computing only
some, but not all, irreps?
THX,
Serge
--
*********************************************************
Serge M. Nakhmanson phone: (630) 252-5205
Assistant Scientist fax: (630) 252-4798
MSD-212, Rm. C-224
Argonne National Laboratory
9700 S. Cass Ave.
Argonne, IL 60439
*********************************************************
From krishnachaitanya.gunturu at gmail.com Wed Nov 5 05:02:39 2008
From: krishnachaitanya.gunturu at gmail.com (Krishna chaitanya)
Date: Wed, 5 Nov 2008 09:32:39 +0530
Subject: [Pw_forum] mpi error while running pw.x
Message-ID: <eb9cf0990811042002h249e1f7bs43754efa8b579181@mail.gmail.com>
Dear Pwscf users,
while running pw.x on a 24 cores clusters (2x2 AMD nodes loaded with
RHEL-AS4) some times it is showing the following error after completing few
BFGS steps. But the problem is not appearing for all the runs. The error
message is
*[cli_0]: aborting job:
Fatal error in MPI_Comm_split: Other MPI error, error stack:
MPI_Comm_split(250).: MPI_Comm_split(comm=0x84000004, color=0, key=0,
new_comm=0x7fbfffdb6c) failed
MPIR_Comm_create(79): Too many communicators*
I am using the following command to run pw.x
* mpirun -machinefile $HOME/mpd.cores -np 24 pw.x -in file.in -npool 1 >
file.out < /dev/null &*
I have tried by changing the pool number but no use. Please help me in this
regard.
Regards
G. Krishna Chaitanya
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From giannozz at democritos.it Wed Nov 5 09:12:41 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 05 Nov 2008 09:12:41 +0100
Subject: [Pw_forum] memory problem
In-Reply-To: <627e0ffa0811041432i1faff684xec92d7b293f49afc@mail.gmail.com>
References: <627e0ffa0811041432i1faff684xec92d7b293f49afc@mail.gmail.com>
Message-ID: <49115579.8060904@democritos.it>
Prasenjit Ghosh wrote:
> per-process dynamical memory: 507.1 Mb
> per-process dynamical memory: 1867.8 Mb
what happens in the middle?
> Oct 31 13:49:45 2008 13128 4 7.02 handleTSRegisterTerm(): TS reports
> task <0> pid <30753> on host<node0833> killed or core dumped
> [...] Can any one please let me know why the job is getting killed?
of course, nobody can
> Is it due to some memory problem?
good guess
> For the same job why does the memory requirement go on increasing?
during a single scf step, the amount of required memory can increase,
but each scf step should take more or less always the same maximum
memory. It is impossible to say more without at least a complete
output. It might be a memory leak, which might come from a bug either
in the code or in the compiler or libraries.
> Also, can you please let me know how the code calculates the memory
> requirement?
with an appropriate (?) system library call. Calculating memory usage
in modern operating systems is a nontrivial task, so you have to hope
that what you get is a meaningful approximation to occupied dynamical
matrix (the static memory, i.e. the code itself including static arrays,
is typically small and can be estimated using "size pw.x" for instance)
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Wed Nov 5 09:15:31 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 05 Nov 2008 09:15:31 +0100
Subject: [Pw_forum] mpi error while running pw.x
In-Reply-To: <eb9cf0990811042002h249e1f7bs43754efa8b579181@mail.gmail.com>
References: <eb9cf0990811042002h249e1f7bs43754efa8b579181@mail.gmail.com>
Message-ID: <49115623.6010808@democritos.it>
Krishna chaitanya wrote:
> while running pw.x
version? compiler and mpi libraries?
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From prasenjit.jnc at gmail.com Wed Nov 5 09:39:38 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Wed, 5 Nov 2008 09:39:38 +0100
Subject: [Pw_forum] memory problem
In-Reply-To: <49115579.8060904@democritos.it>
References: <627e0ffa0811041432i1faff684xec92d7b293f49afc@mail.gmail.com>
<49115579.8060904@democritos.it>
Message-ID: <627e0ffa0811050039w2f662ed6wcb4ce4d9464f703d@mail.gmail.com>
Hi Paolo,
Thanks for your reply.
> > per-process dynamical memory: 507.1 Mb
> > per-process dynamical memory: 1867.8 Mb
>
> what happens in the middle?
507.1 Mb was the memory required at the beginning of one of the scf cycles.
Then the job was exited because the calculation time was over.......Then I
restart the calculation and the memory requirement jumps to 1867.8 Mb
> Is it due to some memory problem?
>
> good guess
>
> > For the same job why does the memory requirement go on increasing?
>
> during a single scf step, the amount of required memory can increase,
> but each scf step should take more or less always the same maximum
> memory.
Do you mean that from one scf cycle to another scf cycle, the memory can
increase while for different scf steps in an scf cycle it should take more
or less the same max. memory?? and if so, why does the memory requirement
from one scf cycle to another increase?....Has it something to do with the
diagonalization sub-routine?
> It is impossible to say more without at least a complete
> output. It might be a memory leak, which might come from a bug either
> in the code or in the compiler or libraries.
>
You can download the output file from the link given below:
http://www.ictp.it/~pghosh/ZnTPP-C70.gs.out
With regards,
Prasenjit.
--
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
+39 3807528672 (M)
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From giannozz at democritos.it Wed Nov 5 10:03:16 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 05 Nov 2008 10:03:16 +0100
Subject: [Pw_forum] help on "wrong total_weight"!
In-Reply-To: <94be399f0811020312t2bc72278gb389e2f4b1b6bae8@mail.gmail.com>
References: <94be399f0811020312t2bc72278gb389e2f4b1b6bae8@mail.gmail.com>
Message-ID: <49116154.30102@democritos.it>
shangy wrote:
> from frc_blk : error # 1
> wrong total_weight
> So, what's wrong with it?
the case you are trying to run is not correctly implemented,
I think. The algorithm transforming D(q) (force contants in
reciprocal space) into D(R) (force constants in real space)
assumes a uniform grid of q and the corresponding grid of R.
In the case of q=0 (i.e. R=0) the logic used inside routine
"wsweight" to assign weights breaks down. I never understood
the logic of that routine so I don't know how to fix it.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Wed Nov 5 10:03:30 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 05 Nov 2008 10:03:30 +0100
Subject: [Pw_forum] memory problem
In-Reply-To: <627e0ffa0811050039w2f662ed6wcb4ce4d9464f703d@mail.gmail.com>
References: <627e0ffa0811041432i1faff684xec92d7b293f49afc@mail.gmail.com> <49115579.8060904@democritos.it>
<627e0ffa0811050039w2f662ed6wcb4ce4d9464f703d@mail.gmail.com>
Message-ID: <49116162.6000108@democritos.it>
Prasenjit Ghosh wrote:
> 507.1 Mb was the memory required at the beginning of one of the scf cycles.
> Then the job was exited because the calculation time was over.......Then
> I restart the calculation and the memory requirement jumps to 1867.8 Mb
so there is something strange when restarting.
> Do you mean that from one scf cycle to another scf cycle, the memory can
> increase while for different scf steps in an scf cycle it should take
> more or less the same max. memory??
it depends on what you call a "cycle" and what you call a "step" ...
Anyway: actually the memory needed by self-consistency is allocated
at the beginning of the scf calculation, not during it, so the
allocated memory should never increase
P
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From degironc at sissa.it Wed Nov 5 10:12:17 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 05 Nov 2008 10:12:17 +0100
Subject: [Pw_forum] help on "wrong total_weight"!
In-Reply-To: <49116154.30102@democritos.it>
References: <94be399f0811020312t2bc72278gb389e2f4b1b6bae8@mail.gmail.com>
<49116154.30102@democritos.it>
Message-ID: <49116371.7000300@sissa.it>
Dear Shangy,
what is your system ... i.e. what are your Bravais lattice vectors and
values of nq1,nq2,nq3 in your phonon grid ?
stefano
Paolo Giannozzi wrote:
> shangy wrote:
>
>
>> from frc_blk : error # 1
>> wrong total_weight
>>
>> So, what's wrong with it?
>>
>
> the case you are trying to run is not correctly implemented,
> I think. The algorithm transforming D(q) (force contants in
> reciprocal space) into D(R) (force constants in real space)
> assumes a uniform grid of q and the corresponding grid of R.
> In the case of q=0 (i.e. R=0) the logic used inside routine
> "wsweight" to assign weights breaks down. I never understood
> the logic of that routine so I don't know how to fix it.
>
> Paolo
>
From prasenjit.jnc at gmail.com Wed Nov 5 10:22:02 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Wed, 5 Nov 2008 10:22:02 +0100
Subject: [Pw_forum] memory problem
In-Reply-To: <49116162.6000108@democritos.it>
References: <627e0ffa0811041432i1faff684xec92d7b293f49afc@mail.gmail.com>
<49115579.8060904@democritos.it>
<627e0ffa0811050039w2f662ed6wcb4ce4d9464f703d@mail.gmail.com>
<49116162.6000108@democritos.it>
Message-ID: <627e0ffa0811050122q453fd95an55158b24a22f9037@mail.gmail.com>
> 507.1 Mb was the memory required at the beginning of one of the scf
> cycles.
> > Then the job was exited because the calculation time was over.......Then
> > I restart the calculation and the memory requirement jumps to 1867.8 Mb
>
> so there is something strange when restarting.
>
Yes, but what is it? Can you please suggest some possible things to check
at??
>
> > Do you mean that from one scf cycle to another scf cycle, the memory can
> > increase while for different scf steps in an scf cycle it should take
> > more or less the same max. memory??
>
> it depends on what you call a "cycle" and what you call a "step" ...
> Anyway: actually the memory needed by self-consistency is allocated
> at the beginning of the scf calculation, not during it, so the
> allocated memory should never increase
> -
>
So why does it increase??
Prasenjit.
--
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
+39 3807528672 (M)
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From giannozz at democritos.it Wed Nov 5 12:14:16 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 5 Nov 2008 12:14:16 +0100
Subject: [Pw_forum] memory problem
In-Reply-To: <627e0ffa0811050122q453fd95an55158b24a22f9037@mail.gmail.com>
References: <627e0ffa0811041432i1faff684xec92d7b293f49afc@mail.gmail.com>
<49115579.8060904@democritos.it>
<627e0ffa0811050039w2f662ed6wcb4ce4d9464f703d@mail.gmail.com>
<49116162.6000108@democritos.it>
<627e0ffa0811050122q453fd95an55158b24a22f9037@mail.gmail.com>
Message-ID: <F89C8298-EA3C-4DA6-A103-6757526FC907@democritos.it>
On Nov 5, 2008, at 10:22 , Prasenjit Ghosh wrote:
> so there is something strange when restarting.
...or maybe there is nothing strange in restarting. Some op.sys. (AIX
for sure)
show the maximum memory usage. Restarting may require a lot of memory,
especially in parallel, but if this memory is deallocated, it is
available for later
usage. Of course, if it is no longer used and not deallocated, this
is a bug.
> Yes, but what is it? Can you please suggest some possible things to
> check at??
first thing to check is what "memstat" actually returns. This can be
checked
with a small program.
In the meantime: don't use "restart". You gain very little anyway.
> So why does it increase??
it doesn't
Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From giannozz at democritos.it Wed Nov 5 14:19:10 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 05 Nov 2008 14:19:10 +0100
Subject: [Pw_forum] Is maxirr=N working in phonon calculations?
In-Reply-To: <4910F174.10508@anl.gov>
References: <4910F174.10508@anl.gov>
Message-ID: <49119D4E.2020000@democritos.it>
Serge Nakhmanson wrote:
> Still the code blasted through all 10 irreps.
not sure whether the "maxirr" option really works. In the CVS
version it was replaced by other options that are useful for
Grid execution (i.e. splitting a long phonon calculation in
many smaller pieces rto be run on different machines). Its main
usage was to prevent the code from crashing for cpu time limit
in a ungraceful way, but option "max_seconds" can do the same.
> Also, is there any system to which irreps are computed first and
> which later? Or is this process completely random, i.e. it would
> be futile to cover a certain frequency window by computing only
> some, but not all, irreps?
I don't think this is going to work. Not sure how exactly
irreps are selected. If no symmetry is present, taht's easy:
atom 1 component x, y,z, atom 2 component x, y, z and so on.
In presence of symmetry, the irreps are obtained via a procedure
in which random matrices are symmetrized, so the order in which
they are produced is quite unpredictable (also the accuracy of
this answer is unpredictable, since it is based on vague
recollections)
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From eyvaz_isaev at yahoo.com Wed Nov 5 17:39:25 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 5 Nov 2008 08:39:25 -0800 (PST)
Subject: [Pw_forum] Projected density of states of phonon
In-Reply-To: <3a749910811010219o26ca43f1nc7eb08fcf3665ea6@mail.gmail.com>
Message-ID: <119997.29760.qm@web65712.mail.ac4.yahoo.com>
Hi,
If you like I can send you a code which can calculate more than projected phonon DOS.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
--- On Sat, 11/1/08, Bipul Rakshit <bipulrr at gmail.com> wrote:
> From: Bipul Rakshit <bipulrr at gmail.com>
> Subject: Re: [Pw_forum] Projected density of states of phonon
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Saturday, November 1, 2008, 12:19 PM
> Hello Pwscf users,
>
> I am calculating phonon of ScAs and ScSb using PWSCF, I
> read a paper
>
> Solid State Commun. 147 (2008) 198
>
> There the author mentioned about projected density of
> states of
> phonon. So can anybody tell me how to find that? Means what
> option we
> have to set in input file to obtain the projected density
> of states of
> phonon.
>
> It will be helpful for me
> thanks
>
> --
> Bipul Rakshit
> PhD Student,
> Barkatullah University,
> Bhopal 462026,
> MP, India
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
From zhaofeng at Princeton.EDU Wed Nov 5 18:18:29 2008
From: zhaofeng at Princeton.EDU (zhaofeng at Princeton.EDU)
Date: Wed, 5 Nov 2008 12:18:29 -0500
Subject: [Pw_forum] Libraries on Blue Gene/L
Message-ID: <4256.1225905509@princeton.edu>
BODY { font-family:Arial, Helvetica, sans-serif;font-size:12px;
}Dear members,
Currently I am porting CP code on BlueGene/L. I have met some
problems that are
related with libraries.
The compilation and linking options are shown below
./configure MPIF90=mpxlf90 CC=mpxlc F77=mpxlf LD=mpxlf90
LDFLAGS="-L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
-lmsglayer.rts -lrts.rts -
ldevices.rts"
BLAS_LIBS="/bgl/local/lib/libblas440.a"
LAPACK_LIBS="/bgl/local/lib/liblapack440.a
/bgl/local/lib/scalapack/libscalapack.a"
CFLAGS="-qarch=440 -qmaxmem=64000"
FFLAGS="-qalias=noaryovrlp -I../include -O3 -qstrict -qarch=440d
-qtune=440 -qsuffix=cpp=f90 -qdpc -qalias=nointpt"
FFT_LIBS="/bgl/local/fftw-3.1.2/lib/libfftw3.a"
There is not problem in obtaining cp.x when "make cp". We test 64
water using 256
processors(128 nodes) with number of task group equal to 2, and the
speed of cp is 6 sec
per step, which is good(If some of you have better suggestions for
configuration which can lead to good performance, that will be so
great).
But we need to us cp-wf as well and find that wannier part takes
also 6 sec per step, which is really
unacceptable.We look into it and find that there are calls of DGEMM
and ZHPEV which are quite time consuming(in wf.f90). For instance,
ZHPEV takes 1.9sec per step and ZGEMM is 0.14 sec per step. Since
ZGEMM and ZHPEV are both the calls in the library of LAPACK, we
conclude it is because of bad choice of lapack library, is it
correct?
Currently the awkward situation is that there aren't ESSL
libraries on our Blue Gene, but some others provided by an IBM'er as
a part of the original training class. So I have little to do with
this lapack library. And I have also searched our forum content a
little bit and found few related result. I am not sure whether it is
enough to choose the correct lapack library. Or we need a complete
ESSL library so that the computing time of ZGEMM and ZHPEV can be
decreased a lot. If it is the former case, can anyone who has lapack
library of ESSL shares with me?
Thank you in advance.
best
zhaofeng li
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From bipulrr at gmail.com Wed Nov 5 18:39:17 2008
From: bipulrr at gmail.com (Bipul Rakshit)
Date: Wed, 5 Nov 2008 23:09:17 +0530
Subject: [Pw_forum] Projected density of states of phonon
In-Reply-To: <119997.29760.qm@web65712.mail.ac4.yahoo.com>
References: <3a749910811010219o26ca43f1nc7eb08fcf3665ea6@mail.gmail.com>
<119997.29760.qm@web65712.mail.ac4.yahoo.com>
Message-ID: <3a749910811050939t64cdd78el649d7c82e514e87e@mail.gmail.com>
Dear Prof. Eyvaz Isaev,
Yes definitely. I would like to work with that code. Its a honor to
work with you. I am waiting.
Thanks
On 11/5/08, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:
> Hi,
>
> If you like I can send you a code which can calculate more than projected
> phonon DOS.
>
> Bests,
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
>
> --- On Sat, 11/1/08, Bipul Rakshit <bipulrr at gmail.com> wrote:
>
>> From: Bipul Rakshit <bipulrr at gmail.com>
>> Subject: Re: [Pw_forum] Projected density of states of phonon
>> To: "PWSCF Forum" <pw_forum at pwscf.org>
>> Date: Saturday, November 1, 2008, 12:19 PM
>> Hello Pwscf users,
>>
>> I am calculating phonon of ScAs and ScSb using PWSCF, I
>> read a paper
>>
>> Solid State Commun. 147 (2008) 198
>>
>> There the author mentioned about projected density of
>> states of
>> phonon. So can anybody tell me how to find that? Means what
>> option we
>> have to set in input file to obtain the projected density
>> of states of
>> phonon.
>>
>> It will be helpful for me
>> thanks
>>
>> --
>> Bipul Rakshit
>> PhD Student,
>> Barkatullah University,
>> Bhopal 462026,
>> MP, India
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Bipul Rakshit
PhD Student,
Barkatullah University,
Bhopal 462026,
MP, India
From giannozz at democritos.it Wed Nov 5 19:02:03 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 05 Nov 2008 19:02:03 +0100
Subject: [Pw_forum] Libraries on Blue Gene/L
In-Reply-To: <4256.1225905509@princeton.edu>
References: <4256.1225905509@princeton.edu>
Message-ID: <4911DF9B.5050008@democritos.it>
zhaofeng at Princeton.EDU wrote:
> [...] We look into it and find that there are calls of DGEMM and ZHPEV
> which are quite time consuming(in wf.f90). [...]
> Since ZGEMM and ZHPEV are both the calls in the library of LAPACK, we
> conclude it is because of bad choice of lapack library, is it correct?
maybe, or maybe this is just part of the story. I don't know what those
routines are used for in wf.f90, but presumably they operate on NxN
matrices, where N is the number of Kohn-Sham states (if not, what
follows may not apply). There used to be many such matrices in both
CP and PW, replicated on all processors, with the related matrix
operations (matrix-matrix multiplication and diagonalization) also
replicated and not parallelized. The conventional wisdom was, "they
are small". When you run on many processors, however, those "small"
matrices gobble up all the memory, while the related matrix operations
gobble up all the CPU. Almost all of them are now distributed across
processors, the related operations parallelized. Unfortunately the
Wannier-function CP code is a different branch that has somewhat
fallen behind the rest of the distribution.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From arunmanna at JNCASR.AC.IN Wed Nov 5 19:39:12 2008
From: arunmanna at JNCASR.AC.IN (Arun Kumar Manna)
Date: Wed, 5 Nov 2008 22:39:12 +0400 (RET)
Subject: [Pw_forum] Regarding raman tensor components
Message-ID: <36281.172.16.1.1.1225910352.squirrel@172.16.1.1>
Dear All,
Could anybody please tell me how the raman tensor components are written in
the output file? Here I have attached the some portion of my output file
containing raman tensors and corresponding frequencies. I got 2
(-ve) frequency values but this should not be happened, it should be close
to zero for gamma point calculation.
I have 2 atom per unit cell.
Raman tensor (A^2)
atom # 1 pol. 1
0.580430157418E+01 0.251559399806E-15 0.000000000000E+00
0.000000000000E+00 -0.275157990883E+01 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.981426367951E+00
atom # 1 pol. 2
-0.503118799612E-15 0.207169333588E+01 0.000000000000E+00
0.207169333588E+01 0.201247519845E-14 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
atom # 1 pol. 3
0.104026700307E-26 0.180179623869E-26 0.178349023792E+01
0.180179623869E-26 0.312080425139E-26 0.000000000000E+00
0.178349023792E+01 0.000000000000E+00 0.000000000000E+00
atom # 2 pol. 1
-0.580430157418E+01 -0.251559399806E-15 0.000000000000E+00
0.000000000000E+00 0.275157990883E+01 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 -0.981426367951E+00
atom # 2 pol. 2
0.503118799612E-15 -0.207169333588E+01 0.000000000000E+00
-0.207169333588E+01 -0.201247519845E-14 0.000000000000E+00
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
atom # 2 pol. 3
0.104026700307E-26 0.180179623869E-26 -0.178349023792E+01
0.180179623869E-26 0.312080425139E-26 0.000000000000E+00
-0.178349023792E+01 0.000000000000E+00 0.000000000000E+00
omega( 1) = -7.762658 [THz] = -258.936116 [cm-1]
omega( 2) = -1.523313 [THz] = -50.812602 [cm-1]
omega( 3) = 2.554965 [THz] = 85.225041 [cm-1]
omega( 4) = 4.840206 [THz] = 161.452955 [cm-1]
omega( 5) = 5.290463 [THz] = 176.472039 [cm-1]
omega( 6) = 40.167212 [THz] = 1339.842894 [cm-1]
Please help me to understand this.
Thanks in advance,
Arun
--
PhD Student
JNCASR, Bangalore-560064
India
--
PhD Student
JNCASR, Bangalore-560064
India
From akohlmey at cmm.chem.upenn.edu Wed Nov 5 21:59:20 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 5 Nov 2008 15:59:20 -0500
Subject: [Pw_forum] Libraries on Blue Gene/L
In-Reply-To: <4256.1225905509@princeton.edu>
References: <4256.1225905509@princeton.edu>
Message-ID: <7b6913e90811051259n179a0327t39dd8529d0a568b6@mail.gmail.com>
hi,
FWIW, the contact for optimized libraries for BG/L is alessandro curioni
at IBM research in zurich <cur at zurich.ibm.com>.
for optimal performance you do not need ESSL, but a specially tuned
LAPACK and mostly BLAS (i.e. DGEMM and related).
On Wed, Nov 5, 2008 at 12:18 PM, <zhaofeng at princeton.edu> wrote:
> Dear members,
>
> Currently I am porting CP code on BlueGene/L. I have met some problems
> that are
> related with libraries.
> The compilation and linking options are shown below
> ./configure MPIF90=mpxlf90 CC=mpxlc F77=mpxlf LD=mpxlf90
> LDFLAGS="-L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts -lmsglayer.rts
> -lrts.rts -
> ldevices.rts"
> BLAS_LIBS="/bgl/local/lib/libblas440.a"
> LAPACK_LIBS="/bgl/local/lib/liblapack440.a
> /bgl/local/lib/scalapack/libscalapack.a"
> CFLAGS="-qarch=440 -qmaxmem=64000"
> FFLAGS="-qalias=noaryovrlp -I../include -O3 -qstrict -qarch=440d -qtune=440
> -qsuffix=cpp=f90 -qdpc -qalias=nointpt"
> FFT_LIBS="/bgl/local/fftw-3.1.2/lib/libfftw3.a"
>
> There is not problem in obtaining cp.x when "make cp". We test 64 water
> using 256
> processors(128 nodes) with number of task group equal to 2, and the speed of
> cp is 6 sec
> per step, which is good(If some of you have better suggestions for
> configuration which can lead to good performance, that will be so great).
> But we need to us cp-wf as well and find that wannier part takes also 6
> sec per step, which is really
> unacceptable.We look into it and find that there are calls of DGEMM and
> ZHPEV which are quite time consuming(in wf.f90). For instance, ZHPEV takes
> 1.9sec per step and ZGEMM is 0.14 sec per step. Since ZGEMM and ZHPEV are
> both the calls in the library of LAPACK, we conclude it is because of bad
no, ZGEMM is part of BLAS and not LAPACK.
nevertheless, this does not necessarily mean, that those are the culprit.
it could just be, that this part of the code is not as parallel as the rest
and thus is doing a lot of redundant work. i saw this quite often with
wannier implementations in different codes.
cheers,
axel.
> choice of lapack library, is it correct?
> Currently the awkward situation is that there aren't ESSL libraries on our
> Blue Gene, but some others provided by an IBM'er as a part of the original
> training class. So I have little to do with this lapack library. And I have
> also searched our forum content a little bit and found few related result. I
> am not sure whether it is enough to choose the correct lapack library. Or we
> need a complete ESSL library so that the computing time of ZGEMM and ZHPEV
> can be decreased a lot. If it is the former case, can anyone who has lapack
> library of ESSL shares with me?
> Thank you in advance.
>
> best
> zhaofeng li
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From nakhmanson at anl.gov Thu Nov 6 02:03:06 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Wed, 05 Nov 2008 19:03:06 -0600
Subject: [Pw_forum] Is maxirr=N working in phonon calculations?
In-Reply-To: <49119D4E.2020000@democritos.it>
References: <4910F174.10508@anl.gov> <49119D4E.2020000@democritos.it>
Message-ID: <4912424A.2080709@anl.gov>
Dear Paolo,
Thank you very much for exhaustively answering my questions, even
the one that I did not ask, i.e., if irreps are picked at random,
then what is the purpose of using "maxirr=N"? :))
Your comment on randomness of irrep generation makes sense to me.
I only know a general answer to how it is done -- by induction
from an (Abelian) group of crystal translations -- but am
rusty on particular numerical algorithms. However, I got an
excellent new book by El-Batanouny and Wooten (ISBN 9780521828451),
all the details should be in there.
THX again,
S.
Paolo Giannozzi wrote:
> Serge Nakhmanson wrote:
>
>> Still the code blasted through all 10 irreps.
>
> not sure whether the "maxirr" option really works. In the CVS
> version it was replaced by other options that are useful for
> Grid execution (i.e. splitting a long phonon calculation in
> many smaller pieces rto be run on different machines). Its main
> usage was to prevent the code from crashing for cpu time limit
> in a ungraceful way, but option "max_seconds" can do the same.
>
>> Also, is there any system to which irreps are computed first and
>> which later? Or is this process completely random, i.e. it would
>> be futile to cover a certain frequency window by computing only
>> some, but not all, irreps?
>
> I don't think this is going to work. Not sure how exactly
> irreps are selected. If no symmetry is present, taht's easy:
> atom 1 component x, y,z, atom 2 component x, y, z and so on.
> In presence of symmetry, the irreps are obtained via a procedure
> in which random matrices are symmetrized, so the order in which
> they are produced is quite unpredictable (also the accuracy of
> this answer is unpredictable, since it is based on vague
> recollections)
>
> Paolo
--
*********************************************************
Serge M. Nakhmanson phone: (630) 252-5205
Assistant Scientist fax: (630) 252-4798
MSD-212, Rm. C-224
Argonne National Laboratory
9700 S. Cass Ave.
Argonne, IL 60439
*********************************************************
From n_madani2008 at yahoo.com Thu Nov 6 08:05:31 2008
From: n_madani2008 at yahoo.com (Noushin Madani)
Date: Wed, 5 Nov 2008 23:05:31 -0800 (PST)
Subject: [Pw_forum] DDDMMMFFFTTT----------
Message-ID: <633602.21147.qm@web45611.mail.sp1.yahoo.com>
?
Dear proffessors,
Dose the software Espresso have the capability of performing "DMFT+LDA" calculations?
Can you kindly help me whit? calculations in this approach??
best regards,
Noushin?Madani
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From sporevoyager at gmail.com Thu Nov 6 08:13:27 2008
From: sporevoyager at gmail.com (shangy)
Date: Thu, 6 Nov 2008 15:13:27 +0800
Subject: [Pw_forum] help on "wrong total_weight"!
In-Reply-To: <49116371.7000300@sissa.it>
References: <94be399f0811020312t2bc72278gb389e2f4b1b6bae8@mail.gmail.com>
<49116154.30102@democritos.it> <49116371.7000300@sissa.it>
Message-ID: <94be399f0811052313y68e428ewa6bcd337268638bf@mail.gmail.com>
Dear Paolo and Stefano:
Thanks for your response!
I'm an newbie bird in this field. I didn't understand the routines
implemented in the SUBROUTINE setupmat, frc_blk and wsweight related with
the error message though I digged it these days. As the last mail said, I
got the good optic frequency (514.4 cm-1) and phonon dos (except some small
jags, Paolo has talked the problem recently) of perfect Si cubic supercell
(64 atoms) with the similar calculation. The capacity of heat deduced form
the phonon-dos with qha method agrees well with the experiments far from the
melting point. Thus, I don't know if my system (there is one vacancy in the
Si cubic supercell (63 atoms)) is a special case that the QE neglect it?
There're two similar error reports in the mailist:
------
http://www.democritos.it/pipermail/pw_forum/2005-March/002237.html
http://www.democritos.it/pipermail/pw_forum/2005-September/002985.html
But no solution is searched in the forum.
The whole inputfile and detail information with the calculation can be found
in the last mail, please see :
------
http://www.democritos.it/pipermail/pw_forum/2008-November/010604.html
I'd like to complete some missed information. The system is a Si cubic
supercell consist of 63 Si atoms and one vacancy. The symmetry of the
optimized vacancy is D2d with 2x2x2 K-points calculation. I want to
calculate the normal modes(the calculation succed with the help of dynmat.x)
and phonon-dos (complained the error message) of the Si-vacancy at gamma
point. The nq1, nq2, nq3 in the q2r.x inputfile are 1,1,1. The Bravais
lattice vectors are a1=(20.7, 0.0, 0.0) a2=(0.0, 20.7, 0.0) a3=(0.0, 0.0,
20.7) (bohr). The missed Si coordinates and K-points in the last mail are as
follows:
----------
ATOMIC_POSITIONS (crystal)
Si 0.001043701 0.001356413 0.001004974
Si 0.001048202 0.001362083 0.501007444
Si 0.001050455 0.501358186 0.001011586
Si 0.001046482 0.501356271 0.501006744
Si 0.501045999 0.001362119 0.001009524
Si 0.501044501 0.001357885 0.501005491
Si 0.501045740 0.501356317 0.001007885
Si 0.001268624 0.252410615 0.251355812
Si 0.000829871 0.252408103 0.750663110
Si 0.000827602 0.750310413 0.251352036
Si 0.001262791 0.750308542 0.750659026
Si 0.500777242 0.253232175 0.253937929
Si 0.501321645 0.253227322 0.748086032
Si 0.501322298 0.749496729 0.253928447
Si 0.500770698 0.749495531 0.748090481
Si 0.250753116 0.000420584 0.250713375
Si 0.250755013 0.002301702 0.751301662
Si 0.256865117 0.502928662 0.256826867
Si 0.256857640 0.499801588 0.745196866
Si 0.751339485 0.002301969 0.250715278
Si 0.751334685 0.000419907 0.751296818
Si 0.745236573 0.499801834 0.256819546
Si 0.745240611 0.502921337 0.745200650
Si 0.251395237 0.252410315 0.001231375
Si 0.253975651 0.253231753 0.500736684
Si 0.251391646 0.750310650 0.000787549
Si 0.253966672 0.749496644 0.501284599
Si 0.750701130 0.252408038 0.000789912
Si 0.748125761 0.253227313 0.501284115
Si 0.750697263 0.750308834 0.001225338
Si 0.748130611 0.749496051 0.500729906
Si 0.375594189 0.125617304 0.375554751
Si 0.375812394 0.127638235 0.875613809
Si 0.387395476 0.621743477 0.387357570
Si 0.376401662 0.625698840 0.874722919
Si 0.875651763 0.127638043 0.375773534
Si 0.876129022 0.126660907 0.876090121
Si 0.874763430 0.625698823 0.376362307
Si 0.874120609 0.626013672 0.874082762
Si 0.125958937 0.126661240 0.125920589
Si 0.126445899 0.127638963 0.626241808
Si 0.127980992 0.626015062 0.127941115
Si 0.127330868 0.625698563 0.625649892
Si 0.626280048 0.127639302 0.126406316
Si 0.626494904 0.125616262 0.626456526
Si 0.625688397 0.625698764 0.127293638
Si 0.614715722 0.621743828 0.614674751
Si 0.127338800 0.377021600 0.376364662
Si 0.127979445 0.376704589 0.874079501
Si 0.126440898 0.875084423 0.375771512
Si 0.125960180 0.876054614 0.876088889
Si 0.614709072 0.380993663 0.387356636
Si 0.625692450 0.377018091 0.874721282
Si 0.626500342 0.877104512 0.375554271
Si 0.626279534 0.875085653 0.875613402
Si 0.376404049 0.377021434 0.127301609
Si 0.387394001 0.380993199 0.614668635
Si 0.375810504 0.875084175 0.126401390
Si 0.375593817 0.877104386 0.626461944
Si 0.874117288 0.376704764 0.127939639
Si 0.874761878 0.377017971 0.625653962
Si 0.876127885 0.876054763 0.125921778
Si 0.875651286 0.875085803 0.626241226
K_POINTS
1
0.0 0.0 0.0 1.0
I'd like to paste the site where the dynamical matrices file writen by the
ph.x again:
http://www.divshare.com/download/5725901-c73
You can check or test it. Please be patient for 15 seconds adversting when
you download it :).
Thanks in advance!
Best regards!
shangy
Graduate School of Chinese Academy of Sciences
2008/11/5 Stefano de Gironcoli <degironc at sissa.it>
> Dear Shangy,
> what is your system ... i.e. what are your Bravais lattice vectors and
> values of nq1,nq2,nq3 in your phonon grid ?
> stefano
>
> Paolo Giannozzi wrote:
> > shangy wrote:
> >
> >
> >> from frc_blk : error # 1
> >> wrong total_weight
> >>
> >> So, what's wrong with it?
> >>
> >
> > the case you are trying to run is not correctly implemented,
> > I think. The algorithm transforming D(q) (force contants in
> > reciprocal space) into D(R) (force constants in real space)
> > assumes a uniform grid of q and the corresponding grid of R.
> > In the case of q=0 (i.e. R=0) the logic used inside routine
> > "wsweight" to assign weights breaks down. I never understood
> > the logic of that routine so I don't know how to fix it.
> >
> > Paolo
> >
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From baroni at sissa.it Thu Nov 6 08:16:54 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 6 Nov 2008 08:16:54 +0100
Subject: [Pw_forum] DDDMMMFFFTTT----------
In-Reply-To: <633602.21147.qm@web45611.mail.sp1.yahoo.com>
References: <633602.21147.qm@web45611.mail.sp1.yahoo.com>
Message-ID: <47A27DE6-F989-4CFA-8DD5-31F67CA38530@sissa.it>
On Nov 6, 2008, at 8:05 AM, Noushin Madani wrote:
>
> Dear proffessors,
> Dose the software Espresso have the capability of performing "DMFT
> +LDA" calculations?
NO
> Can you kindly help me whit calculations in this approach??
not at this time
SB
> best regards,
> Noushin Madani
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
La morale est une logique de l'action comme la logique est une morale
de la pens?e - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From baroni at sissa.it Thu Nov 6 08:25:06 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 6 Nov 2008 08:25:06 +0100
Subject: [Pw_forum] Is maxirr=N working in phonon calculations?
In-Reply-To: <4912424A.2080709@anl.gov>
References: <4910F174.10508@anl.gov> <49119D4E.2020000@democritos.it>
<4912424A.2080709@anl.gov>
Message-ID: <D6C67D08-BAC1-4E67-8FC4-283582F3C81B@sissa.it>
On Nov 6, 2008, at 2:03 AM, Serge Nakhmanson wrote:
> Dear Paolo,
>
> Thank you very much for exhaustively answering my questions, even
> the one that I did not ask, i.e., if irreps are picked at random,
> then what is the purpose of using "maxirr=N"? :))
>
> Your comment on randomness of irrep generation makes sense to me.
> I only know a general answer to how it is done -- by induction
> from an (Abelian) group of crystal translations -- but am
> rusty on particular numerical algorithms. However, I got an
> excellent new book by El-Batanouny and Wooten (ISBN 9780521828451),
> all the details should be in there.
I do not know about the book, but I am afraid that what is implemented
in the code is not anything worth reporting in a book. The idea is as
follows. The code already contains all the weaponery for simmetrizing
all kind of stuff with respect to the small group of the point in the
Brillouin zone we are working at. In particular, you fill the
dynamical matrix with random numbers and then symmetrize it. The
resulting matrix will commute with all the operations of the small
group, and its eigenvectors will therefore realize a number of
irreducible representation of the group. As simple as that. Do not ask
me about the details of the implementation, though. The documentation
(as poor as it may be) is the code itself ...
Cheers - SB
>
>
> THX again,
>
> S.
>
> Paolo Giannozzi wrote:
>> Serge Nakhmanson wrote:
>>
>>> Still the code blasted through all 10 irreps.
>>
>> not sure whether the "maxirr" option really works. In the CVS
>> version it was replaced by other options that are useful for
>> Grid execution (i.e. splitting a long phonon calculation in
>> many smaller pieces rto be run on different machines). Its main
>> usage was to prevent the code from crashing for cpu time limit
>> in a ungraceful way, but option "max_seconds" can do the same.
>>
>>> Also, is there any system to which irreps are computed first and
>>> which later? Or is this process completely random, i.e. it would
>>> be futile to cover a certain frequency window by computing only
>>> some, but not all, irreps?
>>
>> I don't think this is going to work. Not sure how exactly
>> irreps are selected. If no symmetry is present, taht's easy:
>> atom 1 component x, y,z, atom 2 component x, y, z and so on.
>> In presence of symmetry, the irreps are obtained via a procedure
>> in which random matrices are symmetrized, so the order in which
>> they are produced is quite unpredictable (also the accuracy of
>> this answer is unpredictable, since it is based on vague
>> recollections)
>>
>> Paolo
>
>
> --
> *********************************************************
> Serge M. Nakhmanson phone: (630) 252-5205
> Assistant Scientist fax: (630) 252-4798
> MSD-212, Rm. C-224
> Argonne National Laboratory
> 9700 S. Cass Ave.
> Argonne, IL 60439
> *********************************************************
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
La morale est une logique de l'action comme la logique est une morale
de la pens?e - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From baroni at sissa.it Thu Nov 6 08:36:38 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 6 Nov 2008 08:36:38 +0100
Subject: [Pw_forum] Is maxirr=N working in phonon calculations?
In-Reply-To: <D6C67D08-BAC1-4E67-8FC4-283582F3C81B@sissa.it>
References: <4910F174.10508@anl.gov> <49119D4E.2020000@democritos.it>
<4912424A.2080709@anl.gov>
<D6C67D08-BAC1-4E67-8FC4-283582F3C81B@sissa.it>
Message-ID: <EB20E624-2D3B-444F-B89A-08D01A63CDB9@sissa.it>
PS: randomness is necessary to make sure (almost sure ...) that
degenerate eigenvectors belong to an irredeucible (rather than
reducible) representation. Stefano
On Nov 6, 2008, at 8:25 AM, Stefano Baroni wrote:
>
> On Nov 6, 2008, at 2:03 AM, Serge Nakhmanson wrote:
>
>> Dear Paolo,
>>
>> Thank you very much for exhaustively answering my questions, even
>> the one that I did not ask, i.e., if irreps are picked at random,
>> then what is the purpose of using "maxirr=N"? :))
>>
>> Your comment on randomness of irrep generation makes sense to me.
>> I only know a general answer to how it is done -- by induction
>> from an (Abelian) group of crystal translations -- but am
>> rusty on particular numerical algorithms. However, I got an
>> excellent new book by El-Batanouny and Wooten (ISBN 9780521828451),
>> all the details should be in there.
>
> I do not know about the book, but I am afraid that what is
> implemented in the code is not anything worth reporting in a book.
> The idea is as follows. The code already contains all the weaponery
> for simmetrizing all kind of stuff with respect to the small group
> of the point in the Brillouin zone we are working at. In particular,
> you fill the dynamical matrix with random numbers and then
> symmetrize it. The resulting matrix will commute with all the
> operations of the small group, and its eigenvectors will therefore
> realize a number of irreducible representation of the group. As
> simple as that. Do not ask me about the details of the
> implementation, though. The documentation (as poor as it may be) is
> the code itself ...
>
> Cheers - SB
>
>>
>>
>> THX again,
>>
>> S.
>>
>> Paolo Giannozzi wrote:
>>> Serge Nakhmanson wrote:
>>>
>>>> Still the code blasted through all 10 irreps.
>>>
>>> not sure whether the "maxirr" option really works. In the CVS
>>> version it was replaced by other options that are useful for
>>> Grid execution (i.e. splitting a long phonon calculation in
>>> many smaller pieces rto be run on different machines). Its main
>>> usage was to prevent the code from crashing for cpu time limit
>>> in a ungraceful way, but option "max_seconds" can do the same.
>>>
>>>> Also, is there any system to which irreps are computed first and
>>>> which later? Or is this process completely random, i.e. it would
>>>> be futile to cover a certain frequency window by computing only
>>>> some, but not all, irreps?
>>>
>>> I don't think this is going to work. Not sure how exactly
>>> irreps are selected. If no symmetry is present, taht's easy:
>>> atom 1 component x, y,z, atom 2 component x, y, z and so on.
>>> In presence of symmetry, the irreps are obtained via a procedure
>>> in which random matrices are symmetrized, so the order in which
>>> they are produced is quite unpredictable (also the accuracy of
>>> this answer is unpredictable, since it is based on vague
>>> recollections)
>>>
>>> Paolo
>>
>>
>> --
>> *********************************************************
>> Serge M. Nakhmanson phone: (630) 252-5205
>> Assistant Scientist fax: (630) 252-4798
>> MSD-212, Rm. C-224
>> Argonne National Laboratory
>> 9700 S. Cass Ave.
>> Argonne, IL 60439
>> *********************************************************
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
> ---
> Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
> Trieste
> http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
> stefanobaroni (skype)
>
> La morale est une logique de l'action comme la logique est une
> morale de la pens?e - Jean Piaget
>
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
La morale est une logique de l'action comme la logique est une morale
de la pens?e - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From giannozz at democritos.it Thu Nov 6 09:00:26 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 06 Nov 2008 09:00:26 +0100
Subject: [Pw_forum] Regarding raman tensor components
In-Reply-To: <36281.172.16.1.1.1225910352.squirrel@172.16.1.1>
References: <36281.172.16.1.1.1225910352.squirrel@172.16.1.1>
Message-ID: <4912A41A.6060808@democritos.it>
Arun Kumar Manna wrote:
> Could anybody please tell me how the raman tensor components are written in
> the output file?
the Raman tensor is the derivative of the dielectric tensor
wrt an atomic displacement
> atom # 1 pol. 1
this is U_x(1) (displacement of atom 1 along x)
> 0.580430157418E+01 0.251559399806E-15 0.000000000000E+00
> 0.000000000000E+00 -0.275157990883E+01 0.000000000000E+00
> 0.000000000000E+00 0.000000000000E+00 0.981426367951E+00
and this is D \epsilon_{\alpha\beta} / D( U_x(1) ), and so on
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Thu Nov 6 09:03:35 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 06 Nov 2008 09:03:35 +0100
Subject: [Pw_forum] Is maxirr=N working in phonon calculations?
In-Reply-To: <4912424A.2080709@anl.gov>
References: <4910F174.10508@anl.gov> <49119D4E.2020000@democritos.it>
<4912424A.2080709@anl.gov>
Message-ID: <4912A4D7.9040403@democritos.it>
Serge Nakhmanson wrote:
> Paolo Giannozzi wrote:
>> not sure whether the "maxirr" option really works.
now I am sure: it doesn't.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From forum.san at gmail.com Thu Nov 6 09:43:48 2008
From: forum.san at gmail.com (Sangamesh B)
Date: Thu, 6 Nov 2008 14:13:48 +0530
Subject: [Pw_forum] Problem in execution of pw.x (qe-4.0.2)
In-Reply-To: <49104887.2000800@sissa.it>
References: <cb60cbc40811040438wbf74268hf6daeb7d7f8cf55e@mail.gmail.com>
<49104887.2000800@sissa.it>
Message-ID: <cb60cbc40811060043k3aab6329p1079c714f5eb54fa@mail.gmail.com>
On Tue, Nov 4, 2008 at 6:35 PM, Lorenzo Paulatto <paulatto at sissa.it> wrote:
> Sangamesh B ha scritto:
>> ###########################################
>> # FROM IOTK LIBRARY, VERSION 1.1.0development
>> # UNRECOVERABLE ERROR (ierr=-1)
>> # ERROR IN: iotk_scan_begin (iotk_scan.spp:155)
>> # CVS Revision: 1.7
>> # Tag not found
>> namel=HEADER
>> #############################################################################
>>
>
> Dear Sangamesh,
> since you are not providing us your input file I can only guess. You
> error can be caused by changing some input options and parameters. If I
> remember correctly, you have to clean the temporary files and directory
> for the job if you change the number of pools.
>
Thanks for the help
> --
> Lorenzo Paulatto
> SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www: http://people.sissa.it/~paulatto/
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
From prasenjit.jnc at gmail.com Thu Nov 6 12:58:12 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Thu, 6 Nov 2008 12:58:12 +0100
Subject: [Pw_forum] compilation problem on sp5@cineca
Message-ID: <627e0ffa0811060358o58aa1732u686243676f367abe@mail.gmail.com>
Hi,
I'm trying to compile espresso on sp5 at cineca with xlf compiler. The
following is the error message:
mpxlf95 -qalias=noaryovrlp:nointptr -I../include -O3 -qstrict
-qarch=auto -qtune=auto -qdpc -Q -qessl -qfree=f90 -qsuffix=cpp=f90
-WF,-D__AIX,-D__XLF,-D__ESSL,-D__MASS,-D__PARA,-D__MPI -I../Modules -I../PW
-I../PH -I../iotk/src -c input.f90
"input.f90", line 282.8: 1511-025 (S) Logical expressions must only be
compared using EQV and NEQV operators.
"input.f90", line 282.22: 1511-025 (S) Logical expressions must only be
compared using EQV and NEQV operators.
"input.f90", line 284.8: 1511-025 (S) Logical expressions must only be
compared using EQV and NEQV operators.
"input.f90", line 284.28: 1511-025 (S) Logical expressions must only be
compared using EQV and NEQV operators.
** iosys === End of Compilation 1 ===
** read_cards === End of Compilation 2 ===
** verify_tmpdir === End of Compilation 3 ===
1501-511 Compilation failed for file input.f90.
make: 1254-004 The error code from the last command is 1.
Stop.
make: 1254-004 The error code from the last command is 2.
It seems the compiler doesn't like the way the logical expressions are
written.
Is there a way to solve it, other than changing the compiler?
With regards,
Prasenjit.
--
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
+39 3807528672 (M)
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From giannozz at democritos.it Thu Nov 6 12:59:34 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 06 Nov 2008 12:59:34 +0100
Subject: [Pw_forum] compilation problem on sp5@cineca
In-Reply-To: <627e0ffa0811060358o58aa1732u686243676f367abe@mail.gmail.com>
References: <627e0ffa0811060358o58aa1732u686243676f367abe@mail.gmail.com>
Message-ID: <4912DC26.5060103@democritos.it>
Prasenjit Ghosh wrote:
> I'm trying to compile espresso
version?
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From prasenjit.jnc at gmail.com Thu Nov 6 13:08:23 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Thu, 6 Nov 2008 13:08:23 +0100
Subject: [Pw_forum] compilation problem on sp5@cineca
In-Reply-To: <4912DC26.5060103@democritos.it>
References: <627e0ffa0811060358o58aa1732u686243676f367abe@mail.gmail.com>
<4912DC26.5060103@democritos.it>
Message-ID: <627e0ffa0811060408p51707c0fue4bd8708dec31e7c@mail.gmail.com>
4.0.1
2008/11/6 Paolo Giannozzi <giannozz at democritos.it>
> Prasenjit Ghosh wrote:
>
> > I'm trying to compile espresso
>
> version?
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
+39 3807528672 (M)
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From dat36 at cam.ac.uk Thu Nov 6 13:09:50 2008
From: dat36 at cam.ac.uk (David Tompsett)
Date: Thu, 06 Nov 2008 12:09:50 +0000
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <Pine.LNX.4.64.0811011908330.2282@localhost.localdomain>
References: <490B39BC.2080306@cam.ac.uk>
<c92002fa0810311309u652cbcc2ob4ec433c35bae3e6@mail.gmail.com>
<Prayer.1.3.1.0811011156550.27996@hermes-1.csi.cam.ac.uk>
<Pine.LNX.4.64.0811011121570.2302@localhost.localdomain>
<Prayer.1.3.1.0811011633190.20751@hermes-1.csi.cam.ac.uk>
<Pine.LNX.4.64.0811011246540.2302@localhost.localdomain>
<Prayer.1.3.1.0811011931440.21596@hermes-1.csi.cam.ac.uk>
<Pine.LNX.4.64.0811011908330.2282@localhost.localdomain>
Message-ID: <4912DE8E.8020403@cam.ac.uk>
Dear Axel and All,
I have tried to run the example01 with the
serial executable and it is successful.
But when I try to run the parallel executable I still receive:
"read_namelists : error".
Also, ifort 9.1.041 is the embedded compiler in my mpif90 and ifort was used to compile the serial version.
Is there anything else that I can do to find out why this read error
occurs only for the parallel executable?
Thanks,
David.
Axel Kohlmeyer wrote:
> On Sat, 1 Nov 2008, D.A. Tompsett wrote:
>
> DT> Dear Alex and All,
> DT> I have tried to get some more info on my compiler.
> DT> I did this by running "module list" in my login environment:
> DT> Currently Loaded Modulefiles:
> DT> 1) dot 8) intel/fce/9.1.041
> DT> 2) torque 9) infinipath/mpi/2.2
> DT> 3) moab 10) infinipath/openfabrics/2.2
> DT> 4) gold/2.1.6.0 11) infinipath/core/2.2
> DT> 5) intel/mkl/9.0.018 12) mpiexec/0.82
> DT> 6) intel/idbe/9.1.046 13) default-infinipath
> DT> 7) intel/cce/9.1.046
> DT>
> DT> I think this indicates that my compiler is intel fortran 9.1.041.
>
> could be, but need not be. you still may have a different fortran
> compiler (gfortran, g95) embedded in your mpif90. are you seeing
> the same problems, when you compile a serial version?
>
> what is the F90 definition in your make.sys gfortran or ifort?
>
> DT>
> DT> Also the output from "uname -a" is: Linux bindloe04
> DT> 2.6.9-67.0.4.EL_lustre.1.6.4.3smp #1 SMP Sun Feb 17 08:05:22 EST 2008
> DT> x86_64 x86_64 x86_64 GNU/Linux
> DT>
> DT> I hope that makes it clearer.
>
> unfortunately, no. this makes both the compiler warnings and
> the problems reading input files very mysterious. i have the
> same compiler on my desktop - only one patchlevel old - and
> i see neither of the two problems that you encounter.
>
> you make sys is the one created from configure?
> and you run 'make clean' after all new runs of configure
> or changing of compiler options? right?
>
> cheers,
> axel.
>
> DT>
> DT> Thanks again,
> DT> David.
> DT>
> DT> On Nov 1 2008, Axel Kohlmeyer wrote:
> DT>
> DT> >On Sat, 1 Nov 2008, D.A. Tompsett wrote:
> DT> >
> DT> > DT> Dear Alex and All, DT> thanks for the help. I understand better what
> DT> > the DT> "read_namelists : error" is now. I am using mpif90 for my
> DT> > compiler on a unix DT> platform.
> DT> >
> DT> >sorry, but this is like answering "i have a red sedan car" when being
> DT> >asked about model and make. what _kind_ of unix and what compiler vendor
> DT> >and version do you have. mpif90 is usually a wrapper and can "contain"
> DT> >any compiler.
> DT> >
> DT> >try running "mpif90 -v" and/or "mpif90 -showme" to get some hints of
> DT> >the compiler and send in the output.
> DT> >and try running "uname -a" to get some info about the kind of unix.
> DT> >
> DT> >thanks,
> DT> > axel.
> DT> >
> DT> >
> DT> > [...] DT> I also paste below all of the warnings sent to stderr during
> DT> > the compile. I DT> am not sure if they are related to my problem: DT> DT>
> DT> > fortcom: Warning: iotk_stream.spp, line 54: A dummy argument with an DT>
> DT> > explicit INTENT(OUT) declaration is not given an explicit value. [VAL]
> DT> > DT> subroutine DT>
> DT> > iotk_stream_read_LOGICAL1(unit,header,val,setpos,getpos,noval,ierr) DT>
> DT> > -------------------------------------------------^ fortcom: Warning: DT>
> DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
> DT> > iotk_stream_read_INTEGER1(unit,header,val,setpos,getpos,noval,ierr) DT>
> DT> > -------------------------------------------------^ fortcom: Warning: DT>
> DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
> DT> > iotk_stream_read_REAL1(unit,header,val,setpos,getpos,noval,ierr) DT>
> DT> > ----------------------------------------------^ fortcom: Warning: DT>
> DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
> DT> > iotk_stream_read_REAL2(unit,header,val,setpos,getpos,noval,ierr) DT>
> DT> > ----------------------------------------------^ fortcom: Warning: DT>
> DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
> DT> > iotk_stream_read_COMPLEX1(unit,header,val,setpos,getpos,noval,ierr) DT>
> DT> > -------------------------------------------------^ fortcom: Warning: DT>
> DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
> DT> > iotk_stream_read_COMPLEX2(unit,header,val,setpos,getpos,noval,ierr) DT>
> DT> > -------------------------------------------------^ fortcom: Warning: DT>
> DT> > iotk_stream.spp, line 54: A dummy argument with an explicit INTENT(OUT)
> DT> > DT> declaration is not given an explicit value. [VAL] subroutine DT>
> DT> > iotk_stream_read_CHARACTER1(unit,header,val,setpos,getpos,noval,ierr) DT>
> DT> > ---------------------------------------------------^ ar: creating
> DT> > libiotk.a DT> fftw.c(27449): warning #188: enumerated type mixed with
> DT> > another type DT> EXPECT_INT(dir); DT> ^ DT> DT> fftw.c(27450): warning
> DT> > #188: enumerated type mixed with another type DT> EXPECT_INT(type); DT>
> DT> > DT> DT> Please let me know if you can see how I might fix this eg. by
> DT> > altering the DT> input file to make the namelist reader happy. DT> DT>
> DT> > Thanks for any help, DT> David. DT>
> DT> >
> DT> >
> DT>
> DT>
>
>
--
David A. Tompsett
Quantum Matter Group
Cavendish Laboratory
J. J. Thomson Avenue
Cambridge CB3 0HE
U.K.
Tel: +44 7907 566351 (mobile)
Fax: +44 1223 337351
http://www-qm.phy.cam.ac.uk/
From giannozz at democritos.it Thu Nov 6 13:13:41 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 06 Nov 2008 13:13:41 +0100
Subject: [Pw_forum] Error in Espresso post-installation Test examples
In-Reply-To: <4912DE8E.8020403@cam.ac.uk>
References: <490B39BC.2080306@cam.ac.uk> <c92002fa0810311309u652cbcc2ob4ec433c35bae3e6@mail.gmail.com> <Prayer.1.3.1.0811011156550.27996@hermes-1.csi.cam.ac.uk> <Pine.LNX.4.64.0811011121570.2302@localhost.localdomain> <Prayer.1.3.1.0811011633190.20751@hermes-1.csi.cam.ac.uk> <Pine.LNX.4.64.0811011246540.2302@localhost.localdomain> <Prayer.1.3.1.0811011931440.21596@hermes-1.csi.cam.ac.uk> <Pine.LNX.4.64.0811011908330.2282@localhost.localdomain>
<4912DE8E.8020403@cam.ac.uk>
Message-ID: <4912DF75.2040106@democritos.it>
David Tompsett wrote:
> Is there anything else that I can do to find out why this read error
> occurs only for the parallel executable?
the reason is well known and documented, and the solution(s) is
also well known: use option -in (or -inp, or -input)
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Thu Nov 6 13:15:06 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 06 Nov 2008 13:15:06 +0100
Subject: [Pw_forum] compilation problem on sp5@cineca
In-Reply-To: <627e0ffa0811060408p51707c0fue4bd8708dec31e7c@mail.gmail.com>
References: <627e0ffa0811060358o58aa1732u686243676f367abe@mail.gmail.com> <4912DC26.5060103@democritos.it>
<627e0ffa0811060408p51707c0fue4bd8708dec31e7c@mail.gmail.com>
Message-ID: <4912DFCA.30206@democritos.it>
Prasenjit Ghosh wrote:
> 4.0.1
there is nothing at lines 282 and 284 of file PW/input.f90
in v.4.0.1, just two comments
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From prasenjit.jnc at gmail.com Thu Nov 6 13:34:32 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Thu, 6 Nov 2008 13:34:32 +0100
Subject: [Pw_forum] compilation problem on sp5@cineca
In-Reply-To: <4912DFCA.30206@democritos.it>
References: <627e0ffa0811060358o58aa1732u686243676f367abe@mail.gmail.com>
<4912DC26.5060103@democritos.it>
<627e0ffa0811060408p51707c0fue4bd8708dec31e7c@mail.gmail.com>
<4912DFCA.30206@democritos.it>
Message-ID: <627e0ffa0811060434t1753e56ducdfe51c8c9d97956@mail.gmail.com>
I'm sorry. I actually did some modification in PW/input.f90.....
I corrected it. Now it compiles properly.
Prasenjit.
2008/11/6 Paolo Giannozzi <giannozz at democritos.it>
> Prasenjit Ghosh wrote:
>
> > 4.0.1
>
> there is nothing at lines 282 and 284 of file PW/input.f90
> in v.4.0.1, just two comments
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
+39 3807528672 (M)
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From mambom1902 at yahoo.com Thu Nov 6 15:09:23 2008
From: mambom1902 at yahoo.com (loc duong ding)
Date: Thu, 6 Nov 2008 06:09:23 -0800 (PST)
Subject: [Pw_forum] espresso 4 _ parallel
Message-ID: <845323.78784.qm@web38801.mail.mud.yahoo.com>
Dear Users,
I use Mpich2 to run Quantum Epresso code. I have a error when I try to run execute file pw.x.
>>mpiexec -machinefile? /home/loc/machinefile -n 8 pw.x -npool 2? < input_Graphite_GGA > output_Graphite_GGA2 &
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 3[cli_3]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 3
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 7[cli_7]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 7
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 2[cli_2]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 2
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 6[cli_6]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 6
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 5[cli_5]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 5
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 4[cli_4]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 4
In the output file, the error is:
rank 7 in job 2? master_49510?? caused collective abort of all ranks
? exit status of rank 7: return code 0
rank 3 in job 2? master_49510?? caused collective abort of all ranks
? exit status of rank 3: return code 0
rank 1 in job 2? master_49510?? caused collective abort of all ranks
? exit status of rank 1: return code 0
I tried to test mpiexec command whith some another execute file?and there was?no problem. The pw.x is also ok when it?was run alone (serial running).
Please give me some suggestion for this error. I also saw this problem in PW_forum but I can find the solution for it.
Best regards,
Duong Dinh Loc.?
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From mambom1902 at yahoo.com Thu Nov 6 15:09:23 2008
From: mambom1902 at yahoo.com (loc duong ding)
Date: Thu, 6 Nov 2008 06:09:23 -0800 (PST)
Subject: [Pw_forum] espresso 4 _ parallel
Message-ID: <845323.78784.qm@web38801.mail.mud.yahoo.com>
Dear Users,
I use Mpich2 to run Quantum Epresso code. I have a error when I try to run execute file pw.x.
>>mpiexec -machinefile? /home/loc/machinefile -n 8 pw.x -npool 2? < input_Graphite_GGA > output_Graphite_GGA2 &
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 3[cli_3]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 3
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 7[cli_7]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 7
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 2[cli_2]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 2
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 6[cli_6]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 6
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 5[cli_5]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 5
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 4[cli_4]: aborting job?????????????????? :
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 4
In the output file, the error is:
rank 7 in job 2? master_49510?? caused collective abort of all ranks
? exit status of rank 7: return code 0
rank 3 in job 2? master_49510?? caused collective abort of all ranks
? exit status of rank 3: return code 0
rank 1 in job 2? master_49510?? caused collective abort of all ranks
? exit status of rank 1: return code 0
I tried to test mpiexec command whith some another execute file?and there was?no problem. The pw.x is also ok when it?was run alone (serial running).
Please give me some suggestion for this error. I also saw this problem in PW_forum but I can find the solution for it.
Best regards,
Duong Dinh Loc.?
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From giannozz at democritos.it Thu Nov 6 15:42:18 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 06 Nov 2008 15:42:18 +0100
Subject: [Pw_forum] espresso 4 _ parallel
In-Reply-To: <845323.78784.qm@web38801.mail.mud.yahoo.com>
References: <845323.78784.qm@web38801.mail.mud.yahoo.com>
Message-ID: <4913024A.1040803@democritos.it>
loc duong ding wrote:
> Please give me some suggestion for this error. I also saw this problem
> in PW_forum but I can find the solution for it.
you didn't look into the documentation. Unless you have evidence
that this is a bug of the code (e.g. reproducibility under some
form in different machines), it is a compiler or mpi library bug.
I never had any problem with openmpi, by the way.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From akohlmey at cmm.chem.upenn.edu Thu Nov 6 16:40:31 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 6 Nov 2008 10:40:31 -0500 (EST)
Subject: [Pw_forum] espresso 4 _ parallel
In-Reply-To: <845323.78784.qm@web38801.mail.mud.yahoo.com>
References: <845323.78784.qm@web38801.mail.mud.yahoo.com>
Message-ID: <Pine.LNX.4.64.0811061038550.2562@localhost.localdomain>
On Thu, 6 Nov 2008, loc duong ding wrote:
DDL> Dear Users,
DDL> I tried to test mpiexec command whith some another execute file?and
DDL> there was?no problem. The pw.x is also ok when it?was run alone
(serial running).
DDL> Please give me some suggestion for this error. I also saw this
problem in PW_forum but I can find the solution for it.
you didn't look close enough! paolo just mentioned it _today_.
your MPI most likely does not forward the stdin to all nodes,
and you have to use the -in (or -inp or -input) flag instead.
cheers,
axel.
Best regards,
Duong Dinh Loc.?
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From thmason24 at yahoo.com Thu Nov 6 16:44:45 2008
From: thmason24 at yahoo.com (Timothy Mason)
Date: Thu, 6 Nov 2008 07:44:45 -0800 (PST)
Subject: [Pw_forum] Total energy does not coverge with ecut
Message-ID: <869411.85628.qm@web81801.mail.mud.yahoo.com>
??? Gentlemen,
My structures do not see to be converging
with increased ecutwfc. ? I'm setting ecutrho to ecutwfc * 12 and using
US PP. ?? below is a table of ecut values vs energies vs difference
from previous steps followed by my input file followed by part of the output
file.??? It appears to begin to converge and 120 ecut but then jumps at
130 and then more at 140. ?? I understood that convergence should be
pretty well achieved by 30 ecut for US PP.? The only thing I change
between runs are the two ecut parameters.? Any ideas as to what I'm
doing wrong or what I should be expecting??
A follow up
question in that I'm trying to do vc-relax based on this scf and the
forces decrease until a value of about 0.0003 and then oscillate around
this value.??? could that be related to the ecut convergence problem
I'm having?
thanks,
Tim Mason,?? University of Missouri St. Louis Department of Physics and astronomy
------------------------------------------------------------------------------------
ecutwfc? total energy??? difference from previous
100??? -48.21607621
105??? -48.21651331????? 0.0004371
110??? -48.21672787????? 0.00021456
120??? -48.21686396????? 0.00013609
130??? -48.2172448??????? 0.00038084
140??? -48.21819748????? 0.00095268
----------------------------------------------------------------------
&CONTROL
calculation = "scf",
prefix = 'n4_scf.out',
tprnfor = .TRUE.
pseudo_dir = '/home/thmmqc/pwscf/psps/US_GGA',
outdir='/home/thmmqc/tmp'
etot_conv_thr = 1.d-8
/
&SYSTEM
ibrav =
0, nat = 8, ntyp = 3,
ecutwfc = 100
ecutrho = 1200
celldm(1) = 1.889725989
/
&ELECTRONS
diagonalization = 'cg',
mixing_mode = 'plain',
mixing_beta = 0.7,
conv_thr = 1.0D-8
/
ATOMIC_SPECIES
Li 6.941000 Li.pbe-n-van.UPF
N 14.006740 N.pbe-van_ak.UPF
H 1.007940 H.pbe-van_ak.UPF
CELL_PARAMETERS
10.52658029 -1.08441956 -0.28831668
-2.96581684 6.61198966 -0.14661465
1.15738394 0.29429438 3.51384172
ATOMIC_POSITIONS {crystal}
Li 0.403906747000 0.720101910000 0.473406799000
Li 0.228004145000 0.310445951000 0.053578743000
?N 0.230067712000 0.303154666000 0.552891390000
?N 0.403264134000 0.730145360000 -0.024840278000
?H 0.185705821000 0.137557379000 0.553855070000
?H 0.132830606000 0.318409519000 0.624406047000
?H 0.486061391000 0.685122024000 -0.095482152000
?H 0.467101514000 0.897467040000 -0.051109646000
K_POINTS automatic
2 2 2 0 0 0
---------------------------------------------------------------------------------------------------------------------
???? Program PWSCF???? v.4.0.2? starts ...
???? Today is? 6Nov2008 at? 8:30: 1
???? Parallel version (MPI)
???? Number of processors in use:?????? 1
???? For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW
???? Current dimensions of program pwscf are:
???? Max number of different atomic species (ntypx) = 10
???? Max number of k-points (npk) =? 40000
???? Max angular momentum in pseudopotentials (lmaxx) =? 3
???? Iterative solution of the
eigenvalue problem
???? Too few procs for parallel algorithm
?????? we need at least 4 procs per pool
???? a serial algorithm will be used
???? Planes per process (thick) : nr3 = 96 npp =? 96 ncplane =51840
???? Planes per process (smooth): nr3s= 54 npps=? 54 ncplanes=17280
?
???? Proc/? planes cols???? G??? planes cols??? G????? columns? G
???? Pool?????? (dense grid)?????? (smooth grid)????? (wavefct grid)
?????? 1???? 96? 32843? 1954809?? 54? 10579?? 357021?? 2893???
51177
?
???? bravais-lattice index???? =??????????? 0
???? lattice parameter (a_0)?? =?????? 1.8897? a.u.
???? unit-cell volume????????? =??? 1595.0644 (a.u.)^3
???? number of atoms/cell????? =??????????? 8
???? number of atomic types??? =??????????? 3
???? number of electrons?????? =??????? 16.00
???? number of Kohn-Sham
states=??????????? 8
???? kinetic-energy cutoff???? =???? 140.0000? Ry
???? charge density cutoff???? =??? 1740.0000? Ry
???? convergence threshold???? =????? 1.0E-08
???? mixing beta?????????????? =?????? 0.7000
???? number of iterations used =??????????? 8? plain???? mixing
???? Exchange-correlation????? =? SLA? PW?? PBE? PBE (1434)
???? celldm(1)=?? 1.889726?
celldm(2)=?? 0.000000? celldm(3)=?? 0.000000
???? celldm(4)=?? 0.000000? celldm(5)=?? 0.000000? celldm(6)=?? 0.000000
???? crystal axes: (cart. coord. in units of a_0)
?????????????? a(1) = ( 10.526580 -1.084420 -0.288317 )?
?????????????? a(2) = ( -2.965817? 6.611990 -0.146615 )?
?????????????? a(3) = (? 1.157384? 0.294294? 3.513842 )?
???? reciprocal axes: (cart. coord. in units 2 pi/a_0)
?????????????? b(1) = (? 0.098478? 0.043373 -0.036069 )?
?????????????? b(2) = (? 0.015762? 0.157902 -0.018417 )?
?????????????? b(3) = (? 0.008738? 0.010147? 0.280861 )?
???? PseudoPot. # 1 for Li read from file Li.pbe-n-van.UPF
???? Pseudo is Ultrasoft + core correction, Zval =? 1.0
???? Generated by new atomic code, or converted to UPF format
???? Using radial grid of? 751 points,? 2 beta functions with:
??????????????? l(1) =?? 1
??????????????? l(2) =?? 1
???? Q(r) pseudized with? 8 coefficients,? rinner
=??? 1.000?? 1.000?? 1.000
???? PseudoPot. # 2 for N? read from file N.pbe-van_ak.UPF
???? Pseudo is Ultrasoft, Zval =? 5.0
???? Generated by new atomic code, or converted to UPF format
???? Using radial grid of? 729 points,? 4 beta functions with:
??????????????? l(1) =?? 0
??????????????? l(2) =?? 0
??????????????? l(3) =?? 1
??????????????? l(4) =?? 1
???? Q(r) pseudized with? 8 coefficients,? rinner =???
0.800?? 0.800?? 0.800
???? PseudoPot. # 3 for H? read from file H.pbe-van_ak.UPF
???? Pseudo is Ultrasoft, Zval =? 1.0
???? Generated by new atomic code, or converted to UPF format
???? Using radial grid of? 615 points,? 1 beta functions with:
??????????????? l(1) =?? 0
???? Q(r) pseudized with? 8 coefficients,? rinner =??? 0.800
???? atomic species?? valence??? mass???? pseudopotential
??????? Li???????????? 1.00???? 6.94100???? Li(
1.00)
??????? N????????????? 5.00??? 14.00674???? N ( 1.00)
??????? H????????????? 1.00???? 1.00794???? H ( 1.00)
???? No symmetry!
?? Cartesian axes
???? site n.???? atom????????????????? positions (a_0 units)
???????? 1?????????? Li? tau(? 1) = (?? 2.6639799?? 4.4626230?? 1.4414460? )
????????
2?????????? Li? tau(? 2) = (?? 1.5413893?? 1.8211812?? 0.0770139? )
???????? 3?????????? N?? tau(? 3) = (?? 2.1626326?? 1.9176784?? 1.8319936? )
???????? 4?????????? N?? tau(? 4) = (?? 2.0507651?? 4.3830957? -0.3106026? )
???????? 5?????????? H?? tau(? 5) = (?? 2.1879002?? 0.8711414?? 1.8724490? )
???????? 6?????????? H?? tau(? 6) =
(?? 1.1765853?? 2.1450355?? 2.1090832? )
???????? 7?????????? H?? tau(? 7) = (?? 2.9741083?? 3.9748254? -0.5760977? )
???????? 8?????????? H?? tau(? 8) = (?? 2.1961052?? 5.4124675? -0.4458462? )
????
???? Self-consistent Calculation
???? iteration #? 1???? ecut=?? 140.00 Ry???? beta=0.70
???? CG style diagonalization
???? ethr =? 1.00E-02,? avg #
of iterations =? 3.3
???? negative rho (up, down):? 0.143E-04 0.000E+00
???
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From paulatto at sissa.it Thu Nov 6 17:08:40 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 06 Nov 2008 17:08:40 +0100
Subject: [Pw_forum] Total energy does not coverge with ecut
In-Reply-To: <869411.85628.qm@web81801.mail.mud.yahoo.com>
References: <869411.85628.qm@web81801.mail.mud.yahoo.com>
Message-ID: <49131688.3040102@sissa.it>
Timothy Mason ha scritto:
>
> Gentlemen,
>
> My structures do not see to be converging with increased ecutwfc.
> I'm setting ecutrho to ecutwfc * 12 and using US PP. below is a
> table of ecut values vs energies vs difference from previous steps
> followed by my input file followed by part of the output file. It
> appears to begin to converge and 120 ecut but then jumps at 130 and
> then more at 140.
>
Dear Timothy,
these are ridiculous cutoff energy for ultrasoft pseudopotentials - they
are very high for norm-conserving too! I suspect the presence of a
high-energy ghost-state in one of the pseudopotential; these kind of
states aren't usually harmful but can suddenly pop-up under some
specifics conditions like high pressure or very high cutoff.
What is happening when you try some reasonable cutoff in the 20-50 Ry range?
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.
Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste
Donations in food, coins, booze and processor time are warmly welcome.
From thmason24 at yahoo.com Thu Nov 6 17:45:05 2008
From: thmason24 at yahoo.com (Timothy Mason)
Date: Thu, 6 Nov 2008 08:45:05 -0800 (PST)
Subject: [Pw_forum] Total energy does not coverge with ecut
In-Reply-To: <49131688.3040102@sissa.it>
Message-ID: <992580.73648.qm@web81806.mail.mud.yahoo.com>
Dear Lorenzo,
here are results for the lower energy range.? Still doesn't seem to be converging.
ecut???? energy????????????? energy differnce
30??????? -48.19258627???
35??????? -48.19503183?????? 0.00244556
40??????? -48.197306?????????? 0.00227417
45??????? -48.20217820?????? 0.0048722
thanks
--- On Thu, 11/6/08, Lorenzo Paulatto <paulatto at sissa.it> wrote:
From: Lorenzo Paulatto <paulatto at sissa.it>
Subject: Re: [Pw_forum] Total energy does not coverge with ecut
To: thmason24 at yahoo.com, "PWSCF Forum" <pw_forum at pwscf.org>
Date: Thursday, November 6, 2008, 10:08 AM
Timothy Mason ha scritto:
>
> Gentlemen,
>
> My structures do not see to be converging with increased ecutwfc.
> I'm setting ecutrho to ecutwfc * 12 and using US PP. below is a
> table of ecut values vs energies vs difference from previous steps
> followed by my input file followed by part of the output file. It
> appears to begin to converge and 120 ecut but then jumps at 130 and
> then more at 140.
>
Dear Timothy,
these are ridiculous cutoff energy for ultrasoft pseudopotentials - they
are very high for norm-conserving too! I suspect the presence of a
high-energy ghost-state in one of the pseudopotential; these kind of
states aren't usually harmful but can suddenly pop-up under some
specifics conditions like high pressure or very high cutoff.
What is happening when you try some reasonable cutoff in the 20-50 Ry range?
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the
last
email you receive from me.
Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste
Donations in food, coins, booze and processor time are warmly welcome.
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From nakhmanson at anl.gov Thu Nov 6 20:03:12 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Thu, 06 Nov 2008 13:03:12 -0600
Subject: [Pw_forum] Is maxirr=N working in phonon calculations?
In-Reply-To: <D6C67D08-BAC1-4E67-8FC4-283582F3C81B@sissa.it>
References: <4910F174.10508@anl.gov>
<49119D4E.2020000@democritos.it> <4912424A.2080709@anl.gov>
<D6C67D08-BAC1-4E67-8FC4-283582F3C81B@sissa.it>
Message-ID: <49133F70.9020108@anl.gov>
Dear Stefano,
Thank you for the clarification.
Serge
Stefano Baroni wrote:
>> I only know a general answer to how it is done -- by induction
>> from an (Abelian) group of crystal translations -- but am
>> rusty on particular numerical algorithms. However, I got an
>> excellent new book by El-Batanouny and Wooten (ISBN 9780521828451),
>> all the details should be in there.
>
> I do not know about the book, but I am afraid that what is implemented
> in the code is not anything worth reporting in a book. The idea is as
> follows. The code already contains all the weaponery for simmetrizing
> all kind of stuff with respect to the small group of the point in the
> Brillouin zone we are working at. In particular, you fill the dynamical
> matrix with random numbers and then symmetrize it. The resulting matrix
> will commute with all the operations of the small group, and its
> eigenvectors will therefore realize a number of irreducible
> representation of the group. As simple as that. Do not ask me about the
> details of the implementation, though. The documentation (as poor as it
> may be) is the code itself ...
--
*********************************************************
Serge M. Nakhmanson phone: (630) 252-5205
Assistant Scientist fax: (630) 252-4798
MSD-212, Rm. C-224
Argonne National Laboratory
9700 S. Cass Ave.
Argonne, IL 60439
*********************************************************
From prasenjit.jnc at gmail.com Thu Nov 6 23:10:40 2008
From: prasenjit.jnc at gmail.com (prasenjit.jnc at gmail.com)
Date: Thu, 06 Nov 2008 14:10:40 -0800
Subject: [Pw_forum] Total energy does not coverge with ecut
Message-ID: <000e0cd2480434b355045b0c911c@google.com>
Sometimes it is also difficult to converge the total energy. So usually it
is better to check the convergence of the quantity you are interested in.
But anyway it is really strange that total energy doesn't converge at such
abnormally high cut off values.
Did you test the pseudopotentials individually?? For eg. did you try
calculating the bond lengths of say a nitrogen molecule & see how the
results are??
With regards,
Prasenjit.
On Nov 6, 2008 5:45pm, Timothy Mason <thmason24 at yahoo.com> wrote:
> Dear Lorenzo,
>
> here are results for the lower energy range. Still doesn't seem to be
converging.
>
> ecut energy energy differnce
> 30 -48.19258627
> 35 -48.19503183 0.00244556
> 40 -48.197306 0.00227417
> 45 -48.20217820 0.0048722
>
> thanks
>
> --- On Thu, 11/6/08, Lorenzo Paulatto paulatto at sissa.it> wrote:
> From: Lorenzo Paulatto paulatto at sissa.it>
> Subject: Re: [Pw_forum] Total energy does not coverge with ecut
> To: thmason24 at yahoo.com, "PWSCF Forum" pw_forum at pwscf.org>
> Date: Thursday, November 6, 2008, 10:08 AM
>
> Timothy Mason ha scritto:
> >
> > Gentlemen,
> >
> > My structures do not see to be converging with increased ecutwfc.
> > I'm setting ecutrho to ecutwfc * 12 and using US PP. below is a
> > table of ecut values vs energies vs difference from previous steps
> > followed by my input file followed by part of the output file. It
> > appears to begin to converge and 120 ecut but then jumps at 130 and
> > then more at 140.
> >
> Dear Timothy,
> these are ridiculous cutoff energy for ultrasoft pseudopotentials - they
> are very high for norm-conserving too! I suspect the presence of a
> high-energy ghost-state in one of the pseudopotential; these kind
> of
> states aren't usually harmful but can suddenly pop-up under some
> specifics conditions like high pressure or very high cutoff.
>
> What is happening when you try some reasonable cutoff in the 20-50 Ry
range?
>
> regards
>
> --
> Lorenzo Paulatto
> SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www: http://people.sissa.it/~paulatto/
>
> Due to budget cuts approved by Italian Minister of Finance and Italian
> Minister "for" Education, University and Research this may be the
> last
> email you receive from me.
>
> Please send any future correspondence, possibly via pigeon, to
> mr. Lorenzo Paulatto
> under Roiano Railway Bridge - Pillar 2
> 34136, Trieste
>
> Donations in food, coins, booze and processor time are warmly welcome.
>
>
>
>
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From njuxuyuehua at gmail.com Fri Nov 7 04:07:14 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 7 Nov 2008 11:07:14 +0800
Subject: [Pw_forum] is there any tools to have a look at the Charge
distribution of Excited state
Message-ID: <aca2feb20811061907o5546c4c1oed8bbaa2569b8a00@mail.gmail.com>
hello all,
i want to have a look at the CHarge distribution of a excited state,such as
a phonon mode(the pwscf _result)
is there any tool to achieve above goal, xcrysden OK?
the input file?
thank you
--
Xu Yuehua
physics Department of Nanjing university
China
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From jameslipd at gmail.com Fri Nov 7 04:20:16 2008
From: jameslipd at gmail.com (Jiaye, Li)
Date: Fri, 7 Nov 2008 11:20:16 +0800
Subject: [Pw_forum] Question about calculating workfunction
Message-ID: <b5d787260811061920y3435b7c7ibd346ff9228ede0d@mail.gmail.com>
Dear all
I am new user of pwscf. Recently I am planning to calculate the work
function of some metal oxide surface. But I don't know where to start first?
The code has been successfully compiled on fedora PC clusters. Could anybody
give me a input file for calculating work function? And I wonder how to
obtain the energy of vaccum space, since it seems that pwscf cannot directly
give rise to that value, so maybe some programs are needed. Would anyone
send me a such file? Thanks in advance.
--
Sincerely
Jiaye Li
==============================================
Li, Jiaye
M.S. in designing and developing novel materials
Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids
Skills:
*ab-initial method, DFT simulation and Force Field simulation
Please contact me at:
1. jameslipd at gmail.com or
2. jameslibd at gmail.com
==============================================
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From nedward at MIT.EDU Fri Nov 7 05:10:07 2008
From: nedward at MIT.EDU (Nicholas E. Singh-Miller)
Date: Thu, 6 Nov 2008 23:10:07 -0500 (EST)
Subject: [Pw_forum] Question about calculating workfunction
In-Reply-To: <b5d787260811061920y3435b7c7ibd346ff9228ede0d@mail.gmail.com>
References: <b5d787260811061920y3435b7c7ibd346ff9228ede0d@mail.gmail.com>
Message-ID: <Pine.GSO.4.64L.0811062308310.7994@grumpy-fuzzball.mit.edu>
Hi,
There is an example in examples/WorkFct_example
-Nick
On Fri, 7 Nov 2008, Jiaye, Li wrote:
> Dear all
>
> I am new user of pwscf. Recently I am planning to calculate the work
> function of some metal oxide surface. But I don't know where to start first?
>
>
> The code has been successfully compiled on fedora PC clusters. Could anybody
> give me a input file for calculating work function? And I wonder how to
> obtain the energy of vaccum space, since it seems that pwscf cannot directly
> give rise to that value, so maybe some programs are needed. Would anyone
> send me a such file? Thanks in advance.
>
>
*****************************************
Nicholas E. Singh-Miller
Ph.D. Candidate
Prof. Marzari Group (quasiamore.mit.edu)
Materials Science and Engineering
Massachusetts Institute of Technology
13-4066
(617)324-0372
*****************************************
From mambom1902 at yahoo.com Fri Nov 7 09:00:46 2008
From: mambom1902 at yahoo.com (loc duong ding)
Date: Fri, 7 Nov 2008 00:00:46 -0800 (PST)
Subject: [Pw_forum] espresso 4 _ parallel
Message-ID: <62280.66511.qm@web38808.mail.mud.yahoo.com>
________________________________
From: loc duong ding <mambom1902 at yahoo.com>
To: Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>
Sent: Thursday, November 6, 2008 5:41:05 PM
Subject: Re: [Pw_forum] espresso 4 _ parallel
I found the error for this case. I tried to change the outdir in the input file to ./ and this run well. I don't know why the error occurs.
I greatly appreciate for your help.
Thank you very much.
Best,
Duong Dinh Loc.
________________________________
From: Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>
To: loc duong ding <mambom1902 at yahoo.com>
Cc: pw_forum at pwscf.org; pw_forum at pwscf.org
Sent: Thursday, November 6, 2008 7:40:31 AM
Subject: Re: [Pw_forum] espresso 4 _ parallel
On Thu, 6 Nov 2008, loc duong ding wrote:
DDL> Dear Users,
DDL> I tried to test mpiexec command whith some another execute file and DDL> there was no problem. The pw.x is also ok when it was run alone (serial running).
DDL> Please give me some suggestion for this error. I also saw this problem in PW_forum but I can find the solution for it.
you didn't look close enough! paolo just mentioned it _today_.
your MPI most likely does not forward the stdin to all nodes,
and you have to use the -in (or -inp or -input) flag instead.
cheers,
axel.
Best regards,
Duong Dinh Loc.
-- =======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
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From mambom1902 at yahoo.com Fri Nov 7 09:02:08 2008
From: mambom1902 at yahoo.com (loc duong ding)
Date: Fri, 7 Nov 2008 00:02:08 -0800 (PST)
Subject: [Pw_forum] espresso 4 _ parallel
Message-ID: <61752.31669.qm@web38802.mail.mud.yahoo.com>
________________________________
From: loc duong ding <mambom1902 at yahoo.com>
To: Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>
Sent: Thursday, November 6, 2008 5:54:40 PM
Subject: Re: [Pw_forum] espresso 4 _ parallel
Another information of my error is that there are no any bug error in the output file.
Best,
Dinh Loc Duong
________________________________
From: Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>
To: loc duong ding <mambom1902 at yahoo.com>
Cc: pw_forum at pwscf.org; pw_forum at pwscf.org
Sent: Thursday, November 6, 2008 7:40:31 AM
Subject: Re: [Pw_forum] espresso 4 _ parallel
On Thu, 6 Nov 2008, loc duong ding wrote:
DDL> Dear Users,
DDL> I tried to test mpiexec command whith some another execute file and DDL> there was no problem. The pw.x is also ok when it was run alone (serial running).
DDL> Please give me some suggestion for this error. I also saw this problem in PW_forum but I can find the solution for it.
you didn't look close enough! paolo just mentioned it _today_.
your MPI most likely does not forward the stdin to all nodes,
and you have to use the -in (or -inp or -input) flag instead.
cheers,
axel.
Best regards,
Duong Dinh Loc.
-- =======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
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From mansourehp at gmail.com Sat Nov 8 11:13:02 2008
From: mansourehp at gmail.com (Mansoureh Pashangpour)
Date: Sat, 8 Nov 2008 13:43:02 +0330
Subject: [Pw_forum] gnuplot
Message-ID: <cbe1626b0811080213w11f97c3k4052b9ac4d5af2c7@mail.gmail.com>
Dear all
I would like to find postscript of a plot (that is figure in figure) in
gnuplot.
thank you inadvance
Mansoureh
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From akohlmey at cmm.chem.upenn.edu Sat Nov 8 12:34:07 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 8 Nov 2008 06:34:07 -0500 (EST)
Subject: [Pw_forum] gnuplot
In-Reply-To: <cbe1626b0811080213w11f97c3k4052b9ac4d5af2c7@mail.gmail.com>
References: <cbe1626b0811080213w11f97c3k4052b9ac4d5af2c7@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0811080632370.11470@localhost.localdomain>
On Sat, 8 Nov 2008, Mansoureh Pashangpour wrote:
MP> Dear all
MP> I would like to find postscript of a plot (that is figure in figure) in
MP> gnuplot.
mansoureh,
in case you didn't notice, this is the mailing list concerning
quantum espresso. i recommend to post your question at the
corresponding forum for _gnuplot_. you chances to get a
competent answer are infinitely higher.
cheers,
axel.
MP> thank you inadvance
MP> Mansoureh
MP>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From kazempoor2000 at yahoo.com Sat Nov 8 18:55:14 2008
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Sat, 8 Nov 2008 09:55:14 -0800 (PST)
Subject: [Pw_forum] GW
Message-ID: <523911.86459.qm@web33107.mail.mud.yahoo.com>
Dear all
Can we do GW calculation with esperesso or did not implemented?
thanks a lot
Ali Kazempour, Isfahan University of Technology
From akohlmey at cmm.chem.upenn.edu Sat Nov 8 19:37:15 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 8 Nov 2008 13:37:15 -0500 (EST)
Subject: [Pw_forum] GW
In-Reply-To: <523911.86459.qm@web33107.mail.mud.yahoo.com>
References: <523911.86459.qm@web33107.mail.mud.yahoo.com>
Message-ID: <Pine.LNX.4.64.0811081335300.3412@localhost.localdomain>
On Sat, 8 Nov 2008, ali kazempoor wrote:
AK> Dear all
AK> Can we do GW calculation with esperesso or did not implemented?
ali,
had you searched the mailing list archive,
you would have found this: http://www.sax-project.org/
axel.
AK> thanks a lot
AK>
AK> Ali Kazempour, Isfahan University of Technology
AK>
AK>
AK>
AK> _______________________________________________
AK> Pw_forum mailing list
AK> Pw_forum at pwscf.org
AK> http://www.democritos.it/mailman/listinfo/pw_forum
AK>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From yuminqian at gmail.com Sun Nov 9 14:51:05 2008
From: yuminqian at gmail.com (yumin qian)
Date: Sun, 9 Nov 2008 21:51:05 +0800
Subject: [Pw_forum] Get wrong symmtry
Message-ID: <aa128b2c0811090551o13965837gf1c608317183ec88@mail.gmail.com>
Dear Prof.
I am doing LaOFeAs ground state calculation , it symmetry blongs to
p4/nmm space group , when I finish the ground state calculation , I
procced to do the phonon calculation of Gamma point , But the output file
tell me that at Gamma point the symmetry is C_4v , but it should be D_4h,
then I look at the x.save fold to find the data-file.xml I find the
symmetry operation is completely different from the D_4h , I also use the
Vasp to do the calculation and I get the D_4h symmetry operation , I check
the possible error of my in put file for SCF calculation the only possible
error is the parameter ibrav=6, and the crystal is indeed a
Tetragonal P (st) cell
where is the errror ? Or what mistake I have made , is there someone to
tell me what's the problem ? Thanks ,I am looking forward to the answer.
this is my input file for ground state SCF calculation
&control
calculation='scf'
restart_mode='from_scratch',
pseudo_dir = '~/software/espresso-4test/pseudo',
outdir='./outscf'
prefix='LaOFeAs',
wf_collect=.true.
tstress = .true.
tprnfor = .true.
/
&system
ibrav = 6, celldm(1) =7.633740 , celldm(3)=2.136,
, nat= 8, ntyp= 4,
ecutwfc = 30.0, ecutrho = 250.0
occupations='smearing', smearing='gaussian', degauss=0.02,
/
&electrons
diagonalization='david'
conv_thr = 1.0e-10
mixing_beta = 0.5
/
ATOMIC_SPECIES
La 138.9 La.pbe-nsp-van.UPF
O 16.00 O.pbe-rrkjus.UPF
Fe 55.85 Fe.pbe-sp-van.UPF
As 74.92 As.pbe-n-van.UPF
ATOMIC_POSITIONS
La 0.2500000000 0.2500000000 0.1461000000
La 0.7500000000 0.7500000000 0.8539000000
O 0.7500000000 0.2500000000 0.0000000000
O 0.2500000000 0.7500000000 0.0000000000
Fe 0.7500000000 0.2500000000 0.5000000000
Fe 0.2500000000 0.7500000000 0.5000000000
As 0.2500000000 0.2500000000 0.6369000000
As 0.7500000000 0.7500000000 0.3631000000
K_POINTS (automatic)
8 8 4 0 0 0
~
--
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel: + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603 Beijing 100190
China
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From akohlmey at cmm.chem.upenn.edu Sun Nov 9 19:14:10 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 9 Nov 2008 13:14:10 -0500 (EST)
Subject: [Pw_forum] Get wrong symmtry
In-Reply-To: <aa128b2c0811090551o13965837gf1c608317183ec88@mail.gmail.com>
References: <aa128b2c0811090551o13965837gf1c608317183ec88@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0811091313350.32555@localhost.localdomain>
On Sun, 9 Nov 2008, yumin qian wrote:
YQ> Dear Prof.
YQ>
YQ> I am doing LaOFeAs ground state calculation , it symmetry blongs to
YQ> p4/nmm space group , when I finish the ground state calculation , I
YQ> procced to do the phonon calculation of Gamma point , But the output file
YQ> tell me that at Gamma point the symmetry is C_4v , but it should be D_4h,
YQ> then I look at the x.save fold to find the data-file.xml I find the
YQ> symmetry operation is completely different from the D_4h , I also use the
YQ> Vasp to do the calculation and I get the D_4h symmetry operation , I check
YQ> the possible error of my in put file for SCF calculation the only possible
YQ> error is the parameter ibrav=6, and the crystal is indeed a
YQ> Tetragonal P (st) cell
YQ> where is the errror ? Or what mistake I have made , is there someone to
how about not having enough numerical accuracy
for the numbers in the z-coordinate?
axel.
YQ> tell me what's the problem ? Thanks ,I am looking forward to the answer.
YQ>
YQ>
YQ> this is my input file for ground state SCF calculation
YQ>
YQ>
YQ> &control
YQ> calculation='scf'
YQ> restart_mode='from_scratch',
YQ> pseudo_dir = '~/software/espresso-4test/pseudo',
YQ> outdir='./outscf'
YQ> prefix='LaOFeAs',
YQ> wf_collect=.true.
YQ> tstress = .true.
YQ> tprnfor = .true.
YQ> /
YQ> &system
YQ> ibrav = 6, celldm(1) =7.633740 , celldm(3)=2.136,
YQ> , nat= 8, ntyp= 4,
YQ> ecutwfc = 30.0, ecutrho = 250.0
YQ> occupations='smearing', smearing='gaussian', degauss=0.02,
YQ> /
YQ> &electrons
YQ> diagonalization='david'
YQ> conv_thr = 1.0e-10
YQ> mixing_beta = 0.5
YQ> /
YQ> ATOMIC_SPECIES
YQ> La 138.9 La.pbe-nsp-van.UPF
YQ> O 16.00 O.pbe-rrkjus.UPF
YQ> Fe 55.85 Fe.pbe-sp-van.UPF
YQ> As 74.92 As.pbe-n-van.UPF
YQ> ATOMIC_POSITIONS
YQ> La 0.2500000000 0.2500000000 0.1461000000
YQ> La 0.7500000000 0.7500000000 0.8539000000
YQ> O 0.7500000000 0.2500000000 0.0000000000
YQ> O 0.2500000000 0.7500000000 0.0000000000
YQ> Fe 0.7500000000 0.2500000000 0.5000000000
YQ> Fe 0.2500000000 0.7500000000 0.5000000000
YQ> As 0.2500000000 0.2500000000 0.6369000000
YQ> As 0.7500000000 0.7500000000 0.3631000000
YQ> K_POINTS (automatic)
YQ> 8 8 4 0 0 0
YQ> ~
YQ>
YQ>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From rcjhawk at gmail.com Sun Nov 9 23:10:41 2008
From: rcjhawk at gmail.com (Michael Mehl)
Date: Sun, 09 Nov 2008 17:10:41 -0500
Subject: [Pw_forum] Get wrong symmtry
In-Reply-To: <Pine.LNX.4.64.0811091313350.32555@localhost.localdomain>
References: <aa128b2c0811090551o13965837gf1c608317183ec88@mail.gmail.com>
<Pine.LNX.4.64.0811091313350.32555@localhost.localdomain>
Message-ID: <49175FE1.7050306@gmail.com>
Axel Kohlmeyer wrote:
> On Sun, 9 Nov 2008, yumin qian wrote:
> how about not having enough numerical accuracy
> for the numbers in the z-coordinate?
>
> axel.
That would appear not to be the case. The requirement for P4/nmm
symmetry is that z for the second atom in a pair be equal to -z (or 1-z)
for the first atom. That's the case here. Whatever the problem is,
it's not in the coordinates.
(See http://cst-www.nrl.navy.mil/lattice/struk/AsCuSiZr.html)
>
> YQ> ATOMIC_POSITIONS
> YQ> La 0.2500000000 0.2500000000 0.1461000000
> YQ> La 0.7500000000 0.7500000000 0.8539000000
> YQ> O 0.7500000000 0.2500000000 0.0000000000
> YQ> O 0.2500000000 0.7500000000 0.0000000000
> YQ> Fe 0.7500000000 0.2500000000 0.5000000000
> YQ> Fe 0.2500000000 0.7500000000 0.5000000000
> YQ> As 0.2500000000 0.2500000000 0.6369000000
> YQ> As 0.7500000000 0.7500000000 0.3631000000
--
Michael Mehl, Naval Research Laboratory, Washington DC.
Sabbatical Duke University through July 2009.
From yuminqian at gmail.com Mon Nov 10 01:25:17 2008
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 10 Nov 2008 08:25:17 +0800
Subject: [Pw_forum] Get wrong symmtry
In-Reply-To: <49175FE1.7050306@gmail.com>
References: <aa128b2c0811090551o13965837gf1c608317183ec88@mail.gmail.com>
<Pine.LNX.4.64.0811091313350.32555@localhost.localdomain>
<49175FE1.7050306@gmail.com>
Message-ID: <aa128b2c0811091625o21550cb2j74c21c963b272383@mail.gmail.com>
Thanks for your reply ,
But what is the problem is ?
I think there is nothing wrong to do with numerical accuracy , there may be
something wrong with the code itself , could anybody give me a suggestion
to the solution of this problem?
2008/11/10 Michael Mehl <rcjhawk at gmail.com>
> Axel Kohlmeyer wrote:
> > On Sun, 9 Nov 2008, yumin qian wrote:
>
> > how about not having enough numerical accuracy
> > for the numbers in the z-coordinate?
> >
> > axel.
>
> That would appear not to be the case. The requirement for P4/nmm
> symmetry is that z for the second atom in a pair be equal to -z (or 1-z)
> for the first atom. That's the case here. Whatever the problem is,
> it's not in the coordinates.
>
> (See http://cst-www.nrl.navy.mil/lattice/struk/AsCuSiZr.html)
>
> >
>
> > YQ> ATOMIC_POSITIONS
> > YQ> La 0.2500000000 0.2500000000 0.1461000000
> > YQ> La 0.7500000000 0.7500000000 0.8539000000
> > YQ> O 0.7500000000 0.2500000000 0.0000000000
> > YQ> O 0.2500000000 0.7500000000 0.0000000000
> > YQ> Fe 0.7500000000 0.2500000000 0.5000000000
> > YQ> Fe 0.2500000000 0.7500000000 0.5000000000
> > YQ> As 0.2500000000 0.2500000000 0.6369000000
> > YQ> As 0.7500000000 0.7500000000 0.3631000000
>
> --
> Michael Mehl, Naval Research Laboratory, Washington DC.
> Sabbatical Duke University through July 2009.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel: + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603 Beijing 100190
China
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From dalcorso at sissa.it Mon Nov 10 07:31:07 2008
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Mon, 10 Nov 2008 07:31:07 +0100
Subject: [Pw_forum] Get wrong symmtry
In-Reply-To: <aa128b2c0811091625o21550cb2j74c21c963b272383@mail.gmail.com>
References: <aa128b2c0811090551o13965837gf1c608317183ec88@mail.gmail.com>
<Pine.LNX.4.64.0811091313350.32555@localhost.localdomain>
<49175FE1.7050306@gmail.com>
<aa128b2c0811091625o21550cb2j74c21c963b272383@mail.gmail.com>
Message-ID: <20081110073107.s4y67y8nk8g4kos8@webmail.sissa.it>
Quoting yumin qian <yuminqian at gmail.com>:
> Thanks for your reply ,
> But what is the problem is ?
> I think there is nothing wrong to do with numerical accuracy , there may be
> something wrong with the code itself , could anybody give me a suggestion
> to the solution of this problem?
This is not a problem of the code. Please check your z coordinates.
Note that they are in units of alat, not in units of c.
Andrea
>
> 2008/11/10 Michael Mehl <rcjhawk at gmail.com>
>
>> Axel Kohlmeyer wrote:
>> > On Sun, 9 Nov 2008, yumin qian wrote:
>>
>> > how about not having enough numerical accuracy
>> > for the numbers in the z-coordinate?
>> >
>> > axel.
>>
>> That would appear not to be the case. The requirement for P4/nmm
>> symmetry is that z for the second atom in a pair be equal to -z (or 1-z)
>> for the first atom. That's the case here. Whatever the problem is,
>> it's not in the coordinates.
>>
>> (See http://cst-www.nrl.navy.mil/lattice/struk/AsCuSiZr.html)
>>
>> >
>>
>> > YQ> ATOMIC_POSITIONS
>> > YQ> La 0.2500000000 0.2500000000 0.1461000000
>> > YQ> La 0.7500000000 0.7500000000 0.8539000000
>> > YQ> O 0.7500000000 0.2500000000 0.0000000000
>> > YQ> O 0.2500000000 0.7500000000 0.0000000000
>> > YQ> Fe 0.7500000000 0.2500000000 0.5000000000
>> > YQ> Fe 0.2500000000 0.7500000000 0.5000000000
>> > YQ> As 0.2500000000 0.2500000000 0.6369000000
>> > YQ> As 0.7500000000 0.7500000000 0.3631000000
>>
>> --
>> Michael Mehl, Naval Research Laboratory, Washington DC.
>> Sabbatical Duke University through July 2009.
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Sincerely Y. M. Qian
> Lab.of Condensed Matter Theory and Materials Computation
> Institute of Physics
> Chinese Academy of Sciences
> Tel: + 8610 8264 9147
> E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
> P.O.Box 603 Beijing 100190
> China
>
----------------------------------------------------------------
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From giannozz at democritos.it Mon Nov 10 08:46:31 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 10 Nov 2008 08:46:31 +0100
Subject: [Pw_forum] Get wrong symmtry
In-Reply-To: <aa128b2c0811091625o21550cb2j74c21c963b272383@mail.gmail.com>
References: <aa128b2c0811090551o13965837gf1c608317183ec88@mail.gmail.com> <Pine.LNX.4.64.0811091313350.32555@localhost.localdomain> <49175FE1.7050306@gmail.com>
<aa128b2c0811091625o21550cb2j74c21c963b272383@mail.gmail.com>
Message-ID: <4917E6D7.50209@democritos.it>
yumin qian wrote:
> But what is the problem is ?
the problem has been explained no less than N! times: see the archives
of this mailing list, items 1.22 and 1.23 of
http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_(PWscf)
The list of possible reasons does not include the trivial one ("symmetry
not found because not there"), of course, but I guess it should be
added. See also here:
http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#Input_data
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From yuminqian at gmail.com Mon Nov 10 08:54:06 2008
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 10 Nov 2008 15:54:06 +0800
Subject: [Pw_forum] Get wrong symmtry
In-Reply-To: <aa128b2c0811091625o21550cb2j74c21c963b272383@mail.gmail.com>
References: <aa128b2c0811090551o13965837gf1c608317183ec88@mail.gmail.com>
<Pine.LNX.4.64.0811091313350.32555@localhost.localdomain>
<49175FE1.7050306@gmail.com>
<aa128b2c0811091625o21550cb2j74c21c963b272383@mail.gmail.com>
Message-ID: <aa128b2c0811092354t4d25b19cq1740d6d3c60f2b43@mail.gmail.com>
thanks for all of you ,
the problem have been solved by adding a parameter to the atomic_position
card.
ATOMIC_POSITIONS {crystal}
2008/11/10 yumin qian <yuminqian at gmail.com>
> Thanks for your reply ,
> But what is the problem is ?
> I think there is nothing wrong to do with numerical accuracy , there may
> be something wrong with the code itself , could anybody give me a suggestion
> to the solution of this problem?
>
> 2008/11/10 Michael Mehl <rcjhawk at gmail.com>
>
> Axel Kohlmeyer wrote:
>> > On Sun, 9 Nov 2008, yumin qian wrote:
>>
>> > how about not having enough numerical accuracy
>> > for the numbers in the z-coordinate?
>> >
>> > axel.
>>
>> That would appear not to be the case. The requirement for P4/nmm
>> symmetry is that z for the second atom in a pair be equal to -z (or 1-z)
>> for the first atom. That's the case here. Whatever the problem is,
>> it's not in the coordinates.
>>
>> (See http://cst-www.nrl.navy.mil/lattice/struk/AsCuSiZr.html)
>>
>> >
>>
>> > YQ> ATOMIC_POSITIONS
>> > YQ> La 0.2500000000 0.2500000000 0.1461000000
>> > YQ> La 0.7500000000 0.7500000000 0.8539000000
>> > YQ> O 0.7500000000 0.2500000000 0.0000000000
>> > YQ> O 0.2500000000 0.7500000000 0.0000000000
>> > YQ> Fe 0.7500000000 0.2500000000 0.5000000000
>> > YQ> Fe 0.2500000000 0.7500000000 0.5000000000
>> > YQ> As 0.2500000000 0.2500000000 0.6369000000
>> > YQ> As 0.7500000000 0.7500000000 0.3631000000
>>
>> --
>> Michael Mehl, Naval Research Laboratory, Washington DC.
>> Sabbatical Duke University through July 2009.
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Sincerely Y. M. Qian
> Lab.of Condensed Matter Theory and Materials Computation
> Institute of Physics
> Chinese Academy of Sciences
> Tel: + 8610 8264 9147
> E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
> P.O.Box 603 Beijing 100190
> China
>
>
--
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel: + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603 Beijing 100190
China
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From lanhaiping at gmail.com Mon Nov 10 10:17:13 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 10 Nov 2008 17:17:13 +0800
Subject: [Pw_forum] Get wrong symmtry
In-Reply-To: <aa128b2c0811092354t4d25b19cq1740d6d3c60f2b43@mail.gmail.com>
References: <aa128b2c0811090551o13965837gf1c608317183ec88@mail.gmail.com>
<Pine.LNX.4.64.0811091313350.32555@localhost.localdomain>
<49175FE1.7050306@gmail.com>
<aa128b2c0811091625o21550cb2j74c21c963b272383@mail.gmail.com>
<aa128b2c0811092354t4d25b19cq1740d6d3c60f2b43@mail.gmail.com>
Message-ID: <c92002fa0811100117x20ee58dbvf4d3cc9504e327f5@mail.gmail.com>
hi, yumin,
you can install a xcrysden to examine your input structures,
just with
" xcrysden --pwi pw.inp"
On Mon, Nov 10, 2008 at 3:54 PM, yumin qian <yuminqian at gmail.com> wrote:
>
> thanks for all of you ,
> the problem have been solved by adding a parameter to the
> atomic_position card.
>
> ATOMIC_POSITIONS {crystal}
> 2008/11/10 yumin qian <yuminqian at gmail.com>
>
> Thanks for your reply ,
>> But what is the problem is ?
>> I think there is nothing wrong to do with numerical accuracy , there may
>> be something wrong with the code itself , could anybody give me a suggestion
>> to the solution of this problem?
>>
>> 2008/11/10 Michael Mehl <rcjhawk at gmail.com>
>>
>> Axel Kohlmeyer wrote:
>>> > On Sun, 9 Nov 2008, yumin qian wrote:
>>>
>>> > how about not having enough numerical accuracy
>>> > for the numbers in the z-coordinate?
>>> >
>>> > axel.
>>>
>>> That would appear not to be the case. The requirement for P4/nmm
>>> symmetry is that z for the second atom in a pair be equal to -z (or 1-z)
>>> for the first atom. That's the case here. Whatever the problem is,
>>> it's not in the coordinates.
>>>
>>> (See http://cst-www.nrl.navy.mil/lattice/struk/AsCuSiZr.html)
>>>
>>> >
>>>
>>> > YQ> ATOMIC_POSITIONS
>>> > YQ> La 0.2500000000 0.2500000000 0.1461000000
>>> > YQ> La 0.7500000000 0.7500000000 0.8539000000
>>> > YQ> O 0.7500000000 0.2500000000 0.0000000000
>>> > YQ> O 0.2500000000 0.7500000000 0.0000000000
>>> > YQ> Fe 0.7500000000 0.2500000000 0.5000000000
>>> > YQ> Fe 0.2500000000 0.7500000000 0.5000000000
>>> > YQ> As 0.2500000000 0.2500000000 0.6369000000
>>> > YQ> As 0.7500000000 0.7500000000 0.3631000000
>>>
>>> --
>>> Michael Mehl, Naval Research Laboratory, Washington DC.
>>> Sabbatical Duke University through July 2009.
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>
>>
>>
>> --
>> Sincerely Y. M. Qian
>> Lab.of Condensed Matter Theory and Materials Computation
>> Institute of Physics
>> Chinese Academy of Sciences
>> Tel: + 8610 8264 9147
>> E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
>> P.O.Box 603 Beijing 100190
>> China
>>
>>
>
>
> --
> Sincerely Y. M. Qian
> Lab.of Condensed Matter Theory and Materials Computation
> Institute of Physics
> Chinese Academy of Sciences
> Tel: + 8610 8264 9147
> E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
> P.O.Box 603 Beijing 100190
> China
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From Adriano.Mosca.Conte at roma2.infn.it Mon Nov 10 10:35:02 2008
From: Adriano.Mosca.Conte at roma2.infn.it (Adriano Mosca Conte)
Date: Mon, 10 Nov 2008 10:35:02 +0100 (CET)
Subject: [Pw_forum] GW
In-Reply-To: <523911.86459.qm@web33107.mail.mud.yahoo.com>
References: <523911.86459.qm@web33107.mail.mud.yahoo.com>
Message-ID: <35713.141.108.248.78.1226309702.squirrel@141.108.248.78>
You can use codes that are interfaced with ESPRESSO such as YAMBO
(www.yambo-code.org) or others.
> Dear all
> Can we do GW calculation with esperesso or did not implemented?
> thanks a lot
>
> Ali Kazempour, Isfahan University of Technology
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Universit? degli Studi Tor Vergata
via della Ricerca Scientifica 1
00133 Roma, Italia
Tel. +39 06 7259 4741
Fax +39 06 2023507
From kazempoor2000 at yahoo.com Mon Nov 10 13:36:32 2008
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Mon, 10 Nov 2008 04:36:32 -0800 (PST)
Subject: [Pw_forum] antiferro
Message-ID: <878548.37520.qm@web33108.mail.mud.yahoo.com>
Daer all
I start the ferromagnetic calculation for the slab of MnAs containing 7 layer,but after finishing the run , the spin polarization of Mn atoms in surface rotate in 180 and make the layer antiferromagnetic ,are this feasible?
Here is my input file:
&CONTROL
title = 'MnAs' ,
calculation = 'relax' ,
restart_mode = 'restart' ,
tstress = .true.,
tprnfor = .true.,
outdir = '/p5/batch/javad/',
pseudo_dir = '/afs/ipp-garching.mpg.de/home/j/javad/espresso-3.2.3/pseudo/' ,
prefix = 'MnAs-surface1' ,
/
&SYSTEM
ibrav = 8,
celldm(1) = 42.498
celldm(2) = 0.28867
celldm(3)= 0.250166
nat = 28,
ntyp = 2,
ecutwfc = 30 ,
ecutrho = 400 ,
occupations = 'smearing' ,
degauss = 0.02 ,
smearing = 'methfessel-paxton' ,
nspin = 2 ,
starting_magnetization(1) = 3.0,
starting_magnetization(2) = 0.01,
/
&ELECTRONS
diagonalization=''
mixing_mode = 'plain'
electron_maxstep = 300,
conv_thr = .0001 ,
/
&IONS
ion_dynamics='bfgs'
/
ATOMIC_SPECIES
Mn 74.92000 Mn.PBE-VAN.UPF
As 54.93000 As.pbe-n-van.UPF
ATOMIC_POSITIONS crystal
Mn 0.0 0.0 0.00000
Mn 0.0 0.0 0.5
As 0.0 0.3333333 0.25
As 0.0 0.66666666 0.75
As 0.08333333 0.1666666 0.75
Mn 0.08333333 0.5 0.00000
Mn 0.083333333 0.5 0.5
As 0.083333333 0.8333333 0.25
Mn 0.1666666 0.0 0.00000
Mn 0.16666666 0.0 0.5
As 0.16666666 0.3333333 0.25
As 0.1666666 0.66666666 0.75
As 0.25 0.1666666 0.75
Mn 0.25 0.5 0.00000
Mn 0.25 0.5 0.5
As 0.25 0.83333333 0.25
Mn 0.3333333 0.0 0.00000
Mn 0.33333333 0.0 0.5
As 0.33333333 0.3333333 0.25
As 0.3333333 0.66666666 0.75
As 0.41666666 0.1666666 0.75
Mn 0.416666666 0.5 0.00000
Mn 0.416666666 0.5 0.5
As 0.416666666 0.83333333 0.25
Mn 0.5 0.0 0.00000
Mn 0.5 0.0 0.5
As 0.5 0.3333333 0.25
As 0.5 0.66666666 0.75
K_POINTS automatic
1 8 8 0 0 1
thanks alot
Ali Kazempour,Isfahan univ. of Tech
From zucco at dipteris.unige.it Mon Nov 10 14:11:03 2008
From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini)
Date: Mon, 10 Nov 2008 14:11:03 +0100
Subject: [Pw_forum] Vectors in rhombohedral cells
Message-ID: <0B09E2D5-3A4E-4A01-9120-B044804884CD@dipteris.unige.it>
Dear all,
working with a rhombohedral cell I've found something that appear to
me to going wrong, and I call you for a help. Probably is only my
mistake but I ask you a confirmation.
The problem arises when I compare the results of a vc-relax output as
below:
...
ibrav = 5,
celldm(1) = 10.9072,
celldm(4) = 0.67279,
....
End of BFGS Geometry Optimization
Final enthalpy = -325.7624962652 Ry
new unit-cell volume = 666.19980 a.u.^3 ( 98.72062 Ang^3 )
CELL_PARAMETERS (alat)
0.411520633 -0.237591548 0.875166762
0.000000000 0.475183096 0.875166762
-0.411520633 -0.237591548 0.875166762
...
and the few summary lines of an scf output of the optimized structure
with c=0.661301537
...
bravais-lattice index = 5
lattice parameter (a_0) = 10.8619 a.u.
unit-cell volume = 661.4872 (a.u.)^3
...
crystal axes: (cart. coord. in units of a_0)
a(1) = ( 0.411521 -0.237592 0.879887 )
a(2) = ( 0.000000 0.475183 0.879887 )
a(3) = ( -0.411521 -0.237592 0.879887 )
You can see the difference in what concerns the volume.
To compute a0 and alpha of the optimized cell I used what is reported
in the PW manual
v1 = a(tx,-ty,tz), v2 = a(0,2ty,tz), v3 = a(-tx,-ty,tz).
where c=cos(alpha) is the cosine of the angle alpha between any pair
of crystallographic vectors, tc, ty, tz are defined as
tx=sqrt((1-c)/2), ty=sqrt((1-c)/6), tz=sqrt((1+2c)/3)
but...if I calculate c (as cos(alpha)) from tx, ty and tz I noticed
that tx and ty are good but tz is not.
From the vc-relax output I obtain:
c from tx ==> 0.661301537
c from ty ==> 0.661301537
c from tz ==> 0.648875292 <=== ?
From scf output I obtain, considering the truncation of the matrix'
elements
c from tx ==> 0.661300933
c from ty ==> 0.661300249
c from tz ==> 0.661301699
Thanks for any help
m.
*******************************************************
Marino Vetuschi Zuccolini
zucco at dipteris.unige.it
Researcher / Geochemist
Laboratory of Geochemistry
DIPartimento per lo studio della TErra e delle sue RISorse -
Universit? di Genova
Tel. ++39 010 3538136 Fax. ++39 010 352169
Corso Europa 26, 16132 - Genova - Italy
From asafis at yahoo.com.br Mon Nov 10 14:59:53 2008
From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=)
Date: Mon, 10 Nov 2008 05:59:53 -0800 (PST)
Subject: [Pw_forum] Warnings
Message-ID: <23376.58658.qm@web52311.mail.re2.yahoo.com>
????
Hello everyone. What are the warnings below? This undermines the final result?
??? Initial potential from superposition of free atoms
???? Check: negative starting charge=(component1):?? -0.002147
???? Check: negative starting charge=(component2):?? -0.002147
Regards
A. S. Santos
Novos endere?os, o Yahoo! que voc? conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com.
http://br.new.mail.yahoo.com/addresses
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From paulatto at sissa.it Mon Nov 10 15:19:49 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 10 Nov 2008 15:19:49 +0100
Subject: [Pw_forum] Warnings
In-Reply-To: <23376.58658.qm@web52311.mail.re2.yahoo.com>
References: <23376.58658.qm@web52311.mail.re2.yahoo.com>
Message-ID: <49184305.5000900@sissa.it>
?lvaro Alves ha scritto:
>
> Hello everyone. What are the warnings below? This undermines the final
> result?
>
> Initial potential from superposition of free atoms
> Check: negative starting charge=(component1): -0.002147
> Check: negative starting charge=(component2): -0.002147
>
Dear Alves,
your question has been asked many times, you can find the answer in the
mailing list archive. For the future I've (just) written a entry in the
!FAQ, you can read it here:
<http://quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#Why_do_I_get_.22negative_starting_charge.22.3F>
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.
Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste
Donations in food, coins, booze and processor time are warmly welcome.
From shruba at gmail.com Mon Nov 10 16:30:09 2008
From: shruba at gmail.com (shruba at gmail.com)
Date: Mon, 10 Nov 2008 10:30:09 -0500
Subject: [Pw_forum] error message from read_pseudo_mesh : error # 1 Reading
pseudo file (R) for Ce
Message-ID: <822f4ec80811100730k7d292a15v1e656aea90fb9099@mail.gmail.com>
Dear all,
I was trying to submit a calculation using ( *
espresso-4.0.3.tar.gz*<http://www.pwscf.org/downloads/PWversion/4.0.3/espresso-4.0.3.tar.gz>(released
2008-10-22)) using this input file and the pseudopotential, which
was provided to us very generously by Dr Fabris,
This input is running normally in a cluster having Opteron processors, and
the os is redhat linux, ( using both LAMMPI and mpich) now when i tried to
run this input in nersc supercomputer cluster, having IBM Cluster 1600 , IBM
p575 POWER 5, Software (original version in parentheses) IBM AIX Version 5.3
ML 4 (5.2 ML 5)
I am getting the error
error message from read_pseudo_mesh : error # 1 Reading pseudo file (R)
for Ce
I am pasting the pseudopotential header and my input, please let me know if
i am missing any information, if you please help me to figure out how to
solve this that will be really great help, thanks for your time
shruba
<PP_INFO>
Generated using Vanderbilt code, version 7 3 4
Author: unknown Generation date: 27 7 2005
Automatically converted from original format
1 The Pseudo was generated with a Scalar-Relativistic Calculation
2.10000000000E+00 Local Potential cutoff radius
nl pn l occ Rcut Rcut US E pseu
4F 4 3 1.00 10.00000000000 1.80000000000 -0.39547555416
5S 5 0 2.00 10.00000000000 1.60000000000 -2.98314000093
5P 5 1 6.00 10.00000000000 1.80000000000 -1.70705941252
5D 5 2 1.00 10.00000000000 1.80000000000 -0.22485386450
6S 6 0 2.00 10.00000000000 1.60000000000 -0.27522397471
</PP_INFO>
input file
&CONTROL
calculation = 'relax'
restart_mode = 'from_scratch',
tprnfor = .TRUE.,
prefix = '9',
pseudo_dir = '/home/shruba/srfeopp/',
/
&SYSTEM
ibrav = 1,
celldm(1) = 35.0
nat =51,
ntyp =2,
nbnd=500,
ecutwfc = 35,
ecutrho = 350,
nspin=2,
multiplicity=1,
occupations = 'smearing',
smearing ='marzari-vanderbilt',
degauss=0.0008,
/
&ELECTRONS
electron_maxstep =400,
/
&ions
ion_dynamics = 'bfgs',
wfc_extrapolation='second_order',
pot_extrapolation='second_order'
ion_positions = 'from_input'
/
ATOMIC_SPECIES
Ce 140.115 Ce4_ps_f1d1-pbe-rc1.0.uspp.UPF
O 16.00 O.pbe-van-bm.UPF
ATOMIC_POSITIONS {angstrom}
Ce 0.240753 0.117800 0.135937
Ce 6.464087 0.131036 0.171093
Ce 4.429110 4.744538 0.151726
Ce 7.493441 3.347170 1.290600
Ce 3.392344 1.520271 -0.956958
Ce 6.509589 2.904330 -2.150325
Ce 4.431329 -0.778173 4.655046
Ce 7.506912 0.613913 3.555310
Ce 3.373915 -1.263157 1.296437
Ce 6.512187 -2.682385 2.427526
Ce 8.599998 3.843615 4.700742
Ce 2.339658 3.806630 4.663235
Ce 5.447009 2.447125 5.789411
Ce 1.359661 0.596837 3.531188
Ce 5.445572 5.176820 3.559495
Ce 1.341018 3.364989 1.304481
Ce 4.412472 1.978056 2.393172
Ce 2.339804 6.639926 2.427280
Ce 2.336563 1.040046 6.987493
O 1.096359 2.117498 -0.704335
O 2.298358 -0.585245 -0.711826
O -0.092844 1.577359 1.916847
O 1.085653 -1.122025 1.922727
O 8.938864 2.384130 2.913119
O 4.411768 0.498645 0.643569
O 5.465176 -2.009996 0.446743
O 7.875984 1.900231 -0.548186
O 7.881522 -0.911806 1.765756
O 5.481604 0.830108 -1.872629
O 6.572420 1.474214 1.837701
O 7.727957 5.065267 2.916824
O 2.166391 5.421034 0.442241
O 3.332956 2.971830 0.649431
O 5.487161 3.913850 1.823983
O 6.685541 4.600396 -0.558270
O 4.578525 6.484106 1.769867
O 4.275459 3.527388 -1.877759
O 7.736974 1.855172 5.557358
O 2.171189 -0.649687 5.394524
O 5.468329 1.017727 4.180748
O 3.363964 0.037689 3.002229
O 6.688818 -1.446701 4.403735
O 4.567571 0.427707 6.703107
O 4.282142 -2.550855 3.091717
O 6.553586 4.537892 5.561983
O 0.949646 2.023619 5.397054
O 3.354910 5.937088 4.407328
O 3.353287 3.123057 6.701842
O 0.944909 4.887132 3.086546
O 4.380494 3.409595 4.185707
O 2.278672 2.462760 3.014481
K_POINTS {automatic}
1 1 1 0 0 0
pseudo potential file,
<PP_HEADER>
0 Version Number
Ce Element
US Ultrasoft pseudopotential
T Nonlinear Core Correction
SLA PW PBE PBE PBE Exchange-Correlation functional
12.00000000000 Z valence
-150.74977779744 Total energy
0.0000000 0.0000000 Suggested cutoff for wfc and rho
3 Max angular momentum component
947 Number of points in mesh
5 5 Number of Wavefunctions, Number of Projectors
Wavefunctions nl l occ
4F 3 1.00
5S 0 2.00
5P 1 6.00
5D 2 1.00
6S 0 2.00
--
shruba gangopadhyay
graduate student
department of chemistry
university of central florida
orlando, FL-32826
'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
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From wjb19 at psu.edu Mon Nov 10 15:59:33 2008
From: wjb19 at psu.edu (WILLIAM J BROUWER)
Date: Mon, 10 Nov 2008 09:59:33 -0500
Subject: [Pw_forum] specifying OH,ON etc in input files
Message-ID: <1226329173l.716912l.0l@psu.edu>
folks, does anyone know how to specify OH, ON etc in an input file? I have a
structure for cancrinite with various ON, OH with a
single x,y,z line in the structure file, how do I describe these explicitly in
ESPRESSO?
cheers,
bill brouwer
Penn State
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From giannozz at democritos.it Mon Nov 10 16:47:49 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 10 Nov 2008 16:47:49 +0100
Subject: [Pw_forum] specifying OH,ON etc in input files
In-Reply-To: <1226329173l.716912l.0l@psu.edu>
References: <1226329173l.716912l.0l@psu.edu>
Message-ID: <491857A5.6000708@democritos.it>
WILLIAM J BROUWER wrote:
> folks, does anyone know how to specify OH, ON etc in an input file?
what are OH, ON ?
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From slgphy at rediffmail.com Mon Nov 10 17:07:55 2008
From: slgphy at rediffmail.com (Shyam )
Date: 10 Nov 2008 16:07:55 -0000
Subject: [Pw_forum] LO -TO Splitting
Message-ID: <20081110160755.17507.qmail@f4mail211.rediffmail.com>
Hello all,I am trying to get the LO-TO splitting in GaAs. But I am
a bit confused about the pseudo potential to be used. I have done
calculations using both the ultrasoft pseudopotential (USPP) and
the normconserving (NCPP). Both of these are giving me almost similar
electronic DOS whereas phonon DOS. The phonon DOS which I have got using USPP is matching with
the reported one and that I have got using NCPP is not matching. The input files used in two cases are as follows,***********************************************************************USPP***********************************************************************
cat > gaas.scf.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
tstress = .true.
tprnfor = .true.
prefix='gaas',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav= 2, celldm(1) =10.68, nat= 2, ntyp= 2,
ecutwfc =18.0, ecutrho =1700,
/
&electrons
conv_thr = 1.0d-8
mixing_beta = 0.7
/
ATOMIC_SPECIES
Ga 69.72 Ga.pbe-nsp-van.UPF
As 74.92 As.pbe-n-van.UPF
ATOMIC_POSITIONS
Ga 0.00 0.00 0.00
As 0.25 0.25 0.25
K_POINTS {automatic}
4 4 4 0 0 0
EOF
$ECHO " running the scf calculation...c"
$PW_COMMAND < gaas.scf.in > gaas.scf.out
check_failure $?
$ECHO " done"
# DOS calculation for GaAs
cat > gaas.dos.in << EOF
&control
calculation='nscf'
prefix='gaas',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav=2, celldm(1) =10.68, nat=2, ntyp=2,
ecutwfc = 18.0, ecutrho = 1700.0, nbnd=10,
occupations='tetrahedra'
/
&electrons
conv_thr = 1.0e-10
mixing_beta = 0.7
/
ATOMIC_SPECIES
Ga 69.720 Ga.pbe-nsp-van.UPF
As 74.922 As.pbe-n-van.UPF
ATOMIC_POSITIONS
Ga 0.0 0.0 0.0
As 0.25 0.25 0.25
K_POINTS {automatic}
12 12 12 0 0 0
EOF
cat > gaas.dos2.in << EOF
&inputpp
outdir='$TMP_DIR/'
prefix='gaas'
fildos='gaas.dos',
Emin=-25.0, Emax=25.0, DeltaE=0.1
/
EOF
$ECHO " running DOS calculation for GaAs...c"
$PW_COMMAND < gaas.dos.in > gaas.dos.out
check_failure $?
$DOS_COMMAND < gaas.dos2.in > gaas.dos2.out
check_failure $?
$ECHO " done"
# phonon calculation on a (444) uniform grid of q-points
cat > gaas.ph.in << EOF
phonons of GaAs
&inputph
tr2_ph=1.0d-12,
prefix='gaas',
ldisp=.true.,
nq1=4, nq2=4, nq3=4
amass(1)=69.72,
amass(2)=74.92,
outdir='$TMP_DIR/',
fildyn='gaas.dyn',
/
EOF
$ECHO " running the phonon calculation ...c"
$PH_COMMAND < gaas.ph.in > gaas.ph.out
check_failure $?
$ECHO " done"
cat > q2r.in <<EOF
&input
fildyn='gaas.dyn', zasr='simple', flfrc='gaas444.fc'
/
EOF
$ECHO " transforming C(q) => C(R)...c"
$Q2R_COMMAND < q2r.in > q2r.out
check_failure $?
$ECHO " done"
cat > matdyn.in <<EOF
&input
asr='simple', amass(1)=69.72, amass(2)=74.922,
flfrc='gaas444.fc', flfrq='gaas.freq'
/
9
0.000 0.0 0.0 0.0
0.125 0.0 0.0 0.0
0.250 0.0 0.0 0.0
0.375 0.0 0.0 0.0
0.500 0.0 0.0 0.0
0.625 0.0 0.0 0.0
0.750 0.0 0.0 0.0
0.875 0.0 0.0 0.0
1.000 0.0 0.0 0.0
EOF
$ECHO " recalculating omega(q) from C(R)...c"
$MATDYN_COMMAND < matdyn.in > matdyn.out
check_failure $?
$ECHO " done"
cat > phdos.in <<EOF
&input
asr='simple', dos=.true. amass(1)=69.72, amass(2)=74.922,
flfrc='gaas444.fc', fldos='gaas.phdos', nk1=6,nk2=6,nk3=6
/
EOF
$ECHO " calculating phonon DOS ...c"
$MATDYN_COMMAND < phdos.in > phdos.out
check_failure $?
$ECHO " done"
$ECHO$ECHO "$EXAMPLE_DIR: done"***********************************************************NCPP***********************************************************
cat > gaas.scf.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
tstress = .true.
tprnfor = .true.
prefix='gaas',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav= 2, celldm(1) =10.68, nat= 2, ntyp= 2,
ecutwfc =60.0, ecutrho=450,
/
&electrons
conv_thr = 1.0d-8
mixing_beta = 0.7
/
ATOMIC_SPECIES
Ga 69.72 Ga.pz-bhs.UPF
As 74.92 As.gon.UPF
ATOMIC_POSITIONS
Ga 0.00 0.00 0.00
As 0.25 0.25 0.25
K_POINTS {automatic}
4 4 4 0 0 0
EOF
$ECHO " running the scf calculation...c"
$PW_COMMAND < gaas.scf.in > gaas.scf.out
check_failure $?
$ECHO " done"
# DOS calculation for GaAs
cat > gaas.dos.in << EOF
&control
calculation='nscf'
prefix='gaas',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav=2, celldm(1) =10.68, nat=2, ntyp=2,
ecutwfc = 60.0, ecutrho = 450.0, nbnd=10,
occupations='tetrahedra'
/
&electrons
conv_thr = 1.0e-10
mixing_beta = 0.7
/
ATOMIC_SPECIES
Ga 69.720 Ga.pz-bhs.UPF
As 74.922 As.gon.UPF
ATOMIC_POSITIONS
Ga 0.0 0.0 0.0
As 0.25 0.25 0.25
K_POINTS {automatic}
12 12 12 0 0 0
EOF
cat > gaas.dos2.in << EOF
&inputpp
outdir='$TMP_DIR/'
prefix='gaas'
fildos='gaas.dos',
Emin=-25.0, Emax=25.0, DeltaE=0.1
/
EOF
$ECHO " running DOS calculation for GaAs...c"
$PW_COMMAND < gaas.dos.in > gaas.dos.out
check_failure $?
$DOS_COMMAND < gaas.dos2.in > gaas.dos2.out
check_failure $?
$ECHO " done"
# phonon calculation on a (444) uniform grid of q-points
cat > gaas.ph.in << EOF
phonons of GaAs
&inputph
tr2_ph=1.0d-12,
prefix='gaas',
ldisp=.true.,
nq1=4, nq2=4, nq3=4
amass(1)=69.72,
amass(2)=74.92,
outdir='$TMP_DIR/',
fildyn='gaas.dyn',
/
EOF
$ECHO " running the phonon calculation ...c"
$PH_COMMAND < gaas.ph.in > gaas.ph.out
check_failure $?
$ECHO " done"
cat > q2r.in <<EOF
&input
fildyn='gaas.dyn', zasr='simple', flfrc='gaas444.fc'
/
EOF
$ECHO " transforming C(q) => C(R)...c"
$Q2R_COMMAND < q2r.in > q2r.out
check_failure $?
$ECHO " done"
cat > matdyn.in <<EOF
&input
asr='simple', amass(1)=69.72, amass(2)=74.922,
flfrc='gaas444.fc', flfrq='gaas.freq'
/
9
0.000 0.0 0.0 0.0
0.125 0.0 0.0 0.0
0.250 0.0 0.0 0.0
0.375 0.0 0.0 0.0
0.500 0.0 0.0 0.0
0.625 0.0 0.0 0.0
0.750 0.0 0.0 0.0
0.875 0.0 0.0 0.0
1.000 0.0 0.0 0.0
EOF
$ECHO " recalculating omega(q) from C(R)...c"
$MATDYN_COMMAND < matdyn.in > matdyn.out
check_failure $?
$ECHO " done"
cat > phdos.in <<EOF
&input
asr='simple', dos=.true. amass(1)=69.72, amass(2)=74.922,
flfrc='gaas444.fc', fldos='gaas.phdos', nk1=6,nk2=6,nk3=6
/
EOF
$ECHO " calculating phonon DOS ...c"
$MATDYN_COMMAND < phdos.in > phdos.out
check_failure $?
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR: done"***********************************************************I will be highly thankful if one could please let me know the way out to this.Thank you.Shyam Lal GuptaIIT KanpurKanpurINDIA-208016.
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From marcel at physik.tu-berlin.de Mon Nov 10 16:57:36 2008
From: marcel at physik.tu-berlin.de (Marcel Mohr)
Date: Mon, 10 Nov 2008 16:57:36 +0100 (CET)
Subject: [Pw_forum] specifying OH,ON etc in input files
In-Reply-To: <1226329173l.716912l.0l@psu.edu>
References: <1226329173l.716912l.0l@psu.edu>
Message-ID: <alpine.BSF.1.10.0811101655490.6928@rosa.physik-pool.tu-berlin.de>
As long as OH and ON are not any new elements, that I do not know, you
have to specify the
coordinate of the O and that of the hydrogen or nitrogen in reasonable
distance in a reasonable direction from your oxygen. The exact position PW
will find itself.
Cheers Marcel
________________________________________________________________________
Marcel Mohr Institut f?r Festk?rperphysik, TU Berlin
marcel(at)physik.tu-berlin.de Sekr. EW 5-4
TEL: +49-30-314 24442 Hardenbergstr. 36
FAX: +49-30-314 27705 10623 Berlin
On Mon, 10 Nov 2008, WILLIAM J BROUWER wrote:
> folks, does anyone know how to specify OH, ON etc in an input file? I have a structure for cancrinite with
> various ON, OH with a single x,y,z line in the structure file, how do I describe these explicitly in ESPRESSO?
>
> cheers,
> bill brouwer
> Penn State
>
>
From slgphy at rediffmail.com Mon Nov 10 17:10:24 2008
From: slgphy at rediffmail.com (Shyam )
Date: 10 Nov 2008 16:10:24 -0000
Subject: [Pw_forum] LO -TO Splitting
Message-ID: <20081110161024.1040.qmail@f4mail-234-223.rediffmail.com>
Hello all,I am trying to get the LO-TO splitting in GaAs. But I am
a bit confused about the pseudo potential to be used. I have done
calculations using both the ultrasoft pseudopotential (USPP) and
the normconserving (NCPP). Both of these are giving me almost similar
electronic DOS whereas phonon DOS differ in two cases. The phonon DOS which I have got using USPP is matching with
the reported one and that I have got using NCPP is not matching. The input files used in two cases are as follows,***********************************************************************USPP***********************************************************************
cat > gaas.scf.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
tstress = .true.
tprnfor = .true.
prefix='gaas',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav= 2, celldm(1) =10.68, nat= 2, ntyp= 2,
ecutwfc =18.0, ecutrho =1700,
/
&electrons
conv_thr = 1.0d-8
mixing_beta = 0.7
/
ATOMIC_SPECIES
Ga 69.72 Ga.pbe-nsp-van.UPF
As 74.92 As.pbe-n-van.UPF
ATOMIC_POSITIONS
Ga 0.00 0.00 0.00
As 0.25 0.25 0.25
K_POINTS {automatic}
4 4 4 0 0 0
EOF
$ECHO " running the scf calculation...c"
$PW_COMMAND < gaas.scf.in > gaas.scf.out
check_failure $?
$ECHO " done"
# DOS calculation for GaAs
cat > gaas.dos.in << EOF
&control
calculation='nscf'
prefix='gaas',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav=2, celldm(1) =10.68, nat=2, ntyp=2,
ecutwfc = 18.0, ecutrho = 1700.0, nbnd=10,
occupations='tetrahedra'
/
&electrons
conv_thr = 1.0e-10
mixing_beta = 0.7
/
ATOMIC_SPECIES
Ga 69.720 Ga.pbe-nsp-van.UPF
As 74.922 As.pbe-n-van.UPF
ATOMIC_POSITIONS
Ga 0.0 0.0 0.0
As 0.25 0.25 0.25
K_POINTS {automatic}
12 12 12 0 0 0
EOF
cat > gaas.dos2.in << EOF
&inputpp
outdir='$TMP_DIR/'
prefix='gaas'
fildos='gaas.dos',
Emin=-25.0, Emax=25.0, DeltaE=0.1
/
EOF
$ECHO " running DOS calculation for GaAs...c"
$PW_COMMAND < gaas.dos.in > gaas.dos.out
check_failure $?
$DOS_COMMAND < gaas.dos2.in > gaas.dos2.out
check_failure $?
$ECHO " done"
# phonon calculation on a (444) uniform grid of q-points
cat > gaas.ph.in << EOF
phonons of GaAs
&inputph
tr2_ph=1.0d-12,
prefix='gaas',
ldisp=.true.,
nq1=4, nq2=4, nq3=4
amass(1)=69.72,
amass(2)=74.92,
outdir='$TMP_DIR/',
fildyn='gaas.dyn',
/
EOF
$ECHO " running the phonon calculation ...c"
$PH_COMMAND < gaas.ph.in > gaas.ph.out
check_failure $?
$ECHO " done"
cat > q2r.in <<EOF
&input
fildyn='gaas.dyn', zasr='simple', flfrc='gaas444.fc'
/
EOF
$ECHO " transforming C(q) => C(R)...c"
$Q2R_COMMAND < q2r.in > q2r.out
check_failure $?
$ECHO " done"
cat > matdyn.in <<EOF
&input
asr='simple', amass(1)=69.72, amass(2)=74.922,
flfrc='gaas444.fc', flfrq='gaas.freq'
/
9
0.000 0.0 0.0 0.0
0.125 0.0 0.0 0.0
0.250 0.0 0.0 0.0
0.375 0.0 0.0 0.0
0.500 0.0 0.0 0.0
0.625 0.0 0.0 0.0
0.750 0.0 0.0 0.0
0.875 0.0 0.0 0.0
1.000 0.0 0.0 0.0
EOF
$ECHO " recalculating omega(q) from C(R)...c"
$MATDYN_COMMAND < matdyn.in > matdyn.out
check_failure $?
$ECHO " done"
cat > phdos.in <<EOF
&input
asr='simple', dos=.true. amass(1)=69.72, amass(2)=74.922,
flfrc='gaas444.fc', fldos='gaas.phdos', nk1=6,nk2=6,nk3=6
/
EOF
$ECHO " calculating phonon DOS ...c"
$MATDYN_COMMAND < phdos.in > phdos.out
check_failure $?
$ECHO " done"
$ECHO$ECHO "$EXAMPLE_DIR: done"***********************************************************NCPP***********************************************************
cat > gaas.scf.in << EOF
&control
calculation='scf'
restart_mode='from_scratch',
tstress = .true.
tprnfor = .true.
prefix='gaas',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav= 2, celldm(1) =10.68, nat= 2, ntyp= 2,
ecutwfc =60.0, ecutrho=450,
/
&electrons
conv_thr = 1.0d-8
mixing_beta = 0.7
/
ATOMIC_SPECIES
Ga 69.72 Ga.pz-bhs.UPF
As 74.92 As.gon.UPF
ATOMIC_POSITIONS
Ga 0.00 0.00 0.00
As 0.25 0.25 0.25
K_POINTS {automatic}
4 4 4 0 0 0
EOF
$ECHO " running the scf calculation...c"
$PW_COMMAND < gaas.scf.in > gaas.scf.out
check_failure $?
$ECHO " done"
# DOS calculation for GaAs
cat > gaas.dos.in << EOF
&control
calculation='nscf'
prefix='gaas',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav=2, celldm(1) =10.68, nat=2, ntyp=2,
ecutwfc = 60.0, ecutrho = 450.0, nbnd=10,
occupations='tetrahedra'
/
&electrons
conv_thr = 1.0e-10
mixing_beta = 0.7
/
ATOMIC_SPECIES
Ga 69.720 Ga.pz-bhs.UPF
As 74.922 As.gon.UPF
ATOMIC_POSITIONS
Ga 0.0 0.0 0.0
As 0.25 0.25 0.25
K_POINTS {automatic}
12 12 12 0 0 0
EOF
cat > gaas.dos2.in << EOF
&inputpp
outdir='$TMP_DIR/'
prefix='gaas'
fildos='gaas.dos',
Emin=-25.0, Emax=25.0, DeltaE=0.1
/
EOF
$ECHO " running DOS calculation for GaAs...c"
$PW_COMMAND < gaas.dos.in > gaas.dos.out
check_failure $?
$DOS_COMMAND < gaas.dos2.in > gaas.dos2.out
check_failure $?
$ECHO " done"
# phonon calculation on a (444) uniform grid of q-points
cat > gaas.ph.in << EOF
phonons of GaAs
&inputph
tr2_ph=1.0d-12,
prefix='gaas',
ldisp=.true.,
nq1=4, nq2=4, nq3=4
amass(1)=69.72,
amass(2)=74.92,
outdir='$TMP_DIR/',
fildyn='gaas.dyn',
/
EOF
$ECHO " running the phonon calculation ...c"
$PH_COMMAND < gaas.ph.in > gaas.ph.out
check_failure $?
$ECHO " done"
cat > q2r.in <<EOF
&input
fildyn='gaas.dyn', zasr='simple', flfrc='gaas444.fc'
/
EOF
$ECHO " transforming C(q) => C(R)...c"
$Q2R_COMMAND < q2r.in > q2r.out
check_failure $?
$ECHO " done"
cat > matdyn.in <<EOF
&input
asr='simple', amass(1)=69.72, amass(2)=74.922,
flfrc='gaas444.fc', flfrq='gaas.freq'
/
9
0.000 0.0 0.0 0.0
0.125 0.0 0.0 0.0
0.250 0.0 0.0 0.0
0.375 0.0 0.0 0.0
0.500 0.0 0.0 0.0
0.625 0.0 0.0 0.0
0.750 0.0 0.0 0.0
0.875 0.0 0.0 0.0
1.000 0.0 0.0 0.0
EOF
$ECHO " recalculating omega(q) from C(R)...c"
$MATDYN_COMMAND < matdyn.in > matdyn.out
check_failure $?
$ECHO " done"
cat > phdos.in <<EOF
&input
asr='simple', dos=.true. amass(1)=69.72, amass(2)=74.922,
flfrc='gaas444.fc', fldos='gaas.phdos', nk1=6,nk2=6,nk3=6
/
EOF
$ECHO " calculating phonon DOS ...c"
$MATDYN_COMMAND < phdos.in > phdos.out
check_failure $?
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR: done"***********************************************************I will be highly thankful if one could please let me know the way out to this.Thank you.Shyam Lal GuptaIIT KanpurKanpurINDIA-208016.
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From wjb19 at psu.edu Mon Nov 10 17:22:34 2008
From: wjb19 at psu.edu (WILLIAM J BROUWER)
Date: Mon, 10 Nov 2008 11:22:34 -0500
Subject: [Pw_forum] specifying OH,ON etc in input files
Message-ID: <1226334154l.782518l.0l@psu.edu>
thank you marcel, much appreciated!
bill brouwer
Penn State
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From vegalew at hotmail.com Mon Nov 10 20:56:46 2008
From: vegalew at hotmail.com (vega)
Date: Tue, 11 Nov 2008 03:56:46 +0800
Subject: [Pw_forum] Could you please help me to cope with the error message
Message-ID: <BAY124-DS45358B5F953046C3888BAA41A0@phx.gbl>
Dear all,
I am suffering from the error message like this,
[node1][0,1,12][btl_tcp_frag.c:202:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed with errno=104
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
libblas.so.3 55A8D51C Unknown Unknown Unknown
pw.x 081CBD7B Unknown Unknown Unknown
pw.x 0823A95E Unknown Unknown Unknown
pw.x 08239C4A Unknown Unknown Unknown
pw.x 081DEDC9 Unknown Unknown Unknown
pw.x 081D4E9C Unknown Unknown Unknown
Unknown FFFFD060 Unknown Unknown Unknown
Stack trace terminated abnormally.
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
mca_oob_tcp.so 55F911B4 Unknown Unknown Unknown
Unknown 00000001 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
pw.x 0813EE72 Unknown Unknown Unknown
pw.x 0813E577 Unknown Unknown Unknown
Stack trace terminated abnormally.
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE40E Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE40E Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
libblas.so.3 55A8C50F Unknown Unknown Unknown
pw.x 081CBD7B Unknown Unknown Unknown
pw.x 0823A95E Unknown Unknown Unknown
pw.x 08239C4A Unknown Unknown Unknown
pw.x 081DEDC9 Unknown Unknown Unknown
pw.x 081D4E9C Unknown Unknown Unknown
Unknown FFFFD060 Unknown Unknown Unknown
Stack trace terminated abnormally.
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE40E Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
libblas.so.3 55A8C50F Unknown Unknown Unknown
pw.x 081CBD7B Unknown Unknown Unknown
pw.x 0823A95E Unknown Unknown Unknown
pw.x 08239C4A Unknown Unknown Unknown
pw.x 081DEDC9 Unknown Unknown Unknown
pw.x 081D4E9C Unknown Unknown Unknown
Unknown FFFFD060 Unknown Unknown Unknown
Stack trace terminated abnormally.
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
Unknown 00000003 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
libblas.so.3 55A8C50B Unknown Unknown Unknown
pw.x 081CBD7B Unknown Unknown Unknown
pw.x 0823A95E Unknown Unknown Unknown
pw.x 08239C4A Unknown Unknown Unknown
pw.x 081DEDC9 Unknown Unknown Unknown
pw.x 081D4E9C Unknown Unknown Unknown
Unknown FFFFCDC0 Unknown Unknown Unknown
Stack trace terminated abnormally.
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
[node1][0,1,12][btl_tcp_frag.c:202:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed with errno=104
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
libblas.so.3 55A8BF47 Unknown Unknown Unknown
pw.x 080EA567 Unknown Unknown Unknown
Stack trace terminated abnormally.
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
libblas.so.3 55A8BF3B Unknown Unknown Unknown
pw.x 081E3C7B Unknown Unknown Unknown
Stack trace terminated abnormally.
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
[node8][0,1,23][btl_tcp_frag.c:202:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed with errno=104
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
. FFFFE410 Unknown Unknown Unknown
mpirun noticed that job rank 14 with PID 3519 on node node3 exited on signal 11 (Segmentation fault).
I could relax 72 atoms successfully with my system using openmpi. But when I wanted to relax 84 atoms, the error message stoped my calculation. Then I tried the mpich2 using the same system. With the help of mpich2 I could relax 120 atoms instead. But the error message bothered me again when I wanted to relax 132 atoms. I was get entangle by his troublesome thing for quite a long time. Could someone give me some suggestions to cope with this?
for better understanding my question, I will show the detail of my systems as follows,
there are 8 nodes in my cluster with the Ethernet.
CPU intel Q6600
Memory 8G per node
Main Board intel S3000AH
hard disk seagate 750G (7200)
OS redhat linux enterprise 4 as 4 update 4
Fortran intel ifort 10.1.015
C intel icc 10.1.015
MPI mpich2/openmpi
FFTW fftw 2.1.5
MKL 10.0.1.014
thank you for reading. any hints will be deeply appreciated.
vega
=================================================================================
Vega Lew (weijia liu)
PH.D Candidate in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
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From eyvaz_isaev at yahoo.com Mon Nov 10 23:24:09 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Mon, 10 Nov 2008 14:24:09 -0800 (PST)
Subject: [Pw_forum] LO -TO Splitting
In-Reply-To: <20081110161024.1040.qmail@f4mail-234-223.rediffmail.com>
Message-ID: <333345.37371.qm@web65706.mail.ac4.yahoo.com>
Hi,
> The phonon DOS which I have got using USPP
> is matching with the reported one and that I have got > using NCPP is not matching.
Did you compare phonon frequencies in dyn-files for USPP and NCPP? If you got wrong (or different) phonon dispersions the phonon DOS will be different, of course.
Did you use a serial or parallel version? Try restart
your job with NCPP, sometime it helps.
Some additional comments, not related to the issue, but might be useful.
> ecutwfc =18.0, ecutrho =1700
ecutrho for USPP is abnormally large, tipically it is around (8-12) times of ecutwfs.
> ecutwfc =60.0, ecutrho=450,
ecutrho for NCPP is 4 times of ecutwfc. There is no reason for using larger ecutrho.
Please also specify the Subject correctly, as your topic is not related to LO-TO splitting, definitely.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
--- On Mon, 11/10/08, Shyam <slgphy at rediffmail.com> wrote:
> From: Shyam <slgphy at rediffmail.com>
> Subject: [Pw_forum] LO -TO Splitting
> To: pw_forum at pwscf.org
> Date: Monday, November 10, 2008, 7:10 PM
> Hello all,I am trying to get the LO-TO splitting in GaAs.
> But I am
> a bit confused about the pseudo potential to be
> used. I have done
> calculations using both the ultrasoft
> pseudopotential (USPP) and
> the normconserving (NCPP). Both of these are
> giving me almost similar
> electronic DOS whereas phonon DOS differ in two
> cases. The phonon DOS which I have got using USPP
> is matching with
> the reported one and that I have got using NCPP is not
> matching. The input files used in two cases are as
> follows,***********************************************************************USPP***********************************************************************
>
>
> cat > gaas.scf.in << EOF
>
> &control
>
> calculation='scf'
>
> restart_mode='from_scratch',
>
> tstress = .true.
>
> tprnfor = .true.
>
> prefix='gaas',
>
> pseudo_dir = '$PSEUDO_DIR/',
>
> outdir='$TMP_DIR/'
>
> /
>
> &system
>
> ibrav= 2, celldm(1) =10.68, nat= 2, ntyp= 2,
>
> ecutwfc =18.0, ecutrho =1700,
>
> /
>
> &electrons
>
> conv_thr = 1.0d-8
>
> mixing_beta = 0.7
>
> /
>
> ATOMIC_SPECIES
>
> Ga 69.72 Ga.pbe-nsp-van.UPF
>
> As 74.92 As.pbe-n-van.UPF
>
> ATOMIC_POSITIONS
>
> Ga 0.00 0.00 0.00
>
> As 0.25 0.25 0.25
>
> K_POINTS {automatic}
>
> 4 4 4 0 0 0
>
> EOF
>
> $ECHO " running the scf calculation...c"
>
> $PW_COMMAND < gaas.scf.in > gaas.scf.out
>
> check_failure $?
>
> $ECHO " done"
>
> # DOS calculation for GaAs
>
> cat > gaas.dos.in << EOF
>
> &control
>
> calculation='nscf'
>
> prefix='gaas',
>
> pseudo_dir = '$PSEUDO_DIR/',
>
> outdir='$TMP_DIR/'
>
> /
>
> &system
>
> ibrav=2, celldm(1) =10.68, nat=2, ntyp=2,
>
> ecutwfc = 18.0, ecutrho = 1700.0, nbnd=10,
>
> occupations='tetrahedra'
>
> /
>
> &electrons
>
> conv_thr = 1.0e-10
>
> mixing_beta = 0.7
>
> /
>
> ATOMIC_SPECIES
>
> Ga 69.720 Ga.pbe-nsp-van.UPF
>
> As 74.922 As.pbe-n-van.UPF
>
> ATOMIC_POSITIONS
>
> Ga 0.0 0.0 0.0
>
> As 0.25 0.25 0.25
>
> K_POINTS {automatic}
>
> 12 12 12 0 0 0
>
> EOF
>
> cat > gaas.dos2.in << EOF
>
> &inputpp
>
> outdir='$TMP_DIR/'
>
> prefix='gaas'
>
> fildos='gaas.dos',
>
> Emin=-25.0, Emax=25.0, DeltaE=0.1
>
> /
>
> EOF
>
> $ECHO " running DOS calculation for GaAs...c"
>
> $PW_COMMAND < gaas.dos.in > gaas.dos.out
>
> check_failure $?
>
> $DOS_COMMAND < gaas.dos2.in > gaas.dos2.out
>
> check_failure $?
>
> $ECHO " done"
>
> # phonon calculation on a (444) uniform grid of q-points
>
> cat > gaas.ph.in << EOF
>
> phonons of GaAs
>
> &inputph
>
> tr2_ph=1.0d-12,
>
> prefix='gaas',
>
> ldisp=.true.,
>
> nq1=4, nq2=4, nq3=4
>
> amass(1)=69.72,
>
> amass(2)=74.92,
>
> outdir='$TMP_DIR/',
>
> fildyn='gaas.dyn',
>
> /
>
> EOF
>
> $ECHO " running the phonon calculation ...c"
>
> $PH_COMMAND < gaas.ph.in > gaas.ph.out
>
> check_failure $?
>
> $ECHO " done"
>
> cat > q2r.in <<EOF
>
> &input
>
> fildyn='gaas.dyn', zasr='simple',
> flfrc='gaas444.fc'
>
> /
>
> EOF
>
> $ECHO " transforming C(q) => C(R)...c"
>
> $Q2R_COMMAND < q2r.in > q2r.out
>
> check_failure $?
>
> $ECHO " done"
>
> cat > matdyn.in <<EOF
>
> &input
>
> asr='simple', amass(1)=69.72, amass(2)=74.922,
>
> flfrc='gaas444.fc', flfrq='gaas.freq'
>
> /
>
> 9
>
> 0.000 0.0 0.0 0.0
>
> 0.125 0.0 0.0 0.0
>
> 0.250 0.0 0.0 0.0
>
> 0.375 0.0 0.0 0.0
>
> 0.500 0.0 0.0 0.0
>
> 0.625 0.0 0.0 0.0
>
> 0.750 0.0 0.0 0.0
>
> 0.875 0.0 0.0 0.0
>
> 1.000 0.0 0.0 0.0
>
> EOF
>
> $ECHO " recalculating omega(q) from C(R)...c"
>
> $MATDYN_COMMAND < matdyn.in > matdyn.out
>
> check_failure $?
>
> $ECHO " done"
>
> cat > phdos.in <<EOF
>
> &input
>
> asr='simple', dos=.true. amass(1)=69.72,
> amass(2)=74.922,
>
> flfrc='gaas444.fc', fldos='gaas.phdos',
> nk1=6,nk2=6,nk3=6
>
> /
>
> EOF
>
> $ECHO " calculating phonon DOS ...c"
>
> $MATDYN_COMMAND < phdos.in > phdos.out
>
> check_failure $?
>
> $ECHO " done"
>
> $ECHO$ECHO "$EXAMPLE_DIR:
> done"***********************************************************NCPP***********************************************************
>
> cat > gaas.scf.in << EOF
>
> &control
>
> calculation='scf'
>
> restart_mode='from_scratch',
>
> tstress = .true.
>
> tprnfor = .true.
>
> prefix='gaas',
>
> pseudo_dir = '$PSEUDO_DIR/',
>
> outdir='$TMP_DIR/'
>
> /
>
> &system
>
> ibrav= 2, celldm(1) =10.68, nat= 2, ntyp= 2,
>
> ecutwfc =60.0, ecutrho=450,
>
> /
>
> &electrons
>
> conv_thr = 1.0d-8
>
> mixing_beta = 0.7
>
> /
>
> ATOMIC_SPECIES
>
> Ga 69.72 Ga.pz-bhs.UPF
>
> As 74.92 As.gon.UPF
>
> ATOMIC_POSITIONS
>
> Ga 0.00 0.00 0.00
>
> As 0.25 0.25 0.25
>
> K_POINTS {automatic}
>
> 4 4 4 0 0 0
>
> EOF
>
> $ECHO " running the scf calculation...c"
>
> $PW_COMMAND < gaas.scf.in > gaas.scf.out
>
> check_failure $?
>
> $ECHO " done"
>
> # DOS calculation for GaAs
>
> cat > gaas.dos.in << EOF
>
> &control
>
> calculation='nscf'
>
> prefix='gaas',
>
> pseudo_dir = '$PSEUDO_DIR/',
>
> outdir='$TMP_DIR/'
>
> /
>
> &system
>
> ibrav=2, celldm(1) =10.68, nat=2, ntyp=2,
>
> ecutwfc = 60.0, ecutrho = 450.0, nbnd=10,
>
> occupations='tetrahedra'
>
> /
>
> &electrons
>
> conv_thr = 1.0e-10
>
> mixing_beta = 0.7
>
> /
>
> ATOMIC_SPECIES
>
> Ga 69.720 Ga.pz-bhs.UPF
>
> As 74.922 As.gon.UPF
>
> ATOMIC_POSITIONS
>
> Ga 0.0 0.0 0.0
>
> As 0.25 0.25 0.25
>
> K_POINTS {automatic}
>
> 12 12 12 0 0 0
>
> EOF
>
> cat > gaas.dos2.in << EOF
>
> &inputpp
>
> outdir='$TMP_DIR/'
>
> prefix='gaas'
>
> fildos='gaas.dos',
>
> Emin=-25.0, Emax=25.0, DeltaE=0.1
>
> /
>
> EOF
>
> $ECHO " running DOS calculation for GaAs...c"
>
> $PW_COMMAND < gaas.dos.in > gaas.dos.out
>
> check_failure $?
>
> $DOS_COMMAND < gaas.dos2.in > gaas.dos2.out
>
> check_failure $?
>
> $ECHO " done"
> # phonon calculation on a (444) uniform grid of q-points
> cat > gaas.ph.in << EOF
> phonons of GaAs
> &inputph
> tr2_ph=1.0d-12,
> prefix='gaas',
> ldisp=.true.,
> nq1=4, nq2=4, nq3=4
> amass(1)=69.72,
> amass(2)=74.92,
> outdir='$TMP_DIR/',
> fildyn='gaas.dyn',
> /
> EOF
> $ECHO " running the phonon calculation ...c"
> $PH_COMMAND < gaas.ph.in > gaas.ph.out
> check_failure $?
> $ECHO " done"
> cat > q2r.in <<EOF
> &input
> fildyn='gaas.dyn', zasr='simple',
> flfrc='gaas444.fc'
> /
> EOF
> $ECHO " transforming C(q) => C(R)...c"
> $Q2R_COMMAND < q2r.in > q2r.out
> check_failure $?
> $ECHO " done"
> cat > matdyn.in <<EOF
> &input
> asr='simple', amass(1)=69.72, amass(2)=74.922,
> flfrc='gaas444.fc', flfrq='gaas.freq'
> /
> 9
> 0.000 0.0 0.0 0.0
> 0.125 0.0 0.0 0.0
> 0.250 0.0 0.0 0.0
> 0.375 0.0 0.0 0.0
> 0.500 0.0 0.0 0.0
> 0.625 0.0 0.0 0.0
> 0.750 0.0 0.0 0.0
> 0.875 0.0 0.0 0.0
> 1.000 0.0 0.0 0.0
> EOF
> $ECHO " recalculating omega(q) from C(R)...c"
> $MATDYN_COMMAND < matdyn.in > matdyn.out
> check_failure $?
> $ECHO " done"
> cat > phdos.in <<EOF
> &input
> asr='simple', dos=.true. amass(1)=69.72,
> amass(2)=74.922,
> flfrc='gaas444.fc', fldos='gaas.phdos',
> nk1=6,nk2=6,nk3=6
> /
> EOF
> $ECHO " calculating phonon DOS ...c"
> $MATDYN_COMMAND < phdos.in > phdos.out
> check_failure $?
> $ECHO " done"
> $ECHO
> $ECHO "$EXAMPLE_DIR:
> done"***********************************************************I
> will be highly thankful if one could please let me know the
> way out to this.Thank you.Shyam Lal GuptaIIT
> KanpurKanpurINDIA-208016.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
From lo_wan_2005 at hotmail.com Tue Nov 11 02:55:55 2008
From: lo_wan_2005 at hotmail.com (Lo_wan_2005XW)
Date: Tue, 11 Nov 2008 09:55:55 +0800
Subject: [Pw_forum] Why my test-calculation is so slowly? SGI4700 for Si
take about 1 hours
Message-ID: <COL103-W652E1E5699E557D9649B17B3150@phx.gbl>
Dear PWscf users
I just download the code and install it in our SGI-4700 without any warnning or error.
After that, I try to do the example-calculation (example01).
My machine is SGI-Altex-4700, so I change the the following line in the file of run_example
$PW_COMMAND < si.scf.$diago.in > si.scf.$diago.out
to
$PARA_PREFIX $PW_COMMAND < si.scf.$diago.in > si.scf.$diago.out
I set
PARA_PREFIX="mpirun -np 12"
After that, I type ./run_example
I can see the following in the screen:
sgi4700:~/Quantum-Espresso/espresso-4.0.3/examples/example01> ./run_example
/disk2/Quantum-Espresso/espresso-4.0.3/examples/example01 : starting
This example shows how to use pw.x to calculate the total energy and
the band structure of four simple systems: Si, Al, Cu, Ni.
executables directory: /disk2/Quantum-Espresso/espresso-4.0.3/bin
pseudo directory: /disk2/Quantum-Espresso/espresso-4.0.3/pseudo
temporary directory: /disk2/tmp
checking that needed directories and files exist... done
running pw.x as: mpirun -np 12 /disk2/Quantum-Espresso/espresso-4.0.3/bin/pw.x -npool 4
running bands.x as: mpirun -np 12 /disk2/Quantum-Espresso/espresso-4.0.3/bin/bands.x -npool 4
cleaning /disk2/xgwan/tmp... done
running the scf calculation for Si...
By using "top", I can find there are 12 pw.x. My machine take about 2 hours to finish this simple calculation. It is quite strange!
I compare the my output and the data saved in referece-directory, it shows that my result, like total energy, is right comparing with the referenced data.
Attached pleased find my output data.
I will appreciate if someone can kindly tell me the possible reason for it.
Thanks
XW
_________________________________________________________________
MSN ????????????????????
http://cn.msn.com
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From lfhuang at theory.issp.ac.cn Tue Nov 11 03:57:03 2008
From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=)
Date: Tue, 11 Nov 2008 10:57:03 +0800
Subject: [Pw_forum] =?utf-8?q?_Why_my_test-calculation_is_so_slowly=3F?=
Message-ID: <20081111025703.21101.qmail@ms.hfcas.ac.cn>
Dear Lo_wan:
I am using SGI too, and I sometimes encounter the problems like yours, which, however, always can be
attributed to two reasons below:
(1) one/some of the nodes in paralleled jobs can not work well ;
(2) or can not commute well.
So, maybe you can change your job subscripts(including reducing No. of nodes), then see what happens.
In addition, I encountered some problems when I compile the packages with f90 compiler, and could you tell me
what is your compiler? Thanks!
Best Wishes!
Yours Sincerely
L.F.Huang
> Date: Tue, 11 Nov 2008 09:55:55 +0800
> From: Lo_wan_2005XW
> Subject: [Pw_forum] Why my test-calculation is so slowly? SGI4700 for
> Si take about 1 hours
> To:
> Message-ID:
> Content-Type: text/plain; charset="gb2312"
>
>
> Dear PWscf users
>
> I just download the code and install it in our SGI-4700 without any warnning or error.
>
> After that, I try to do the example-calculation (example01).
>
> My machine is SGI-Altex-4700, so I change the the following line in the file of run_example
>
>
>
> $PW_COMMAND si.scf.$diago.out
>
>
>
> to
>
>
>
> $PARA_PREFIX $PW_COMMAND si.scf.$diago.out
>
>
>
> I set
>
>
>
> PARA_PREFIX="mpirun -np 12"
>
>
>
> After that, I type ./run_example
>
> I can see the following in the screen:
>
>
>
> sgi4700:~/Quantum-Espresso/espresso-4.0.3/examples/example01> ./run_example
>
> /disk2/Quantum-Espresso/espresso-4.0.3/examples/example01 : starting
>
> This example shows how to use pw.x to calculate the total energy and
> the band structure of four simple systems: Si, Al, Cu, Ni.
>
> executables directory: /disk2/Quantum-Espresso/espresso-4.0.3/bin
> pseudo directory: /disk2/Quantum-Espresso/espresso-4.0.3/pseudo
> temporary directory: /disk2/tmp
> checking that needed directories and files exist... done
>
> running pw.x as: mpirun -np 12 /disk2/Quantum-Espresso/espresso-4.0.3/bin/pw.x -npool 4
> running bands.x as: mpirun -np 12 /disk2/Quantum-Espresso/espresso-4.0.3/bin/bands.x -npool 4
>
> cleaning /disk2/xgwan/tmp... done
> running the scf calculation for Si...
>
>
>
>
>
>
>
> By using "top", I can find there are 12 pw.x. My machine take about 2 hours to finish this simple calculation. It is quite strange!
> I compare the my output and the data saved in referece-directory, it shows that my result, like total energy, is right comparing with the referenced data.
>
> Attached pleased find my output data.
>
> I will appreciate if someone can kindly tell me the possible reason for it.
>
> Thanks
>
> XW
>
------
======================================================================
L.F.Huang(???) lfhuang at theory.issp.ac.cn
======================================================================
Add: Research Laboratory for Computational Materials Sciences,
Instutue of Solid State Physics,the Chinese Academy of Sciences,
P.O.Box 1129, Hefei 230031, P.R.China
Tel: 86-551-5591464-328(office)
Fax: 86-551-5591434
Web: http://theory.issp.ac.cn (website of our theory group)
http://www.issp.ac.cn (website of our institute)
======================================================================
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From lo_wan_2005 at hotmail.com Tue Nov 11 04:51:57 2008
From: lo_wan_2005 at hotmail.com (Lo_wan_2005XW)
Date: Tue, 11 Nov 2008 11:51:57 +0800
Subject: [Pw_forum] Why my test-calculation is so slowly? SGI4700 for Si
take about 1 hours
In-Reply-To: <Pine.LNX.4.64.0811102150280.2412@localhost.localdomain>
References: <COL103-W652E1E5699E557D9649B17B3150@phx.gbl>
<Pine.LNX.4.64.0811102150280.2412@localhost.localdomain>
Message-ID: <COL103-W1B11C33CDD2DE87A53FD9B3150@phx.gbl>
Dear axel
Thank you very much for your help!
Just following your suggestion, I export OMP_NUM_THREADS=1, the calculation finish within several seconds!
Thank you very much for your help!
The machine I used is SGI-Altex-4700. After I download the code, I just do
1) configure
2) make all
I donot know if I still other set or configurations to optimize my calculation in SGI-Altex-4700?
Thanks
Xiangang Wan
Department of Physics
Nanjing University
P.R. China
> Date: Mon, 10 Nov 2008 21:55:58 -0500
> From: akohlmey at cmm.chem.upenn.edu
> To: lo_wan_2005 at hotmail.com
> Subject: Re: [Pw_forum] Why my test-calculation is so slowly? SGI4700 for Si take about 1 hours
>
> On Tue, 11 Nov 2008, Lo_wan_2005XW wrote:
>
> XW>
> XW> Dear PWscf users
>
> dear xw,
>
> please don't forget to specify your full name and affiliation.
>
> you are a victim of not overly smart sysadmins and the strange
> choices of intel. you are most likely linking to MKL and as of
> version 10.0 it automatically multi-threads across _all_ available
> cpu 'cores'. on an SGI altix this has disasterous consequences
> for the performance. you have to set OMP_NUM_THREADS=1 and
> it will be _much_ less of a problem (check out the mailing list
> archive for multiple occurances of this "feature".
>
> please not that the first test examples don't overly scale
> as well (for testing, you may be better off with the contents
> of the tests directory using only 2-4 processors.
>
> cheers,
> axel.
>
> p.s.: if your sysadmins are not totally ignorant, please
> ask them to at export OMP_NUM_THREADS=1 to the default
> environment, and they'll avoid a lot of problems with
> jobs not running overly efficient.
>
> XW>
> XW> I just download the code and install it in our SGI-4700 without any warnning or error.
> XW>
> XW> After that, I try to do the example-calculation (example01).
> XW>
> XW> My machine is SGI-Altex-4700, so I change the the following line in the file of run_example
> XW>
> XW>
> XW>
> XW> $PW_COMMAND < si.scf.$diago.in > si.scf.$diago.out
> XW>
> XW>
> XW>
> XW> to
> XW>
> XW>
> XW>
> XW> $PARA_PREFIX $PW_COMMAND < si.scf.$diago.in > si.scf.$diago.out
> XW>
> XW>
> XW>
> XW> I set
> XW>
> XW>
> XW>
> XW> PARA_PREFIX="mpirun -np 12"
> XW>
> XW>
> XW>
> XW> After that, I type ./run_example
> XW>
> XW> I can see the following in the screen:
> XW>
> XW>
> XW>
> XW> sgi4700:~/Quantum-Espresso/espresso-4.0.3/examples/example01> ./run_example
> XW>
> XW> /disk2/Quantum-Espresso/espresso-4.0.3/examples/example01 : starting
> XW>
> XW> This example shows how to use pw.x to calculate the total energy and
> XW> the band structure of four simple systems: Si, Al, Cu, Ni.
> XW>
> XW> executables directory: /disk2/Quantum-Espresso/espresso-4.0.3/bin
> XW> pseudo directory: /disk2/Quantum-Espresso/espresso-4.0.3/pseudo
> XW> temporary directory: /disk2/tmp
> XW> checking that needed directories and files exist... done
> XW>
> XW> running pw.x as: mpirun -np 12 /disk2/Quantum-Espresso/espresso-4.0.3/bin/pw.x -npool 4
> XW> running bands.x as: mpirun -np 12 /disk2/Quantum-Espresso/espresso-4.0.3/bin/bands.x -npool 4
> XW>
> XW> cleaning /disk2/xgwan/tmp... done
> XW> running the scf calculation for Si...
> XW>
> XW>
> XW>
> XW>
> XW>
> XW>
> XW>
> XW> By using "top", I can find there are 12 pw.x. My machine take about 2 hours to finish this simple calculation. It is quite strange!
> XW> I compare the my output and the data saved in referece-directory, it shows that my result, like total energy, is right comparing with the referenced data.
> XW>
> XW> Attached pleased find my output data.
> XW>
> XW> I will appreciate if someone can kindly tell me the possible reason for it.
> XW>
> XW> Thanks
> XW>
> XW> XW
> XW>
> XW> _________________________________________________________________
> XW> MSN ????????????????????????????????????????
> XW> http://cn.msn.com
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
_________________________________________________________________
MSN???????????????????
http://im.live.cn/newsexpress
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From w2agz at pacbell.net Tue Nov 11 05:43:28 2008
From: w2agz at pacbell.net (Paul M. Grant)
Date: Mon, 10 Nov 2008 20:43:28 -0800
Subject: [Pw_forum] Two More Questions on k-points Generation
Message-ID: <02be01c943b8$0b2705c0$21751140$@net>
In Example 01, the number of k-points for Al is 60 in the scf step.I would
have thought it would have been a power of 3 for an fcc cell (eg.,
4x4x4=64). How was this and the respective weights generated?
What subroutine in the pw.x compiled and linked executable actually calls
the input NAMELIST, in particular to generate the kpoints array passing
appropriate arguments (e.g., Automatic)?
-Paul
Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com <http://www.w2agz.com/>
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From jelle.van.sijl at falw.vu.nl Tue Nov 11 10:17:04 2008
From: jelle.van.sijl at falw.vu.nl (Jelle van Sijl)
Date: Tue, 11 Nov 2008 10:17:04 +0100 (CET)
Subject: [Pw_forum] job submission script
Message-ID: <f6379f34ea8b50f5c29a9e52dde644a6.squirrel@webmail.falw.vu>
Dear All,
I am having difficulties writing a good job submission script for pwscf in
parallel on a cluster with sometimes very slow NFS performance.
example job: 23h 4m CPU time for 23h 50m wall time
User files are stored in /home/user (this is the slow part)
scratch space on each node is a variable (TMPDIR), which is fast.
When I submit the job (see script below) from the directory on /home/user,
pwscf stores everything in that folder but the repeated IO operations slow
down the job.
I already set disc_io=low and wf_collect=true
How can I work efficiently on the scratch space of each node, but still
find all output in /home/user after a successful run?
thanks in advance,
Jelle van Sijl
ps: I replaced my loginname on the cluster with 'user'
--
drs. Jelle van Sijl
PhD student, Department of Petrology
Faculty of Earth and Life Sciences (FALW)
VU University Amsterdam, De Boelelaan 1085
1081 HV Amsterdam, The Netherlands
Phone +31 (0)20 5987403
http://www.falw.vu.nl/petrology
#!/bin/bash
#
# Job script for running parallel pwscf 4.0.1
# on lisa. Created 11-08-2008 by Jelle van Sijl
#
# This is a job requesting 4 cores.
# request 2 nodes, 2 cores per node and
# each node equipped with the infiniband network:
#PBS -lnodes=2:ppn=2:infiniband:cores2
#PBS -lwalltime=01:00:00
#PBS -joe
# Edit this part:
export INP=INPUT
export OUT=OUTPUT
# Leave the rest.
#
# ---- start of MVAPICH related code:
# test if ~/.mpd.conf exists, create it if not:
if [ ! -e ~/.mpd.conf ]
then
echo MPD_SECRETWORD=$USER$RANDOM$PPID$$ > ~/.mpd.conf
chmod 600 ~/.mpd.conf
fi
# determine the number of processes to start:
nprocs=`wc -l < $PBS_NODEFILE`
# determine the number of nodes:
nnodes=`sort -u $PBS_NODEFILE | wc -l`
# start the mpd daemons:
/usr/local/mvapich2-intel-0.9.8/bin/mpdboot -n $nnodes -f $PBS_NODEFILE
# ---- End of MVAPICH related code
export EXE=/home/user/espresso-4.0.1/bin/pw.x
export mpiexec=/usr/local/mvapich2-intel-0.9.8/bin/mpiexec
#export mpicopy=/usr/local/mpicopy/bin/mpicpbin.openib
$mpiexec -n $nprocs $EXE < $INP > $OUT
From paulatto at sissa.it Tue Nov 11 10:48:23 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Tue, 11 Nov 2008 10:48:23 +0100
Subject: [Pw_forum] job submission script
In-Reply-To: <f6379f34ea8b50f5c29a9e52dde644a6.squirrel@webmail.falw.vu>
References: <f6379f34ea8b50f5c29a9e52dde644a6.squirrel@webmail.falw.vu>
Message-ID: <491954E7.2020705@sissa.it>
Jelle van Sijl ha scritto:
> When I submit the job (see script below) from the directory on /home/user,
> pwscf stores everything in that folder but the repeated IO operations slow
> down the job.
>
Dear Jelle,
you should set outdir='/tmp/NameIt' in the control namelist; in this way
every process will save its own data on its local disk. You can later
recollect the data by hand using scp (with password-less login or with
expect).
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.
Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste
Donations in food, coins, booze and processor time are warmly welcome.
From sclauzer at sissa.it Tue Nov 11 11:41:17 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Tue, 11 Nov 2008 11:41:17 +0100
Subject: [Pw_forum] Two More Questions on k-points Generation
In-Reply-To: <02be01c943b8$0b2705c0$21751140$@net>
References: <02be01c943b8$0b2705c0$21751140$@net>
Message-ID: <4919614D.4010907@sissa.it>
Dear Paul
Paul M. Grant wrote:
> In Example 01, the number of k-points for Al is 60 in the scf step.I would
> have thought it would have been a power of 3 for an fcc cell (eg.,
> 4x4x4=64).
Not necessarily, since some k-points are equivalent to others because of symmetry. Only
the first non-equivalent k-point in a list of uniformly spaced k-points is considered and
its weight is proportional to the number of equivalent points.
> How was this and the respective weights generated?
First the uniform grid is generated, eventually shifted according to the Monkhorst-Pack
scheme (you should find plenty of discussion about that on the forum archive). Then each
symmetry of the system is applied to each vector in the grid and if the transformed vector
is already in the list (and has already been considered), then the starting vector is
considered as equivalent to that prevoiusly checked and retained in the list.
>
> What subroutine in the pw.x compiled and linked executable actually calls
> the input NAMELIST, in particular to generate the kpoints array passing
> appropriate arguments (e.g., Automatic)?
The automatic generation of k-points is performed by subroutine setupkpoint or
kpoint_grid, which are called by setup. Some missing point might be added later by
irreducible_BZ if the symmetry of the crystal (lattice+basis) is lower than that of the
lattice alone.
If you know the correct weights, you can give a k-point list explicitly (as done in the
example you mentioned - BTW, the weights are renormalized so that the total sum gives 1 or
2, depending if you're using nspin=2 or 1, resp.). A k-point grid equivalent to that in
the example could have been obtained automatically by specifying
K_POINTS automatic
8 8 8 1 1 1
The coordinates of k-point are very different from those given explicitly in the example,
but the result you get (i.e. total energy) is exactly the same.
You may want to play a bit with the kpoints.x tool, which also generates grids of k-point
and also optionally shows you the full list of points, telling you which is equivalent to
which.
Best regards,
Gabriele Sclauzero
>
> -Paul
>
> Paul M. Grant, PhD
> Principal, W2AGZ Technologies
> Visiting Scholar, Applied Physics, Stanford (2005-2008)
> EPRI Science Fellow (Retired)
> IBM Research Staff Member Emeritus
> w2agz at pacbell.net
> http://www.w2agz.com <http://www.w2agz.com/>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
--
La legge n. 133 uccide l'Universit? e la Ricerca italiana!
Save Italian Brains! (http://saveitalianbrains.wordpress.com/)
o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student |
| c/o: SISSA & CNR-INFM Democritos, |
| via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511 |
| skype: gurlonotturno |
o ------------------------------------------------ o
From fabris at democritos.it Tue Nov 11 12:16:09 2008
From: fabris at democritos.it (Stefano Fabris)
Date: Tue, 11 Nov 2008 12:16:09 +0100
Subject: [Pw_forum] error message from read_pseudo_mesh : error # 1
Reading pseudo file (R) for Ce
In-Reply-To: <822f4ec80811100730k7d292a15v1e656aea90fb9099@mail.gmail.com>
References: <822f4ec80811100730k7d292a15v1e656aea90fb9099@mail.gmail.com>
Message-ID: <FB9A089A-0651-4A12-B50D-40A919AA2536@democritos.it>
Dear Shruba,
it is indeed surprising that an UPF file is correctly read on the
Opteron cluster but not on the IBM SP5 one. We have been using the
same pseudo on both Opteron and IBM SP5 and never got this error
message. My 0-level suggestion would be to check if the pseudo file
contains non printable characters such as ^M or similar.
Stefano
On 10 Nov 2008, at 16:30, shruba at gmail.com wrote:
> Dear all,
> I was trying to submit a calculation using
> ( espresso-4.0.3.tar.gz (released 2008-10-22)) using this input
> file and the pseudopotential, which was provided to us very
> generously by Dr Fabris,
> This input is running normally in a cluster having Opteron
> processors, and the os is redhat linux, ( using both LAMMPI and
> mpich) now when i tried to run this input in nersc supercomputer
> cluster, having IBM Cluster 1600 , IBM p575 POWER 5, Software
> (original version in parentheses) IBM AIX Version 5.3 ML 4 (5.2 ML 5)
> I am getting the error
> error message from read_pseudo_mesh : error # 1 Reading pseudo
> file (R) for Ce
> I am pasting the pseudopotential header and my input, please let me
> know if i am missing any information, if you please help me to
> figure out how to solve this that will be really great help, thanks
> for your time
> shruba
>
> <PP_INFO>
> Generated using Vanderbilt code, version 7 3 4
> Author: unknown Generation date: 27 7 2005
> Automatically converted from original format
> 1 The Pseudo was generated with a Scalar-Relativistic
> Calculation
> 2.10000000000E+00 Local Potential cutoff radius
> nl pn l occ Rcut Rcut US E
> pseu
> 4F 4 3 1.00 10.00000000000 1.80000000000
> -0.39547555416
> 5S 5 0 2.00 10.00000000000 1.60000000000
> -2.98314000093
> 5P 5 1 6.00 10.00000000000 1.80000000000
> -1.70705941252
> 5D 5 2 1.00 10.00000000000 1.80000000000
> -0.22485386450
> 6S 6 0 2.00 10.00000000000 1.60000000000
> -0.27522397471
> </PP_INFO>
>
> input file
> &CONTROL
> calculation = 'relax'
> restart_mode = 'from_scratch',
> tprnfor = .TRUE.,
> prefix = '9',
> pseudo_dir = '/home/shruba/srfeopp/',
>
> /
>
> &SYSTEM
> ibrav = 1,
> celldm(1) = 35.0
> nat =51,
> ntyp =2,
> nbnd=500,
> ecutwfc = 35,
> ecutrho = 350,
> nspin=2,
> multiplicity=1,
> occupations = 'smearing',
> smearing ='marzari-vanderbilt',
> degauss=0.0008,
>
> /
> &ELECTRONS
> electron_maxstep =400,
> /
> &ions
> ion_dynamics = 'bfgs',
> wfc_extrapolation='second_order',
> pot_extrapolation='second_order'
> ion_positions = 'from_input'
> /
>
> ATOMIC_SPECIES
> Ce 140.115 Ce4_ps_f1d1-pbe-rc1.0.uspp.UPF
> O 16.00 O.pbe-van-bm.UPF
> ATOMIC_POSITIONS {angstrom}
> Ce 0.240753 0.117800 0.135937
> Ce 6.464087 0.131036 0.171093
> Ce 4.429110 4.744538 0.151726
> Ce 7.493441 3.347170 1.290600
> Ce 3.392344 1.520271 -0.956958
> Ce 6.509589 2.904330 -2.150325
> Ce 4.431329 -0.778173 4.655046
> Ce 7.506912 0.613913 3.555310
> Ce 3.373915 -1.263157 1.296437
> Ce 6.512187 -2.682385 2.427526
> Ce 8.599998 3.843615 4.700742
> Ce 2.339658 3.806630 4.663235
> Ce 5.447009 2.447125 5.789411
> Ce 1.359661 0.596837 3.531188
> Ce 5.445572 5.176820 3.559495
> Ce 1.341018 3.364989 1.304481
> Ce 4.412472 1.978056 2.393172
> Ce 2.339804 6.639926 2.427280
> Ce 2.336563 1.040046 6.987493
> O 1.096359 2.117498 -0.704335
> O 2.298358 -0.585245 -0.711826
> O -0.092844 1.577359 1.916847
> O 1.085653 -1.122025 1.922727
> O 8.938864 2.384130 2.913119
> O 4.411768 0.498645 0.643569
> O 5.465176 -2.009996 0.446743
> O 7.875984 1.900231 -0.548186
> O 7.881522 -0.911806 1.765756
> O 5.481604 0.830108 -1.872629
> O 6.572420 1.474214 1.837701
> O 7.727957 5.065267 2.916824
> O 2.166391 5.421034 0.442241
> O 3.332956 2.971830 0.649431
> O 5.487161 3.913850 1.823983
> O 6.685541 4.600396 -0.558270
> O 4.578525 6.484106 1.769867
> O 4.275459 3.527388 -1.877759
> O 7.736974 1.855172 5.557358
> O 2.171189 -0.649687 5.394524
> O 5.468329 1.017727 4.180748
> O 3.363964 0.037689 3.002229
> O 6.688818 -1.446701 4.403735
> O 4.567571 0.427707 6.703107
> O 4.282142 -2.550855 3.091717
> O 6.553586 4.537892 5.561983
> O 0.949646 2.023619 5.397054
> O 3.354910 5.937088 4.407328
> O 3.353287 3.123057 6.701842
> O 0.944909 4.887132 3.086546
> O 4.380494 3.409595 4.185707
> O 2.278672 2.462760 3.014481
> K_POINTS {automatic}
> 1 1 1 0 0 0
>
> pseudo potential file,
> <PP_HEADER>
> 0 Version Number
> Ce Element
> US Ultrasoft pseudopotential
> T Nonlinear Core Correction
> SLA PW PBE PBE PBE Exchange-Correlation functional
> 12.00000000000 Z valence
> -150.74977779744 Total energy
> 0.0000000 0.0000000 Suggested cutoff for wfc and rho
> 3 Max angular momentum component
> 947 Number of points in mesh
> 5 5 Number of Wavefunctions, Number of Projectors
> Wavefunctions nl l occ
> 4F 3 1.00
> 5S 0 2.00
> 5P 1 6.00
> 5D 2 1.00
> 6S 0 2.00
>
>
> --
> shruba gangopadhyay
> graduate student
> department of chemistry
> university of central florida
> orlando, FL-32826
> 'friendship doubles joys and reduces sorrows by half' (Francis Bacon).
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Fabris
Theory at Elettra Group
CNR-INFM DEMOCRITOS National Simulation Center
c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE
website: www.democritos.it/the-group
email: fabris at democritos.it tel: +39 040 375-8735 fax: -8776
---
From giannozz at democritos.it Tue Nov 11 12:31:01 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 11 Nov 2008 12:31:01 +0100
Subject: [Pw_forum] error message from read_pseudo_mesh : error # 1
Reading pseudo file (R) for Ce
In-Reply-To: <822f4ec80811100730k7d292a15v1e656aea90fb9099@mail.gmail.com>
References: <822f4ec80811100730k7d292a15v1e656aea90fb9099@mail.gmail.com>
Message-ID: <49196CF5.5080702@democritos.it>
shruba at gmail.com wrote:
> error message from read_pseudo_mesh : error # 1 Reading pseudo file
> (R) for Ce
go into the pseudopotential file, locate <PP_R> and following lines
until </PP_R>, verify if there is something wrong. Your file might
be corrupted.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From thmason24 at yahoo.com Tue Nov 11 21:05:41 2008
From: thmason24 at yahoo.com (Timothy Mason)
Date: Tue, 11 Nov 2008 12:05:41 -0800 (PST)
Subject: [Pw_forum] Total energy does not coverge with ecut
In-Reply-To: <000e0cd2480434b355045b0c911c@google.com>
Message-ID: <910570.49147.qm@web81804.mail.mud.yahoo.com>
I have not attempted your suggestion however I did trade out the PSPS with different PSPSs.?? I'm now using
?Li.pz-n-vbc.UPF
?N.pbe-rrkjus.UPF
?H.pbe-rrkjus.UPF
and they seem to converge nicely.
is there problem with the ones I was using??? here they are for reference
Li 6.941000 Li.pbe-n-van.UPF
N 14.006740 N.pbe-van_ak.UPF
H 1.007940 H.pbe-van_ak.UPF
I'm not sure of the best way to select them from the website.
thanks for the help.
--- On Thu, 11/6/08, prasenjit.jnc at gmail.com <prasenjit.jnc at gmail.com> wrote:
From: prasenjit.jnc at gmail.com <prasenjit.jnc at gmail.com>
Subject: Re: Re: [Pw_forum] Total energy does not coverge with ecut
To: "Timothy Mason" <thmason24 at yahoo.com>, "PWSCF Forum" <pw_forum at pwscf.org>
Date: Thursday, November 6, 2008, 4:10 PM
Sometimes it is also difficult to converge the total energy. So usually it is better to check the convergence of the quantity you are interested in.
But anyway it is really strange that total energy doesn't converge at such abnormally high cut off values.
Did you test the pseudopotentials individually?? For eg. did you try calculating the bond lengths of say a nitrogen molecule & see how the results are??
With regards,
Prasenjit.
On Nov 6, 2008 5:45pm, Timothy Mason <thmason24 at yahoo.com> wrote:
> Dear Lorenzo,
>
> here are results for the lower energy range. Still doesn't seem to be converging.
>
> ecut energy energy differnce
> 30 -48.19258627
> 35 -48.19503183 0.00244556
> 40 -48.197306 0.00227417
> 45 -48.20217820 0.0048722
>
> thanks
>
> --- On Thu, 11/6/08, Lorenzo Paulatto paulatto at sissa.it> wrote:
> From: Lorenzo Paulatto paulatto at sissa.it>
> Subject: Re: [Pw_forum] Total energy does not coverge with ecut
> To: thmason24 at yahoo.com, "PWSCF Forum" pw_forum at pwscf.org>
> Date: Thursday, November 6, 2008, 10:08 AM
>
> Timothy Mason ha scritto:
> >
> > Gentlemen,
> >
> > My structures do not see to be converging with increased ecutwfc.
> > I'm setting ecutrho to ecutwfc * 12 and using US PP. below is a
> > table of ecut values vs energies vs difference from previous steps
> > followed by my input file followed by part of the output file. It
> > appears to begin to converge and 120 ecut but then jumps at 130 and
> > then more at 140.
> >
> Dear Timothy,
> these are ridiculous cutoff energy for ultrasoft pseudopotentials - they
> are very high for norm-conserving too! I suspect the presence of a
> high-energy ghost-state in one of the pseudopotential; these kind
> of
> states aren't usually harmful but can suddenly pop-up under some
> specifics conditions like high pressure or very high cutoff.
>
> What is happening when you try some reasonable cutoff in the 20-50 Ry range?
>
> regards
>
> --
> Lorenzo Paulatto
> SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www: http://people.sissa.it/~paulatto/
>
> Due to budget cuts approved by Italian Minister of Finance and Italian
> Minister "for" Education, University and Research this may be the
> last
> email you receive from me.
>
> Please send any future correspondence, possibly via pigeon, to
> mr. Lorenzo Paulatto
> under Roiano Railway Bridge - Pillar 2
> 34136, Trieste
>
> Donations in food, coins, booze and processor time are warmly welcome.
>
>
>
>
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From eyvaz_isaev at yahoo.com Wed Nov 12 00:13:38 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 11 Nov 2008 15:13:38 -0800 (PST)
Subject: [Pw_forum] Total energy does not converge with ecut
In-Reply-To: <235216.38300.qm@web81803.mail.mud.yahoo.com>
Message-ID: <737088.86937.qm@web65715.mail.ac4.yahoo.com>
Timothy,
--- On Wed, 11/12/08, Timothy Mason <thmason24 at yahoo.com> wrote:
>
> sadly there is no typo. ?
Then quite strange how could you proceed your calculations. readpp.f90 should stop pw.x
> Those are indeed the PsPs I was using(hopefully I've
> havn't exposed myself as hopeless). I have
> witnessed that sometimes the calculations stop which seems
> to be structure dependent.
If you are absolutely sure that the structure is correct, this one actually might be a reason for doubts about a PsP quality (transferability).
Otherwise, check your structure via XCrysDen.
> is there a reference regarding guidelines for selecting
> Pseudopotentials?
I do not think so. It will be not so democratic.
This should be only your choice, and depends on your experience.
The gold rule is the use of PsPs with the same XC-functional, at the same time you can mix different type of PsPs (normconserving, ultrasoft, and, hopefully, PAW now).
> in general its a bad ideal to mixmatch types of
> pseudopotentials?
>
Presumably, mismatch, but not mixmatch. In general, and in particular, it is a bad idea with respect to XC-type only, indeed. Otherwise, see above.
> thanks a lot for your help.
Welcome.
Bests,
Eyvaz.
>
>
> --- On Tue, 11/11/08, Eyvaz Isaev
> <eyvaz_isaev at yahoo.com> wrote:
> From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> Subject: Re: [Pw_forum] Total energy does not coverge with
> ecut
> To: thmason24 at yahoo.com
> Date: Tuesday, November 11, 2008, 2:51 PM
>
> Hi Timothy,
>
>
> --On Tue, 11/11/08, Timothy Mason
> <thmason24 at yahoo.com> wrote:
> > Subject: Re: [Pw_forum] Total energy does not coverge
> with ecut
> >
> > I'm now using
> >
> > ?Li.pz-n-vbc.UPF
> > ?N.pbe-rrkjus.UPF
> > ?H.pbe-rrkjus.UPF
> >
> > and they seem to converge nicely.
> >
>
> Quite strange. The program had to be stopped, because you
> mentioned PsPs with
> different XC-functionals.
>
> I would suggest there is a typos with Li.pz.....
> If so, and you meant Li.pbe.... then it is OK.
> Nevertheless, nobody can tell
> you which PsP is better for your system until you perform a
> test for yourself.
>
> Good Espresso time!
>
> bests,
> Eyvaz.
>
> > is there problem with the ones I was using??? here
> they
> > are for reference
> >
> > Li 6.941000 Li.pbe-n-van.UPF
> > N 14.006740 N.pbe-van_ak.UPF
> > H 1.007940 H.pbe-van_ak.UPF
> >
> > I'm not sure of the best way to select them from
> the
> > website.
> >
> > thanks for the help.
> >
> >
> >
> >
> >
> >
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of
> Steel & Alloys,
> Russia,
> Department of Physics, Chemistry, and Biology (IFM),
> Linkoping University,
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se,
> eyvaz_isaev at yahoo.com
From sanjeev0302 at rediffmail.com Wed Nov 12 17:31:13 2008
From: sanjeev0302 at rediffmail.com (sanjeev gupta)
Date: 12 Nov 2008 16:31:13 -0000
Subject: [Pw_forum] PWSCF calculation for Nanostructures
Message-ID: <20081112163113.11543.qmail@f4mail-234-122.rediffmail.com>
Dear PWSCF users,
I am using Quantum espresso package for DFT calculation for noble nitride systems. My main interest in electron-phonon calculation and Raman tensor etc. Sir, I want to know, what will be change in SCF or NSCF file for nanostructures calculation? or where is difference in bulfk or nano? I want to do calculation on nanostructre?, what i do ?
Please help me .
Kind Regards
sanjeev gupta
S. K. Gupta
PhD Candidate,
Dept. of Physics,
Bhavnagar University.
Bhavnagar, 364 002., Gujarat.
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From eyvaz_isaev at yahoo.com Wed Nov 12 17:51:23 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 12 Nov 2008 08:51:23 -0800 (PST)
Subject: [Pw_forum] Request
In-Reply-To: <9c021210811112234q35d83d8q1a0e805d74e48685@mail.gmail.com>
Message-ID: <219.98005.qm@web65716.mail.ac4.yahoo.com>
Dear Sanjeev,
Mainly you should define your (nano)structure, i.e. atomic positions and then visualize them with XCrysDen.
Then see /examples/example07 and /examples/example15 directory how to set up parameters for such kind calculations.
But be sure, electron-phonon calculations are very time-demanding, especially for (nano)structures.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
--- On Wed, 11/12/08, Sanjeev Kumar Gupta <skgupta.physics at gmail.com> wrote:
> From: Sanjeev Kumar Gupta <skgupta.physics at gmail.com>
> Subject: Request
> To: "Eyvaz Isaev" <eyvaz_isaev at yahoo.com>
> Date: Wednesday, November 12, 2008, 9:34 AM
> Respected Sir,
> Myself Sanjeev Gupta, reserach student from India, working
> in the field of
> computational condensed matter physics. I am using Quantum
> espresso package
> for DFT calculation. My main interest in electron-phonon
> calculation and
> Raman tensor etc.
>
> Sir, I want to know, what will be change in SCF or NSCF
> file for
> nanostructures calculation?
>
> or somewhere is difference? I want to do calculation on
> nanostructre?, what
> i do ?
> Please help me .
>
> Kind Regards
> sanjeev gupta
>
>
> --
>
>
>
>
>
>
>
> S. K. Gupta
> PhD Candidate,
> Dept. of Physics,
> Bhavnagar University.
> Bhavnagar, 364 002., Gujarat.
From lanhaiping at gmail.com Wed Nov 12 18:37:47 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Thu, 13 Nov 2008 01:37:47 +0800
Subject: [Pw_forum] PWSCF calculation for Nanostructures
In-Reply-To: <20081112163113.11543.qmail@f4mail-234-122.rediffmail.com>
References: <20081112163113.11543.qmail@f4mail-234-122.rediffmail.com>
Message-ID: <c92002fa0811120937v6eacb73fmfe6ec67e9a142421@mail.gmail.com>
As far As i know,
for nanostructures, time is demanding for e-ph calculations.
with respect to the difference between nano and bulk systems,
it seems you should introduce certain vacuum layers to define so-called
nano systems due to periodic scheme used in QE.
regards
On Thu, Nov 13, 2008 at 12:31 AM, sanjeev gupta
<sanjeev0302 at rediffmail.com>wrote:
>
> Dear PWSCF users,
>
> I am using Quantum espresso package for DFT calculation for noble nitride
> systems. My main interest in electron-phonon calculation and Raman tensor
> etc. Sir, I want to know, what will be change in SCF or NSCF file for
> nanostructures calculation? or where is difference in bulfk or nano? I want
> to do calculation on nanostructre?, what i do ?
> Please help me .
>
> Kind Regards
> sanjeev gupta
> S. K. Gupta
> PhD Candidate,
> Dept. of Physics,
> Bhavnagar University.
> Bhavnagar, 364 002., Gujarat.
>
>
> [image: Rediff Shopping]<http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198 at Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From sanjeev0302 at rediffmail.com Thu Nov 13 12:49:14 2008
From: sanjeev0302 at rediffmail.com (sanjeev gupta)
Date: 13 Nov 2008 11:49:14 -0000
Subject: [Pw_forum] PWSCF calculation for Nanostructures
Message-ID: <20081113114914.22587.qmail@f4mail-235-240.rediffmail.com>
Thank you sir. ?
Please explain more "it seems you should introduce certain vacuum layers to define so-called nano systems due to periodic scheme used in QE" For nano", the non-periodic scheme will used. How I introduced vacuum layers?
Please suggest me more.
kind regards
sanjeev gupta
On Wed, 12 Nov 2008 lan haiping wrote :
>As far As i know,
>for nanostructures, time is demanding for e-ph calculations.
>
>with respect to the difference between nano and bulk systems,
>it seems you should introduce certain vacuum layers to define so-called
>nano systems due to periodic scheme used in QE.
>
>regards
>
>On Thu, Nov 13, 2008 at 12:31 AM, sanjeev gupta
><sanjeev0302 at rediffmail.com>wrote:
>
> >
> > Dear PWSCF users,
> >
> > I am using Quantum espresso package for DFT calculation for noble nitride
> > systems. My main interest in electron-phonon calculation and Raman tensor
> > etc. Sir, I want to know, what will be change in SCF or NSCF file for
> > nanostructures calculation? or where is difference in bulfk or nano? I want
> > to do calculation on nanostructre?, what i do ?
> > Please help me .
> >
> > Kind Regards
> > sanjeev gupta
> > S. K. Gupta
> > PhD Candidate,
> > Dept. of Physics,
> > Bhavnagar University.
> > Bhavnagar, 364 002., Gujarat.
> >
> >
> > [image: Rediff Shopping]<http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198 at Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
>
>
>--
>Hai-Ping Lan
>Department of Electronics ,
>Peking University , Bejing, 100871
>lanhaiping at gmail.com, hplan at pku.edu.cn
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
S. K. Gupta
PhD Candidate,
Dept. of Physics,
Bhavnagar University.
Bhavnagar, 364 002., Gujarat.
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From prasenjit.jnc at gmail.com Thu Nov 13 13:42:51 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Thu, 13 Nov 2008 13:42:51 +0100
Subject: [Pw_forum] PWSCF calculation for Nanostructures
In-Reply-To: <20081113114914.22587.qmail@f4mail-235-240.rediffmail.com>
References: <20081113114914.22587.qmail@f4mail-235-240.rediffmail.com>
Message-ID: <627e0ffa0811130442w16d461d4t796cfa7ef2007184@mail.gmail.com>
Sanjeev,
Its the same thing which I explained to you earlier.......Why gon't you go
through this paper......Reviews of Modern Physics, vol 64, page 1045 (1992)
by M. C. Payne et al.......In Section IIC, of the paper they have explained
everything.
Prasenjit
2008/11/13 sanjeev gupta <sanjeev0302 at rediffmail.com>
>
> Thank you sir.
>
> Please explain more "it seems you should introduce certain vacuum layers
> to define so-called nano systems due to periodic scheme used in QE" For
> nano", the non-periodic scheme will used. How I introduced vacuum layers?
>
> Please suggest me more.
> kind regards
> sanjeev gupta
>
> On Wed, 12 Nov 2008 lan haiping wrote :
>
> >As far As i know,
> >for nanostructures, time is demanding for e-ph calculations.
> >
> >with respect to the difference between nano and bulk systems,
> >it seems you should introduce certain vacuum layers to define so-called
> >nano systems due to periodic scheme used in QE.
> >
> >regards
> >
> >On Thu, Nov 13, 2008 at 12:31 AM, sanjeev gupta
> ><sanjeev0302 at rediffmail.com>wrote:
> >
> > >
> > > Dear PWSCF users,
> > >
> > > I am using Quantum espresso package for DFT calculation for noble
> nitride
> > > systems. My main interest in electron-phonon calculation and Raman
> tensor
> > > etc. Sir, I want to know, what will be change in SCF or NSCF file for
> > > nanostructures calculation? or where is difference in bulfk or nano? I
> want
> > > to do calculation on nanostructre?, what i do ?
> > > Please help me .
> > >
> > > Kind Regards
> > > sanjeev gupta
> > > S. K. Gupta
> > > PhD Candidate,
> > > Dept. of Physics,
> > > Bhavnagar University.
> > > Bhavnagar, 364 002., Gujarat.
> > >
> > >
> > > [image: Rediff Shopping]<
> http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198 at Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null
> >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> > >
> >
> >
> >--
> >Hai-Ping Lan
> >Department of Electronics ,
> >Peking University , Bejing, 100871
> >lanhaiping at gmail.com, hplan at pku.edu.cn
> >_______________________________________________
> >Pw_forum mailing list
> >Pw_forum at pwscf.org
> >http://www.democritos.it/mailman/listinfo/pw_forum
> S. K. Gupta
> PhD Candidate,
> Dept. of Physics,
> Bhavnagar University.
> Bhavnagar, 364 002., Gujarat.
>
>
> [image: Rediff Shopping]<http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198 at Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
+39 3807528672 (M)
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From prasenjit.jnc at gmail.com Thu Nov 13 13:44:18 2008
From: prasenjit.jnc at gmail.com (Prasenjit Ghosh)
Date: Thu, 13 Nov 2008 13:44:18 +0100
Subject: [Pw_forum] PWSCF calculation for Nanostructures
In-Reply-To: <20081113114914.22587.qmail@f4mail-235-240.rediffmail.com>
References: <20081113114914.22587.qmail@f4mail-235-240.rediffmail.com>
Message-ID: <627e0ffa0811130444k14c723d3pdb8b339c87e1ee06@mail.gmail.com>
Sanjeev,
Its the same thing which I explained to you earlier.......Why gon't you go
through this paper......Reviews of Modern Physics, vol 64, page 1045 (1992)
by M. C. Payne et al.......In Section IIC (Periodic supercells), of the
paper they have explained everything.
Prasenjit
2008/11/13 sanjeev gupta <sanjeev0302 at rediffmail.com>
>
> Thank you sir.
>
> Please explain more "it seems you should introduce certain vacuum layers
> to define so-called nano systems due to periodic scheme used in QE" For
> nano", the non-periodic scheme will used. How I introduced vacuum layers?
>
> Please suggest me more.
> kind regards
> sanjeev gupta
>
> On Wed, 12 Nov 2008 lan haiping wrote :
>
> >As far As i know,
> >for nanostructures, time is demanding for e-ph calculations.
> >
> >with respect to the difference between nano and bulk systems,
> >it seems you should introduce certain vacuum layers to define so-called
> >nano systems due to periodic scheme used in QE.
> >
> >regards
> >
> >On Thu, Nov 13, 2008 at 12:31 AM, sanjeev gupta
> ><sanjeev0302 at rediffmail.com>wrote:
> >
> > >
> > > Dear PWSCF users,
> > >
> > > I am using Quantum espresso package for DFT calculation for noble
> nitride
> > > systems. My main interest in electron-phonon calculation and Raman
> tensor
> > > etc. Sir, I want to know, what will be change in SCF or NSCF file for
> > > nanostructures calculation? or where is difference in bulfk or nano? I
> want
> > > to do calculation on nanostructre?, what i do ?
> > > Please help me .
> > >
> > > Kind Regards
> > > sanjeev gupta
> > > S. K. Gupta
> > > PhD Candidate,
> > > Dept. of Physics,
> > > Bhavnagar University.
> > > Bhavnagar, 364 002., Gujarat.
> > >
> > >
> > > [image: Rediff Shopping]<
> http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198 at Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null
> >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> > >
> >
> >
> >--
> >Hai-Ping Lan
> >Department of Electronics ,
> >Peking University , Bejing, 100871
> >lanhaiping at gmail.com, hplan at pku.edu.cn
> >_______________________________________________
> >Pw_forum mailing list
> >Pw_forum at pwscf.org
> >http://www.democritos.it/mailman/listinfo/pw_forum
> S. K. Gupta
> PhD Candidate,
> Dept. of Physics,
> Bhavnagar University.
> Bhavnagar, 364 002., Gujarat.
>
>
> [image: Rediff Shopping]<http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198 at Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
+39 3807528672 (M)
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From oulihui666 at 126.com Fri Nov 14 03:36:36 2008
From: oulihui666 at 126.com (oulihui666)
Date: Fri, 14 Nov 2008 10:36:36 +0800 (CST)
Subject: [Pw_forum] How to get vacuum level
Message-ID: <28605520.482401226630196176.JavaMail.coremail@bj126app81.126.com>
Dear pwscf users,
I want to calculate work function, I have got the fermi level, so I must get the vacuum level.
work = (vacuum level) - (fermi level)
My input file displayed as follows:
(1)scf calculation:
&control
calculation='scf'
restart_mode='from_scratch',
prefix='Al',
pseudo_dir = './',
outdir='./'
/
&system
ibrav= 0, nat=11, ntyp= 1,
ecutwfc =16,
occupations='smearing', smearing='methfessel-paxton', degauss=0.01
/
&electrons
conv_thr = 1.0d-8
mixing_beta = 0.7
/
CELL_PARAMETERS cubic
5.41176 0 0
0 5.41176 0
0 0 60.9909
ATOMIC_SPECIES
Al 13.867 Al.vbc.UPF
ATOMIC_POSITIONS {angstrom}
Al 0 0 0
Al 1.43189 1.43189 2.025
Al 0 0 4.05
Al 1.43189 1.43189 6.075
Al 0 0 8.1
Al 1.43189 1.43189 10.125
Al 0 0 12.15
Al 1.43189 1.43189 14.175
Al 0 0 16.2
Al 1.43189 1.43189 18.225
Al 0 0 20.25
K_POINTS {automatic}
8 8 1 0 0 0
(2)Electrostatic potential calculation:
&inputpp
prefix = 'Al'
outdir = './'
filplot = 'Al.pot'
plot_num= 11
/
(3)macroscopic averages calculation: average.x.
1
Al.pot
1.D0
5000
3
2.95
Finally, I get a output file, column 1: coordinate u, defined over a mesh of npt=5000 points along the direction idir=3, column 2: averaged quantity V,
column 3: macroscopically averaged quantity V, I should how to get the vacuum level? any suggestion will be appreciated.
Thank you
Lihui Ou
--
======================================
Lihui Ou
PH.D Candidate in Electrochemistry
College of Chemistry and Molecular Science
Wuhan University,430072,Hubei Province,China
E-mail:oulihui666 at 126.com
======================================
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From lanhaiping at gmail.com Fri Nov 14 04:36:59 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Fri, 14 Nov 2008 11:36:59 +0800
Subject: [Pw_forum] How to get vacuum level
In-Reply-To: <28605520.482401226630196176.JavaMail.coremail@bj126app81.126.com>
References: <28605520.482401226630196176.JavaMail.coremail@bj126app81.126.com>
Message-ID: <c92002fa0811131936i5216daep2c416306b7306d97@mail.gmail.com>
in fact , this question has been asked for many times in the forum. Just do
a refined search with 'workfunction ' or '
vacuum level ' keywords in google or other engines will
help you a lot. And there is also a example about how
to do workfunction's calculation supplied with QE, which
you can find in $QE/examples/WorkFct_example.
how to define vacuum level ? a simple or handwaving picture is to do plane
average of electrostatic potential
perpendicular to vacuum layer. If your vacuum layer is
thick enough, you should find a constant value in the vacuum layer region.
This value , you then can refer to
so-called vacuum level.
On Fri, Nov 14, 2008 at 10:36 AM, oulihui666 <oulihui666 at 126.com> wrote:
> Dear pwscf users,
> I want to calculate work function, I have got the fermi level, so I must
> get the vacuum level.
> *work = (vacuum level) - (fermi level)*
>
> My input file displayed as follows:
>
> (1)scf calculation:
>
> &control
> calculation='scf'
> restart_mode='from_scratch',
> prefix='Al',
> pseudo_dir = './',
> outdir='./'
> /
> &system
> ibrav= 0, nat=11, ntyp= 1,
> ecutwfc =16,
> occupations='smearing', smearing='methfessel-paxton', degauss=0.01
> /
> &electrons
> conv_thr = 1.0d-8
> mixing_beta = 0.7
> /
> CELL_PARAMETERS cubic
> 5.41176 0 0
> 0 5.41176 0
> 0 0 60.9909
> ATOMIC_SPECIES
> Al 13.867 Al.vbc.UPF
> ATOMIC_POSITIONS {angstrom}
> Al 0 0 0
> Al 1.43189 1.43189 2.025
> Al 0 0 4.05
> Al 1.43189 1.43189 6.075
> Al 0 0 8.1
> Al 1.43189 1.43189 10.125
> Al 0 0 12.15
> Al 1.43189 1.43189 14.175
> Al 0 0 16.2
> Al 1.43189 143189 18.225
> Al 0 0 20.25
> K_POINTS {automatic}
> 8 8 1 0 0 0
>
> (2)Electrostatic potential calculation:
>
> &inputpp
> prefix = 'Al'
> outdir = './'
> filplot = 'Al.pot'
> plot_num= 11
> /
>
> (3)macroscopic averages calculation: average.x.
>
> 1
> Al.pot
> 1.D0
> 5000
> 3
> 2.95
>
> Finally, I get a output file, column 1: coordinate u, *defined over a mesh
> of npt=5000 point*s along the direction idir=3, column 2: *averaged
> quantity* V,
>
> column 3: *macroscopically averaged quantity V*, I should how to get the
> vacuum level? any suggestion will be appreciated.
>
>
>
> Thank you
>
> Lihui Ou
>
> --
> ======================================
> Lihui Ou
> PH.D Candidate in Electrochemistry
> College of Chemistry and Molecular Science
> Wuhan University,*430072*,Hubei Province,China
> *E-mail:oulihui666 at 126.com*
> ======================================
>
>
> ------------------------------
> ????10??,?????? <http://www.yeah.net>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From baroni at sissa.it Fri Nov 14 07:48:37 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 14 Nov 2008 07:48:37 +0100
Subject: [Pw_forum] How to get vacuum level
In-Reply-To: <28605520.482401226630196176.JavaMail.coremail@bj126app81.126.com>
References: <28605520.482401226630196176.JavaMail.coremail@bj126app81.126.com>
Message-ID: <4515AD73-79AF-4674-8BE0-16EAB6A1D852@sissa.it>
Work function = (average potential in the vacuum) - (Fermi Energy)
So you had the solution already, the missing (and not very surprising)
step is the identification of the vacuum level with the average of the
potential "out in the vacuum" (as discussed many, many times in this
forum as well as many, many times in the literature)
SB
On Nov 14, 2008, at 3:36 AM, oulihui666 wrote:
> Dear pwscf users,
> I want to calculate work function, I have got the fermi level, so I
> must get the vacuum level.
> work = (vacuum level) - (fermi level)
> My input file displayed as follows:
> (1)scf calculation:
> &control
> calculation='scf'
> restart_mode='from_scratch',
> prefix='Al',
> pseudo_dir = './',
> outdir='./'
> /
> &system
> ibrav= 0, nat=11, ntyp= 1,
> ecutwfc =16,
> occupations='smearing', smearing='methfessel-paxton', degauss=0.01
> /
> &electrons
> conv_thr = 1.0d-8
> mixing_beta = 0.7
> /
> CELL_PARAMETERS cubic
> 5.41176 0 0
> 0 5.41176 0
> 0 0 60.9909
> ATOMIC_SPECIES
> Al 13.867 Al.vbc.UPF
> ATOMIC_POSITIONS {angstrom}
> Al 0 0 0
> Al 1.43189 1.43189 2.025
> Al 0 0 4.05
> Al 1.43189 1.43189 6.075
> Al 0 0 8.1
> Al 1.43189 1.43189 10.125
> Al 0 0 12.15
> Al 1.43189 1.43189 14.175
> Al 0 0 16.2
> Al 1.43189 143189 18.225
> Al 0 0 20.25
> K_POINTS {automatic}
> 8 8 1 0 0 0
> (2)Electrostatic potential calculation:
> &inputpp
> prefix = 'Al'
> outdir = './'
> filplot = 'Al.pot'
> plot_num= 11
> /
> (3)macroscopic averages calculation: average.x.
> 1
> Al.pot
> 1.D0
> 5000
> 3
> 2.95
> Finally, I get a output file, column 1: coordinate u, defined over a
> mesh of npt=5000 points along the direction idir=3, column 2:
> averaged quantity V,
> column 3: macroscopically averaged quantity V, I should how to get
> the vacuum level? any suggestion will be appreciated.
>
> Thank you
> Lihui Ou
>
> --
> ======================================
> Lihui Ou
> PH.D Candidate in Electrochemistry
> College of Chemistry and Molecular Science
> Wuhan University,430072,Hubei Province,China
> E-mail:oulihui666 at 126.com
> ======================================
>
>
> ????10??,??????
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
La morale est une logique de l'action comme la logique est une morale
de la pens?e - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From marzari at MIT.EDU Fri Nov 14 07:58:56 2008
From: marzari at MIT.EDU (Nicola Marzari)
Date: Fri, 14 Nov 2008 09:58:56 +0300
Subject: [Pw_forum] How to get vacuum level
In-Reply-To: <28605520.482401226630196176.JavaMail.coremail@bj126app81.126.com>
References: <28605520.482401226630196176.JavaMail.coremail@bj126app81.126.com>
Message-ID: <491D21B0.9090406@mit.edu>
oulihui666 wrote:
> Dear pwscf users,
> I want to calculate work function, I have got the fermi level, so I must
> get the vacuum level.
Dear Lihui,
on top of what Stefano Baroni just mentioned, there was a post not
more than 3 days ago from Nicholas Singh-Miller pointing out to a
tutorial on how to do this in detail.
nicola
> ======================================
> Lihui Ou
> PH.D Candidate in Electrochemistry
> College of Chemistry and Molecular Science
> Wuhan University,/430072/,Hubei Province,China
> /E-mail:oulihui666 at 126.com <mailto:oulihui666 at 126.com>/
> ======================================
--
---------------------------------------------------------------------
Prof Nicola Marzari Department of Materials Science and Engineering
13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu
From babderre at physics.auth.gr Fri Nov 14 14:38:54 2008
From: babderre at physics.auth.gr (babderre at physics.auth.gr)
Date: Fri, 14 Nov 2008 15:38:54 +0200
Subject: [Pw_forum] Bi-fully relativistic
Message-ID: <1226669934.491d7f6ecbb2c@mail.physics.auth.gr>
Dear pwscf users,
I need fully relativistic pseudopotential
for Bi to calculate the band structure of
GaBi with spin-orbit.
If anyone can help me.
Belabbes
Aristotle University of Thessaloniki.
http://parsem.physics.auth.gr/belabbes.htm
From giannozz at democritos.it Fri Nov 14 16:57:56 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 14 Nov 2008 16:57:56 +0100
Subject: [Pw_forum] Could you please help me to cope with the error
message
In-Reply-To: <BAY124-DS45358B5F953046C3888BAA41A0@phx.gbl>
References: <BAY124-DS45358B5F953046C3888BAA41A0@phx.gbl>
Message-ID: <491DA004.9090607@democritos.it>
vega wrote:
> I am suffering from the error message like this,
> [node1][0,1,12][btl_tcp_frag.c:202:mca_btl_tcp_frag_recv]
> mca_btl_tcp_frag_recv: readv failed with errno=104
> forrtl: error (78): process killed (SIGTERM)
as explained many times: unless you have evidence of the opposite,
this kind of obscure errors is likely due to buggy compiler or buggy
libraries or even flakey hardware.
> I could relax 72 atoms successfully with my system using openmpi. But
> when I wanted to relax 84 atoms, the error message stoped my
> calculation. Then I tried the mpich2 using the same system. With the
> help of mpich2 I could relax 120 atoms instead. But the error message
> bothered me again when I wanted to relax 132 atoms.
this might indicate a problem with excessive memory requirements
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Fri Nov 14 17:05:20 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 14 Nov 2008 17:05:20 +0100
Subject: [Pw_forum] Total energy does not coverge with ecut
In-Reply-To: <910570.49147.qm@web81804.mail.mud.yahoo.com>
References: <910570.49147.qm@web81804.mail.mud.yahoo.com>
Message-ID: <491DA1C0.9080802@democritos.it>
Timothy Mason wrote:
> I have not attempted your suggestion however I did trade out the PSPS
> with different PSPSs. I'm now using
>
> Li.pz-n-vbc.UPF
> N.pbe-rrkjus.UPF
> H.pbe-rrkjus.UPF
>
> and they seem to converge nicely.
>
> is there problem with the ones I was using? here they are for reference
>
> Li 6.941000 Li.pbe-n-van.UPF
> N 14.006740 N.pbe-van_ak.UPF
> H 1.007940 H.pbe-van_ak.UPF
hard to say, without an example
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From roccad at gmail.com Sat Nov 15 02:32:06 2008
From: roccad at gmail.com (dario rocca)
Date: Fri, 14 Nov 2008 17:32:06 -0800
Subject: [Pw_forum] Total energy does not coverge with ecut
In-Reply-To: <910570.49147.qm@web81804.mail.mud.yahoo.com>
References: <000e0cd2480434b355045b0c911c@google.com>
<910570.49147.qm@web81804.mail.mud.yahoo.com>
Message-ID: <cb6486310811141732j68679f5bu6bdc858dc113c044@mail.gmail.com>
It seems that now you are using pseusopotentials generated with different
functionals (pz and pbe).
In my experience it is hard to converge ultrasoft with respect to ecutrho:
at a certain point the total enegy starts
oscillating or it goes down very slowly. This could be the reason of the
behavior that you see, namely the
results for different ecutwfc does not converge because none of them is
fully converged with respect to
ecutrho. From this point of view I found that rrkj ultrasoft have a much
better behavior. If I remember well they are optimized to use a smaller
number of plane-waves to describe the augmentation
charge. I would follow the suggestion "So usually it is better to check the
convergence of the quantity you are interested in"
Dario
On Tue, Nov 11, 2008 at 12:05 PM, Timothy Mason <thmason24 at yahoo.com> wrote:
> I have not attempted your suggestion however I did trade out the PSPS with
> different PSPSs. I'm now using
>
> Li.pz-n-vbc.UPF
> N.pbe-rrkjus.UPF
> H.pbe-rrkjus.UPF
>
> and they seem to converge nicely.
>
> is there problem with the ones I was using? here they are for reference
>
> Li 6.941000 Li.pbe-n-van.UPF
> N 14.006740 N.pbe-van_ak.UPF
> H 1.007940 H.pbe-van_ak.UPF
>
> I'm not sure of the best way to select them from the website.
>
> thanks for the help.
>
>
>
>
>
>
>
> --- On *Thu, 11/6/08, prasenjit.jnc at gmail.com <prasenjit.jnc at gmail.com>*wrote:
>
> From: prasenjit.jnc at gmail.com <prasenjit.jnc at gmail.com>
> Subject: Re: Re: [Pw_forum] Total energy does not coverge with ecut
> To: "Timothy Mason" <thmason24 at yahoo.com>, "PWSCF Forum" <
> pw_forum at pwscf.org>
> Date: Thursday, November 6, 2008, 4:10 PM
>
>
> Sometimes it is also difficult to converge the total energy. So usually it
> is better to check the convergence of the quantity you are interested in.
>
> But anyway it is really strange that total energy doesn't converge at such
> abnormally high cut off values.
>
> Did you test the pseudopotentials individually?? For eg. did you try
> calculating the bond lengths of say a nitrogen molecule & see how the
> results are??
>
> With regards,
>
> Prasenjit.
>
> On Nov 6, 2008 5:45pm, Timothy Mason <thmason24 at yahoo.com> wrote:
> > Dear Lorenzo,
> >
> > here are results for the lower energy range. Still doesn't seem to be
> converging.
> >
> > ecut energy energy differnce
> > 30 -48.19258627
> > 35 -48.19503183 0.00244556
> > 40 -48.197306 0.00227417
> > 45 -48.20217820 0.0048722
> >
> > thanks
> >
> > --- On Thu, 11/6/08, Lorenzo Paulatto paulatto at sissa.it> wrote:
> > From: Lorenzo Paulatto paulatto at sissa.it>
> > Subject: Re: [Pw_forum] Total energy does not coverge with ecut
> > To: thmason24 at yahoo.com, "PWSCF Forum" pw_forum at pwscf.org>
> > Date: Thursday, November 6, 2008, 10:08 AM
> >
> > Timothy Mason ha scritto:
> > >
> > > Gentlemen,
> > >
> > > My structures do not see to be converging with increased ecutwfc.
> > > I'm setting ecutrho to ecutwfc * 12 and using US PP. below is a
> > > table of ecut values vs energies vs difference from previous steps
> > > followed by my input file followed by part of the output file. It
> > > appears to begin to converge and 120 ecut but then jumps at 130 and
> > > then more at 140.
> > >
> > Dear Timothy,
> > these are ridiculous cutoff energy for ultrasoft pseudopotentials - they
> > are very high for norm-conserving too! I suspect the presence of a
> > high-energy ghost-state in one of the pseudopotential; these kind
> > of
> > states aren't usually harmful but can suddenly pop-up under some
> > specifics conditions like high pressure or very high cutoff.
> >
> > What is happening when you try some reasonable cutoff in the 20-50 Ry
> range?
> >
> > regards
> >
> > --
> > Lorenzo Paulatto
> > SISSA & DEMOCRITOS (Trieste)
> > phone: +39 040 3787 511
> > skype: paulatz
> > www: http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
> >
> > Due to budget cuts approved by Italian Minister of Finance and Italian
> > Minister "for" Education, University and Research this may be the
> > last
> > email you receive from me.
> >
> > Please send any future correspondence, possibly via pigeon, to
> > mr. Lorenzo Paulatto
> > under Roiano Railway Bridge - Pillar 2
> > 34136, Trieste
> >
> > Donations in food, coins, booze and processor time are warmly welcome.
> >
> >
> >
> >
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From frnkhzi at yahoo.com Sat Nov 15 06:56:37 2008
From: frnkhzi at yahoo.com (fereydoon khazali)
Date: Fri, 14 Nov 2008 21:56:37 -0800 (PST)
Subject: [Pw_forum] (no subject)
Message-ID: <304110.55227.qm@web30102.mail.mud.yahoo.com>
All dear
Please send me an input file for slab.
thanks
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From asaaravindh at yahoo.co.in Sat Nov 15 07:26:53 2008
From: asaaravindh at yahoo.co.in (asa aravindh)
Date: Sat, 15 Nov 2008 11:56:53 +0530 (IST)
Subject: [Pw_forum] convergence problem
Message-ID: <626089.39518.qm@web7905.mail.in.yahoo.com>
Dear all..
I was trying to do scf and nscf calculations on ZnO nanowires using pwscf
scf has run successfully, while nscf shows this warning in between..
Band Structure Calculation
CG style diagonalization
c_bands: 2 eigenvalues not converged
.....................................
but the code works even after this and finishes the nscf run. After looking into the forum I got the impression that this might be due to the algorithm "david", which I was using .So I changed to "CG" . Again the same situation is repeating.
My question is whether my results will be accurate if this warnig persists??
If I do further calculations like transport taking this scf and nscf outputs how far my calculations will be reliable??
can anybody please help me in this regard...........
Thanks in advance
asa
Be the first one to try the new Messenger 9 Beta! Go to http://in.messenger.yahoo.com/win/
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From eyvaz_isaev at yahoo.com Sat Nov 15 13:46:41 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 15 Nov 2008 04:46:41 -0800 (PST)
Subject: [Pw_forum] (no subject)
In-Reply-To: <304110.55227.qm@web30102.mail.mud.yahoo.com>
Message-ID: <901139.66497.qm@web65712.mail.ac4.yahoo.com>
Dear Fereydoon,
Already you have it. Please see /examples/example03 with Al(001) slab. Besides, you need to read some papers how to deal with such kind calculations. For example, Payne et al. in Review of Modern Physics, vol. 64, p.1045 (1992).
There are also textbooks "Surface Physics" of Zengwil, and "Principles of Surface Physics" by Bechstedt.
Please also do not forget specify your affiliation as it is default in this forum.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
--- On Sat, 11/15/08, fereydoon khazali <frnkhzi at yahoo.com> wrote:
> From: fereydoon khazali <frnkhzi at yahoo.com>
> Subject: [Pw_forum] (no subject)
> To: Pw_forum at pwscf.org
> Date: Saturday, November 15, 2008, 8:56 AM
> All dear
> Please send me an input file for slab.
> thanks
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
From eyvaz_isaev at yahoo.com Sat Nov 15 14:04:14 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 15 Nov 2008 05:04:14 -0800 (PST)
Subject: [Pw_forum] convergence problem
In-Reply-To: <626089.39518.qm@web7905.mail.in.yahoo.com>
Message-ID: <262570.76464.qm@web65712.mail.ac4.yahoo.com>
Dear Asa,
I think you can trust these results. Please have a look at Troubleshooting in User's Guide: "warning : N eigenvectors not converged ..."
We appreciate if you will specify your affiliation.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
--- On Sat, 11/15/08, asa aravindh <asaaravindh at yahoo.co.in> wrote:
> From: asa aravindh <asaaravindh at yahoo.co.in>
> Subject: [Pw_forum] convergence problem
> To: pw_forum at pwscf.org
> Date: Saturday, November 15, 2008, 9:26 AM
> Dear all..
> I was trying to do scf and nscf calculations on ZnO
> nanowires using pwscf
> scf has run successfully, while nscf shows this warning in
> between..
> Band Structure Calculation
> CG style diagonalization
> c_bands: 2 eigenvalues not converged
> .....................................
> but the code works even after this and finishes the nscf
> run. After looking into the forum I got the impression that
> this might be due to the algorithm "david", which
> I was using .So I changed to "CG" . Again the same
> situation is repeating.
> My question is whether my results will be accurate if this
> warnig persists??
> If I do further calculations like transport taking this scf
> and nscf outputs how far my calculations will be reliable??
> can anybody please help me in this regard...........
> Thanks in advance
> asa
>
>
> Be the first one to try the new Messenger 9 Beta! Go
> to
> http://in.messenger.yahoo.com/win/_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
From chenhanghuipwscf at gmail.com Sat Nov 15 19:27:53 2008
From: chenhanghuipwscf at gmail.com (hanghui chen)
Date: Sat, 15 Nov 2008 13:27:53 -0500
Subject: [Pw_forum] sawtooth method
Message-ID: <22ae3ca40811151027s7cfd5c64m3336acc7706cbc0d@mail.gmail.com>
Dear PWSCF users,
I calculate a symmetric STO slab (separated by vacuum) and turn on a
symmetric sawtooth potential (the turning point is right at the center of
the STO slab). I fix all the atoms. Without the sawtooth potential, the
forces are symmetric and there are no forces in the central layer. However,
when I turn on the sawtooth potential which I set to be symmetric, the
forces on the atoms are NO longer symmetric and the forces in the layer are
NO longer zero. The input file and the forces (turning on sawtooth
potential) are given below.
Why are the forces NOT symmetric but the configuration (including the
sawtooth potential) is symmetric? Does the turning point in the material
cause any anomaly?
Thank you very much.
Hanghui Chen
Department of Physics, Yale University
Input file:
&CONTROL
calculation='scf'
wf_collect=.true.
pseudo_dir = './psp'
outdir='.'
wfcdir='/scratch'
prefix='test1'
disk_io='low'
verbosity='high'
tprnfor = .true.
tstress = .true.
dt=80.D0
tefield=.true.
/
&SYSTEM
ibrav= 6
celldm(1) = 7.27
celldm(3) = 6.0
nat= 12
ntyp= 3
ecutwfc = 30.0
ecutrho = 180.0
occupations='smearing'
smearing='gauss'
degauss=0.005
edir=3
emaxpos=0.5
eopreg=0.5
eamp=0.01
/
&ELECTRONS
diagonalization='david'
mixing_beta = 0.7D0
diago_david_ndim = 4
mixing_mode= 'local-TF'
electron_maxstep = 300
startingpot = 'file'
conv_thr= 1.d-8
/
&IONS
ion_dynamics = 'bfgs'
phase_space = 'full'
pot_extrapolation = 'first_order'
wfc_extrapolation = 'first_order'
/
&CELL
cell_dynamics = 'damp-w'
/
ATOMIC_SPECIES
Sr 87.62 038-Sr-ca-sp-vgrp.uspp.format.UPF
Ti 47.90 022-Ti-ca-sp-vgrp.uspp.format.UPF
O 16.00 008-O-ca--vgrp.uspp.format.UPF
ATOMIC_POSITIONS alat
Sr 0.00 0.00 2.00
O 0.50 0.50 2.00
Ti 0.50 0.50 2.50
O 0.50 0.00 2.50
O 0.00 0.50 2.50
Sr 0.00 0.00 3.00
O 0.50 0.50 3.00
Ti 0.50 0.50 3.50
O 0.50 0.00 3.50
O 0.00 0.50 3.50
Sr 0.00 0.00 4.00
O 0.50 0.50 4.00
K_POINTS {automatic}
8 8 1 0 0 0
Forces:
atom 1 type 1 force = 0.00000001 -0.00000001 -0.09670746
atom 2 type 3 force = 0.00000000 0.00000000 -0.21698818
atom 3 type 2 force = 0.00000000 0.00000001 -0.17490285
atom 4 type 3 force = 0.00000000 0.00000000 -0.17341486
atom 5 type 3 force = 0.00000001 0.00000000 -0.17341491
atom 6 type 1 force = -0.00000002 0.00000000 0.06540405
atom 7 type 3 force = -0.00000001 -0.00000001 -0.01253063
atom 8 type 2 force = 0.00000001 0.00000001 0.32344891
atom 9 type 3 force = 0.00000000 0.00000000 0.08311003
atom 10 type 3 force = 0.00000000 0.00000000 0.08311005
atom 11 type 1 force = 0.00000000 0.00000000 0.16600421
atom 12 type 3 force = 0.00000001 0.00000000 0.12688164
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From chenhanghuipwscf at gmail.com Sun Nov 16 07:27:57 2008
From: chenhanghuipwscf at gmail.com (hanghui chen)
Date: Sun, 16 Nov 2008 01:27:57 -0500
Subject: [Pw_forum] a possible problem in the routine add_efield.f90
Message-ID: <22ae3ca40811152227m52d98444le4d554ea16b12600@mail.gmail.com>
Dear PWSCF users,
In my previous email, I reported that if I calculated a
symmetric
system (both the material and the external sawtooth potential are
symmetric), I found that the forces are not symmetric. I think I may find
the reason.
The total force in the presence of sawtooth potential has two parts:
one is from the variation of Kohn-Sham functional; the other is from
sawtooth potential which in the code is "forcefield" (see the routine
forces.f90). The additional force is calculated by the routine
add_efield.f90. However in routine add_efield.f90, it only calculates the
magnitude of the force but does not specify the direction (the additional
force only has one direction). Therefore all the forces in the 'reversed
region' are not correctly calculated because the direction of
'forcefield'
is NOT reversed as is the external electric field.
I sincerely hope that the people who wrote the routine
add_efield.f90
can reexamine the code and add the directions to the "forcefield".
No offense intended.
Thank you very much.
Hanghui Chen
Department of Physics, Yale University
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From baroni at sissa.it Sun Nov 16 16:36:47 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Sun, 16 Nov 2008 16:36:47 +0100
Subject: [Pw_forum] a possible problem in the routine add_efield.f90
In-Reply-To: <22ae3ca40811152227m52d98444le4d554ea16b12600@mail.gmail.com>
References: <22ae3ca40811152227m52d98444le4d554ea16b12600@mail.gmail.com>
Message-ID: <D7FFD11D-BFB4-48EA-9515-7E1E888A8DAF@sissa.it>
Dear Hanghui:
On Nov 16, 2008, at 7:27 AM, hanghui chen wrote:
> Dear PWSCF users,
> In my previous email, I reported that if I calculated
> a symmetric
> system (both the material and the external sawtooth potential are
> symmetric), I found that the forces are not symmetric. I think I
> may find
> the reason.
> The total force in the presence of sawtooth potential has
> two parts:
> one is from the variation of Kohn-Sham functional; the other is
> from
> sawtooth potential which in the code is "forcefield" (see the
> routine
> forces.f90). The additional force is calculated by the routine
> add_efield.f90. However in routine add_efield.f90, it only
> calculates the
> magnitude of the force but does not specify the direction (the
> additional
> force only has one direction). Therefore all the forces in the
> 'reversed
> region' are not correctly calculated because the direction of
> 'forcefield'
> is NOT reversed as is the external electric field.
thank you very much for your thorough analysis
> I sincerely hope that the people who wrote the routine
> add_efield.f90
> can reexamine the code and add the directions to the "forcefield".
I hope the same as well, however I would be even happier if you would
volunteer to fix the code yourself and to submit the fix to the QE
community
> No offense intended.
of course, nobody would fel offended by your interest
cheers - SB
>
> Thank you very much.
> Hanghui Chen
> Department of Physics, Yale University
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
La morale est une logique de l'action comme la logique est une morale
de la pens?e - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From giannozz at democritos.it Sun Nov 16 18:39:24 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 16 Nov 2008 18:39:24 +0100
Subject: [Pw_forum] a possible problem in the routine add_efield.f90
In-Reply-To: <22ae3ca40811152227m52d98444le4d554ea16b12600@mail.gmail.com>
References: <22ae3ca40811152227m52d98444le4d554ea16b12600@mail.gmail.com>
Message-ID: <FFD92F7B-60C0-499D-A551-E1C9433098D1@democritos.it>
On Nov 16, 2008, at 7:27 , hanghui chen wrote:
> The additional force is calculated by the routine add_efield.f90.
> However in routine add_efield.f90, it only calculates the magnitude
> of the force but does not specify the direction (the additional force
> only has one direction). Therefore all the forces in the 'reversed
> region' are not correctly calculated because the direction of
> 'forcefield'
> is NOT reversed as is the external electric field.
I think the sawtooth potential was meant to reproduce the case of a
homogeneous electric field on a slab. The sawtooth potential is supposed
to reverse in the vacuum region and to yield a constant electric
field in the
region where atoms are. An electric field reversing in the middle of
the layers
was not considered a physical case, I guess. Of course this
limitation should
be documented, or else the unexpected placement of the reversal should
produce an error, or else this case should be implemented (assuming
it has
any physical interest, which is far from obvious to me).
Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From asaaravindh at yahoo.co.in Mon Nov 17 04:46:14 2008
From: asaaravindh at yahoo.co.in (asa aravindh)
Date: Mon, 17 Nov 2008 09:16:14 +0530 (IST)
Subject: [Pw_forum] Pw_forum Digest, Vol 17, Issue 32
References: <mailman.1.1226821760.30079.pw_forum@pwscf.org>
Message-ID: <648317.95308.qm@web7904.mail.in.yahoo.com>
Dear Prof.Eyvaz Isaev,
Thanks for your reply.
I have looked into the user guide and got the impression that the warning I am getting willnot seriously affect further calcualtions.
regards
Assa Aravindh.S
Research Scholar
Theory and Computational Studies Section
Material Science Division
Indira gandhi Centre for Atomic Research
Kalpakkam - 603102, India
________________________________
From: "pw_forum-request at pwscf.org" <pw_forum-request at pwscf.org>
To: pw_forum at pwscf.org
Sent: Sunday, 16 November, 2008 1:19:20 PM
Subject: Pw_forum Digest, Vol 17, Issue 32
Send Pw_forum mailing list submissions to
pw_forum at pwscf.org
To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Pw_forum digest..."
Today's Topics:
1. Re: (no subject) (Eyvaz Isaev)
2. Re: convergence problem (Eyvaz Isaev)
3. sawtooth method (hanghui chen)
4. a possible problem in the routine add_efield.f90 (hanghui chen)
----------------------------------------------------------------------
Message: 1
Date: Sat, 15 Nov 2008 04:46:41 -0800 (PST)
From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
Subject: Re: [Pw_forum] (no subject)
To: pw_forum at pwscf.org
Message-ID: <901139.66497.qm at web65712.mail.ac4.yahoo.com>
Content-Type: text/plain; charset=us-ascii
Dear Fereydoon,
Already you have it. Please see /examples/example03 with Al(001) slab. Besides, you need to read some papers how to deal with such kind calculations. For example, Payne et al. in Review of Modern Physics, vol. 64, p.1045 (1992).
There are also textbooks "Surface Physics" of Zengwil, and "Principles of Surface Physics" by Bechstedt.
Please also do not forget specify your affiliation as it is default in this forum.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
--- On Sat, 11/15/08, fereydoon khazali <frnkhzi at yahoo.com> wrote:
> From: fereydoon khazali <frnkhzi at yahoo.com>
> Subject: [Pw_forum] (no subject)
> To: Pw_forum at pwscf.org
> Date: Saturday, November 15, 2008, 8:56 AM
> All dear
> Please send me an input file for slab.
> thanks
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
------------------------------
Message: 2
Date: Sat, 15 Nov 2008 05:04:14 -0800 (PST)
From: Eyvaz Isaev <eyvaz_isaev at yahoo.com>
Subject: Re: [Pw_forum] convergence problem
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <262570.76464.qm at web65712.mail.ac4.yahoo.com>
Content-Type: text/plain; charset=us-ascii
Dear Asa,
I think you can trust these results. Please have a look at Troubleshooting in User's Guide: "warning : N eigenvectors not converged ..."
We appreciate if you will specify your affiliation.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
--- On Sat, 11/15/08, asa aravindh <asaaravindh at yahoo.co.in> wrote:
> From: asa aravindh <asaaravindh at yahoo.co.in>
> Subject: [Pw_forum] convergence problem
> To: pw_forum at pwscf.org
> Date: Saturday, November 15, 2008, 9:26 AM
> Dear all..
> I was trying to do scf and nscf calculations on ZnO
> nanowires using pwscf
> scf has run successfully, while nscf shows this warning in
> between..
> Band Structure Calculation
> CG style diagonalization
> c_bands: 2 eigenvalues not converged
> .....................................
> but the code works even after this and finishes the nscf
> run. After looking into the forum I got the impression that
> this might be due to the algorithm "david", which
> I was using .So I changed to "CG" . Again the same
> situation is repeating.
> My question is whether my results will be accurate if this
> warnig persists??
> If I do further calculations like transport taking this scf
> and nscf outputs how far my calculations will be reliable??
> can anybody please help me in this regard...........
> Thanks in advance
> asa
>
>
> Be the first one to try the new Messenger 9 Beta! Go
> to
> http://in.messenger.yahoo.com/win/_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
------------------------------
Message: 3
Date: Sat, 15 Nov 2008 13:27:53 -0500
From: "hanghui chen" <chenhanghuipwscf at gmail.com>
Subject: [Pw_forum] sawtooth method
To: pw_forum at pwscf.org
Message-ID:
<22ae3ca40811151027s7cfd5c64m3336acc7706cbc0d at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear PWSCF users,
I calculate a symmetric STO slab (separated by vacuum) and turn on a
symmetric sawtooth potential (the turning point is right at the center of
the STO slab). I fix all the atoms. Without the sawtooth potential, the
forces are symmetric and there are no forces in the central layer. However,
when I turn on the sawtooth potential which I set to be symmetric, the
forces on the atoms are NO longer symmetric and the forces in the layer are
NO longer zero. The input file and the forces (turning on sawtooth
potential) are given below.
Why are the forces NOT symmetric but the configuration (including the
sawtooth potential) is symmetric? Does the turning point in the material
cause any anomaly?
Thank you very much.
Hanghui Chen
Department of Physics, Yale University
Input file:
&CONTROL
calculation='scf'
wf_collect=.true.
pseudo_dir = './psp'
outdir='.'
wfcdir='/scratch'
prefix='test1'
disk_io='low'
verbosity='high'
tprnfor = .true.
tstress = .true.
dt=80.D0
tefield=.true.
/
&SYSTEM
ibrav= 6
celldm(1) = 7.27
celldm(3) = 6.0
nat= 12
ntyp= 3
ecutwfc = 30.0
ecutrho = 180.0
occupations='smearing'
smearing='gauss'
degauss=0.005
edir=3
emaxpos=0.5
eopreg=0.5
eamp=0.01
/
&ELECTRONS
diagonalization='david'
mixing_beta = 0.7D0
diago_david_ndim = 4
mixing_mode= 'local-TF'
electron_maxstep = 300
startingpot = 'file'
conv_thr= 1.d-8
/
&IONS
ion_dynamics = 'bfgs'
phase_space = 'full'
pot_extrapolation = 'first_order'
wfc_extrapolation = 'first_order'
/
&CELL
cell_dynamics = 'damp-w'
/
ATOMIC_SPECIES
Sr 87.62 038-Sr-ca-sp-vgrp.uspp.format.UPF
Ti 47.90 022-Ti-ca-sp-vgrp.uspp.format.UPF
O 16.00 008-O-ca--vgrp.uspp.format.UPF
ATOMIC_POSITIONS alat
Sr 0.00 0.00 2.00
O 0.50 0.50 2.00
Ti 0.50 0.50 2.50
O 0.50 0.00 2.50
O 0.00 0.50 2.50
Sr 0.00 0.00 3.00
O 0.50 0.50 3.00
Ti 0.50 0.50 3.50
O 0.50 0.00 3.50
O 0.00 0.50 3.50
Sr 0.00 0.00 4.00
O 0.50 0.50 4.00
K_POINTS {automatic}
8 8 1 0 0 0
Forces:
atom 1 type 1 force = 0.00000001 -0.00000001 -0.09670746
atom 2 type 3 force = 0.00000000 0.00000000 -0.21698818
atom 3 type 2 force = 0.00000000 0.00000001 -0.17490285
atom 4 type 3 force = 0.00000000 0.00000000 -0.17341486
atom 5 type 3 force = 0.00000001 0.00000000 -0.17341491
atom 6 type 1 force = -0.00000002 0.00000000 0.06540405
atom 7 type 3 force = -0.00000001 -0.00000001 -0.01253063
atom 8 type 2 force = 0.00000001 0.00000001 0.32344891
atom 9 type 3 force = 0.00000000 0.00000000 0.08311003
atom 10 type 3 force = 0.00000000 0.00000000 0.08311005
atom 11 type 1 force = 0.00000000 0.00000000 0.16600421
atom 12 type 3 force = 0.00000001 0.00000000 0.12688164
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------------------------------
Message: 4
Date: Sun, 16 Nov 2008 01:27:57 -0500
From: "hanghui chen" <chenhanghuipwscf at gmail.com>
Subject: [Pw_forum] a possible problem in the routine add_efield.f90
To: pw_forum at pwscf.org
Message-ID:
<22ae3ca40811152227m52d98444le4d554ea16b12600 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear PWSCF users,
In my previous email, I reported that if I calculated a
symmetric
system (both the material and the external sawtooth potential are
symmetric), I found that the forces are not symmetric. I think I may find
the reason.
The total force in the presence of sawtooth potential has two parts:
one is from the variation of Kohn-Sham functional; the other is from
sawtooth potential which in the code is "forcefield" (see the routine
forces.f90). The additional force is calculated by the routine
add_efield.f90. However in routine add_efield.f90, it only calculates the
magnitude of the force but does not specify the direction (the additional
force only has one direction). Therefore all the forces in the 'reversed
region' are not correctly calculated because the direction of
'forcefield'
is NOT reversed as is the external electric field.
I sincerely hope that the people who wrote the routine
add_efield.f90
can reexamine the code and add the directions to the "forcefield".
No offense intended.
Thank you very much.
Hanghui Chen
Department of Physics, Yale University
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------------------------------
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From djaithania at hotmail.com Mon Nov 17 10:10:19 2008
From: djaithania at hotmail.com (hania djani-ait aissa)
Date: Mon, 17 Nov 2008 09:10:19 +0000
Subject: [Pw_forum] problem with polarization
Message-ID: <BLU115-W38CB99B1A96D71D34390D2D2130@phx.gbl>
Dear all,
i am trying to calculate polarization in ferroelectric materials with Aurivillius structure (tetragonal and orthorombic), but i often get two anomalies: negative polarization and polarization close to the "quantum" polarization. as an example: P= -0.23 (mod 0.248) C/m2.
could someone explain me that? i'll be grateful.
Hania Djani
Phd student
centre for development of advanced technologies
Algiers, Algeria
_________________________________________________________________
Appelez vos amis de PC ? PC -- C'EST GRATUIT
http://get.live.com/messenger/overview
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From yuminqian at gmail.com Mon Nov 17 10:56:10 2008
From: yuminqian at gmail.com (yumin qian)
Date: Mon, 17 Nov 2008 17:56:10 +0800
Subject: [Pw_forum] phonon mode and atom displacements
Message-ID: <aa128b2c0811170156p4b6121dbu6a2d6252b24ffa6a@mail.gmail.com>
> Atomic displacements:
> There are 16 irreducible representations
>
> Representation 1 2 modes - To be done
> Phonon polarizations are as follows:
>
mode # 1 mode # 2
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( -0.70711 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( -0.70711 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.70711 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.70711 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000
I wander how the atoms ,in the unit cell are displaced, for a real
calculation
> what's the relation between polariztion vector and atoms displacements
>
and the relation between phonon mode , how to use the symmetry group to
get the atoms displacements pattern , if the crystal have inversion
symmetry ,
so is it correct to say a particular phonon mode have or not have
inversion symmetry.
>
> --
> Sincerely Y. M. Qian
> Lab.of Condensed Matter Theory and Materials Computation
> Institute of Physics
> Chinese Academy of Sciences
> Tel: + 8610 8264 9147
> E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
> P.O.Box 603 Beijing 100190
> China
>
>
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From wangqj1 at 126.com Mon Nov 17 13:52:40 2008
From: wangqj1 at 126.com (wangqj1)
Date: Mon, 17 Nov 2008 20:52:40 +0800 (CST)
Subject: [Pw_forum] the vcsmd.f90
Message-ID: <6566271.772501226926360117.JavaMail.coremail@bj126app28.126.com>
Dear all
After I installed the espresso-4.0.3,I use pw.x to do vc-relax,but it turned up as following and stoped:
total stress (Ry/bohr**3) (kbar) P= 43.49
0.00029630 0.00000000 0.00000000 43.59 0.00 0.00
0.00000000 0.00029630 0.00000000 0.00 43.59 0.00
0.00000000 0.00000000 0.00029429 0.00 0.00 43.29
At line 151 of file vcsmd.f90
Fortran runtime error: Bad real number in item 33 of list input
I don't know what's wrong , I installed Federo core 8 which bring fortran95 compiler of itself . What should I do ?
Any help will be appreciated !
Q J Wang
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From degironc at sissa.it Mon Nov 17 14:19:32 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 17 Nov 2008 14:19:32 +0100
Subject: [Pw_forum] the vcsmd.f90
In-Reply-To: <6566271.772501226926360117.JavaMail.coremail@bj126app28.126.com>
References: <6566271.772501226926360117.JavaMail.coremail@bj126app28.126.com>
Message-ID: <49216F64.4050509@sissa.it>
Dear QJ Wang,
does this occur at the first iteration of a new run or after some
iterations? Or is it a continuation run ?
line 151 is a reading line from a file that should have been generated
previously.
a guess is that the file has been corrupted or is not accessible or that
a previously generated file (with a different number of items in it) has
been left behind.
Hope this help
.... please don't forget to provide your affiliation.
Stefano de Gironcoli - SISSA and DEMOCRITOS
wangqj1 wrote:
> Dear all
> After I installed the espresso-4.0.3,I use pw.x to do vc-relax,but it
> turned up as following and stoped:
> total stress (Ry/bohr**3) (kbar) P= 43.49
> 0.00029630 0.00000000 0.00000000 43.59 0.00 0.00
> 0.00000000 0.00029630 0.00000000 0.00 43.59 0.00
> 0.00000000 0.00000000 0.00029429 0.00 0.00 43.29
> At line 151 of file vcsmd.f90
> Fortran runtime error: Bad real number in item 33 of list input
> I don't know what's wrong , I installed Federo core 8 which bring
> fortran95 compiler of itself . What should I do ?
> Any help will be appreciated !
> Q J Wang
>
>
> ------------------------------------------------------------------------
> ????????10????,???????????? <http://www.yeah.net>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
From krishnachaitanya.gunturu at gmail.com Tue Nov 18 05:16:28 2008
From: krishnachaitanya.gunturu at gmail.com (Krishna chaitanya)
Date: Tue, 18 Nov 2008 09:46:28 +0530
Subject: [Pw_forum] problem with primitive cell
Message-ID: <eb9cf0990811172016wbae5beu6723b097ffec0306@mail.gmail.com>
Hi,
I am trying to calculate surface energy of MgO surface layers using PWSCF.
For that i have used 2 methods given as
1)Ens={En-n(En-En-1)}/2A
here n=no of layers, En and En-1 are total energies of n and n-1 layers,
A=surface area of primitive cell
2)Ens=(En-mEbulk)/2A
here m=no of primitive units present in surface, Ebulk=total energy of
primitive unit cell
I have got converged surfae energy 0.004au/bohr**2 by using method 1, but by
using method 2 i got very different energies and not converged by varying
number of layers. When i checked with xcrysden the periodic repetetion in
primitive cell is not good. Initially i have followed by cartesian
coordinates but the number of symmetry operations observed as 1, but when
followed by fractional coordinates symmetry operations are 48 now.
MgO conventional cell is in FCC bravis lattice group and i have used the
following input for the primitive cell description
&SYSTEM
ibrav = 2,
A = 2.977768,
B = 2.977768,
C = 2.977768,
cosAB = 0.5,
cosAC = 0.5,
cosBC = 0.5,
nat = 2,
ntyp = 2,
ecutwfc = 25,
ecutrho = 200,
/
&ELECTRONS
electron_maxstep = 500,
diago_david_ndim = 6,
/
&IONS
ion_dynamics = 'bfgs',
/
ATOMIC_SPECIES
O 16.000 O.pw91-van_ak.UPF
Mg 24.305 Mg.pw91-np-van.UPF
ATOMIC_POSITIONS crystal
Mg 0.00000000 0.00000000 0.00000000
O 0.50000000 0.50000000 0.50000000
K_POINTS automatic
4 4 4 0 0 0
Please suggest me where i have done mistake and thanks in advance
G. Krishna Chaitanya
Senior research fellow
C/o Dr. Bhanuprakash K.
Inorganic Chemistry Division
Indian Institute of Chemical Technology
Hyderabad, India
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From yuminqian at gmail.com Tue Nov 18 08:22:36 2008
From: yuminqian at gmail.com (yumin qian)
Date: Tue, 18 Nov 2008 15:22:36 +0800
Subject: [Pw_forum] atoms displacements and symmetry
Message-ID: <aa128b2c0811172322p3a173f75r64c38036b2399ff5@mail.gmail.com>
Dear Prof.
I did a phonon calculation for a p4/nmm crystal at Gamma point
but when I look at the output
file there appares several representation and blocks data of phonon
polarization
Atomic displacements:
There are 16 irreducible representations
Representation 1 2 modes - To be done
Phonon polarizations are as follows:
mode # 1 mode # 2
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( -0.70711 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( -0.70711 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.70711 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.70711 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000 )
( 0.00000 0.00000 ) ( 0.00000 0.00000
I wander how the atoms in the unit cell are displaced, for a real
calculation
what's the relation between polariztion vector and atoms displacements
and the relation between phonon mode , how to use the symmetry group to
get the phonon polarization and atoms displacements pattern , if the
crystal have inversion symmetry ,
so is it correct to say a particular phonon mode have or not have
inversion symmetry.
Can anyone anwser my question , I will be very gratefull .--
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel: + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603 Beijing 100190
China
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From degironc at sissa.it Tue Nov 18 08:57:14 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 18 Nov 2008 08:57:14 +0100
Subject: [Pw_forum] problem with primitive cell
In-Reply-To: <eb9cf0990811172016wbae5beu6723b097ffec0306@mail.gmail.com>
References: <eb9cf0990811172016wbae5beu6723b097ffec0306@mail.gmail.com>
Message-ID: <4922755A.2050009@sissa.it>
Dear Krishna chaitanya ,
the problem with eq 2 is that it defines the surface energy as a
(small) difference between large numbers and tiny inaccuracies in the
calculation of Ebulk (due to different k-point sampling or limited
self-consistency) are amplified by the factor proportional to the number
of layer.
One way the surfare can be calculated is to rewrite eq 2 as
En = n Ebulk + 2 A Ens
and then extract Ebulk and Ens from a linear fit of calculated En for
large enough n.
The slope of the resulting straight line is related to Ebulk and
should be close to the directly calculated value in a bulk cell while
the intersection with the vertical axis gives you the surface energy
(times 2A).
Hope this helps,
Stefano de Gironcoli - SISSA and DEMOCRITOS
Krishna chaitanya wrote:
> Hi,
>
> I am trying to calculate surface energy of MgO surface layers using
> PWSCF. For that i have used 2 methods given as
>
> 1)Ens={En-n(En-En-1)}/2A
> here n=no of layers, En and En-1 are total energies of n and n-1
> layers, A=surface area of primitive cell
>
> 2)Ens=(En-n Ebulk)/2A
> here m=no of primitive units present in surface, Ebulk=total energy
> of primitive unit cell
>
> I have got converged surfae energy 0.004au/bohr**2 by using method 1,
> but by using method 2 i got very different energies and not converged
> by varying number of layers. When i checked with xcrysden the periodic
> repetetion in primitive cell is not good. Initially i have followed by
> cartesian coordinates but the number of symmetry operations observed
> as 1, but when followed by fractional coordinates symmetry operations
> are 48 now.
>
>
> MgO conventional cell is in FCC bravis lattice group and i have used
> the following input for the primitive cell description
>
> &SYSTEM
>
> ibrav = 2,
>
> A = 2.977768,
>
> B = 2.977768,
>
> C = 2.977768,
>
> cosAB = 0.5,
>
> cosAC = 0.5,
>
> cosBC = 0.5,
>
> nat = 2,
>
> ntyp = 2,
>
> ecutwfc = 25,
>
> ecutrho = 200,
>
> /
>
> &ELECTRONS
>
> electron_maxstep = 500,
>
> diago_david_ndim = 6,
>
> /
>
> &IONS
>
> ion_dynamics = 'bfgs',
>
> /
>
> ATOMIC_SPECIES
>
> O 16.000 O.pw91-van_ak.UPF
>
> Mg 24.305 Mg.pw91-np-van.UPF
>
> ATOMIC_POSITIONS crystal
>
> Mg 0.00000000 0.00000000 0.00000000
>
> O 0.50000000 0.50000000 0.50000000
>
> K_POINTS automatic
>
> 4 4 4 0 0 0
>
>
>
> Please suggest me where i have done mistake and thanks in advance
>
> G. Krishna Chaitanya
> Senior research fellow
> C/o Dr. Bhanuprakash K.
> Inorganic Chemistry Division
> Indian Institute of Chemical Technology
> Hyderabad, India
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
From giannozz at democritos.it Tue Nov 18 09:03:28 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 18 Nov 2008 09:03:28 +0100
Subject: [Pw_forum] atoms displacements and symmetry
In-Reply-To: <aa128b2c0811172322p3a173f75r64c38036b2399ff5@mail.gmail.com>
References: <aa128b2c0811172322p3a173f75r64c38036b2399ff5@mail.gmail.com>
Message-ID: <492276D0.6090803@democritos.it>
yumin qian wrote:
> Can anyone anwser my question
surely somebody can, but if you keep asking too many things
at the time, in vague and confused terms, nobody will.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From yuminqian at gmail.com Tue Nov 18 09:25:53 2008
From: yuminqian at gmail.com (yumin qian)
Date: Tue, 18 Nov 2008 16:25:53 +0800
Subject: [Pw_forum] atoms displacements and symmetry
In-Reply-To: <492276D0.6090803@democritos.it>
References: <aa128b2c0811172322p3a173f75r64c38036b2399ff5@mail.gmail.com>
<492276D0.6090803@democritos.it>
Message-ID: <aa128b2c0811180025u340205d6vf04562d9b5f1e8b9@mail.gmail.com>
Thanks , it's very kind of you to give me suggestion about how to ask
question when I have somethind unclear . Thank you very much .
2008/11/18 Paolo Giannozzi <giannozz at democritos.it>
> yumin qian wrote:
>
> > Can anyone anwser my question
>
> surely somebody can, but if you keep asking too many things
> at the time, in vague and confused terms, nobody will.
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Sincerely Y. M. Qian
Lab.of Condensed Matter Theory and Materials Computation
Institute of Physics
Chinese Academy of Sciences
Tel: + 8610 8264 9147
E-Mail:yuminqian at gmail.com <E-Mail%3Ayuminqian at gmail.com>
P.O.Box 603 Beijing 100190
China
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From sunshoutian168 at yahoo.com.cn Tue Nov 18 10:15:20 2008
From: sunshoutian168 at yahoo.com.cn (shoutian sun)
Date: Tue, 18 Nov 2008 17:15:20 +0800 (CST)
Subject: [Pw_forum] error of phonon in example07
Message-ID: <571976.2958.qm@web15301.mail.cnb.yahoo.com>
Dear all,
I have a problem of calculating the example07 in the espresso-4.0.3/examples/.
When I run run_example, error happened as fallows:
running the scf calculation with dense k-point grid... done
running the scf calculation... done
running the el-ph calculation..../run_example: line 176: 21025
$PH_COMMAND <al.elph.in >al.elph.out
Error condition encountered during test: exit status = 134
Could anyone help me?
--------------------------------------------------------------------------
By the way, the computer I am using to compile PWscf is AMD64.
when ./configure, then make all , and the compiling was done.
___________________________________________________________
?????????????????
http://card.mail.cn.yahoo.com/
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From degironc at sissa.it Tue Nov 18 10:27:20 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 18 Nov 2008 10:27:20 +0100
Subject: [Pw_forum] error of phonon in example07
In-Reply-To: <571976.2958.qm@web15301.mail.cnb.yahoo.com>
References: <571976.2958.qm@web15301.mail.cnb.yahoo.com>
Message-ID: <49228A78.1030902@sissa.it>
shoutian sun wrote:
> Dear all,
> I have a problem of calculating the example07 in the
> espresso-4.0.3/examples/.
> When I run run_example, error happened as fallows:
>
> running the scf calculation with dense k-point grid... done
> running the scf calculation... done
> running the el-ph calculation..../run_example: line 176: 21025
> $PH_COMMAND <al.elph.in >al.elph.out
> Error condition encountered during test: exit status = 134
>
Dear Shoutian Sun,
this is the error in the SCRIPT... the (hopefully more informative)
error message in the phonon calculation should be contained in the
al.elph.out file....
Don't forget to add you affiliation in your posts.
best,
Stefano de Gironcoli - SISSA and DEMOCRITOS
> Could anyone help me?
> --------------------------------------------------------------------------
> By the way, the computer I am using to compile PWscf is AMD64.
> when ./configure, then make all , and the compiling was done.
>
>
> ------------------------------------------------------------------------
> ?????????????????
> <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
From vegalew at hotmail.com Tue Nov 18 17:51:52 2008
From: vegalew at hotmail.com (vega lew)
Date: Wed, 19 Nov 2008 00:51:52 +0800
Subject: [Pw_forum] Could you please help me to cope with the
error message
In-Reply-To: <491DA004.9090607@democritos.it>
References: <BAY124-DS45358B5F953046C3888BAA41A0@phx.gbl>
<491DA004.9090607@democritos.it>
Message-ID: <BAY124-W35C2CBCE1A3372610422BBA4120@phx.gbl>
Dear sir,
thank you so much for your suggestions.
> > I am suffering from the error message like this,> > [node1][0,1,12][btl_tcp_frag.c:202:mca_btl_tcp_frag_recv] > > mca_btl_tcp_frag_recv: readv failed with errno=104> > forrtl: error (78): process killed (SIGTERM)> > as explained many times: unless you have evidence of the opposite,> this kind of obscure errors is likely due to buggy compiler or buggy> libraries or even flakey hardware.
My Fortran / C compilers was intel 10.1.015 version. And MKL was 10.0.1.014. I could relax 72 atoms(openmpi) and 120 atoms(MPICH2) successfully using the compilers and MKL. If this version of compilers and MKL was not suitable for my hardware, could you please tell me which compiler and MKL was appropriate for my computers. Which compiler would be best choice for Q-E?
By the way, my clusters have 8 computers composed of intel Q6600 cpu(quadcore), intel S3000AH mother boards, and 8G(2Gx4) physical memory per node (so 64G in total for the whole cluster). The OS was redhat enterprise linux 4 update 4 for x86_64bit, therefore, the em64t verison of compiler and mkl was installed on the system.
> this might indicate a problem with excessive memory requirements
I tested the tasks using openmpi and MPICH2 respectively. QE with MPICH2 could relax 120 atoms, but QE with openmpi could relax 72 atoms. If the memory was not sufficient , why the relaxation of 84 atoms crashed using QE with openmpi but not the case for QE with MPICH2. And why QE with MPICH2 could calculate nearly the twice than the QE with openmpi?
My system to be calculated was composed of 48 Ti atoms 96 O atoms with a slab model. the ultrasoft pseudo(PW91) was downloaded for the pwscf website directly. The ecutwfc and ecutrho was 50 Ry and 500 Ry respectively.
Do you think 64G memory was not enough for such a task?
thank you for reading and kindly advised. I really appreciate your replying.
vega
Vega Lew (weijia liu)PH.D Candidate in Chemical EngineeringState Key Laboratory of Materials-oriented Chemical EngineeringCollege of Chemistry and Chemical EngineeringNanjing University of Technology, 210009, Nanjing, Jiangsu, China> Date: Fri, 14 Nov 2008 16:57:56 +0100> From: giannozz at democritos.it> To: pw_forum at pwscf.org> Subject: Re: [Pw_forum] Could you please help me to cope with the error message> > vega wrote:> > > I am suffering from the error message like this,> > [node1][0,1,12][btl_tcp_frag.c:202:mca_btl_tcp_frag_recv] > > mca_btl_tcp_frag_recv: readv failed with errno=104> > forrtl: error (78): process killed (SIGTERM)> > as explained many times: unless you have evidence of the opposite,> this kind of obscure errors is likely due to buggy compiler or buggy> libraries or even flakey hardware.> > > I could relax 72 atoms successfully with my system using openmpi. But > > when I wanted to relax 84 atoms, the error message stoped my > > calculation. Then I tried the mpich2 using the same system. With the > > help of mpich2 I could relax 120 atoms instead. But the error message > > bothered me again when I wanted to relax 132 atoms.> > this might indicate a problem with excessive memory requirements> > Paolo> -- > Paolo Giannozzi, Democritos and University of Udine, Italy> _______________________________________________> Pw_forum mailing list> Pw_forum at pwscf.org> http://www.democritos.it/mailman/listinfo/pw_forum
_________________________________________________________________
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From vegalew at hotmail.com Tue Nov 18 17:58:52 2008
From: vegalew at hotmail.com (vega lew)
Date: Wed, 19 Nov 2008 00:58:52 +0800
Subject: [Pw_forum] /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so:
warning: warning: feupdateenv is not implemented and will always fail
Message-ID: <BAY124-W2640C47644715796EA4640A4120@phx.gbl>
Dear all,
I recompile the QE 4.0.3 with intel compiler 11.0. I found there was an warning during the "make all" process.
the warning was like this,
"/opt/intel/Compiler/11.0/069/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail"
Do you think the warning will have a bad effect on the QE?
vegaVega Lew (weijia liu)PH.D Candidate in Chemical EngineeringState Key Laboratory of Materials-oriented Chemical EngineeringCollege of Chemistry and Chemical EngineeringNanjing University of Technology, 210009, Nanjing, Jiangsu, China
_________________________________________________________________
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From giannozz at democritos.it Tue Nov 18 18:02:22 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 18 Nov 2008 18:02:22 +0100
Subject: [Pw_forum] /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so:
warning: warning: feupdateenv is not implemented and will always fail
In-Reply-To: <BAY124-W2640C47644715796EA4640A4120@phx.gbl>
References: <BAY124-W2640C47644715796EA4640A4120@phx.gbl>
Message-ID: <4922F51E.7010204@democritos.it>
vega lew wrote:
> I recompile the QE 4.0.3 with intel compiler 11.0.
oh my. Yet another version of the Intel compiler, with new and
better bugs
> I found there was an warning during the "make all" process.
> the warning was like this,
> "/opt/intel/Compiler/11.0/069/lib/intel64/libimf.so: warning: warning:
> feupdateenv is not implemented and will always fail"
> Do you think the warning will have a bad effect on the QE?
no, no effect at all
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From akohlmey at cmm.chem.upenn.edu Tue Nov 18 18:08:47 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 18 Nov 2008 12:08:47 -0500 (EST)
Subject: [Pw_forum] /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so:
warning: warning: feupdateenv is not implemented and will always fail
In-Reply-To: <4922F51E.7010204@democritos.it>
References: <BAY124-W2640C47644715796EA4640A4120@phx.gbl>
<4922F51E.7010204@democritos.it>
Message-ID: <Pine.LNX.4.64.0811181205490.2561@localhost.localdomain>
On Tue, 18 Nov 2008, Paolo Giannozzi wrote:
PG> vega lew wrote:
PG>
PG> > I recompile the QE 4.0.3 with intel compiler 11.0.
PG>
PG> oh my. Yet another version of the Intel compiler, with new and
PG> better bugs
yes. paolo. expect the worst. as far as i know,
this one was a bit 'rushed' to match the release of
the new 'nehalem' processor family (core i7) and
ensure the validity of SPEC benchmark results...
PG>
PG> > I found there was an warning during the "make all" process.
PG> > the warning was like this,
PG> > "/opt/intel/Compiler/11.0/069/lib/intel64/libimf.so: warning: warning:
PG> > feupdateenv is not implemented and will always fail"
PG> > Do you think the warning will have a bad effect on the QE?
PG>
PG> no, no effect at all
not to mention that every effing intel fortran compiler
since version 8.1 or so has been printing this message...
cheers,
axel.
PG>
PG> Paolo
PG>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From vegalew at hotmail.com Tue Nov 18 18:11:16 2008
From: vegalew at hotmail.com (vega lew)
Date: Wed, 19 Nov 2008 01:11:16 +0800
Subject: [Pw_forum] /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so:
warning: warning: feupdateenv is not implemented and will always fail
In-Reply-To: <4922F51E.7010204@democritos.it>
References: <BAY124-W2640C47644715796EA4640A4120@phx.gbl>
<4922F51E.7010204@democritos.it>
Message-ID: <BAY124-W144B621972C672E98CFB9EA4120@phx.gbl>
Dear sir,
> oh my. Yet another version of the Intel compiler, with new and> better bugs
which compiler was best and stable for QE? 9.1? 9.0? and what about the mkl?
if intel was not good enough. Do you think gfortran or other compilers would be better for QE on intel computers?
vega
Vega Lew (weijia liu)PH.D Candidate in Chemical EngineeringState Key Laboratory of Materials-oriented Chemical EngineeringCollege of Chemistry and Chemical EngineeringNanjing University of Technology, 210009, Nanjing, Jiangsu, China> Date: Tue, 18 Nov 2008 18:02:22 +0100> From: giannozz at democritos.it> To: pw_forum at pwscf.org> Subject: Re: [Pw_forum] /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail> > vega lew wrote:> > > I recompile the QE 4.0.3 with intel compiler 11.0.> > oh my. Yet another version of the Intel compiler, with new and> better bugs> > > I found there was an warning during the "make all" process.> > the warning was like this,> > "/opt/intel/Compiler/11.0/069/lib/intel64/libimf.so: warning: warning: > > feupdateenv is not implemented and will always fail"> > Do you think the warning will have a bad effect on the QE?> > no, no effect at all> > Paolo> -- > Paolo Giannozzi, Democritos and University of Udine, Italy> _______________________________________________> Pw_forum mailing list> Pw_forum at pwscf.org> http://www.democritos.it/mailman/listinfo/pw_forum
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From Giovanni.Cantele at na.infn.it Tue Nov 18 18:07:28 2008
From: Giovanni.Cantele at na.infn.it (Giovanni Cantele)
Date: Tue, 18 Nov 2008 18:07:28 +0100
Subject: [Pw_forum] /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so:
warning: warning: feupdateenv is not implemented and will always fail
In-Reply-To: <BAY124-W2640C47644715796EA4640A4120@phx.gbl>
References: <BAY124-W2640C47644715796EA4640A4120@phx.gbl>
Message-ID: <4922F650.5080805@na.infn.it>
vega lew wrote:
> Dear all,
>
> I recompile the QE 4.0.3 with intel compiler 11.0. I found there was
> an warning during the "make all" process.
> the warning was like this,
> "/opt/intel/Compiler/11.0/069/lib/intel64/libimf.so: warning: warning:
> feupdateenv is not implemented and will always fail"
> Do you think the warning will have a bad effect on the QE?
maybe not, if I well remember I found a similar message. Anyway, to my
experience Mr. Google often has
an answer to this kind of questions (disclaimer: an answer is other than
a right answer!!!!)
http://www.ualberta.ca/AICT/RESEARCH/LinuxClusters/doc/icc91/Release_Notes.htm
at this (google-suggested) link I found:
|libimf| Linking Change on Intel EM64T
In some earlier versions of Intel C++ Compiler, applications built for
Intel EM64T linked by default to the dynamic (shared object) version of
|libimf|, even though other libraries were linked statically. In the
current version, |libimf| is linked statically unless |-i-dynamic| is
used. This matches the behavior on IA-32 systems. You should use
|-i-dynamic| to specify the dynamic Intel libraries if you are linking
against shared objects built by Intel compilers.
A side effect of this change is that users may see the following message
from the linker:
|warning: feupdateenv is not implemented and will always fail|
This warning is due to a mismatch of library types and can be ignored.
The warning will not appear if |-i-dynamic| is used.
Giovanni
--
Dr. Giovanni Cantele
Coherentia CNR-INFM and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario di Monte S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Fax: +39 081 676346
E-mail: giovanni.cantele at cnr.it
giovanni.cantele at na.infn.it
Web: http://people.na.infn.it/~cantele
Research Group: http://www.nanomat.unina.it
From akohlmey at cmm.chem.upenn.edu Tue Nov 18 18:26:18 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 18 Nov 2008 12:26:18 -0500 (EST)
Subject: [Pw_forum] /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so:
warning: warning: feupdateenv is not implemented and will always fail
In-Reply-To: <BAY124-W144B621972C672E98CFB9EA4120@phx.gbl>
References: <BAY124-W2640C47644715796EA4640A4120@phx.gbl>
<4922F51E.7010204@democritos.it>
<BAY124-W144B621972C672E98CFB9EA4120@phx.gbl>
Message-ID: <Pine.LNX.4.64.0811181217320.2561@localhost.localdomain>
On Wed, 19 Nov 2008, vega lew wrote:
VL>
VL> Dear sir,
VL>
VL> > oh my. Yet another version of the Intel compiler, with new and> better bugs
VL> which compiler was best and stable for QE? 9.1? 9.0? and what about the mkl?
what on earth makes you think that the compiler is the culprit
of your problems. as paolo suggested, you have to provide _proof_
(to yourself mostly) of what is going wrong.
there are a bunch of issues with intel compilers that have been
discussed here many, many times. if one takes them all into account
there is no harm in using intel. various versions have been working
find for me on a large number of machine and also for codes that are
much more demanding in terms of correctness of the implementation of
fortran95 than Q-E. the key issue is to know what you are doing
and to not push the compiler too far (i.e. reduce the optimization
level and avoid excessive IPO or SSE optimizations). moreover, there
are additional complications with MKL 10 due to the way it multi-threads
across available processors unless OMP_NUM_THREADS is set to 1 on
all machines or one uses the proper linking sequence. all of that
has been discussed here many times and is well documented in the
intel provided documentation.
my suspicion is more that you are running either out of stack memory
or in general out of memory, but that is something that you can
monitor easily (and information of i am using x atoms, or y cutoff
does not help, there are many more parameters that determine how
much memory a calculation requires) and test systematically. since
you don't provide crucial details that allow any qualified statements
you'll have to learn to live with no proper help.
my prediction is that randomly swapping compilers or MPI libraries
will only increase your (and our) confusion, but not provide
any proper resolution.
cheers,
axel.
VL>
VL> if intel was not good enough. Do you think gfortran or other compilers would be better for QE on intel computers?
VL>
VL> vega
VL> Vega Lew (weijia liu)PH.D Candidate in Chemical EngineeringState Key Laboratory of Materials-oriented Chemical EngineeringCollege of Chemistry and Chemical EngineeringNanjing University of Technology, 210009, Nanjing, Jiangsu, China> Date: Tue, 18 Nov 2008 18:02:22 +0100> From: giannozz at democritos.it> To: pw_forum at pwscf.org> Subject: Re: [Pw_forum] /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail> > vega lew wrote:> > > I recompile the QE 4.0.3 with intel compiler 11.0.> > oh my. Yet another version of the Intel compiler, with new and> better bugs> > > I found there was an warning during the "make all" process.> > the warning was like this,> > "/opt/intel/Compiler/11.0/069/lib/intel64/libimf.so: warning: warning: > > feupdateenv is not implemented and will always fail"> > Do you think the warning will have a bad effect on the QE?> > no, no effect at all> > Paolo> -- > Paolo Giannozzi, Democritos and!
University of Udine, Italy> _______________________________________________> Pw_forum mailing list> Pw_forum at pwscf.org> http://www.democritos.it/mailman/listinfo/pw_forum
VL> _________________________________________________________________
VL> Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy!
VL> http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From giannozz at democritos.it Tue Nov 18 18:33:26 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 18 Nov 2008 18:33:26 +0100
Subject: [Pw_forum] /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so:
warning: warning: feupdateenv is not implemented and will always fail
In-Reply-To: <Pine.LNX.4.64.0811181217320.2561@localhost.localdomain>
References: <BAY124-W2640C47644715796EA4640A4120@phx.gbl> <4922F51E.7010204@democritos.it> <BAY124-W144B621972C672E98CFB9EA4120@phx.gbl>
<Pine.LNX.4.64.0811181217320.2561@localhost.localdomain>
Message-ID: <4922FC66.6090805@democritos.it>
Axel Kohlmeyer wrote:
> my suspicion is more that you are running either out of stack
> memory or in general out of memory, but that is something that
> you can monitor easily
well..."you can monitor", ok, but "easily" ... maybe easily
for you, Axel! Anyway: I heard that MPI sometimes allocates
sizable amounts of memory.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From akohlmey at cmm.chem.upenn.edu Tue Nov 18 18:44:18 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 18 Nov 2008 12:44:18 -0500 (EST)
Subject: [Pw_forum] /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so:
warning: warning: feupdateenv is not implemented and will always fail
In-Reply-To: <4922FC66.6090805@democritos.it>
References: <BAY124-W2640C47644715796EA4640A4120@phx.gbl>
<4922F51E.7010204@democritos.it>
<BAY124-W144B621972C672E98CFB9EA4120@phx.gbl>
<Pine.LNX.4.64.0811181217320.2561@localhost.localdomain>
<4922FC66.6090805@democritos.it>
Message-ID: <Pine.LNX.4.64.0811181236570.2561@localhost.localdomain>
On Tue, 18 Nov 2008, Paolo Giannozzi wrote:
PG> Axel Kohlmeyer wrote:
PG>
PG> > my suspicion is more that you are running either out of stack memory or in
PG> > general out of memory, but that is something that
PG> > you can monitor easily
PG>
PG> well..."you can monitor", ok, but "easily" ... maybe easily
PG> for you, Axel! Anyway: I heard that MPI sometimes allocates
PG> sizable amounts of memory.
once has to carefully differentiate between reserved address space
and memory used. the first happens a lot on "RDMA" infrastructures
like infiniband or myrinet. a process may show several GB under VIRT
(when monitoring with top) but the more important columns are
RES and DATA (which may need to be explicitly enabled) which
show the resident set size and the data segment size.
in any case, if we would know what the exact error messages are
and what the exact input was, we could do a much better guess
at what was going on.
axel.
PG>
PG> Paolo
PG>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From ski2 at mail.uh.edu Tue Nov 18 22:12:51 2008
From: ski2 at mail.uh.edu (ski2 at mail.uh.edu)
Date: Tue, 18 Nov 2008 15:12:51 -0600
Subject: [Pw_forum] ultrasoft pseudopotential and direct space analysis
Message-ID: <f60ed36cc02.4922db73@mail.uh.edu>
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Dear users and
developers,
From arunmanna at jncasr.ac.in Wed Nov 19 05:14:30 2008
From: arunmanna at jncasr.ac.in (Arun Kumar Manna)
Date: Wed, 19 Nov 2008 08:14:30 +0400 (RET)
Subject: [Pw_forum] problem with phonon calculation
Message-ID: <37276.172.16.1.1.1227068070.squirrel@172.16.1.1>
Dear All,
I am getting error during calculation of phonon at gamma point.
Error message is following:
Calling punch_plot_e
Writing on file drho
Computing Pc [DH,Drho] |psi>
Derivative coefficient: 0.001000 Threshold: 1.00E-12
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from cdiaghg : error # 176
info =/= 0
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
After successful scf run, for phonon calculation, the following input I
have used.
phonons of Grap at Gamma
&inputph
tr2_ph=1.0d-12,
prefix='grap',
trans=.true.,
lraman=.true.,
amass(1)=12.00,
outdir='/sfs3/usr/local/48atom_grap',
fildyn='grap.dynG',
/
0.0 0.0 0.0
But the above input for phonon calculation is ok for small system(I have
checked with 10 atoms per unit cell).
For my case, the system contains 48 atom per unit cell
Could anyone please help me how will I handled such big system?.
Thanks in advanced,
Arun
--
PhD Student
JNCASR, Bangalore-560064
India
From giannozz at democritos.it Wed Nov 19 11:12:41 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 19 Nov 2008 11:12:41 +0100
Subject: [Pw_forum] problem with phonon calculation
In-Reply-To: <37276.172.16.1.1.1227068070.squirrel@172.16.1.1>
References: <37276.172.16.1.1.1227068070.squirrel@172.16.1.1>
Message-ID: <4923E699.6020500@democritos.it>
Arun Kumar Manna wrote:
> Computing Pc [DH,Drho] |psi>
> ...]
> from cdiaghg : error # 176
> info =/= 0
this is unfortunately one of the worst cases to fix: an error inside
a lapack routine, with no obvious reason (I assume that your system
is ok: otherwise some error would have shown up much earlier). Are
you running in parallel or serially? and what libraries are you using?
sometimes machine-optimized libraries are very fast but not so reliable.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Wed Nov 19 11:17:47 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 19 Nov 2008 11:17:47 +0100
Subject: [Pw_forum] ultrasoft pseudopotential and direct space analysis
In-Reply-To: <f60ed36cc02.4922db73@mail.uh.edu>
References: <f60ed36cc02.4922db73@mail.uh.edu>
Message-ID: <4923E7CB.9070904@democritos.it>
ski2 at mail.uh.edu wrote:
> From the Pw_forum Archives, I learned ultrasoft PPs may not be
> desirable for ELF analysis
it's not that they are not desirable: the complete calculation of
ELF is not implemented
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From igor at ffh.bg.ac.yu Wed Nov 19 10:08:42 2008
From: igor at ffh.bg.ac.yu (Igor Pasti)
Date: Wed, 19 Nov 2008 10:08:42 +0100
Subject: [Pw_forum] question about PDOS
Message-ID: <1227085722.4923d79a41831@mail.ffh.bg.ac.yu>
Dear QE users,
I am dealing with PDOS of some binary alloys using projwfc.x. I am wondering if
there is some cut off radius for projection around atom of interest in order to
reduce PDOS contribution form neighboring atoms (as there is no such parameter
in the input file) or this radius can be considered to be infinite. I know that
some ab initio codes use value of 2 a.u. around atom of interest.
Thank you very much,
Igor
--
Igor Pasti, PhD student, Faculty of Physical Chemistry, Belgrade University
Studentski trg 12, Belgrade
From giannozz at democritos.it Wed Nov 19 12:40:13 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 19 Nov 2008 12:40:13 +0100
Subject: [Pw_forum] problem with phonon calculation
In-Reply-To: <39830.172.16.1.1.1227094169.squirrel@172.16.1.1>
References: <37276.172.16.1.1.1227068070.squirrel@172.16.1.1>
<4923E699.6020500@democritos.it>
<39830.172.16.1.1.1227094169.squirrel@172.16.1.1>
Message-ID: <4923FB1D.4000700@democritos.it>
Arun Kumar Manna wrote:
> I am running in parallel in super computer and that includes
> lapack libraries.
which supercomputer, and which lapack libraries? try to use
internal lapack libraries instead of system libraries
> Please help me to solve this problem?
please stop asking impossible things. I take responsibility
ONLY for bugs in the code. Unless you have evidence that there
is a bug in the code, there is nothing I (or anybody else
working on quantum-espresso) can do.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Thu Nov 20 10:05:54 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 20 Nov 2008 10:05:54 +0100
Subject: [Pw_forum] question about PDOS
In-Reply-To: <1227085722.4923d79a41831@mail.ffh.bg.ac.yu>
References: <1227085722.4923d79a41831@mail.ffh.bg.ac.yu>
Message-ID: <49252872.4070503@democritos.it>
Igor Pasti wrote:
> I am dealing with PDOS of some binary alloys using projwfc.x.
> I am wondering if there is some cut off radius for projection
> around atom of interest in order to reduce PDOS contribution
> from neighboring atoms
there isn't. Projection is performed in reciprocal space.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From nakhmanson at anl.gov Thu Nov 20 00:45:18 2008
From: nakhmanson at anl.gov (Serge Nakhmanson)
Date: Wed, 19 Nov 2008 17:45:18 -0600
Subject: [Pw_forum] matdyn.x: why are input/output k-points in the units of
2pi/a_0?
Message-ID: <4924A50E.6070403@anl.gov>
Dear PWSCF developers,
I have used espresso 3.* and 4.* to do phonon calculations
at various individual k-points in the BZ. My typical
routine was
pw.x (scf) + pw.x (k, nscf) + ph.x (k) + dynmat.x (k)
PW manual for phonon calculations with &PHONON namelist
calls for units of 2pi/a for xqq(i). As I understand, these
are what you call "crystal coordinates" for k-points. So,
for example, xqq = (0.5, 0.5, 0.5) for a tetragonal system
would bring me into a corner of my BZ. All my experience
confirms that this procedure works well and gives me phonons
at the appropriate k-points.
Currently, I am using version 4.0.2 to learn how to compute
phonon dispersions across the BZ. Here, my routine is the
following:
pw.x (scf) + ph.x (k_grid) + q2r.x (to get IFC(r))
Then I use my own script (not kpoints.x) to generate k-point paths
that I feed into matdyn.x to produce the dispersions. The description
of matdyn input says the following about the k-points:
! (q(i,n), i=1,3) nq q-points in 2pi/a units
I automatically assumed that matdyn.x also expects input
k-points in the "crystal coordinates" and produces output
in the same coordinate system. However, now my impression is
that it actually works with k-points that are in what you
call "cartesian in units of 2pi/a_0." E.g., in tetragonal
systems with c != a, when I feed my "crystal" k-points to
matdyn.x, I either do not get full dispersion curves or I
get them repeated many times over (depending on my c/a ratio),
when the Z direction is involved.
I don't know whether such an arrangement is intentional or a
bug (I did not see this among the 4.0.3 bug fixes) but it
surely is confusing and inconvenient (for me, at least), and
it also seems to be inconsistent with the rest of the code.
I fixed my own copy of matdyn.f90 to work in "crystal" coordinates
(simple!) and I dare to suggest that it may be a good idea to make
this change "official," since it will still be a drag fixing this
each time a new version of espresso comes out. However, if it
*has to* operate in 2pi/a_0 units, at least it would be prudent
to put an expanded comment about this into matdyn.f90. A
great alternative option would be to make matdyn.x recognize
both coordinate systems by flipping an input switch.
I have trolled the forum looking for any previous reports of
this problem but found nothing. Still, if you are already aware
of this issue or consider it somewhat insignificant, I would like
to apologize for taking so much of your time (it turned out to be
a relatively long post). And seriously, thank you for your
effort!
THX,
Serge
--
*********************************************************
Serge M. Nakhmanson phone: (630) 252-5205
Assistant Scientist fax: (630) 252-4798
MSD-212, Rm. C-224
Argonne National Laboratory
9700 S. Cass Ave.
Argonne, IL 60439
*********************************************************
From greatnaol at gmail.com Thu Nov 20 12:34:10 2008
From: greatnaol at gmail.com (Naol Regassa)
Date: Thu, 20 Nov 2008 14:34:10 +0300
Subject: [Pw_forum] (no subject)
Message-ID: <97e4b88e0811200334g14d4b703v2923e40bc455e92d@mail.gmail.com>
Dear all
In density of state calculation of Nickel, when I tried to execute
inputpp I got an error which describes, ./pwscf.save non existent. I
did it checking the prefix and outdir again but the same thing happen.
What do you advise me?
Tamene, East Africa
From giannozz at democritos.it Thu Nov 20 13:00:39 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 20 Nov 2008 13:00:39 +0100
Subject: [Pw_forum] matdyn.x: why are input/output k-points in the units
of 2pi/a_0?
In-Reply-To: <4924A50E.6070403@anl.gov>
References: <4924A50E.6070403@anl.gov>
Message-ID: <49255167.6030608@democritos.it>
Serge Nakhmanson wrote:
> PW manual for phonon calculations with &PHONON namelist
> calls for units of 2pi/a for xqq(i). As I understand, these
> are what you call "crystal coordinates" for k-points.
no: crystal coordinates are in units of the crystal axis
of the reciprocal space
> for example, xqq = (0.5, 0.5, 0.5) for a tetragonal system
> would bring me into a corner of my BZ.
I don't think so: xqq = (0.5, 0.5, 0.5*(a/c)) would
> All my experience confirms that this procedure works well
> and gives me phonons at the appropriate k-points.
Very strange
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From yukihiro_okuno at fujifilm.co.jp Thu Nov 20 12:38:46 2008
From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp)
Date: Thu, 20 Nov 2008 20:38:46 +0900
Subject: [Pw_forum] On the UPF file format and pseudo-wave function
Message-ID: <OFF47716D1.FD88EADF-ON49257507.003EB25A-49257507.003FF973@mta.fujifilm.co.jp>
Dear PWSCF users and developer.
I want to know the detail about UPF file.
In the "pseudo_types" Module in PWSCF program,
there are variables chi, and pswfc, and which means pseudo atomic
wave function and what is the difference between chi and pswfc.
On the pswfc, it seems that if values of pswfc is stored in the
calculation,
there must be the tag " has_wfc = "T" " in UPF file and in the example
UPF file, only paw type potential file include such a tag, and also
there are tag "PP_CHI" which is not written in manual of UPF file format.
chi means pseudo-wave function ?
Sincerely.
Yukihiro Okuno.
From paulatto at sissa.it Thu Nov 20 14:26:06 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 20 Nov 2008 14:26:06 +0100
Subject: [Pw_forum] On the UPF file format and pseudo-wave function
In-Reply-To: <OFF47716D1.FD88EADF-ON49257507.003EB25A-49257507.003FF973@mta.fujifilm.co.jp>
References: <OFF47716D1.FD88EADF-ON49257507.003EB25A-49257507.003FF973@mta.fujifilm.co.jp>
Message-ID: <4925656E.4020009@sissa.it>
yukihiro_okuno at fujifilm.co.jp ha scritto:
> chi means pseudo-wave function ?
>
Yes, they are pseudo atomic wavefunctions. They are always saved for PAW
datasets, but they can be always saved by setting the lsave_wfc switch
in the ld1 input file.
This also remind me that should fix the documentation and publish it.
.regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.
Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste
Donations in food, coins, booze and processor time are warmly welcome.
From paulatto at sissa.it Thu Nov 20 14:28:09 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 20 Nov 2008 14:28:09 +0100
Subject: [Pw_forum] (no subject)
In-Reply-To: <97e4b88e0811200334g14d4b703v2923e40bc455e92d@mail.gmail.com>
References: <97e4b88e0811200334g14d4b703v2923e40bc455e92d@mail.gmail.com>
Message-ID: <492565E9.1040501@sissa.it>
Naol Regassa ha scritto:
> Dear all
>
> In density of state calculation of Nickel, when I tried to execute
> inputpp I got an error which describes, ./pwscf.save non existent. I
> did it checking the prefix and outdir again but the same thing happen.
> What do you advise me?
>
if you've sate outdir to the current directory (e.g. "./") or a
relative-path directory (e.g. "./outdir") you must execute pp.x from the
exact same location of pw.x.
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.
Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste
Donations in food, coins, booze and processor time are warmly welcome.
From jameslipd at gmail.com Thu Nov 20 14:40:14 2008
From: jameslipd at gmail.com (Jiaye, Li)
Date: Thu, 20 Nov 2008 21:40:14 +0800
Subject: [Pw_forum] Slab relaxation
Message-ID: <b5d787260811200540i1d433aeg84904586e669cd29@mail.gmail.com>
Dear All
I met with a problem when I am trying to relax the geometry of MgO (001)
slab, the error message occured:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
task # 0
from system_checkin : error # 1
ecutwfc out of range
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Therefore pw.x didn't work. But the test of the examples reported no
problem. I cannot figure out what's wrong with it, could anybody help me?
Thanks in advance.
This is my input file:
&CONTROL
calculation = "relax" ,
pseudo_dir = "/home/blade/jamesli/source/pwscf/espresso-4.0.3/pseudo" ,
outdir = "/home/blade/temp-pwscf" ,
etot_conv_thr = 1.D-4 ,
forc_conv_thr = 1.D-3 ,
nstep = 200 ,
/
&SYSTEM
ibrav = 6 ,
A = 4.2112 ,
B = 4.2112 ,
C = 17.1056 ,
cosAB = 0 ,
cosBC = 0 ,
cosAC = 0 ,
nat = 8,
ntyp = 2,
occupations = "tetrahedra" ,
nspin = 2 ,
/
&ELECTRONS
electron_maxstep = 100,
conv_thr = 1.D-6 ,
/
ATOMIC_SPECIES
Mg 24.3050 Mg.pw91-np-van.UPF
O 15.9994 O.pw91-van_ak.UPF
ATOMIC_POSITIONS
Mg 0.00000 0.50000 0.12309 1 1 1
Mg 0.00000 0.00000 0.00000 0 0 0
Mg 0.50000 0.50000 0.00000 0 0 0
Mg 0.50000 0.00000 0.12309 1 1 1
O 0.50000 0.00000 0.00000 0 0 0
O 0.50000 0.50000 0.12309 1 1 1
O 0.00000 0.00000 0.12309 1 1 1
O 0.00000 0.50000 0.00000 0 0 0
K_POINTS {automatic}
2 2 1 0 0 0
--
Sincerely
Jiaye Li
==============================================
Li, Jiaye
M.S. in designing and developing novel materials
Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids
Skills:
*ab-initial method, DFT simulation and Force Field simulation
Please contact me at:
1. jameslipd at gmail.com or
2. jameslibd at gmail.com
==============================================
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From giannozz at democritos.it Thu Nov 20 14:56:02 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 20 Nov 2008 14:56:02 +0100
Subject: [Pw_forum] Slab relaxation
In-Reply-To: <b5d787260811200540i1d433aeg84904586e669cd29@mail.gmail.com>
References: <b5d787260811200540i1d433aeg84904586e669cd29@mail.gmail.com>
Message-ID: <49256C72.4040507@democritos.it>
Jiaye, Li wrote:
> ecutwfc out of range
> Therefore pw.x didn't work. But the test of the examples reported no
> problem. I cannot figure out what's wrong with it
you need to set a value for the cutoff, "ecutwfc". It is one of
the handful of parameters that MUST be specified in input
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From paulatto at sissa.it Thu Nov 20 14:56:12 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 20 Nov 2008 14:56:12 +0100
Subject: [Pw_forum] Slab relaxation
In-Reply-To: <b5d787260811200540i1d433aeg84904586e669cd29@mail.gmail.com>
References: <b5d787260811200540i1d433aeg84904586e669cd29@mail.gmail.com>
Message-ID: <49256C7C.7010606@sissa.it>
Jiaye, Li ha scritto:
> ecutwfc out of range
Dear Li Jiaye,
the ecutwfc (energy cutoff for plane expansion of wavefunctions)
parameter is compulsory, there is no default for it as it depends on the
pseudopotentials you're using. Please refer to documentation and
examples for details.
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.
Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste
Donations in food, coins, booze and processor time are warmly welcome.
From eyvaz_isaev at yahoo.com Thu Nov 20 15:00:46 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 20 Nov 2008 06:00:46 -0800 (PST)
Subject: [Pw_forum] Slab relaxation
In-Reply-To: <b5d787260811200540i1d433aeg84904586e669cd29@mail.gmail.com>
Message-ID: <367569.86589.qm@web65712.mail.ac4.yahoo.com>
Hi,
You did not specify neither ecutwfc, nor ecutrho. Please search in PWSCF forum how to choose them.
Besides, I never heard about magnetism in MgO, so, nspin=2 is not required. Nevertheless, if you are absolutely sure MgO(001) surface has magnetic moments, then you should specify starting_magnetization keyword, otherwise you waste time, as by default starting_magnetazion()=0.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
--- On Thu, 11/20/08, Jiaye, Li <jameslipd at gmail.com> wrote:
> From: Jiaye, Li <jameslipd at gmail.com>
> Subject: [Pw_forum] Slab relaxation
> To: pw_forum at pwscf.org
> Date: Thursday, November 20, 2008, 4:40 PM
> Dear All
>
> I met with a problem when I am trying to relax the geometry
> of MgO (001)
> slab, the error message occured:
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> task # 0
> from system_checkin : error # 1
> ecutwfc out of range
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Therefore pw.x didn't work. But the test of the
> examples reported no
> problem. I cannot figure out what's wrong with it,
> could anybody help me?
> Thanks in advance.
>
> This is my input file:
> &CONTROL
> calculation = "relax" ,
> pseudo_dir =
> "/home/blade/jamesli/source/pwscf/espresso-4.0.3/pseudo"
> ,
> outdir = "/home/blade/temp-pwscf" ,
> etot_conv_thr = 1.D-4 ,
> forc_conv_thr = 1.D-3 ,
> nstep = 200 ,
> /
> &SYSTEM
> ibrav = 6 ,
> A = 4.2112 ,
> B = 4.2112 ,
> C = 17.1056 ,
> cosAB = 0 ,
> cosBC = 0 ,
> cosAC = 0 ,
> nat = 8,
> ntyp = 2,
> occupations = "tetrahedra" ,
> nspin = 2 ,
> /
> &ELECTRONS
> electron_maxstep = 100,
> conv_thr = 1.D-6 ,
> /
> ATOMIC_SPECIES
> Mg 24.3050 Mg.pw91-np-van.UPF
> O 15.9994 O.pw91-van_ak.UPF
> ATOMIC_POSITIONS
> Mg 0.00000 0.50000 0.12309 1 1 1
> Mg 0.00000 0.00000 0.00000 0 0 0
> Mg 0.50000 0.50000 0.00000 0 0 0
> Mg 0.50000 0.00000 0.12309 1 1 1
> O 0.50000 0.00000 0.00000 0 0 0
> O 0.50000 0.50000 0.12309 1 1 1
> O 0.00000 0.00000 0.12309 1 1 1
> O 0.00000 0.50000 0.00000 0 0 0
> K_POINTS {automatic}
> 2 2 1 0 0 0
>
>
> --
> Sincerely
>
> Jiaye Li
>
>
>
> ==============================================
> Li, Jiaye
>
> M.S. in designing and developing novel materials
>
> Research experience:
> *ALD precursor. ie. Metal complexes
> *Surface modification. ie. Indium tin oxide, SiO2
> *Gas storage and adsorption. ie. Ionic Liquids
>
> Skills:
> *ab-initial method, DFT simulation and Force Field
> simulation
>
> Please contact me at:
> 1. jameslipd at gmail.com or
> 2. jameslibd at gmail.com
>
> ==============================================
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
From calderin at physics.queensu.ca Thu Nov 20 22:52:29 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Thu, 20 Nov 2008 16:52:29 -0500 (EST)
Subject: [Pw_forum] IBM JS20 pw tests problems
Message-ID: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
Hello everyone,
I am getting some large discrepancies and errors when executing pw tests
on a couple of ibms clusters. Here is a report for the first one.
This is the arch.:
Machine: IBM JS20 Blade Center
OS: Linux 2.6.5-7.244-pseries64
Compilers: xlf suite 10.1
espresso 4.0.3, configured with ARCH = ppc64, make.sys file modified to
account for missing stuff (an example for the serial version is attached).
All parallel and serial version, with or without optimization, give the
same errors or discrepancies in the pw tests suite. The same errors are
also reproduced when using espresso's blas and lapack. A log of the pw
tests is attached.
Main problems:
Apart from some large discrepancies these are the most colorful errors:
- berry tests ask to increase ecutrho
- paw-atom_l=2 blows up with a segmentation fault
I thought that the tests my be outdated but they work fine on Linux/Intel
Clusters Tool/Mkl.
I could not find any reports on these problems.
The segmentation fault may be a compiler problem but what about all the rest.
Thanks,
Lazaro
--
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario K7L 3N6, Canada
+1 613 533 6000 ext 74811
calderin at physics.queensu.ca
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From akohlmey at cmm.chem.upenn.edu Thu Nov 20 23:12:40 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 20 Nov 2008 17:12:40 -0500 (EST)
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
Message-ID: <Pine.LNX.4.64.0811201704580.2387@localhost.localdomain>
On Thu, 20 Nov 2008, Lazaro Calderin wrote:
LC> Hello everyone,
hello lazaro,
LC> I am getting some large discrepancies and errors when executing pw tests
LC> on a couple of ibms clusters. Here is a report for the first one.
actually, the discrepancies are not _that_ large, and
most likely due the fact that the reference was run with
fftw as FFT library, while you are using ESSL. fftw supports
many more FFT grid sizes than ESSL and as a consequence
you have differences in energies. try compiling without ESSL
and against the shipped internal fft and see if you still
have those differences...
LC>
LC> This is the arch.:
LC>
LC> Machine: IBM JS20 Blade Center
LC> OS: Linux 2.6.5-7.244-pseries64
LC> Compilers: xlf suite 10.1
LC>
LC> espresso 4.0.3, configured with ARCH = ppc64, make.sys file modified to
LC> account for missing stuff (an example for the serial version is attached).
LC>
LC> All parallel and serial version, with or without optimization, give the
LC> same errors or discrepancies in the pw tests suite. The same errors are
which confirms my comments about the fft grids causing the
energy differences.
LC> also reproduced when using espresso's blas and lapack. A log of the pw
LC> tests is attached.
LC>
LC> Main problems:
LC> Apart from some large discrepancies these are the most colorful errors:
LC>
LC> - berry tests ask to increase ecutrho
LC> - paw-atom_l=2 blows up with a segmentation fault
those need to be investigated in more detail. the ecutrho
thing may be related to the grid sizes (check and compare
the two output files for the fft grids). the paw problem
should not happen, but this is rather new code. since you
get a segfault, it would be helpful, if you could trigger
a coredump and provide a stack trace, so that the author
of the code can have a closer look...
LC> I thought that the tests my be outdated but they work fine on Linux/Intel
LC> Clusters Tool/Mkl.
LC>
LC> I could not find any reports on these problems.
LC> The segmentation fault may be a compiler problem but what about all
LC> the rest.
true, but making code work with multiple compilers is usually
a good thing. some compilers are overly forgiving towards
some programming practices that are not 100% standard. it is
always helpfult to track these issues down...
cheers,
axel.
LC>
LC> Thanks,
LC> Lazaro
LC>
LC>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From yaldachem at gmail.com Fri Nov 21 11:01:58 2008
From: yaldachem at gmail.com (yaldaa kh)
Date: Fri, 21 Nov 2008 02:01:58 -0800
Subject: [Pw_forum] (no subject)
Message-ID: <47431d9f0811210201p24b096c4wb08f3f5f10add139@mail.gmail.com>
Dear all new friends
I am msc. student in chemistry and my thesis is about adsorption of gases on
transient metal surface(teoretical).Please guide me to do this.start from
where?tell me some reference to explain surface compu.
thanks a lot
yalda.
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From giannozz at democritos.it Fri Nov 21 11:15:52 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 21 Nov 2008 11:15:52 +0100
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
Message-ID: <49268A58.4090107@democritos.it>
Lazaro Calderin wrote:
> I am getting some large discrepancies and errors when executing pw
> tests on a couple of ibms clusters.
no, you are getting many small discrepancies (none of which seems to
me serious) and two errors, namely:
> - berry tests ask to increase ecutrho
> - paw-atom_l=2 blows up with a segmentation fault
that deserve to be investigated. It is hard to say more without at
least the output files (berry.out and paw-atom_l=2.out), though,
or even better, some more precise pointer to what went wrong.
Q-E sort of works on recent Linux IBM machines with xlf compiler,
but it is of course much less tested than on PC-class machines.
By the way: if you run on the MareNostrum Barcelona supercomputer,
use "./configure ARCH=ppc64-mn"
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Fri Nov 21 12:40:35 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 21 Nov 2008 12:40:35 +0100
Subject: [Pw_forum] On the UPF file format and pseudo-wave function
In-Reply-To: <OFF47716D1.FD88EADF-ON49257507.003EB25A-49257507.003FF973@mta.fujifilm.co.jp>
References: <OFF47716D1.FD88EADF-ON49257507.003EB25A-49257507.003FF973@mta.fujifilm.co.jp>
Message-ID: <49269E33.30903@democritos.it>
yukihiro_okuno at fujifilm.co.jp wrote:
> I want to know the detail about UPF file.
available documentation (not guaranteed to be updated) here:
http://www.quantum-espresso.org/wiki/index.php/UPF
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From jorge.gallardo at cab.cnea.gov.ar Fri Nov 21 13:34:29 2008
From: jorge.gallardo at cab.cnea.gov.ar (jorge.gallardo at cab.cnea.gov.ar)
Date: Fri, 21 Nov 2008 10:34:29 -0200 (ARST)
Subject: [Pw_forum] electronic density
In-Reply-To: <49269E33.30903@democritos.it>
References: <OFF47716D1.FD88EADF-ON49257507.003EB25A-49257507.003FF973@mta.fujifilm.co.jp>
<49269E33.30903@democritos.it>
Message-ID: <45023.200.0.233.50.1227270869.squirrel@mail.cab.cnea.gov.ar>
hello!
somebody knows if there is a way to get the average electronic density
(the same if it was a jellium) of a crystal in the files x.y.out from
pw.x, pp.x, etc... ?
thanks
jorge
From baroni at sissa.it Fri Nov 21 14:27:19 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 21 Nov 2008 14:27:19 +0100
Subject: [Pw_forum] electronic density
In-Reply-To: <45023.200.0.233.50.1227270869.squirrel@mail.cab.cnea.gov.ar>
References: <OFF47716D1.FD88EADF-ON49257507.003EB25A-49257507.003FF973@mta.fujifilm.co.jp>
<49269E33.30903@democritos.it>
<45023.200.0.233.50.1227270869.squirrel@mail.cab.cnea.gov.ar>
Message-ID: <9966E640-05A8-4CA9-BCF8-B903C30F9A5E@sissa.it>
(number of electrons in the unit cell) / (volume of the unit cell)
no need of quantum espresso, not even of a computer
SB
On Nov 21, 2008, at 1:34 PM, jorge.gallardo at cab.cnea.gov.ar wrote:
> hello!
> somebody knows if there is a way to get the average electronic density
> (the same if it was a jellium) of a crystal in the files x.y.out from
> pw.x, pp.x, etc... ?
>
> thanks
>
> jorge
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
La morale est une logique de l'action comme la logique est une morale
de la pens?e - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From jorge.gallardo at cab.cnea.gov.ar Fri Nov 21 15:08:37 2008
From: jorge.gallardo at cab.cnea.gov.ar (jorge.gallardo at cab.cnea.gov.ar)
Date: Fri, 21 Nov 2008 12:08:37 -0200 (ARST)
Subject: [Pw_forum] electronic density
In-Reply-To: <9966E640-05A8-4CA9-BCF8-B903C30F9A5E@sissa.it>
References: <OFF47716D1.FD88EADF-ON49257507.003EB25A-49257507.003FF973@mta.fujifilm.co.jp>
<49269E33.30903@democritos.it>
<45023.200.0.233.50.1227270869.squirrel@mail.cab.cnea.gov.ar>
<9966E640-05A8-4CA9-BCF8-B903C30F9A5E@sissa.it>
Message-ID: <38716.200.0.233.50.1227276517.squirrel@mail.cab.cnea.gov.ar>
> (number of electrons in the unit cell) / (volume of the unit cell)
>
> no need of quantum espresso, not even of a computer
> SB
>
> On Nov 21, 2008, at 1:34 PM, jorge.gallardo at cab.cnea.gov.ar wrote:
>
I'm sorry, I was very synthetic in my question before. I did mean:
1) supposing we are using pseudo-potentials (I think pw.x not), the
electron density taking into account only the valence electrons (as is
considered by some [what?] pseudopotential program in quantum espresso).
2) If we are relaxing the crystal structure (from what we don't known but
only an approximation of lattice parameter), there is a way to get the
electron density from the output files?
thanks
From sclauzer at sissa.it Fri Nov 21 15:41:20 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Fri, 21 Nov 2008 15:41:20 +0100
Subject: [Pw_forum] antiferro
In-Reply-To: <878548.37520.qm@web33108.mail.mud.yahoo.com>
References: <878548.37520.qm@web33108.mail.mud.yahoo.com>
Message-ID: <4926C890.7030708@sissa.it>
ali kazempoor wrote:
> Daer all
> I start the ferromagnetic calculation for the slab of MnAs containing 7 layer,but after
>
> finishing the run , the spin polarization of Mn atoms in surface rotate in 180
> and make the layer antiferromagnetic ,are this feasible?
Actually I don't know anything about the physics of your system, but since the spin
polarization in collinear calculations is a scalar between -1 and 1, I would reply yes, it
is possible to find opposite spin polarization on non equivalent atoms.
> starting_magnetization(1) = 3.0,
> starting_magnetization(2) = 0.01,
Be careful of your value of starting_magnetization(1)! It must between -1 and 1! I thought
that the program would perform a check, but I see that this is not the case. You should
find this warning in your output file:
Initial potential from superposition of free atoms
Check: negative starting charge=(component1): -0.009305
Check: negative starting charge=(component2): -193.251520
which I don't know if it is later treated properly in the code. So I suggest you to start
with a correct value of magnetization.
> degauss = 0.02 ,
This may be not small enough for spin polarized calculations, please check convergence.
> diagonalization=''
> mixing_mode = 'plain'
> electron_maxstep = 300,
you do not need to specify these fields, and you should not unless you know exactly what
are the consequences. Defaults are usually good
> conv_thr = .0001 ,
This looks too small to me. The default is 10^-6, but some people uses even 10^-8
Regards,
GS
--
La legge n. 133 uccide l'Universit? e la Ricerca italiana!
Save Italian Brains! (http://saveitalianbrains.wordpress.com/)
o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student |
| c/o: SISSA & CNR-INFM Democritos, |
| via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511 |
| skype: gurlonotturno |
o ------------------------------------------------ o
From sclauzer at sissa.it Fri Nov 21 15:56:49 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Fri, 21 Nov 2008 15:56:49 +0100
Subject: [Pw_forum] electronic density
In-Reply-To: <38716.200.0.233.50.1227276517.squirrel@mail.cab.cnea.gov.ar>
References: <OFF47716D1.FD88EADF-ON49257507.003EB25A-49257507.003FF973@mta.fujifilm.co.jp> <49269E33.30903@democritos.it> <45023.200.0.233.50.1227270869.squirrel@mail.cab.cnea.gov.ar> <9966E640-05A8-4CA9-BCF8-B903C30F9A5E@sissa.it>
<38716.200.0.233.50.1227276517.squirrel@mail.cab.cnea.gov.ar>
Message-ID: <4926CC31.5030502@sissa.it>
jorge.gallardo at cab.cnea.gov.ar wrote:
>> (number of electrons in the unit cell) / (volume of the unit cell)
>>
>> no need of quantum espresso, not even of a computer
>> SB
>>
>> On Nov 21, 2008, at 1:34 PM, jorge.gallardo at cab.cnea.gov.ar wrote:
>>
>
> I'm sorry, I was very synthetic in my question before. I did mean:
>
> 1) supposing we are using pseudo-potentials (I think pw.x not),
Actually you are. Pseudopotentials are always used for each of the species you have in
your system
> the
> electron density taking into account only the valence electrons (as is
> considered by some [what?] pseudopotential program in quantum espresso).
The number of electrons on output is the number of valence electrons.
>
> 2) If we are relaxing the crystal structure (from what we don't known but
> only an approximation of lattice parameter), there is a way to get the
> electron density from the output files?
The same way as before, if you use variable cell relax at each relaxations step the volume
changes and so the electron density (according to the formula above).
GS
>
>
> thanks
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
La legge n. 133 uccide l'Universit? e la Ricerca italiana!
Save Italian Brains! (http://saveitalianbrains.wordpress.com/)
o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student |
| c/o: SISSA & CNR-INFM Democritos, |
| via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511 |
| skype: gurlonotturno |
o ------------------------------------------------ o
From schmidt at chem.wisc.edu Fri Nov 21 15:59:22 2008
From: schmidt at chem.wisc.edu (JR Schmidt)
Date: Fri, 21 Nov 2008 08:59:22 -0600
Subject: [Pw_forum] Problems with integrated charge for a large supercell
relaxation
Message-ID: <4926CCCA.8030504@chem.wisc.edu>
I am having problems with a calculation repeatedly aborting during a
supercell relaxation. After MANY successful (force / displacement)
iterations, and when the force on the atoms is quite small (i.e. near
convergence of the optimization), the calculation aborts with the error:
WARNING: integrated charge= 405.28031513, expected= 408.00000000
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from electrons : error # 1
charge is wrong
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I checked the archives, and this problem has come up before for
supercell calculations. I realize that the most obvious explanations are:
(1) Bad geometry
(2) Bad cutoffs
With regards to (1), I have essentially ruled out by:
* Checking the geometry in xcrysden.
* Noting that if I restart the relaxation from the final geometry of
the failed relaxation, the resulting SCF converges just fine, and the
optimization continues (although the approximate Hessian is lost, so the
optimization does not proceed very well).
With regards to (2), I am using an ultrasoft PP. For ectuwfc I am using
30 Ry, which works fine for all the SCF calculations. I tried
increasing ecutrho from 200 Ry to 300 Ry (which I think is quite
conservative) to no avail.
Is there something happening in the course of the optimization (say, for
example, an atom moving from one side of the unit cell to another across
the boundary?) that would render the previous charge density a horrible
guess, and cause the optimization to bomb out?
I don't think the optimization itself is leading to unreasonable
geometries, as I looked at the final result (right before the crash); it
looks fine. Also, as I mentioned, I can successfully restart
('from_scratch', but with the final geometry) the optimization from that
point.
Thanks for any guidance.
--
J.R. Schmidt
Assistant Professor of Chemistry
Room 8305D
Department of Chemistry
University of Wisconsin-Madison
1101 University Ave
Madison, WI 53706
Phone: (608) 262-2996
Fax: (608) 262-9918
E-mail: schmidt at chem.wisc.edu
http://www.chem.wisc.edu/people/profiles/schmidt.php
From paulatto at sissa.it Fri Nov 21 16:05:43 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Fri, 21 Nov 2008 16:05:43 +0100
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
Message-ID: <4926CE47.3090707@sissa.it>
Lazaro Calderin ha scritto:
> - paw-atom_l=2 blows up with a segmentation fault
> The segmentation fault may be a compiler problem but what about all the rest.
>
Il may be, but I'm not really sure. I have access to an xlf 10.01
compiler myself, I will run some example and see what happens. Thank you
for reporting.
bye
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.
Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste
Donations in food, coins, booze and processor time are warmly welcome.
From sclauzer at sissa.it Fri Nov 21 16:13:47 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Fri, 21 Nov 2008 16:13:47 +0100
Subject: [Pw_forum] Problems with integrated charge for a large
supercell relaxation
In-Reply-To: <4926CCCA.8030504@chem.wisc.edu>
References: <4926CCCA.8030504@chem.wisc.edu>
Message-ID: <4926D02B.5070202@sissa.it>
JR Schmidt wrote:
> I am having problems with a calculation repeatedly aborting during a
> supercell relaxation. After MANY successful (force / displacement)
> iterations, and when the force on the atoms is quite small (i.e. near
> convergence of the optimization), the calculation aborts with the error:
>
> WARNING: integrated charge= 405.28031513, expected= 408.00000000
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> from electrons : error # 1
> charge is wrong
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> I checked the archives, and this problem has come up before for
> supercell calculations. I realize that the most obvious explanations are:
>
> (1) Bad geometry
> (2) Bad cutoffs
Maybe I'm wrong, but this could happen also if your charge density and/or wfc files are
not written correctly in the outdir. Is your problem reproducible, or did it happen just
only once?
If it is reproducible, please specify version of QE, input file and exact point of crash
in the program (i.e. first diagonalization step or before diagonalization or etc.).
GS
>
> With regards to (1), I have essentially ruled out by:
> * Checking the geometry in xcrysden.
> * Noting that if I restart the relaxation from the final geometry of
> the failed relaxation, the resulting SCF converges just fine, and the
> optimization continues (although the approximate Hessian is lost, so the
> optimization does not proceed very well).
>
> With regards to (2), I am using an ultrasoft PP. For ectuwfc I am using
> 30 Ry, which works fine for all the SCF calculations. I tried
> increasing ecutrho from 200 Ry to 300 Ry (which I think is quite
> conservative) to no avail.
>
> Is there something happening in the course of the optimization (say, for
> example, an atom moving from one side of the unit cell to another across
> the boundary?) that would render the previous charge density a horrible
> guess, and cause the optimization to bomb out?
>
> I don't think the optimization itself is leading to unreasonable
> geometries, as I looked at the final result (right before the crash); it
> looks fine. Also, as I mentioned, I can successfully restart
> ('from_scratch', but with the final geometry) the optimization from that
> point.
>
> Thanks for any guidance.
>
--
La legge n. 133 uccide l'Universit? e la Ricerca italiana!
Save Italian Brains! (http://saveitalianbrains.wordpress.com/)
o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student |
| c/o: SISSA & CNR-INFM Democritos, |
| via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511 |
| skype: gurlonotturno |
o ------------------------------------------------ o
From giannozz at democritos.it Fri Nov 21 16:25:30 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 21 Nov 2008 16:25:30 +0100
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
Message-ID: <4926D2EA.3000901@democritos.it>
Lazaro Calderin wrote:
> - berry tests ask to increase ecutrho
remove the option tqr=.true., calculating the augmentation functions
in real space. It is really useful with ultrasoft PP's, when it works,
but sometimes it doesn't. There might be a bug that is triggered by
the different FFT grid wrt to the test case
> - paw-atom_l=2 blows up with a segmentation fault
works on a sp5 with xlf v. 10
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Fri Nov 21 16:27:23 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 21 Nov 2008 16:27:23 +0100
Subject: [Pw_forum] Problems with integrated charge for a large
supercell relaxation
In-Reply-To: <4926CCCA.8030504@chem.wisc.edu>
References: <4926CCCA.8030504@chem.wisc.edu>
Message-ID: <4926D35B.8000306@democritos.it>
JR Schmidt wrote:
> from electrons : error # 1
> charge is wrong
did you look for signs of strange things happening in the
diagonalization (e.g. a large number of states not converged)
immediately before th ecrash?
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From schmidt at chem.wisc.edu Fri Nov 21 16:27:37 2008
From: schmidt at chem.wisc.edu (JR Schmidt)
Date: Fri, 21 Nov 2008 09:27:37 -0600
Subject: [Pw_forum] Problems with integrated charge for a large
supercell relaxation
In-Reply-To: <4926D02B.5070202@sissa.it>
References: <4926CCCA.8030504@chem.wisc.edu> <4926D02B.5070202@sissa.it>
Message-ID: <4926D369.9020903@chem.wisc.edu>
> Maybe I'm wrong, but this could happen also if your charge density and/or wfc files are
> not written correctly in the outdir. Is your problem reproducible, or did it happen just
> only once?
>
>
I have not tried to reproduce the problem (i.e. restarting with the
exact same input file, and checking whether the calculation crashes at
the exact same location). However it is reproducible that I have
restarted the optimization from the final geometry of a crash, and I
(eventually) get another crash to some point in that optimization. I
have repeated this process several times in trying to get the
optimization completely converged.
> If it is reproducible, please specify version of QE, input file and exact point of crash
> in the program (i.e. first diagonalization step or before diagonalization or etc.).
>
This is Quantum Espresso 4.0.3, built using Intel compiler (10.0.023)
and MKL. I don't have the EXACT input file (sorry, I pasted in the
final geometry, and restarted the calculation, as I have done several
times before), but I have attached the most recent copy. The only
change is the updated geometry. (It has bombed with several different
starting geometries, so I don't think this should matter too much).
Here is the tail end out the output file ( a bit long, since there are
102 atoms). To my eye it appears to bomb out either during (or after)
the first SCF iteration at the new geometry. I just restarted from this
geometry, and the SCF appears to be converging fine (on iteration 7).
......
atom 101 type 3 force = -0.00140546 0.00260677 -0.00229403
atom 102 type 4 force = 0.00113588 -0.00072455 0.00196843
Total force = 0.022483 Total SCF correction = 0.000528
number of scf cycles = 16
number of bfgs steps = 14
energy old = -2431.4214008699 Ry
energy new = -2431.4219781799 Ry
CASE: energy _new < energy _old
new trust radius = 0.2665190437 bohr
new conv_thr = 0.0000004229 Ry
ATOMIC_POSITIONS (crystal)
O -0.329526429 -0.408808816 -0.012099766
O -0.434130483 -0.133157596 -0.214645373
O -0.431633645 -0.137892036 -0.006222829
O -0.278739310 -0.137128307 -0.090430586
O -0.100796783 -0.133159579 -0.214645086
H -0.441325581 -0.252176776 -0.233419076
H -0.411465954 -0.261947028 -0.009668170
H -0.293198596 -0.263177630 -0.067937580
H -0.107996346 -0.252172931 -0.233425559
O -0.416139923 0.128063905 0.318233951
O -0.387554176 0.130743077 -0.095310465
O -0.231602139 0.121569046 -0.208319176
O -0.385187700 0.130283862 0.092084327
O -0.228069787 0.124872768 -0.000766583
H -0.414453983 0.240587177 0.346900657
H -0.387329888 0.256725038 -0.095834561
H -0.222947359 0.237077505 -0.231649927
H -0.386094008 0.256259527 0.086575194
H -0.226779193 0.250970084 0.001914462
Mg -0.330991031 -0.014427540 -0.192166380
Mg -0.497243217 -0.030011345 0.093631363
Al -0.331794917 -0.000095089 -0.000003813
Mg -0.165624155 -0.016743806 -0.112469566
H -0.324402886 0.485070589 -0.046289780
O -0.082806392 0.128072098 0.318229105
O -0.054221084 0.130739878 -0.095310811
O 0.101730579 0.121568812 -0.208320229
O 0.250526744 0.128071895 0.318229999
H -0.081114562 0.240578345 0.346910401
H -0.053997473 0.256722791 -0.095833694
H 0.110387035 0.237074293 -0.231653767
H 0.252220884 0.240568947 0.346919719
Mg 0.002342215 -0.014428825 -0.192166459
O -0.486233882 -0.424944563 0.282468035
O -0.152902975 -0.424923950 0.282492893
O -0.448007797 -0.126099255 0.206038361
O -0.283488958 -0.136554136 0.094529944
O -0.098299797 -0.137895360 -0.006223184
O -0.257561493 -0.101812753 0.317114709
O -0.114674360 -0.126099495 0.206038458
H -0.467450272 -0.317062175 0.248499575
H -0.291008934 -0.260107629 0.078208802
H -0.078129058 -0.261950747 -0.009670096
H -0.248296246 -0.226700066 0.324685699
H -0.134117474 -0.317064934 0.248508527
O -0.229665447 0.139240693 0.203078789
H -0.233063301 0.263904916 0.196793737
Al -0.501107767 0.009829988 0.278096233
Mg -0.336471868 -0.016800421 0.208322765
Mg -0.163909767 -0.030017008 0.093629991
Al -0.167774872 0.009833816 0.278094317
H -0.494739902 0.490454516 0.236028417
H -0.161399446 0.490435633 0.236068761
O 0.003804988 -0.408812995 -0.012106498
O 0.337138877 -0.408804925 -0.012093574
O 0.180427795 -0.424925471 0.282486058
O 0.054594580 -0.137128116 -0.090430868
O 0.232535390 -0.133160703 -0.214644526
O 0.049845721 -0.136538951 0.094532164
O 0.235033412 -0.137890297 -0.006222681
O 0.387927780 -0.137129390 -0.090429923
O 0.075771524 -0.101811984 0.317115958
O 0.218657640 -0.126095548 0.206037887
O 0.383177974 -0.136551218 0.094530340
H 0.040133700 -0.263179077 -0.067937349
H 0.225335947 -0.252174684 -0.233424395
H 0.042325773 -0.260119034 0.078212695
H 0.255202765 -0.261945796 -0.009665528
H 0.373468841 -0.263176671 -0.067936303
H 0.085034231 -0.226700669 0.324685923
H 0.199212753 -0.317065153 0.248503220
H 0.375657119 -0.260105586 0.078209622
O -0.051853965 0.130283000 0.092084073
O 0.105261922 0.124873294 -0.000766854
O 0.279112337 0.130741515 -0.095311270
O 0.103667183 0.139245587 0.203079965
O 0.281479746 0.130286931 0.092084294
H -0.052759999 0.256257517 0.086573734
H 0.106548978 0.250973287 0.001912919
H 0.279338295 0.256723045 -0.095839763
H 0.100263104 0.263910378 0.196803259
H 0.280573963 0.256261905 0.086574484
Al 0.001538118 -0.000097303 -0.000004398
Mg 0.167708308 -0.016742424 -0.112469608
Mg 0.335675475 -0.014432215 -0.192166679
Mg -0.003138919 -0.016797335 0.208322152
Mg 0.169422697 -0.030009048 0.093629753
Al 0.334871513 -0.000093607 -0.000003512
Al 0.165557590 0.009835476 0.278095025
Mg 0.330195719 -0.016800923 0.208321902
H 0.008911038 0.485090356 -0.046320964
H 0.342249011 0.485073821 -0.046284985
H 0.171967586 0.490411142 0.236064816
O 0.435063458 0.121565766 -0.208319977
O 0.438596656 0.124875637 -0.000767504
O 0.437002567 0.139241010 0.203081804
H 0.443718781 0.237073493 -0.231652853
H 0.439886884 0.250971398 0.001913823
H 0.433598762 0.263906152 0.196807410
Mg 0.501042400 -0.016741373 -0.112469566
O 0.409105089 -0.101818787 0.317114407
H 0.418368050 -0.226706829 0.324683215
Writing output data file pwscf.save
Check: negative starting charge= -0.002078
NEW-OLD atomic charge density approx. for the potential
Check: negative starting charge= -0.002019
negative rho (up, down): 0.997E-02 0.000E+00
total cpu time spent up to now is 34788.51 secs
per-process dynamical memory: 957.7 Mb
Self-consistent Calculation
iteration # 1 ecut= 30.00 Ry beta=0.70
Davidson diagonalization with overlap
ethr = 1.00E-06, avg # of iterations = 4.0
negative rho (up, down): 0.101E-01 0.000E+00
total cpu time spent up to now is 35129.06 secs
WARNING: integrated charge= 405.28031513, expected= 408.00000000
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
from electrons : error # 1
charge is wrong
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
--
J.R. Schmidt
Assistant Professor of Chemistry
Room 8305D
Department of Chemistry
University of Wisconsin-Madison
1101 University Ave
Madison, WI 53706
Phone: (608) 262-2996
Fax: (608) 262-9918
E-mail: schmidt at chem.wisc.edu
http://www.chem.wisc.edu/people/profiles/schmidt.php
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From baroni at sissa.it Fri Nov 21 17:11:50 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 21 Nov 2008 17:11:50 +0100
Subject: [Pw_forum] electronic density
In-Reply-To: <38716.200.0.233.50.1227276517.squirrel@mail.cab.cnea.gov.ar>
References: <OFF47716D1.FD88EADF-ON49257507.003EB25A-49257507.003FF973@mta.fujifilm.co.jp>
<49269E33.30903@democritos.it>
<45023.200.0.233.50.1227270869.squirrel@mail.cab.cnea.gov.ar>
<9966E640-05A8-4CA9-BCF8-B903C30F9A5E@sissa.it>
<38716.200.0.233.50.1227276517.squirrel@mail.cab.cnea.gov.ar>
Message-ID: <AF5FDFC1-CA47-4E62-AFA1-A19C32E01AFA@sissa.it>
I am sorry as well - I still do not understand the question
On Nov 21, 2008, at 3:08 PM, jorge.gallardo at cab.cnea.gov.ar wrote:
>> (number of electrons in the unit cell) / (volume of the unit cell)
>>
>> no need of quantum espresso, not even of a computer
>> SB
>>
>> On Nov 21, 2008, at 1:34 PM, jorge.gallardo at cab.cnea.gov.ar wrote:
>>
>
> I'm sorry, I was very synthetic in my question before. I did mean:
>
> 1) supposing we are using pseudo-potentials (I think pw.x not), the
> electron density taking into account only the valence electrons (as is
> considered by some [what?] pseudopotential program in quantum
> espresso).
(number of VALENCE electrons in the unit cell) / (volume of the unit
cell)
> 2) If we are relaxing the crystal structure (from what we don't
> known but
> only an approximation of lattice parameter), there is a way to get the
> electron density from the output files?
(number of VALENCE electrons in the EQUILIBRIUM unit cell) / (volume
of the EQUILIBRIUM unit cell)
SB
>
>
>
> thanks
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
La morale est une logique de l'action comme la logique est une morale
de la pens?e - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From giannozz at democritos.it Fri Nov 21 17:29:33 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 21 Nov 2008 17:29:33 +0100
Subject: [Pw_forum] Problems with integrated charge for a large
supercell relaxation
In-Reply-To: <4926D369.9020903@chem.wisc.edu>
References: <4926CCCA.8030504@chem.wisc.edu> <4926D02B.5070202@sissa.it>
<4926D369.9020903@chem.wisc.edu>
Message-ID: <4926E1ED.7000207@democritos.it>
Your system is treated as an insulator. If for some reason it
becomes metallic or semimetallic, you may run into trouble.
Add a few more bands and a small broadening, just in case.
Note that
K_POINTS Gamma
(uses "Gamma tricks") will be faster and take less memory
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From giannozz at democritos.it Fri Nov 21 18:21:24 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 21 Nov 2008 18:21:24 +0100
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
Message-ID: <4926EE14.4030001@democritos.it>
Lazaro Calderin wrote:
> - berry tests ask to increase ecutrho
actually, the berry test is correct: the charge density with
the augmentation part calculated in real space is a little
bit inaccurate. With a slightly different FFT grid the check
on consistency is no longer passed. With higher charge cutoff
the error disappears.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From calderin at physics.queensu.ca Fri Nov 21 21:03:57 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Fri, 21 Nov 2008 15:03:57 -0500 (EST)
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <4926EE14.4030001@democritos.it>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
<4926EE14.4030001@democritos.it>
Message-ID: <49414.130.15.24.220.1227297837.squirrel@physics.queensu.ca>
Hi Axel and Paolo,
As you said most of the discrepancies are acceptable but these two bother
me :
Checking metaGGA...discrepancy in total energy detected
discrepancy in force detected
Reference: 0.2336, You got: 0.2338
Error= .0002
Checking noncolin-constrain_atomic...discrepancy in total energy detected
Reference: -55.690313, You got: -55.687460
Error= .002853
Thanks, L.
--
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario K7L 3N6, Canada
+1 613 533 6000 ext 74811
calderin at physics.queensu.ca
From calderin at physics.queensu.ca Fri Nov 21 21:20:45 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Fri, 21 Nov 2008 15:20:45 -0500 (EST)
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <Pine.LNX.4.64.0811201704580.2387@localhost.localdomain>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
<Pine.LNX.4.64.0811201704580.2387@localhost.localdomain>
Message-ID: <44588.130.15.24.220.1227298845.squirrel@physics.queensu.ca>
Hi Axel
> fftw supports
> many more FFT grid sizes than ESSL and as a consequence
> you have differences in energies. try compiling without ESSL
> and against the shipped internal fft and see if you still
> have those differences...
I see .. I will try this test.
> LC> - berry tests ask to increase ecutrho
> LC> - paw-atom_l=2 blows up with a segmentation fault
>
> those need to be investigated in more detail. the ecutrho
> thing may be related to the grid sizes (check and compare
> the two output files for the fft grids). the paw problem
> should not happen, but this is rather new code. since you
> get a segfault, it would be helpful, if you could trigger
> a coredump and provide a stack trace, so that the author
> of the code can have a closer look...
Ok ... I'll try to get more specific info on the segfault problem.
Thanks a lot Axel.
--
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario K7L 3N6, Canada
+1 613 533 6000 ext 74811
calderin at physics.queensu.ca
From calderin at physics.queensu.ca Fri Nov 21 21:23:29 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Fri, 21 Nov 2008 15:23:29 -0500 (EST)
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <4926D2EA.3000901@democritos.it>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
<4926D2EA.3000901@democritos.it>
Message-ID: <44617.130.15.24.220.1227299009.squirrel@physics.queensu.ca>
>> - paw-atom_l=2 blows up with a segmentation fault
>
> works on a sp5 with xlf v. 10
Paolo could you send me the make.sys file to have a look.
Thanks a lot, L.
--
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario K7L 3N6, Canada
+1 613 533 6000 ext 74811
calderin at physics.queensu.ca
From schmidt at chem.wisc.edu Fri Nov 21 22:02:46 2008
From: schmidt at chem.wisc.edu (JR Schmidt)
Date: Fri, 21 Nov 2008 15:02:46 -0600
Subject: [Pw_forum] Problems with integrated charge for a large
supercell relaxation
In-Reply-To: <4926E1ED.7000207@democritos.it>
References: <4926CCCA.8030504@chem.wisc.edu>
<4926D02B.5070202@sissa.it> <4926D369.9020903@chem.wisc.edu>
<4926E1ED.7000207@democritos.it>
Message-ID: <492721F6.3050607@chem.wisc.edu>
Just to follow up on the problem of the integrated charge --
> Your system is treated as an insulator. If for some reason it
> becomes metallic or semimetallic, you may run into trouble.
> Add a few more bands and a small broadening, just in case.
>
I went back and verified this system. Even at the geometry where the
optimization failed, I took that geometry and did and SCF calculation
with extra bands. The band gap (at that geometry ) is 3.1 Ry (as would
be expected for this strong metal oxide insulator), so I don't think
that is the problem.
As I mentioned in the initial email, it is also odd that I can restart
the SCF or optimization from the 'failed' geometry and go for quite a
few optimization cycles before another crash
> Note that
> K_POINTS Gamma
> (uses "Gamma tricks") will be faster and take less memory
>
Fantastic! I was looking for a different (gamma-specific )executable,
but I couldn't find one. Now I know why.
--
J.R. Schmidt
Assistant Professor of Chemistry
Room 8305D
Department of Chemistry
University of Wisconsin-Madison
1101 University Ave
Madison, WI 53706
Phone: (608) 262-2996
Fax: (608) 262-9918
E-mail: schmidt at chem.wisc.edu
http://www.chem.wisc.edu/people/profiles/schmidt.php
From giannozz at democritos.it Fri Nov 21 22:32:27 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 21 Nov 2008 22:32:27 +0100
Subject: [Pw_forum] Problems with integrated charge for a large
supercell relaxation
In-Reply-To: <492721F6.3050607@chem.wisc.edu>
References: <4926CCCA.8030504@chem.wisc.edu>
<4926D02B.5070202@sissa.it> <4926D369.9020903@chem.wisc.edu>
<4926E1ED.7000207@democritos.it> <492721F6.3050607@chem.wisc.edu>
Message-ID: <02444A8D-33C3-447A-B5AE-C5671D3A2EBD@democritos.it>
On Nov 21, 2008, at 22:02 , JR Schmidt wrote:
> Even at the geometry where the optimization failed, I took that
> geometry
> and did and SCF calculation with extra bands. The band gap (at that
> geometry ) is 3.1 Ry
at convergence. There is no guarantee that the system will be an
insulator at the beginning of self-consistency
Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From giannozz at democritos.it Fri Nov 21 22:33:16 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 21 Nov 2008 22:33:16 +0100
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <44617.130.15.24.220.1227299009.squirrel@physics.queensu.ca>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
<4926D2EA.3000901@democritos.it>
<44617.130.15.24.220.1227299009.squirrel@physics.queensu.ca>
Message-ID: <3287B619-0398-4978-850C-8EDC097530B5@democritos.it>
On Nov 21, 2008, at 21:23 , Lazaro Calderin wrote:
> Paolo could you send me the make.sys file to have a look.
I can't right now, but there is nothing special in it
Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From calderin at physics.queensu.ca Fri Nov 21 23:11:51 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Fri, 21 Nov 2008 17:11:51 -0500 (EST)
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <Pine.LNX.4.64.0811201704580.2387@localhost.localdomain>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
<Pine.LNX.4.64.0811201704580.2387@localhost.localdomain>
Message-ID: <52517.130.15.24.220.1227305511.squirrel@physics.queensu.ca>
Axel Kohlmeyer wrote:
> since you
> get a segfault, it would be helpful, if you could trigger
> a coredump and provide a stack trace, so that the author
> of the code can have a closer look...
recompiled with -qsigtrap but can not get a core dump.
here is the stack trace
#0 0x000000001017ed0c in .__paw_onecenter_NMOD_paw_divergence ()
#1 0x00000000101856e8 in .__paw_onecenter_NMOD_paw_gcxc_potential ()
#2 0x0000000010186940 in .__paw_onecenter_NMOD_paw_xc_potential ()
#3 0x00000000101899a8 in .__paw_onecenter_NMOD_paw_potential ()
#4 0x0000000010191050 in .potinit ()
#5 0x000000001013f5ec in .init_run ()
#6 0x0000000010002e34 in .pwscf ()
Thanks, Lazaro
--
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario K7L 3N6, Canada
+1 613 533 6000 ext 74811
calderin at physics.queensu.ca
From frnkhzi at yahoo.com Sat Nov 22 06:58:20 2008
From: frnkhzi at yahoo.com (fereydoon khazali)
Date: Fri, 21 Nov 2008 21:58:20 -0800 (PST)
Subject: [Pw_forum] slab
Message-ID: <133162.67255.qm@web30103.mail.mud.yahoo.com>
dear all
please answer?these q.
1-what is the difference of slab input file from 3d crystal input file?
2-for example, 4 layer slab means slab has for atomic layer or supercell has 4 slab layer?
thanks
?
?
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From paulatto at sissa.it Sat Nov 22 12:39:16 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Sat, 22 Nov 2008 12:39:16 +0100 (CET)
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <3287B619-0398-4978-850C-8EDC097530B5@democritos.it>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
<4926D2EA.3000901@democritos.it>
<44617.130.15.24.220.1227299009.squirrel@physics.queensu.ca>
<3287B619-0398-4978-850C-8EDC097530B5@democritos.it>
Message-ID: <12136.79.16.6.235.1227353956.squirrel@webmail.sissa.it>
On Ven, Novembre 21, 2008 22:33, Paolo Giannozzi wrote:
> I can't right now, but there is nothing special in it
I'm attaching mine.
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
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From baroni at sissa.it Sat Nov 22 14:14:02 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Sat, 22 Nov 2008 14:14:02 +0100
Subject: [Pw_forum] slab
In-Reply-To: <133162.67255.qm@web30103.mail.mud.yahoo.com>
References: <133162.67255.qm@web30103.mail.mud.yahoo.com>
Message-ID: <CC541A59-4B13-46FD-BB54-8EA937FC29A1@sissa.it>
On Nov 22, 2008, at 6:58 AM, fereydoon khazali wrote:
Dear Mr X,
> dear all
> please answer these q.
please, sign your posts and provide your affiliation
> 1-what is the difference of slab input file from 3d crystal input
> file?
that the first describes a slab (which by definition is an alternance
of atomic layers with empty space, aimed at mimicking a surface),
while the second describes a system "with atoms all over the place"
> 2-for example, 4 layer slab means slab has for atomic layer or
> supercell has 4 slab layer?
both: the supercell consists of a slab, plus some empty space that (by
definition of "emptiness") does not contain any atoms. hence, (number
of atoms in the slab) = (number of atoms in the supercell)
> thanks
yoy are most welcome
SB
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
La morale est une logique de l'action comme la logique est une morale
de la pens?e - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From rdmeneze at yahoo.com.br Sat Nov 22 23:06:11 2008
From: rdmeneze at yahoo.com.br (Rafael Dias Menezes)
Date: Sat, 22 Nov 2008 14:06:11 -0800 (PST)
Subject: [Pw_forum] problem with TPSS (Tao-Perdew-Staroverov-Scuseria)
meta-GGA for silicon
Message-ID: <882438.76946.qm@web65706.mail.ac4.yahoo.com>
Hi people,
I'm doing some tests with the TPSS (Tao-Perdew-Staroverov-Scuseria) meta-GGA for silicon pseudo potential available in quantum-espresso web site (http://www.quantum-espresso.org/pseudo/1.3/UPF/Si.tpss-mt.UPF).
My current test is perform the self convergency cicle in a single isolated silicon atom in a big box. In this test the energy con't converge and I got this error message :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
task # 0
from rdiaghg : error # 16
info =/= 0
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
If I change the pseudo potential the calculations converge, like is espected.
Can someone help me with this little problem?
thanks,
Rafael Dias Menezes
Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
From rdmeneze at yahoo.com.br Sat Nov 22 23:20:05 2008
From: rdmeneze at yahoo.com.br (Rafael Dias Menezes)
Date: Sat, 22 Nov 2008 14:20:05 -0800 (PST)
Subject: [Pw_forum] Is possible convert ABINIT pseudo potentials file to UPF
format?
Message-ID: <659719.42866.qm@web65701.mail.ac4.yahoo.com>
Hi,
I got the upftools programs that come with quantum espresso package to convert some pseudo potentials from abinit package to upf format. In this operation I got several errors with all the upftools programs.
Someone can inform if is possible to do this conversation?
thanks,
Rafael Dias
Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
From giannozz at democritos.it Sun Nov 23 21:57:02 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 23 Nov 2008 21:57:02 +0100
Subject: [Pw_forum] Is possible convert ABINIT pseudo potentials file to
UPF format?
In-Reply-To: <659719.42866.qm@web65701.mail.ac4.yahoo.com>
References: <659719.42866.qm@web65701.mail.ac4.yahoo.com>
Message-ID: <68042E3C-FD59-4E15-9A23-A8F0DB3414DC@democritos.it>
On Nov 22, 2008, at 23:20 , Rafael Dias Menezes wrote:
> I got the upftools programs that come with quantum espresso package
> to convert some pseudo potentials from abinit package to upf
> format. In this operation I got several errors with all the
> upftools programs.
only pseudopotentials in the FHI (Fritz Haber Institute) format
can be converted using the fhi2upf utility.
Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From giannozz at democritos.it Sun Nov 23 22:04:40 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 23 Nov 2008 22:04:40 +0100
Subject: [Pw_forum] problem with TPSS (Tao-Perdew-Staroverov-Scuseria)
meta-GGA for silicon
In-Reply-To: <882438.76946.qm@web65706.mail.ac4.yahoo.com>
References: <882438.76946.qm@web65706.mail.ac4.yahoo.com>
Message-ID: <4E9EE02E-1B41-4182-8351-77E2C7ED1E6E@democritos.it>
On Nov 22, 2008, at 23:06 , Rafael Dias Menezes wrote:
> I'm doing some tests with the TPSS (Tao-Perdew-Staroverov-Scuseria)
> meta-GGA for silicon pseudo potential available in quantum-espresso
> web site (http://www.quantum-espresso.org/pseudo/1.3/UPF/Si.tpss-
> mt.UPF) [...] I got this error message [...]:
> from rdiaghg : error # 16
TPSS is quite nasty from a numerical point of view. Try to use lapack
from sources
instead of optimized libraries. On my Macintosh I get this problem
when testing
tests/metaGGA.in with atlas loaded; it disappears if I link lapack
instead.
Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
From njuxuyuehua at gmail.com Mon Nov 24 09:13:02 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Mon, 24 Nov 2008 16:13:02 +0800
Subject: [Pw_forum] why the results obtained from pwscf have so big
difference with experiment
Message-ID: <aca2feb20811240013h3ab078fcuaeee711abf4404ba@mail.gmail.com>
hello :
i am doing relax calculation, and my cell lattice parameter is obtained
from experiment.
The hexagonal crystal has unit cell dimensions 4.5181 ? (a) and 7.3560 ? (c)
(90?, 90?, 120?, 4 molecules, at 250 K) <ref4.html#r382>
the force on every atoms is OK
but the STRSS SECTION is:
entering subroutine stress ...
total stress (Ry/bohr**3) (kbar) P=
-13.55
-0.00009429 -0.00000007 -0.00000009 -13.87 -0.01 -0.01
-0.00000007 -0.00008866 -0.00000020 -0.01 -13.04 -0.03
-0.00000009 -0.00000020 -0.00009344 -0.01 -0.03 -13.75
why P is so big ?
I add K Pionts, but the results is still like that ?
should i do vc-relax?
thank you !
--
Xu Yuehua
physics Department of Nanjing university
China
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From giannozz at democritos.it Mon Nov 24 09:23:56 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 24 Nov 2008 09:23:56 +0100
Subject: [Pw_forum] why the results obtained from pwscf have so
big difference with experiment
In-Reply-To: <aca2feb20811240013h3ab078fcuaeee711abf4404ba@mail.gmail.com>
References: <aca2feb20811240013h3ab078fcuaeee711abf4404ba@mail.gmail.com>
Message-ID: <492A649C.5020808@democritos.it>
xu yuehua wrote:
> why P is so big ?
try to estimate how much the volume should change in order to
offset the pressure, before claiming that "P is big"
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From njuxuyuehua at gmail.com Mon Nov 24 09:38:09 2008
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Mon, 24 Nov 2008 16:38:09 +0800
Subject: [Pw_forum] why the results obtained from pwscf have so big
difference with experiment
In-Reply-To: <492A649C.5020808@democritos.it>
References: <aca2feb20811240013h3ab078fcuaeee711abf4404ba@mail.gmail.com>
<492A649C.5020808@democritos.it>
Message-ID: <aca2feb20811240038m6c6176f5t581a0d0c78dfa730@mail.gmail.com>
en, in general, the P is somewhat big,(i have a look at the forum posted
before)
but if i should estimate the change of volume, what is the dV/da (c)
criterion?
2008/11/24 Paolo Giannozzi <giannozz at democritos.it>
> xu yuehua wrote:
>
> > why P is so big ?
>
> try to estimate how much the volume should change in order to
> offset the pressure, before claiming that "P is big"
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Xu Yuehua
physics Department of Nanjing university
China
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From baroni at sissa.it Mon Nov 24 12:11:22 2008
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 24 Nov 2008 12:11:22 +0100
Subject: [Pw_forum] why the results obtained from pwscf have so big
difference with experiment
In-Reply-To: <aca2feb20811240038m6c6176f5t581a0d0c78dfa730@mail.gmail.com>
References: <aca2feb20811240013h3ab078fcuaeee711abf4404ba@mail.gmail.com>
<492A649C.5020808@democritos.it>
<aca2feb20811240038m6c6176f5t581a0d0c78dfa730@mail.gmail.com>
Message-ID: <E3908A2A-AE37-47D6-9527-445D48AF2714@sissa.it>
\Delta V \approx { {\partial E\over \partial V} \over {\partial^2 E
\over \partial V^2}}
the trace of the stress tensor gives the numerator; the denominator
can be estimated by finite-difference differentiation
the rest is left as an exercise ...
SB
On Nov 24, 2008, at 9:38 AM, xu yuehua wrote:
> en, in general, the P is somewhat big,(i have a look at the forum
> posted before)
> but if i should estimate the change of volume, what is the dV/da (c)
> criterion?
>
>
> 2008/11/24 Paolo Giannozzi <giannozz at democritos.it>
> xu yuehua wrote:
>
> > why P is so big ?
>
> try to estimate how much the volume should change in order to
> offset the pressure, before claiming that "P is big"
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --
> Xu Yuehua
> physics Department of Nanjing university
> China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
La morale est une logique de l'action comme la logique est une morale
de la pens?e - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From giannozz at democritos.it Mon Nov 24 12:27:48 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 24 Nov 2008 12:27:48 +0100
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <49414.130.15.24.220.1227297837.squirrel@physics.queensu.ca>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca> <4926EE14.4030001@democritos.it>
<49414.130.15.24.220.1227297837.squirrel@physics.queensu.ca>
Message-ID: <492A8FB4.3040108@democritos.it>
Lazaro Calderin wrote:
> Checking metaGGA...discrepancy in total energy detected
> discrepancy in force detected
> Reference: 0.2336, You got: 0.2338
as I mentioned recently, metaGGA is sometimes nasty from a numerical
point of view. It doesn't look that serious to me.
> Checking noncolin-constrain_atomicnoncolin-constrain_atomic...discrepancy in total energy detected
> Reference: -55.690313, You got: -55.687460
this is not so small. Noncolinear calculations with constraints are
also rather nasty. Please have a look at the differences between
noncolin-constrain_atomic.out and noncolin-constrain_atomic.ref
and report suspicious differences
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From calderin at physics.queensu.ca Mon Nov 24 16:22:40 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Mon, 24 Nov 2008 10:22:40 -0500 (EST)
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <12136.79.16.6.235.1227353956.squirrel@webmail.sissa.it>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
<4926D2EA.3000901@democritos.it>
<44617.130.15.24.220.1227299009.squirrel@physics.queensu.ca>
<3287B619-0398-4978-850C-8EDC097530B5@democritos.it>
<12136.79.16.6.235.1227353956.squirrel@webmail.sissa.it>
Message-ID: <58148.130.15.24.220.1227540160.squirrel@physics.queensu.ca>
Thanks, Lorenzo.
Your file is for AIX which is also helpful for me because I am also trying
to get espresso running on that arch.
Is your file for the cvs version?
The differences between yours and the one generated by configure are in
some include dirs and the multigrid library missing, but that is fine for
4.0.3.
Thanks, Lazaro
--
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario K7L 3N6, Canada
+1 613 533 6000 ext 74811
calderin at physics.queensu.ca
> On Ven, Novembre 21, 2008 22:33, Paolo Giannozzi wrote:
>> I can't right now, but there is nothing special in it
>
> I'm attaching mine.
>
> --
> Lorenzo Paulatto
> SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www: http://people.sissa.it/~paulatto/
>
>
>
> ----------------------------------------------------------------
> SISSA Webmail https://webmail.sissa.it/
> Powered by SquirrelMail
> http://www.squirrelmail.org/_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
From paulatto at sissa.it Mon Nov 24 16:46:34 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 24 Nov 2008 16:46:34 +0100
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <58148.130.15.24.220.1227540160.squirrel@physics.queensu.ca>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca> <4926D2EA.3000901@democritos.it> <44617.130.15.24.220.1227299009.squirrel@physics.queensu.ca> <3287B619-0398-4978-850C-8EDC097530B5@democritos.it> <12136.79.16.6.235.1227353956.squirrel@webmail.sissa.it>
<58148.130.15.24.220.1227540160.squirrel@physics.queensu.ca>
Message-ID: <492ACC5A.8070807@sissa.it>
Lazaro Calderin ha scritto:
> Is your file for the cvs version?
>
yes, it is
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.
Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste
Donations in food, coins, booze and processor time are warmly welcome.
From calderin at physics.queensu.ca Mon Nov 24 17:44:10 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Mon, 24 Nov 2008 11:44:10 -0500 (EST)
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <492A8FB4.3040108@democritos.it>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
<4926EE14.4030001@democritos.it>
<49414.130.15.24.220.1227297837.squirrel@physics.queensu.ca>
<492A8FB4.3040108@democritos.it>
Message-ID: <37735.130.15.24.220.1227545050.squirrel@physics.queensu.ca>
>> Checking
>> noncolin-constrain_atomicnoncolin-constrain_atomic...discrepancy in
>> total energy detected
>> Reference: -55.690313, You got: -55.687460
>
> this is not so small. Noncolinear calculations with constraints are
> also rather nasty. Please have a look at the differences between
> noncolin-constrain_atomic.out and noncolin-constrain_atomic.ref
> and report suspicious differences
Well .. the most suspicious difference seems to be in the fft grids:
From bogus@does.not.exist.com Wed Nov 19 23:20:46 2008
From: bogus@does.not.exist.com ()
Date: Wed, 19 Nov 2008 22:20:46 -0000
Subject: No subject
Message-ID: <mailman.0.1227545067.15649.pw_forum@pwscf.org>
---
From bogus@does.not.exist.com Wed Nov 19 23:20:46 2008
From: bogus@does.not.exist.com ()
Date: Wed, 19 Nov 2008 22:20:46 -0000
Subject: No subject
Message-ID: <mailman.1.1227545067.15649.pw_forum@pwscf.org>
Lazaro
--
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario K7L 3N6, Canada
+1 613 533 6000 ext 74811
calderin at physics.queensu.ca
From giannozz at democritos.it Mon Nov 24 17:50:00 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 24 Nov 2008 17:50:00 +0100
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <37735.130.15.24.220.1227545050.squirrel@physics.queensu.ca>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca> <4926EE14.4030001@democritos.it> <49414.130.15.24.220.1227297837.squirrel@physics.queensu.ca> <492A8FB4.3040108@democritos.it>
<37735.130.15.24.220.1227545050.squirrel@physics.queensu.ca>
Message-ID: <492ADB38.1080302@democritos.it>
Lazaro Calderin wrote:
> Well .. the most suspicious difference seems to be in the fft grids:
>
>>From .out
> < G cutoff = 137.8834 ( 3367 G-vectors) FFT grid: ( 22, 22, 22)
> < G cutoff = 68.9417 ( 1205 G-vectors) smooth grid: ( 16, 16, 16)
> ---
>>From .ref
>> G cutoff = 137.8834 ( 3367 G-vectors) FFT grid: ( 24, 24, 24)
>> G cutoff = 68.9417 ( 1205 G-vectors) smooth grid: ( 15, 15, 15)
try to set the charge grid to 24 (nr1=24,nr2=24,nr3=24 in
namelist system) and see if it makes a difference
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From calderin at physics.queensu.ca Mon Nov 24 18:04:09 2008
From: calderin at physics.queensu.ca (Lazaro Calderin)
Date: Mon, 24 Nov 2008 12:04:09 -0500 (EST)
Subject: [Pw_forum] IBM JS20 pw tests problems
In-Reply-To: <492ADB38.1080302@democritos.it>
References: <43045.130.15.24.220.1227217949.squirrel@physics.queensu.ca>
<4926EE14.4030001@democritos.it>
<49414.130.15.24.220.1227297837.squirrel@physics.queensu.ca>
<492A8FB4.3040108@democritos.it>
<37735.130.15.24.220.1227545050.squirrel@physics.queensu.ca>
<492ADB38.1080302@democritos.it>
Message-ID: <50496.130.15.24.220.1227546249.squirrel@physics.queensu.ca>
Thanks Paolo,
> try to set the charge grid to 24 (nr1=24,nr2=24,nr3=24 in
> namelist system) and see if it makes a difference
The difference in total energies becomes less than 1e-6.
Lazaro
--
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario K7L 3N6, Canada
+1 613 533 6000 ext 74811
calderin at physics.queensu.ca
From lanhaiping at gmail.com Mon Nov 24 22:24:45 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Tue, 25 Nov 2008 05:24:45 +0800
Subject: [Pw_forum] a strange behavior for QE-v4 compared with QE-v3
Message-ID: <c92002fa0811241324k769a45b6rda0f8e4b3cf43fa9@mail.gmail.com>
Dear All,
I am performing a series tests on a RHEL-intel 4-core 2cpu workstation with
ifort 9 and mpi-1.2.6.
A strange behavior is found for QE v4 when i carry out parallel
executation. For example, i just ran the script supplied in
$QE/example/example10. Using 'top' command, i found load in each cpu is
highly unbalanced :
%cpu %mem
151 0.2 0:20.38 pw.x
130 0.2 0:19.40 pw.x
103 0.2 0:19.99 pw.x
92 0.2 0:13.82 pw.x
81 0.2 0:17.89 pw.x
79 0.2 0:14.01 pw.x
76 0.2 0:14.01 pw.x
74 0.2 0:14.02 pw.x
But this situation doesnot happen when i try to run the same work with
QE-v3.
Would you please give me some hints or suggestion to tune the performance
for
QE v4 ?
Thanks in advance, and best regards!
Hai-Ping
--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From jdai3 at mail.ustc.edu.cn Tue Nov 25 09:45:56 2008
From: jdai3 at mail.ustc.edu.cn (Dai)
Date: Tue, 25 Nov 2008 16:45:56 +0800
Subject: [Pw_forum] About el-ph coupling
Message-ID: <427602732.18187@ustc.edu.cn>
Dear all;
In phonon calculations, is it possible to take the effects of magnon into consideration? More simply, if I perform a phonon calculation using FM and AFM configurations, will there be any difference in the phonon spectrum and the coupling constant? Thanks.
2008-11-25
Best regards,
Jun Dai
=============================================================
Jun Dai
Ph.D. Candidate,
Hefei National Laboratory For Physical Sciences at the Microscale,
University of Science and Technology of China,
Hefei, Anhui, 230026,
People's Republic of China
=============================================================
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From eyvaz_isaev at yahoo.com Tue Nov 25 13:32:48 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 25 Nov 2008 04:32:48 -0800 (PST)
Subject: [Pw_forum] About el-ph coupling
In-Reply-To: <427602732.18187@ustc.edu.cn>
Message-ID: <358577.63719.qm@web65709.mail.ac4.yahoo.com>
Hi,
--- On Tue, 11/25/08, Dai <jdai3 at mail.ustc.edu.cn> wrote:
> More simply, if I perform a
> phonon calculation using FM and AFM configurations, will
> there be any difference in the phonon spectrum and the
> coupling constant?
from phq_readin:
IF (elph.AND.lsda) CALL errore ('phq_readin', 'El-ph and spin not implemented', 1)
At least, for QE_4.0 and earlier versions.
As concerns an influence of different magnetic ordering (FM and AFM), yes, you can see the difference in the phonon spectrum. Of course, in this case you should use the same structure for both FM and AFM calculations, but introducing AFM ordering you reduce the symmetry.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
From thmason24 at yahoo.com Tue Nov 25 16:00:50 2008
From: thmason24 at yahoo.com (Timothy Mason)
Date: Tue, 25 Nov 2008 07:00:50 -0800 (PST)
Subject: [Pw_forum] vc-relax
In-Reply-To: <BLU110-W30E6084D4162C675D1A7E9D4110@phx.gbl>
Message-ID: <304300.28407.qm@web81806.mail.mud.yahoo.com>
I have two perhaps fundamental questions related to vc-relax.
?
1) Can?someone give me an idea of what role wmass plays in VC relax??? it does seem to affect my convergence but it would be nice to have a better understanding so I'm not just?shooting in the dark.? How does the algorithm use this parameter?
?
2)? this question is perhaps more fundamental.?? Even though the toal forces and stresses eventually?oscillate about a point,?? the energy itself ALWAYS decreases although asymptotically.?? is this an indication that I actually am converging but it will take a long time?
?
Thanks in advance for your help.
?
Tim Mason? (university of Missouri St. Louis)
?
?
?
--- On Fri, 11/14/08, Eric Abel <etabel at hotmail.com> wrote:
From: Eric Abel <etabel at hotmail.com>
Subject: RE: vc-relax PWSCF
To: thmason24 at yahoo.com
Date: Friday, November 14, 2008, 11:00 PM
#yiv1108401564 .hmmessage P
{
margin:0px;padding:0px;}
#yiv1108401564 {
font-size:10pt;font-family:Verdana;}
Not sure what your end goal is, but in general vc-relax shouldn't be necessary.? Rather, the lattice?parameters, as well as the atomic?positions?can be very accurately determined using x-ray or neutron diffraction.? These should therefore be the starting point for your study.? From there, I would then relax the structure using the simple 'relax' routine, which keeps the?lattice parameters?fixed, but varies the atomic positions within the unit cell.? This ensures that all of the atoms are in their potential minimum.? If the relaxed structure is drastically different from the experimental structure, this indicates something wrong with the pseudopotentials or other input parameters mentioned below.? This step isn't so necessary if all you are investigating is electronic properties, but it is absolutely essentialy for anything to do with lattice dynamics.
?
Anyway, it sounds like you have some foundation calculation to do (it took me a good two weeks non-stop to optimize my input parameters).? I am happy to continue helping you, but you should also utilize the pw_forum.??By now there is a huge knowledgebase of Q & A on all topics.? This is where I learned most of what I know.? My discussions with Marzari and Co. only fine tuned some of the details.
?
Good Luck, and feel free to ask me for any additional guidance.
?
Eric
Date: Fri, 14 Nov 2008 06:38:53 -0800
From: thmason24 at yahoo.com
Subject: RE: vc-relax PWSCF
To: etabel at hotmail.com
Dear Eric,
?
the reason I want to use VC relax is that?our first guess also includes a first guess of the lattice vectors and I have no reason to think that they are optimized.? Am?I missing the point of VC-relax???
1) Good info on the Kpoint density.?? Hopefully 8 8 8 will give me the convergence I need.
sounds like these computations willl be more expensive than I anticipated.
?
I'm?quite new to this so I'm not sure what's all involved in thouroughly research the space.?? I make sure it converges on ecut and Kpoint for an scf run.?? I believe its not metallic so I leave smearing alone.?
?
2)?I thought 'damp' was suppose to do better at the final convergence so i chose that over 'sd'.???I believe I did try a run with 'bfgs'? and didn't see a difference.
?
?
i really appreciate you taking the time to look.
?
?
?
--- On Thu, 11/13/08, Eric Abel <etabel at hotmail.com> wrote:
From: Eric Abel <etabel at hotmail.com>
Subject: RE: vc-relax PWSCF
To: thmason24 at yahoo.com
Date: Thursday, November 13, 2008, 10:01 PM
#yiv1108401564 .ExternalClass #EC_yiv1630627734 .EC_hmmessage P
{padding:0px;}
#yiv1108401564 .ExternalClass #EC_yiv1630627734
{font-size:10pt;font-family:Verdana;}
Well, at first glance I don't see anything grossly wrong.?? The first question I feel compelled to ask, is why you wish to do a vc-relax?? As you saw, I asked a lot of questions on the issue, and (being a student at MIT) had the opportunity to sit down with Dr. Marzari, and some of his grad students who were actively developing PWSCF code, and I found that sometimes we make life too dificult for ourselves by performing unnecessary calculations.?
?
?
?
Anyway, assuming vc-relax is indeed something you care about, I do have a?few?things stick out however:
?
1.? Your k-point density seems a little coarse.? I wouldn't run at anything less than 8 8 8, especially for vc-relax.? You may even need a grid as tight as 16 16 16, or even 24 24 24.? Have you thoroughly investigated this space?? The relax will be more sensitive to this than just the band calculations.
?
2.? I was running with 'bfgs' ion dynamics.? I believe this is the default.? Do you have a specific reason for running with 'damp'?
?
3.? You should also play with the mixing beta, smearing parameters, and ecutwfc/ecutrho.? Dr. Marzari showed me nice plots of the convergence of the?total force as a function of all of these parameters, which really illustrated to me the importance of finding asymtote, as the results can be drastically affected.
?
Date: Thu, 13 Nov 2008 06:22:53 -0800
From: thmason24 at yahoo.com
Subject: RE: vc-relax PWSCF
To: etabel at hotmail.com
Great.
my struggle is that I can't get my structure to converge as tightly as I'd like it to.?? I'd like to get the forces down to 0.0004 Ryd/a.u? but they generally start oscillating around 0.02.?? Quite confusing to me since the total energy continues to decline although asymptotically.?? I'm including my input file as a reference.?? Did you run into this and remember how you solved it?
thanks so much for taking a look.
&CONTROL
calculation = "vc-relax",
prefix = 'n14.out',
tprnfor = .TRUE.
pseudo_dir = '/home/thmmqc/pwscf/psps/US_GGA',
outdir='/home/thmmqc/tmp'
forc_conv_thr = 0.0004,
nstep = 100
/
&SYSTEM
ibrav = 0, nat = 8, ntyp = 3,
ecutwfc = 40
ecutrho = 480
celldm(1) = 1.889725989
/
&ELECTRONS
mixing_mode = 'plain',
mixing_beta = 0.7,
conv_thr = 1.0D-8,
/
&IONS
ion_dynamics? = 'damp',
ion_damping? = 0.2,
ion_positions = 'from_input',
upscale = 100,
/
&CELL
cell_dynamics = "damp-pr",
/
ATOMIC_SPECIES
Li 6.941000 Li.pbe-n-van.UPF
N 14.006740 N.pbe-rrkjus.UPF
H 1.007940 H.pbe-rrkjus.UPF
CELL_PARAMETERS
5.67649703 0.09921379 0.92493840
1.07129347 6.96479879 -0.12086294
-1.34503851 0.22123471 3.75667723
ATOMIC_POSITIONS {crystal}
Li 0.116794697000 0.651673872000 0.623162333000
Li 0.175318460000 0.437682929000 0.133625687000
?N 0.091275887000 0.737412816000 0.118429764000
?N 0.198322191000 0.351690647000 0.637630892000
?H -0.076285944000 0.821236835000 0.075907461000
?H 0.202774564000 0.839292956000 0.150103014000
?H 0.081850214000 0.253355665000 0.605178356000
?H 0.363204688000 0.263855155000 0.679010850000
K_POINTS automatic
4 4 4 0 0 0
--- On Thu, 11/13/08, Eric Abel <etabel at hotmail.com> wrote:
From: Eric Abel <etabel at hotmail.com>
Subject: RE: vc-relax PWSCF
To: thmason24 at yahoo.com
Date: Thursday, November 13, 2008, 2:29 AM
#yiv1108401564 .ExternalClass #EC_yiv1630627734 .EC_ExternalClass #EC_EC_yiv1948518543 .EC_EC_hmmessage P
{padding:0px;}
#yiv1108401564 .ExternalClass #EC_yiv1630627734 .EC_ExternalClass #EC_EC_yiv1948518543
{font-size:10pt;font-family:Verdana;}
"done quite a bit" might be an overstatement.? I got it to work, but that was over a year ago.? You can shoot some questions my way, and I'll do my best to try to help.
?
Eric
Date: Tue, 11 Nov 2008 12:46:53 -0800
From: thmason24 at yahoo.com
Subject: vc-relax PWSCF
To: etabel at hotmail.com
Hi Eric,
My name is Tim Mason.?? I'm a grad student at University of Missouri St. Louis.
I saw your name on the PWSCF forums.?? You seem to have done quite a bit with VC-relax.??? I'm not sure how experienced you ended up getting but would you be willing to answer a few basic questions?
thanks,
Tim
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From jdai3 at mail.ustc.edu.cn Tue Nov 25 16:11:52 2008
From: jdai3 at mail.ustc.edu.cn (Dai)
Date: Tue, 25 Nov 2008 23:11:52 +0800
Subject: [Pw_forum] About el-ph coupling
Message-ID: <427625889.23888@ustc.edu.cn>
Dear Prof. Isaev and all,
Thanks for reply. Do you konw any software packages that can deal with this kind of issue?
2008-11-25
Best regards,
Jun Dai
=============================================================
Jun Dai
Ph.D. Candidate,
Hefei National Laboratory For Physical Sciences at the Microscale,
University of Science and Technology of China,
Hefei, Anhui, 230026,
People's Republic of China
=============================================================
???? Eyvaz Isaev
????? 2008-11-25 20:33:59
???? PWSCF Forum
???
??? Re: [Pw_forum] About el-ph coupling
Hi,
--- On Tue, 11/25/08, Dai <jdai3 at mail.ustc.edu.cn> wrote:
> More simply, if I perform a
> phonon calculation using FM and AFM configurations, will
> there be any difference in the phonon spectrum and the
> coupling constant?
from phq_readin:
IF (elph.AND.lsda) CALL errore ('phq_readin', 'El-ph and spin not implemented', 1)
At least, for QE_4.0 and earlier versions.
As concerns an influence of different magnetic ordering (FM and AFM), yes, you can see the difference in the phonon spectrum. Of course, in this case you should use the same structure for both FM and AFM calculations, but introducing AFM ordering you reduce the symmetry.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From degironc at sissa.it Tue Nov 25 18:48:36 2008
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Tue, 25 Nov 2008 18:48:36 +0100
Subject: [Pw_forum] vc-relax
In-Reply-To: <304300.28407.qm@web81806.mail.mud.yahoo.com>
References: <304300.28407.qm@web81806.mail.mud.yahoo.com>
Message-ID: <492C3A74.4040808@sissa.it>
there are two main algorithms in variable cell shape relaxation: a
damped dynamics and a bfgs-like relaxation.
in the damped dynamics case there are two flavors, Parrinello-Rahman and
Wentzcovitch, and the value of the cell mass is different in the two
cases because the underlying Lagrangian is different. There is a default
value that should be not too wrong. A good value should be something
that gives similar frequencies for the internal vibrations and for the
cell oscillationos so that they are optimally coupled.
In the (recently introduced) bfgs algorithm there is no need of
specifying the cell mass.
Stefano de Gironcoli - SISSA and DEMOCRITOS
Timothy Mason wrote:
> I have two perhaps fundamental questions related to vc-relax.
>
> 1) Can someone give me an idea of what role wmass plays in VC relax?
> it does seem to affect my convergence but it would be nice to have a
> better understanding so I'm not just shooting in the dark. How does
> the algorithm use this parameter?
>
> 2) this question is perhaps more fundamental. Even though the toal
> forces and stresses eventually oscillate about a point, the energy
> itself ALWAYS decreases although asymptotically. is this an
> indication that I actually am converging but it will take a long time?
>
> Thanks in advance for your help.
>
> Tim Mason (university of Missouri St. Louis)
>
> --- On *Fri, 11/14/08, Eric Abel /<etabel at hotmail.com>/* wrote:
>
> From: Eric Abel <etabel at hotmail.com>
> Subject: RE: vc-relax PWSCF
> To: thmason24 at yahoo.com
> Date: Friday, November 14, 2008, 11:00 PM
>
> Not sure what your end goal is, but in general vc-relax shouldn't
> be necessary. Rather, the lattice parameters, as well as the
> atomic positions can be very accurately determined using x-ray or
> neutron diffraction. These should therefore be the starting point
> for your study. From there, I would then relax the structure
> using the simple 'relax' routine, which keeps the lattice
> parameters fixed, but varies the atomic positions within the unit
> cell. This ensures that all of the atoms are in their potential
> minimum. If the relaxed structure is drastically different from
> the experimental structure, this indicates something wrong with
> the pseudopotentials or other input parameters mentioned below.
> This step isn't so necessary if all you are investigating is
> electronic properties, but it is absolutely essentialy for
> anything to do with lattice dynamics.
>
> Anyway, it sounds like you have some foundation calculation to do
> (it took me a good two weeks non-stop to optimize my input
> parameters). I am happy to continue helping you, but you should
> also utilize the pw_forum. By now there is a huge knowledgebase
> of Q & A on all topics. This is where I learned most of what I
> know. My discussions with Marzari and Co. only fine tuned some of
> the details.
>
> Good Luck, and feel free to ask me for any additional guidance.
>
> Eric
>
>
> ------------------------------------------------------------------------
>
> Date: Fri, 14 Nov 2008 06:38:53 -0800
> From: thmason24 at yahoo.com
> Subject: RE: vc-relax PWSCF
> To: etabel at hotmail.com
>
>
> Dear Eric,
>
> the reason I want to use VC relax is that our first guess also
> includes a first guess of the lattice vectors and I have no reason
> to think that they are optimized. Am I missing the point of
> VC-relax?
>
> 1) Good info on the Kpoint density. Hopefully 8 8 8 will give me
> the convergence I need.
> sounds like these computations willl be more expensive than I
> anticipated.
>
> I'm quite new to this so I'm not sure what's all involved in
> thouroughly research the space. I make sure it converges on ecut
> and Kpoint for an scf run. I believe its not metallic so I leave
> smearing alone.
>
> 2) I thought 'damp' was suppose to do better at the final
> convergence so i chose that over 'sd'. I believe I did try a run
> with 'bfgs' and didn't see a difference.
>
>
> i really appreciate you taking the time to look.
>
>
>
>
> --- On *Thu, 11/13/08, Eric Abel /<etabel at hotmail.com>/* wrote:
>
> From: Eric Abel <etabel at hotmail.com>
> Subject: RE: vc-relax PWSCF
> To: thmason24 at yahoo.com
> Date: Thursday, November 13, 2008, 10:01 PM
>
> Well, at first glance I don't see anything grossly wrong.
> The first question I feel compelled to ask, is why you wish to
> do a vc-relax? As you saw, I asked a lot of questions on the
> issue, and (being a student at MIT) had the opportunity to sit
> down with Dr. Marzari, and some of his grad students who were
> actively developing PWSCF code, and I found that sometimes we
> make life too dificult for ourselves by performing unnecessary
> calculations.
>
>
>
>
>
> Anyway, assuming vc-relax is indeed something you care about,
> I do have a few things stick out however:
>
> 1. Your k-point density seems a little coarse. I wouldn't
> run at anything less than 8 8 8, especially for vc-relax. You
> may even need a grid as tight as 16 16 16, or even 24 24 24.
> Have you thoroughly investigated this space? The relax will
> be more sensitive to this than just the band calculations.
>
> 2. I was running with 'bfgs' ion dynamics. I believe this is
> the default. Do you have a specific reason for running with
> 'damp'?
>
> 3. You should also play with the mixing beta, smearing
> parameters, and ecutwfc/ecutrho. Dr. Marzari showed me nice
> plots of the convergence of the total force as a function of
> all of these parameters, which really illustrated to me the
> importance of finding asymtote, as the results can be
> drastically affected.
>
>
>
> ------------------------------------------------------------------------
>
> Date: Thu, 13 Nov 2008 06:22:53 -0800
> From: thmason24 at yahoo.com
> Subject: RE: vc-relax PWSCF
> To: etabel at hotmail.com
>
>
> Great.
>
> my struggle is that I can't get my structure to converge as
> tightly as I'd like it to. I'd like to get the forces down
> to 0.0004 Ryd/a.u but they generally start oscillating around
> 0.02. Quite confusing to me since the total energy continues
> to decline although asymptotically. I'm including my input
> file as a reference. Did you run into this and remember how
> you solved it?
>
> thanks so much for taking a look.
>
> &CONTROL
> calculation = "vc-relax",
> prefix = 'n14.out',
> tprnfor = .TRUE.
> pseudo_dir = '/home/thmmqc/pwscf/psps/US_GGA',
> outdir='/home/thmmqc/tmp'
> forc_conv_thr = 0.0004,
> nstep = 100
> /
>
> &SYSTEM
> ibrav = 0, nat = 8, ntyp = 3,
> ecutwfc = 40
> ecutrho = 480
> celldm(1) = 1.889725989
> /
>
> &ELECTRONS
> mixing_mode = 'plain',
> mixing_beta = 0.7,
> conv_thr = 1.0D-8,
> /
>
> &IONS
> ion_dynamics = 'damp',
> ion_damping = 0.2,
> ion_positions = 'from_input',
> upscale = 100,
> /
>
> &CELL
> cell_dynamics = "damp-pr",
> /
>
> ATOMIC_SPECIES
> Li 6.941000 Li.pbe-n-van.UPF
> N 14.006740 N.pbe-rrkjus.UPF
> H 1.007940 H.pbe-rrkjus.UPF
>
> CELL_PARAMETERS
> 5.67649703 0.09921379 0.92493840
> 1.07129347 6.96479879 -0.12086294
> -1.34503851 0.22123471 3.75667723
>
> ATOMIC_POSITIONS {crystal}
> Li 0.116794697000 0.651673872000 0.623162333000
> Li 0.175318460000 0.437682929000 0.133625687000
> N 0.091275887000 0.737412816000 0.118429764000
> N 0.198322191000 0.351690647000 0.637630892000
> H -0.076285944000 0.821236835000 0.075907461000
> H 0.202774564000 0.839292956000 0.150103014000
> H 0.081850214000 0.253355665000 0.605178356000
> H 0.363204688000 0.263855155000 0.679010850000
>
> K_POINTS automatic
> 4 4 4 0 0 0
>
>
>
>
>
>
>
>
>
>
> --- On *Thu, 11/13/08, Eric Abel /<etabel at hotmail.com>/* wrote:
>
> From: Eric Abel <etabel at hotmail.com>
> Subject: RE: vc-relax PWSCF
> To: thmason24 at yahoo.com
> Date: Thursday, November 13, 2008, 2:29 AM
>
> "done quite a bit" might be an overstatement. I got it to
> work, but that was over a year ago. You can shoot some
> questions my way, and I'll do my best to try to help.
>
> Eric
>
>
> ------------------------------------------------------------------------
>
> Date: Tue, 11 Nov 2008 12:46:53 -0800
> From: thmason24 at yahoo.com
> Subject: vc-relax PWSCF
> To: etabel at hotmail.com
>
>
> Hi Eric,
>
> My name is Tim Mason. I'm a grad student at University
> of Missouri St. Louis.
>
> I saw your name on the PWSCF forums. You seem to have
> done quite a bit with VC-relax. I'm not sure how
> experienced you ended up getting but would you be willing
> to answer a few basic questions?
>
> thanks,
>
> Tim
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
From giannozz at democritos.it Tue Nov 25 18:55:41 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 25 Nov 2008 18:55:41 +0100
Subject: [Pw_forum] a strange behavior for QE-v4 compared with QE-v3
In-Reply-To: <c92002fa0811241324k769a45b6rda0f8e4b3cf43fa9@mail.gmail.com>
References: <c92002fa0811241324k769a45b6rda0f8e4b3cf43fa9@mail.gmail.com>
Message-ID: <492C3C1D.5060609@democritos.it>
lan haiping wrote:
> A strange behavior is found for QE v4 when i carry out parallel
> executation [...] But this situation doesnot happen when i try
> to run the same work with QE-v3.
it's hard to say anything meaningful based on the output of "top"
and little more. There are several parallelization levles in QE,
as explained here:
http://www.quantum-espresso.org/wiki/index.php/Running_on_parallel_machines
I don't remember what happened between v.3 and v.4, but whatever
happened, it is unlikely to make parallelism less effective.
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From lanhaiping at gmail.com Tue Nov 25 19:58:24 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Wed, 26 Nov 2008 02:58:24 +0800
Subject: [Pw_forum] a strange behavior for QE-v4 compared with QE-v3
In-Reply-To: <492C3C1D.5060609@democritos.it>
References: <c92002fa0811241324k769a45b6rda0f8e4b3cf43fa9@mail.gmail.com>
<492C3C1D.5060609@democritos.it>
Message-ID: <c92002fa0811251058n299f5e7ch89508c14d0cf4fb8@mail.gmail.com>
Dear Paolo,
thanks for explaination.
But this behavior is really strange i have ever come to.
i have tried to rebuild the mpich and the QE, and nothing is
gained. Another strange problem is that the work i execute parallelly
with QE-v4 sometimes come to idle without execuation or output
information.
is there any other suggestion to figure what the problem with it ?
thanks
On Wed, Nov 26, 2008 at 1:55 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:
> lan haiping wrote:
>
> > A strange behavior is found for QE v4 when i carry out parallel
> > executation [...] But this situation doesnot happen when i try
> > to run the same work with QE-v3.
>
> it's hard to say anything meaningful based on the output of "top"
> and little more. There are several parallelization levles in QE,
> as explained here:
> http://www.quantum-espresso.org/wiki/index.php/Running_on_parallel_machines
> I don't remember what happened between v.3 and v.4, but whatever
> happened, it is unlikely to make parallelism less effective.
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From quantumdft at gmail.com Wed Nov 26 09:18:38 2008
From: quantumdft at gmail.com (vega lew)
Date: Wed, 26 Nov 2008 16:18:38 +0800
Subject: [Pw_forum] binding energy for water adsorption at certain surface
Message-ID: <412f6c680811260018t129946c4y16041aed3783b832@mail.gmail.com>
Dear all,
I want to calculate the binding energy for water adsorption at certain
surface. So I first put an water molecule at some sites of the surface, and
relaxed the whole systems( water and the upper half of the surface slab,
lower slab was fixed). After relax calculations finished, I copy the slab
atoms and the water molecule coordinates separately into two inputfiles(the
dimension of the supercell, and other parameters such as k point sampling,
ecut, et al. were not changed) and performed a SCF calculation to get the
single point energy. Then I substrated the two single point energy (water
molecule and the surface slab) from the final energy for the whole system
reported by former relaxed calculation.
this procedure was quite well when the adsorptions were in a molecular
style. But if the water molecule dissociated at the surface, the subsequent
SCF calculations of the dissociated water molecules were not converged. How
could I cope with this? To increase the ecut, k-point, empty bands? to
decrease the broadening, mixing beta? Or setting the mixing mode to
'local-TF'? If the convergence could be achieved by doing this, do you think
I could use the this value to calculate the binding energy directly while
the scf calculation of the slab and the former relax calculation were using
different parameters (such as ecut, number of k-points, mixing beta et
al.)?
the input file of the scf calculation of water is show as follows (the water
was in a dissociated configuration. and surface slab was removed to perform
scf calculation),
&CONTROL
title = '*********_water'
,
calculation = 'scf'
,
restart_mode = 'from_scratch'
,
outdir = '/tmp/' ,
wfcdir = '/tmp/'
,
pseudo_dir = '/home/vega/espresso-4.0/pseudo/' ,
prefix = '********_water'
,
disk_io = 'none'
,
nstep = 1000
,
/
&SYSTEM
ibrav =
8,
celldm(1) =24.8624,
celldm(2) = 0.8520,
celldm(3) = 1.6964,
nat =
3,
ntyp =
2,
nosym = .ture.
,
ecutwfc = 30,
ecutrho = 300,
/
&ELECTRONS
/
ATOMIC_SPECIES
# Ti 47.86700 Ti.pw91-sp-van_ak.UPF
O 15.99940 O.pw91-van_ak.UPF
H 1.00794
H.pw91-van_ak.UPF
ATOMIC_POSITIONS crystal
O -0.672041076 0.333142157 0.526904777
H -0.486792757 0.330778459 0.505140407
H -0.739833562 0.333472512 0.544633120
K_POINTS gamma
thank you for reading.
any hints on my questiosn will be deeply appreciated.
vega
--
==================================================================================
Vega Lew ( weijia liu)
PH.D Candidate in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
******************************************************************************************************************
Email: vegalew at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing,
Jiangsu, China
******************************************************************************************************************
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From akohlmey at cmm.chem.upenn.edu Wed Nov 26 09:29:42 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 26 Nov 2008 09:29:42 +0100
Subject: [Pw_forum] a strange behavior for QE-v4 compared with QE-v3
In-Reply-To: <c92002fa0811251058n299f5e7ch89508c14d0cf4fb8@mail.gmail.com>
References: <c92002fa0811241324k769a45b6rda0f8e4b3cf43fa9@mail.gmail.com>
<492C3C1D.5060609@democritos.it>
<c92002fa0811251058n299f5e7ch89508c14d0cf4fb8@mail.gmail.com>
Message-ID: <7b6913e90811260029h413ab777ufb90f12e7b702236@mail.gmail.com>
this looks a lot like you are using two different versions
of MKL for the two compiles and thus are another "victim"
of the automatic threading of MKL v10. you should not
have a process with >100% CPU with a regular compile.
now if you have 8 cores and 8 MPI tasks and each of them
threads across 8 cores, you have a) a severe overload of
the scheduler and b) a big mess and all kinds of bad
performance issues.
try setting OMP_NUM_THREADS=1 and check if that
changes the behavior.
cheers,
axel.
On 11/25/08, lan haiping <lanhaiping at gmail.com> wrote:
> Dear Paolo,
> thanks for explaination.
> But this behavior is really strange i have ever come to.
> i have tried to rebuild the mpich and the QE, and nothing is
> gained. Another strange problem is that the work i execute parallelly
> with QE-v4 sometimes come to idle without execuation or output
> information.
>
> is there any other suggestion to figure what the problem with it ?
>
> thanks
>
> On Wed, Nov 26, 2008 at 1:55 AM, Paolo Giannozzi
> <giannozz at democritos.it>wrote:
>
>> lan haiping wrote:
>>
>> > A strange behavior is found for QE v4 when i carry out parallel
>> > executation [...] But this situation doesnot happen when i try
>> > to run the same work with QE-v3.
>>
>> it's hard to say anything meaningful based on the output of "top"
>> and little more. There are several parallelization levles in QE,
>> as explained here:
>> http://www.quantum-espresso.org/wiki/index.php/Running_on_parallel_machines
>> I don't remember what happened between v.3 and v.4, but whatever
>> happened, it is unlikely to make parallelism less effective.
>>
>> Paolo
>> --
>> Paolo Giannozzi, Democritos and University of Udine, Italy
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From fabio at che.tohoku.ac.jp Wed Nov 26 12:23:47 2008
From: fabio at che.tohoku.ac.jp (fabio)
Date: Wed, 26 Nov 2008 20:23:47 +0900
Subject: [Pw_forum] Postdoc position available
Message-ID: <001c01c94fb9$739fb400$ca241fac@YOUR2FFD4502BB>
Dear Everyone,
A postdoc position is available in my laboratory at Tohoku University
(Japan) to investigate the structure and properties of molecular liquids
confined at interfaces. The research will be performed in close
collaboration with the experimental group of Professor Kazue Kurihara
(IMRAM, Tohoku University), leader of the JST-CREST project: "Foundation of
Nano-Interface Technology by the Surface Forces Measurement". The title
project, started on October 1-st 2008, will run for five years (till March
2014).
The ideal candidate will have a Ph.D in Chemistry, Physics, or Materials
Science, and experience with the application of first-principles and
classical MD simulation methods to complex materials and/or molecular
systems. A previous postdoctoral experience is not necessary. However,
strong enthusiasm for solving challenging problems and cheerful disposition
(good nature) are both a plus.
Conditions: 1 year contract with possibility of extension to a second year.
Upon review of the candidate?s performance, the contract may be extended up
to the fifth year.
Starting date: April 1st 2009
Working place: Department of Applied Chemistry, Graduate School of
Engineering, Tohoku University, Sendai (Japan).
Contact: Dr. Fabio Pichierri, G-COE Laboratory, Department of Applied
Chemistry, Graduate School of Engineering, Tohoku University, 980-8579
Sendai (Japan). E-mail: fabio AT che.tohoku.ac.jp
Application (by E-mail, PDF file preferred): please send a CV including a
list of publications, a short description of research experience, and the
names of two references.
Deadline for receipt of applications: December 31, 2008.
----
Fabio Pichierri, G-COE Laboratory, Department of Applied Chemistry, Graduate
School of Engineering, Tohoku University, 980-8579 Sendai (Japan).
E-mail: fabio AT che.tohoku.ac.jp
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From giannozz at democritos.it Wed Nov 26 12:31:24 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 26 Nov 2008 12:31:24 +0100
Subject: [Pw_forum] binding energy for water adsorption at certain
surface
In-Reply-To: <412f6c680811260018t129946c4y16041aed3783b832@mail.gmail.com>
References: <412f6c680811260018t129946c4y16041aed3783b832@mail.gmail.com>
Message-ID: <492D338C.7050907@democritos.it>
vega lew wrote:
> I want to calculate the binding energy for water adsorption at certain
> surface.
binding energy = E(water+surface)-E(surface)-E(water).
All energies should be calculated with the same cell,
cutoff, k-points, at the equilibrium geometry of the
respective system, i.e. E(water) for an isolated water
molecule, not the water molecule in the geometry after
adsorption
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From quantumdft at gmail.com Wed Nov 26 12:57:46 2008
From: quantumdft at gmail.com (vega lew)
Date: Wed, 26 Nov 2008 19:57:46 +0800
Subject: [Pw_forum] binding energy for water adsorption at certain
surface
In-Reply-To: <492D338C.7050907@democritos.it>
References: <412f6c680811260018t129946c4y16041aed3783b832@mail.gmail.com>
<492D338C.7050907@democritos.it>
Message-ID: <412f6c680811260357u3f8d2ab5wa078d605de02f9bc@mail.gmail.com>
Dear sir,
Thank you very much for your reply.
It's very kind of you to point out my misunderstanding on calculation of
binding energy.
Now, my work seems to be further improved. Thank you again.
vega
On Wed, Nov 26, 2008 at 7:31 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:
> vega lew wrote:
>
> > I want to calculate the binding energy for water adsorption at certain
> > surface.
>
> binding energy = E(water+surface)-E(surface)-E(water).
> All energies should be calculated with the same cell,
> cutoff, k-points, at the equilibrium geometry of the
> respective system, i.e. E(water) for an isolated water
> molecule, not the water molecule in the geometry after
> adsorption
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
==================================================================================
Vega Lew ( weijia liu)
PH.D Candidate in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
******************************************************************************************************************
Email: vegalew at gmail.com
Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing,
Jiangsu, China
******************************************************************************************************************
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From schmidt at chem.wisc.edu Wed Nov 26 15:52:52 2008
From: schmidt at chem.wisc.edu (JR Schmidt)
Date: Wed, 26 Nov 2008 08:52:52 -0600
Subject: [Pw_forum] a strange behavior for QE-v4 compared with QE-v3
In-Reply-To: <7b6913e90811260029h413ab777ufb90f12e7b702236@mail.gmail.com>
References: <c92002fa0811241324k769a45b6rda0f8e4b3cf43fa9@mail.gmail.com> <492C3C1D.5060609@democritos.it> <c92002fa0811251058n299f5e7ch89508c14d0cf4fb8@mail.gmail.com>
<7b6913e90811260029h413ab777ufb90f12e7b702236@mail.gmail.com>
Message-ID: <492D62C4.8090303@chem.wisc.edu>
I ran into this same issue. Let me say that (for whatever reason)
setting OMP_NUM_THREADS, or MKL_NUM_THREADS did not seem to fix the
problem. MKL was still creating many threads per process, though
perhaps only one thread was active at at time.
I found a better solution, offering increased performance at least for
parallel jobs, was to link with the MKL serial library. This can be
done by modifying the following lines in make.sys (for MKL 10)
BLAS_LIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
LAPACK_LIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
then doing:
make clean (probably unnecessary)
make
Although this gives WORSE performance when you are only running a single
job (since it does not thread to take advantage of the other cores), if
you are trying to fully utilize your nodes by running several jobs or
parallel jobs, using the threaded library results in a giant mess.
> this looks a lot like you are using two different versions
> of MKL for the two compiles and thus are another "victim"
> of the automatic threading of MKL v10. you should not
> have a process with >100% CPU with a regular compile.
> now if you have 8 cores and 8 MPI tasks and each of them
> threads across 8 cores, you have a) a severe overload of
> the scheduler and b) a big mess and all kinds of bad
> performance issues.
>
> try setting OMP_NUM_THREADS=1 and check if that
> changes the behavior.
>
--
J.R. Schmidt
Assistant Professor of Chemistry
Room 8305D
Department of Chemistry
University of Wisconsin-Madison
1101 University Ave
Madison, WI 53706
Phone: (608) 262-2996
Fax: (608) 262-9918
E-mail: schmidt at chem.wisc.edu
http://www.chem.wisc.edu/people/profiles/schmidt.php
From paulatto at sissa.it Wed Nov 26 16:07:33 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 26 Nov 2008 16:07:33 +0100
Subject: [Pw_forum] a strange behavior for QE-v4 compared with QE-v3
In-Reply-To: <492D62C4.8090303@chem.wisc.edu>
References: <c92002fa0811241324k769a45b6rda0f8e4b3cf43fa9@mail.gmail.com> <492C3C1D.5060609@democritos.it> <c92002fa0811251058n299f5e7ch89508c14d0cf4fb8@mail.gmail.com> <7b6913e90811260029h413ab777ufb90f12e7b702236@mail.gmail.com>
<492D62C4.8090303@chem.wisc.edu>
Message-ID: <492D6635.8050204@sissa.it>
JR Schmidt ha scritto:
> I ran into this same issue. Let me say that (for whatever reason)
> setting OMP_NUM_THREADS, or MKL_NUM_THREADS did not seem to fix the
> problem. MKL was still creating many threads per process, though
>
If you are running a job on several nodes it may be tricky to ensure
the OMP_NUM_THREADS variable is set correctly on all of them. Using the
-x option of mpirun can be a solution, if you use open-mpi
bye
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
Due to budget cuts approved by Italian Minister of Finance and Italian
Minister "for" Education, University and Research this may be the last
email you receive from me.
Please send any future correspondence, possibly via pigeon, to
mr. Lorenzo Paulatto
under Roiano Railway Bridge - Pillar 2
34136, Trieste
Donations in food, coins, booze and processor time are warmly welcome.
From meghdad_saeedian at yahoo.com Wed Nov 26 17:30:00 2008
From: meghdad_saeedian at yahoo.com (meghdad saeedian)
Date: Wed, 26 Nov 2008 08:30:00 -0800 (PST)
Subject: [Pw_forum] exchange correlation subroutine
Message-ID: <508344.5269.qm@web31405.mail.mud.yahoo.com>
?
?
Hi every one.
I want to know, does exchange correlation program packd in the one subroutine and where is it?
Thanks for any comment.
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From akohlmey at cmm.chem.upenn.edu Wed Nov 26 17:44:31 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 26 Nov 2008 17:44:31 +0100
Subject: [Pw_forum] exchange correlation subroutine
In-Reply-To: <508344.5269.qm@web31405.mail.mud.yahoo.com>
References: <508344.5269.qm@web31405.mail.mud.yahoo.com>
Message-ID: <7b6913e90811260844g3a27b5ebk959e835d5dc1ecea@mail.gmail.com>
grep is your friend... ;-)
cheers,
axel.
On 11/26/08, meghdad saeedian <meghdad_saeedian at yahoo.com> wrote:
>
>
> Hi every one.
> I want to know, does exchange correlation program packd in the one
> subroutine and where is it?
> Thanks for any comment.
>
>
>
>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From lanhaiping at gmail.com Wed Nov 26 17:48:09 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Thu, 27 Nov 2008 00:48:09 +0800
Subject: [Pw_forum] a strange behavior for QE-v4 compared with QE-v3
In-Reply-To: <7b6913e90811260029h413ab777ufb90f12e7b702236@mail.gmail.com>
References: <c92002fa0811241324k769a45b6rda0f8e4b3cf43fa9@mail.gmail.com>
<492C3C1D.5060609@democritos.it>
<c92002fa0811251058n299f5e7ch89508c14d0cf4fb8@mail.gmail.com>
<7b6913e90811260029h413ab777ufb90f12e7b702236@mail.gmail.com>
Message-ID: <c92002fa0811260848k4a325a2co26e797c90950cf02@mail.gmail.com>
thanks , Axel.
This scheme does work .
best
On Wed, Nov 26, 2008 at 4:29 PM, Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu
> wrote:
> this looks a lot like you are using two different versions
> of MKL for the two compiles and thus are another "victim"
> of the automatic threading of MKL v10. you should not
> have a process with >100% CPU with a regular compile.
> now if you have 8 cores and 8 MPI tasks and each of them
> threads across 8 cores, you have a) a severe overload of
> the scheduler and b) a big mess and all kinds of bad
> performance issues.
>
> try setting OMP_NUM_THREADS=1 and check if that
> changes the behavior.
>
> cheers,
> axel.
>
>
>
> On 11/25/08, lan haiping <lanhaiping at gmail.com> wrote:
> > Dear Paolo,
> > thanks for explaination.
> > But this behavior is really strange i have ever come to.
> > i have tried to rebuild the mpich and the QE, and nothing is
> > gained. Another strange problem is that the work i execute parallelly
> > with QE-v4 sometimes come to idle without execuation or output
> > information.
> >
> > is there any other suggestion to figure what the problem with it ?
> >
> > thanks
> >
> > On Wed, Nov 26, 2008 at 1:55 AM, Paolo Giannozzi
> > <giannozz at democritos.it>wrote:
> >
> >> lan haiping wrote:
> >>
> >> > A strange behavior is found for QE v4 when i carry out parallel
> >> > executation [...] But this situation doesnot happen when i try
> >> > to run the same work with QE-v3.
> >>
> >> it's hard to say anything meaningful based on the output of "top"
> >> and little more. There are several parallelization levles in QE,
> >> as explained here:
> >>
> http://www.quantum-espresso.org/wiki/index.php/Running_on_parallel_machines
> >> I don't remember what happened between v.3 and v.4, but whatever
> >> happened, it is unlikely to make parallelism less effective.
> >>
> >> Paolo
> >> --
> >> Paolo Giannozzi, Democritos and University of Udine, Italy
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >>
> >
> >
> >
> > --
> > Hai-Ping Lan
> > Department of Electronics ,
> > Peking University , Bejing, 100871
> > lanhaiping at gmail.com, hplan at pku.edu.cn
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From lanhaiping at gmail.com Wed Nov 26 17:49:51 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Thu, 27 Nov 2008 00:49:51 +0800
Subject: [Pw_forum] a strange behavior for QE-v4 compared with QE-v3
In-Reply-To: <492D62C4.8090303@chem.wisc.edu>
References: <c92002fa0811241324k769a45b6rda0f8e4b3cf43fa9@mail.gmail.com>
<492C3C1D.5060609@democritos.it>
<c92002fa0811251058n299f5e7ch89508c14d0cf4fb8@mail.gmail.com>
<7b6913e90811260029h413ab777ufb90f12e7b702236@mail.gmail.com>
<492D62C4.8090303@chem.wisc.edu>
Message-ID: <c92002fa0811260849t3a3906e4l289718de9e378c51@mail.gmail.com>
Hi, Schmidt, i will try your method to build QE for other
machines. thanks for your sharing.
best
On Wed, Nov 26, 2008 at 10:52 PM, JR Schmidt <schmidt at chem.wisc.edu> wrote:
> I ran into this same issue. Let me say that (for whatever reason)
> setting OMP_NUM_THREADS, or MKL_NUM_THREADS did not seem to fix the
> problem. MKL was still creating many threads per process, though
> perhaps only one thread was active at at time.
>
> I found a better solution, offering increased performance at least for
> parallel jobs, was to link with the MKL serial library. This can be
> done by modifying the following lines in make.sys (for MKL 10)
>
> BLAS_LIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
> LAPACK_LIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
>
> then doing:
> make clean (probably unnecessary)
> make
>
> Although this gives WORSE performance when you are only running a single
> job (since it does not thread to take advantage of the other cores), if
> you are trying to fully utilize your nodes by running several jobs or
> parallel jobs, using the threaded library results in a giant mess.
>
> > this looks a lot like you are using two different versions
> > of MKL for the two compiles and thus are another "victim"
> > of the automatic threading of MKL v10. you should not
> > have a process with >100% CPU with a regular compile.
> > now if you have 8 cores and 8 MPI tasks and each of them
> > threads across 8 cores, you have a) a severe overload of
> > the scheduler and b) a big mess and all kinds of bad
> > performance issues.
> >
> > try setting OMP_NUM_THREADS=1 and check if that
> > changes the behavior.
> >
> --
> J.R. Schmidt
> Assistant Professor of Chemistry
> Room 8305D
> Department of Chemistry
> University of Wisconsin-Madison
> 1101 University Ave
> Madison, WI 53706
>
> Phone: (608) 262-2996
> Fax: (608) 262-9918
> E-mail: schmidt at chem.wisc.edu
> http://www.chem.wisc.edu/people/profiles/schmidt.php
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From Giovanni.Cantele at na.infn.it Wed Nov 26 17:46:51 2008
From: Giovanni.Cantele at na.infn.it (Giovanni Cantele)
Date: Wed, 26 Nov 2008 17:46:51 +0100
Subject: [Pw_forum] exchange correlation subroutine
In-Reply-To: <508344.5269.qm@web31405.mail.mud.yahoo.com>
References: <508344.5269.qm@web31405.mail.mud.yahoo.com>
Message-ID: <492D7D7B.3000102@na.infn.it>
meghdad saeedian wrote:
>
>
> Hi every one.
> I want to know, does exchange correlation program packd in the one
> subroutine and where is it?
> Thanks for any comment.
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
I understand you need to know where different XC functionals are coded.
You can start having a look to the following files:
flib/functionals.f90
flib/more_functionals.f90
flib/lsda_functionals.f90
Modules/functionals.f90
Things like that may be (sometimes) easily found by browsing the QE
directory tree and using the "grep" command.
Giovanni
--
Dr. Giovanni Cantele
Coherentia CNR-INFM and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario di Monte S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Fax: +39 081 676346
E-mail: giovanni.cantele at cnr.it
giovanni.cantele at na.infn.it
Web: http://people.na.infn.it/~cantele
Research Group: http://www.nanomat.unina.it
From manoj at phys.ufl.edu Thu Nov 27 00:26:11 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Wed, 26 Nov 2008 18:26:11 -0500 (EST)
Subject: [Pw_forum] complex band
In-Reply-To: <Pine.GSO.4.21.0810201748530.1564-100000@neptune.phys.ufl.edu>
Message-ID: <Pine.GSO.4.21.0811261812130.10614-100000@neptune.phys.ufl.edu>
Dear Alexander, PWSCF users and developers,
I have a technical question in one of the subroutines used to calculate
complex band. The subroutine 'init_gper.f90' under PWCOND directory is
used to calculate number of G perpendicular vectors within the energy
cutoff by using [k_{\perp}+G_{\perp}]^2.le.E_{cut}. I understand the
counting of Gper, but i dont understand how do they construct the Gper
vectors. For example what is 'ngpsh'? It is defined as 'no. of shells for
G', but i really dont understand what this is. I dont understand after
line 50 of the code in init_gper.f90. Mainly what does the following
piece of code do
do i=1,nrx
do j=1,nry
icount=0
do iw=1, ngpsh
if (abs(norm2-gnorm2(iw)).gt.eps) then
icount=icount+1
else
nshell(i,j)=iw
endif
enddo
if (icount.eq.ngpsh) then
ngpsh=ngpsh+1
gnorm2(ngpsh)=norm2
nshell(i,j)=ngpsh
endif
endif
enddo
enddo
I understand it is not a good way of asking question, but I am completely
lost. Any help will be appreciated.
Regards,
Manoj
From chenhanghuipwscf at gmail.com Thu Nov 27 06:54:48 2008
From: chenhanghuipwscf at gmail.com (hanghui chen)
Date: Thu, 27 Nov 2008 00:54:48 -0500
Subject: [Pw_forum] structure relaxation in the sawtooth method
Message-ID: <22ae3ca40811262154u22f110adi50ae4b4b2db3821c@mail.gmail.com>
Dear PWSCF users,
I know this question may be too technical, but I would like to give a
try.
I am implementing how to do structure relaxation in the presence of a
sawtooth potential with atoms in the reversed region (I know it is a very
weird idea.). I already fixed the forces so that the forces on the atoms in
the reversed region are correctly calculated.
I would like to know: even if the forces are correctly calculated, do I
need to update anything in the move_ions.f90 so that structure relaxation
can be correctly executed. Before the version 4.0.2, the structure
relaxation in the sawtooth method is not correctly implemented because the
electric field disappears after the first run. Can anyone tell me how this
bug is fixed? It will be very useful if I want to implement a new
feature concerning the sawtooth method (though a very weird feature).
Thank you very much.
Hanghui Chen
Department of Physics,
Yale University
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From giannozz at democritos.it Thu Nov 27 09:07:10 2008
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 27 Nov 2008 09:07:10 +0100
Subject: [Pw_forum] structure relaxation in the sawtooth method
In-Reply-To: <22ae3ca40811262154u22f110adi50ae4b4b2db3821c@mail.gmail.com>
References: <22ae3ca40811262154u22f110adi50ae4b4b2db3821c@mail.gmail.com>
Message-ID: <492E552E.9010306@democritos.it>
hanghui chen wrote:
> Before the version 4.0.2, the structure relaxation in the sawtooth
> method is not correctly implemented because the electric field disappears
> after the first run. Can anyone tell me how this bug is fixed?
it was fixed here:
http://www.democritos.it:8888/O-sesame/chngview?cn=6133
Please get this and verify if the bug you mention is fixed:
http://www.pwscf.org/downloads/PWversion/4.0.4/espresso-4.0.4.tar.gz
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
From paulatto at sissa.it Thu Nov 27 10:20:32 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 27 Nov 2008 10:20:32 +0100 (CET)
Subject: [Pw_forum] structure relaxation in the sawtooth method
In-Reply-To: <22ae3ca40811262154u22f110adi50ae4b4b2db3821c@mail.gmail.com>
References: <22ae3ca40811262154u22f110adi50ae4b4b2db3821c@mail.gmail.com>
Message-ID: <29210.79.1.62.65.1227777632.squirrel@webmail.sissa.it>
On Gio, Novembre 27, 2008 06:54, hanghui chen wrote:
> I am implementing how to do structure relaxation in the presence of a
> sawtooth potential with atoms in the reversed region (I know it is a very
> weird idea.).
We have been talking for a while on fixing that subroutine, it is quite
garbled at the moment. If you cannot understand what some specific
instruction is doing, and you think your question would be too technical
for this mailing list, feel free to ask me personally.
To answer your question, I don't think any update in ions is necessary.
Forces contribution from ext efield are written to the global variable
forcefield (from module extfield); this variable is than used in
forces.f90 to add the efield contribution.
cheers
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
----------------------------------------------------------------
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From rdmeneze at yahoo.com.br Thu Nov 27 15:44:55 2008
From: rdmeneze at yahoo.com.br (Rafael Dias Menezes)
Date: Thu, 27 Nov 2008 06:44:55 -0800 (PST)
Subject: [Pw_forum] problem with TPSS (Tao-Perdew-Staroverov-Scuseria)
meta-GGA for silicon
Message-ID: <778134.92069.qm@web65702.mail.ac4.yahoo.com>
On Nov 23, 2008 at 22:04 , Paolo Giannozzi wrote:
>TPSS is quite nasty from a numerical point of view. Try to use lapack
>from sources instead of optimized libraries. On my Macintosh I get
>this problem when testing tests/metaGGA.in with atlas loaded;
>it disappears if I link lapack instead.
Thank you, Paolo for the trick.
Really this error disappear but the calculation to silicon atom in a big box don't converge. I did 100 interactions and the convergency isn't reach.
Can someone get me a direction in this simple calculus? Maybe I'm missing the setup of some input variable do pwscf.
thanks,
Rafael Dias
Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
From akohlmey at cmm.chem.upenn.edu Thu Nov 27 17:01:03 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 27 Nov 2008 17:01:03 +0100
Subject: [Pw_forum] problem with TPSS (Tao-Perdew-Staroverov-Scuseria)
meta-GGA for silicon
In-Reply-To: <778134.92069.qm@web65702.mail.ac4.yahoo.com>
References: <778134.92069.qm@web65702.mail.ac4.yahoo.com>
Message-ID: <7b6913e90811270801i5d0f49er6636d74deee130f6@mail.gmail.com>
rafael,
please keep in mind, that a single atom in a large box
is a bit of a pathological case, since you tend to pick up
all the noise from the "vacuum" area, which is most likely
the source of your numerical instabilities. if it is just for
testing, you'll probably get better results with a bulk crystal
system (and it'll be faster, too).
cheers,
axel.
On 11/27/08, Rafael Dias Menezes <rdmeneze at yahoo.com.br> wrote:
> On Nov 23, 2008 at 22:04 , Paolo Giannozzi wrote:
>
>>TPSS is quite nasty from a numerical point of view. Try to use lapack
>>from sources instead of optimized libraries. On my Macintosh I get
>>this problem when testing tests/metaGGA.in with atlas loaded;
>>it disappears if I link lapack instead.
>
> Thank you, Paolo for the trick.
>
> Really this error disappear but the calculation to silicon atom in a big box
> don't converge. I did 100 interactions and the convergency isn't reach.
>
> Can someone get me a direction in this simple calculus? Maybe I'm missing
> the setup of some input variable do pwscf.
>
> thanks,
> Rafael Dias
>
>
>
> Veja quais s?o os assuntos do momento no Yahoo! +Buscados
> http://br.maisbuscados.yahoo.com
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From ykhuang0731 at gmail.com Thu Nov 27 20:21:32 2008
From: ykhuang0731 at gmail.com (Yi-Kai Huang)
Date: Fri, 28 Nov 2008 03:21:32 +0800
Subject: [Pw_forum] Calculation of band diagram of cobalt ferrite
Message-ID: <2643f0f10811271121v758415e5nf93552916ed99dcb@mail.gmail.com>
Dear all,
I tried to calculate band diagram of cobalt ferrite (antiferromagnetic
material) by using example05.
However, the band diagram I get is blank. In my scf.out file, there
are lines showing that
" CG style diagonalization c_bands: 1 eigenvalues not converged"
I am not sure is it related to my blank band diagram.
Below is my input file. (I did not change anything other than material
description)
&system
ibrav= 2, celldm(1) =15.87, nat= 14, ntyp= 3,
ecutwfc = 55
ecutrho = 450
nspin = 2
starting_magnetization(1) = 0.7
starting_magnetization(2) = -0.6
nbnd = 32
occupations = 'smearing'
degauss = 0.008
smearing = 'cold'
lda_plus_u = .true.,
Hubbard_U(1) = 4.0,
Hubbard_U(2) = 4.5,
/
&electrons
diagonalization = 'cg'
mixing_mode = 'plain'
mixing_beta = 0.7
conv_thr = 1.0d-8
Thanks for the help!
Kenny
From paulatto at sissa.it Thu Nov 27 23:26:09 2008
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 27 Nov 2008 23:26:09 +0100 (CET)
Subject: [Pw_forum] Calculation of band diagram of cobalt ferrite
In-Reply-To: <2643f0f10811271121v758415e5nf93552916ed99dcb@mail.gmail.com>
References: <2643f0f10811271121v758415e5nf93552916ed99dcb@mail.gmail.com>
Message-ID: <11066.79.1.62.65.1227824769.squirrel@webmail.sissa.it>
On Gio, Novembre 27, 2008 20:21, Yi-Kai Huang wrote:
> However, the band diagram I get is blank.
if you have not changed the plotband input files, it is likely that you
have plotted an energy range that misses all the bands! Check the energy
of the eigenvalues in the output files of the scf calculation and tune the
plotband input accordingly.
regards
--
Lorenzo Paulatto
SISSA & DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www: http://people.sissa.it/~paulatto/
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From smogunov at sissa.it Fri Nov 28 08:59:46 2008
From: smogunov at sissa.it (Alexander)
Date: Fri, 28 Nov 2008 08:59:46 +0100
Subject: [Pw_forum] complex band
In-Reply-To: <Pine.GSO.4.21.0811261812130.10614-100000@neptune.phys.ufl.edu>
References: <Pine.GSO.4.21.0811261812130.10614-100000@neptune.phys.ufl.edu>
Message-ID: <200811280859.46256.smogunov@sissa.it>
Dear Manoj
Ngper is the total number of g_perp=G_perp+k_perp with |g_perp|^2<E_cut
which are arranged into the shells. Each shell contains g_perp having the same
norm which is very useful because many calculations with g_perp depend only
on their norms. The number of shells is ngpsh. gnsh(ngpsh) is the norm for
each shell, ninsh(ngpsh) is the number of g_perp in the shell.
The array nshell is the auxiliary array used further to arrange the g_perp
vectors in the shells.
Hope this helps you,
regards, Alexander
and ngpsh is the number of shells
On Thursday 27 November 2008 00:26, Manoj Srivastava wrote:
> Dear Alexander, PWSCF users and developers,
> I have a technical question in one of the subroutines used to calculate
> complex band. The subroutine 'init_gper.f90' under PWCOND directory is
> used to calculate number of G perpendicular vectors within the energy
> cutoff by using [k_{\perp}+G_{\perp}]^2.le.E_{cut}. I understand the
> counting of Gper, but i dont understand how do they construct the Gper
> vectors. For example what is 'ngpsh'? It is defined as 'no. of shells for
> G', but i really dont understand what this is. I dont understand after
> line 50 of the code in init_gper.f90. Mainly what does the following
> piece of code do
>
> do i=1,nrx
> do j=1,nry
> icount=0
> do iw=1, ngpsh
> if (abs(norm2-gnorm2(iw)).gt.eps) then
> icount=icount+1
> else
> nshell(i,j)=iw
> endif
> enddo
> if (icount.eq.ngpsh) then
> ngpsh=ngpsh+1
> gnorm2(ngpsh)=norm2
> nshell(i,j)=ngpsh
> endif
> endif
> enddo
> enddo
> I understand it is not a good way of asking question, but I am completely
> lost. Any help will be appreciated.
>
> Regards,
> Manoj
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
From ari.p.seitsonen at iki.fi Fri Nov 28 11:56:11 2008
From: ari.p.seitsonen at iki.fi (Ari P Seitsonen)
Date: Fri, 28 Nov 2008 11:56:11 +0100 (CET)
Subject: [Pw_forum] problem with TPSS (Tao-Perdew-Staroverov-Scuseria)
meta-GGA for silicon
In-Reply-To: <7b6913e90811270801i5d0f49er6636d74deee130f6@mail.gmail.com>
References: <778134.92069.qm@web65702.mail.ac4.yahoo.com>
<7b6913e90811270801i5d0f49er6636d74deee130f6@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0811281148470.11168@peridot.impmc.jussieu.fr>
Dear Rafael,
Adding to Axel's comment; you might experience the problem of
"non-spherical" atom in Si since in the free atom you have two p-electrons
to put on three degenerate (spin-up) states. Thus there will be a fight
(= usually no convergence) which one of p_x, p_y and p_z will get them if
tried straightforwardly. What one can try is to modify the cell slightly
making it non-cubic, eg tetragonal and then seeing if the calculation
converges. Additionally you might try adding more mixing of the previous
charge density.
Summa summarum, this problem might not be due to the implemenation of
TPSS but a "pathodological example".
Greetings from Paris,
apsi
PS This topic keeps on popping up on the mailing lists of different codes
quite regularly. Apparently the people do not know that the topic was
discussed already decades ago. ;)
"Energies of atoms with nonspherical charge densities calculated with
nonlocal density-functional theory"
Frank W Kutzler and G S Painter
Phys Rev Lett 59, 1285 (1987)
DOI: 10.1103/PhysRevLett.59.1285
On Thu, 27 Nov 2008, Axel Kohlmeyer wrote:
> rafael,
>
> please keep in mind, that a single atom in a large box
> is a bit of a pathological case, since you tend to pick up
> all the noise from the "vacuum" area, which is most likely
> the source of your numerical instabilities. if it is just for
> testing, you'll probably get better results with a bulk crystal
> system (and it'll be faster, too).
>
> cheers,
> axel.
>
> On 11/27/08, Rafael Dias Menezes <rdmeneze at yahoo.com.br> wrote:
>> On Nov 23, 2008 at 22:04 , Paolo Giannozzi wrote:
>>
>>> TPSS is quite nasty from a numerical point of view. Try to use lapack
>>> from sources instead of optimized libraries. On my Macintosh I get
>>> this problem when testing tests/metaGGA.in with atlas loaded;
>>> it disappears if I link lapack instead.
>>
>> Thank you, Paolo for the trick.
>>
>> Really this error disappear but the calculation to silicon atom in a big box
>> don't converge. I did 100 interactions and the convergency isn't reach.
>>
>> Can someone get me a direction in this simple calculus? Maybe I'm missing
>> the setup of some input variable do pwscf.
>>
>> thanks,
>> Rafael Dias
>>
>>
>>
>> Veja quais s?o os assuntos do momento no Yahoo! +Buscados
>> http://br.maisbuscados.yahoo.com
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
>
--
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
IMPMC, CNRS & Universit? Pierre et Marie Curie
Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820
From sclauzer at sissa.it Fri Nov 28 15:39:28 2008
From: sclauzer at sissa.it (Gabriele Sclauzero)
Date: Fri, 28 Nov 2008 15:39:28 +0100
Subject: [Pw_forum] problem with TPSS (Tao-Perdew-Staroverov-Scuseria)
meta-GGA for silicon
In-Reply-To: <Pine.LNX.4.64.0811281148470.11168@peridot.impmc.jussieu.fr>
References: <778134.92069.qm@web65702.mail.ac4.yahoo.com> <7b6913e90811270801i5d0f49er6636d74deee130f6@mail.gmail.com>
<Pine.LNX.4.64.0811281148470.11168@peridot.impmc.jussieu.fr>
Message-ID: <493002A0.8010903@sissa.it>
Ari P Seitsonen wrote:
>
> Dear Rafael,
>
> Adding to Axel's comment; you might experience the problem of
> "non-spherical" atom in Si since in the free atom you have two
> p-electrons to put on three degenerate (spin-up) states. Thus there will
> be a fight (= usually no convergence) which one of p_x, p_y and p_z will
> get them if tried straightforwardly. What one can try is to modify the
> cell slightly making it non-cubic,
This solution is nice, I'll try it someday. Anyway, the pw.x flag:
nosym=.true.
could do the job in this case (and it is often useful for computing atoms or molecules in
supercells).
You can even fix occupations in the more problematic cases, by setting:
occupations = 'from_input'
and specifying the desired occupations at the end of the namelists.
NB: works only with gamma point
Hope this helps,
regards
GS
>>>
>>>
>>
>>
>>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
--
La legge n. 133 uccide l'Universit? e la Ricerca italiana!
Save Italian Brains! (http://saveitalianbrains.wordpress.com/)
o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student |
| c/o: SISSA & CNR-INFM Democritos, |
| via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511 |
| skype: gurlonotturno |
o ------------------------------------------------ o
From rdmeneze at yahoo.com.br Fri Nov 28 19:26:52 2008
From: rdmeneze at yahoo.com.br (Rafael Dias Menezes)
Date: Fri, 28 Nov 2008 10:26:52 -0800 (PST)
Subject: [Pw_forum] problem with TPSS (Tao-Perdew-Staroverov-Scuseria)
meta-GGA for silicon
In-Reply-To: <493002A0.8010903@sissa.it>
Message-ID: <818240.29415.qm@web65705.mail.ac4.yahoo.com>
Hi everybody,
thank you for the help.
That's hug
Rafael Dias
--- Em sex, 28/11/08, Gabriele Sclauzero <sclauzer at sissa.it> escreveu:
> De: Gabriele Sclauzero <sclauzer at sissa.it>
> Assunto: Re: [Pw_forum] problem with TPSS (Tao-Perdew-Staroverov-Scuseria) meta-GGA for silicon
> Para: "PWSCF Forum" <pw_forum at pwscf.org>
> Data: Sexta-feira, 28 de Novembro de 2008, 12:39
> Ari P Seitsonen wrote:
> >
> > Dear Rafael,
> >
> > Adding to Axel's comment; you might experience
> the problem of
> > "non-spherical" atom in Si since in the free
> atom you have two
> > p-electrons to put on three degenerate (spin-up)
> states. Thus there will
> > be a fight (= usually no convergence) which one of
> p_x, p_y and p_z will
> > get them if tried straightforwardly. What one can try
> is to modify the
> > cell slightly making it non-cubic,
>
> This solution is nice, I'll try it someday. Anyway, the
> pw.x flag:
>
> nosym=.true.
>
> could do the job in this case (and it is often useful for
> computing atoms or molecules in
> supercells).
> You can even fix occupations in the more problematic cases,
> by setting:
>
> occupations = 'from_input'
>
> and specifying the desired occupations at the end of the
> namelists.
>
> NB: works only with gamma point
>
> Hope this helps,
>
> regards
>
> GS
>
> >>>
> >>>
> >>
> >>
> >>
> >
> >
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> --
>
> La legge n. 133 uccide l'Universit? e la Ricerca
> italiana!
>
> Save Italian Brains!
> (http://saveitalianbrains.wordpress.com/)
>
> o ------------------------------------------------ o
> | Gabriele Sclauzero, PhD Student |
> | c/o: SISSA & CNR-INFM Democritos, |
> | via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it |
> | phone: +39 040 3787 511 |
> | skype: gurlonotturno |
> o ------------------------------------------------ o
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
From frnkhzi at yahoo.com Sat Nov 29 13:42:15 2008
From: frnkhzi at yahoo.com (fereydoon khazali)
Date: Sat, 29 Nov 2008 04:42:15 -0800 (PST)
Subject: [Pw_forum] slab
Message-ID: <88705.84554.qm@web30102.mail.mud.yahoo.com>
Dear All
Is this input file?correct for 5-layer slab of Ag(001)? vacuum thickness about 8.18 ang. & surface geometry is (2*2)
?
&CONTROL
calculation = "scf",
title = 'Ag-slab (001) oxygen adsorbed '
pseudo_dir = "/home/f/espresso-4.0/pseudo",
outdir = "/home/f/tmp",
/
&SYSTEM
ibrav = 6,
celldm(1) = 15.458,
celldm(3) = 3.956,
nat = 48,
ntyp = 2,
ecutwfc = 27.D0,
ecutrho = 216.,
occupations = "smearing",
smearing = "gaussian",
degauss = 0.03D0,
/
&ELECTRONS
conv_thr = 1.D-7,
mixing_beta = 0.3D0,
/
&IONS
ion_dynamics = "damp",
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
Ag 1.D0 Al_pbe-d-rrkusj.UPF
O 1.0 O.pbe-rrkjus.PUF
ATOMIC_POSITIONS {bohr}
Ag ?0.0000????? 0.00000?????? 30.5759
Ag? 7.7290????? 0.00000?????? 30.5759
Ag? 0.0000????? 7.72900?????? 30.5759
Ag? 3.8645????? 3.86450?????? 30.5759
Ag? 3.8645???? 11.5935??????? 30.5759
Ag? 7.7290????? 7.72900?????? 30.5759
Ag? 11.5935??? 3.8645???????? 30.5759
Ag? 11.5935?? 11.5935??????? 30.5759
Ag? 0.0000???? 3.8645???????? 34.4404
Ag? 0.0000??? 11.5935??????? 34.4404
Ag? 3.8645?? ?0.0000????????? 34.4404
Ag? 11.5935? ?0.0000???????? 34.4404
Ag? 7.729???? 3.8645????????? 34.4404
Ag? 7.729??? 11.5935???????? 34.4404
Ag? 3.8645??? 7.7290???????? 34.4404
Ag? 11.5935?? 7.7290??????? 34.4404
Ag? 0.0000??? 0.000?????????? 38.3049
Ag? 7.7290?? ?0.000?????????? 38.3049
Ag? 0.0000??? 7.729?????????? 38.3049
Ag? 3.8645??? 3.8645???????? 38.3049
Ag? 3.8645?? 11.5935??????? 38.3049
Ag? 7.7290???? 7.7290??????? 38.3049
Ag? 11.5935??? 3.8645???????38.3049
Ag? 11.5935?? 11.5935??????38.3049
Ag? 0.00000??? 3.864500???? 26.7114
Ag? 0.00000?? 11.59350????? 26.7114
Ag? 3.86450?? 0.0000000??? 26.7114
Ag? 11.5935? ?0.0?????????????? 26.7114
Ag? 7.729????? 3.8645????????? 26.7114
Ag? 7.729???? 11.5935???????? 26.7114
Ag? 3.8645??? 7.729??????????? 26.7114
Ag? 11.5935? ?7.729???????????26.7114
Ag? 0.0000??? 0.00000??????????? 22.8469
Ag? 7.7290??? 0.00000??????????? 22.8469
Ag? 0.0000??? 7.72900??????????? 22.8469
Ag? 3.8645??? 3.86450??????????? 22.8469
Ag? 3.8645??? 11.5935??????????? 22.8469
Ag? 7.7290???? 7.72900?????????? 22.8469
Ag? 11.5935??? 3.8645??????????? 22.8469
Ag? 11.5935?? 11.5935?????????? 22.8469
O?? 3.8645??? 3.86450??????????? 40.3049
O?? 3.8645??? 11.5935??????????? 40.3049
O?? 11.5935??? 3.8645??????????? 40.3049
O?? 11.5935?? 11.5935???????????40.3049
O?? 3.8645????? 3.86450????????? 20.8469
O?? 3.8645????? 11.5935????????? 20.8469
O?? 11.5935???? 3.8645?????????? 20.8469
O?? 11.5935??? 11.5935???????? ?20.8469
K_POINTS automatic
4 4 1
?
?
?
thanks
fereydoon Kh.
?
?
?
?
?
?
?
?
?
?
?
?
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From eyvaz_isaev at yahoo.com Sun Nov 30 00:02:07 2008
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Sat, 29 Nov 2008 15:02:07 -0800 (PST)
Subject: [Pw_forum] slab
In-Reply-To: <88705.84554.qm@web30102.mail.mud.yahoo.com>
Message-ID: <551486.33262.qm@web65704.mail.ac4.yahoo.com>
Dear Fereydoon,
It looks more or less correct except &IONS section which is excess as you specified "scf", i.e. to perform only self-consistent calculation. If you are going to do atomic-relaxation calculations, then you should use "relax".
I think the use of default parameters is more preferable unless you experience troubles or you know what you are doing.
For example, please read INPUT_PW about "wfc_extrapolation" and see pseudopotentials you applied.
If you learn more about your geometry you can reduce twice the number of atoms you considered.
Nevertheless, it should be only your responsibility to accept whether your input file is correct.
And finally, please provide your affiliation. That is default Netiquette in this forum.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia,
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden
Condensed Matter Theory Group, Uppsala University, Sweden
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
--- On Sat, 11/29/08, fereydoon khazali <frnkhzi at yahoo.com> wrote:
> From: fereydoon khazali <frnkhzi at yahoo.com>
> Subject: [Pw_forum] slab
> To: Pw_forum at pwscf.org
> Date: Saturday, November 29, 2008, 3:42 PM
> Dear All
> Is this input file?correct for 5-layer slab of Ag(001)?
> vacuum thickness about 8.18 ang. & surface geometry is
> (2*2)
> ?
> &CONTROL
> calculation = "scf",
> title = 'Ag-slab (001) oxygen adsorbed '
> pseudo_dir = "/home/f/espresso-4.0/pseudo",
> outdir = "/home/f/tmp",
> /
> &SYSTEM
> ibrav = 6,
> celldm(1) = 15.458,
> celldm(3) = 3.956,
> nat = 48,
> ntyp = 2,
> ecutwfc = 27.D0,
> ecutrho = 216.,
> occupations = "smearing",
> smearing = "gaussian",
> degauss = 0.03D0,
> /
> &ELECTRONS
> conv_thr = 1.D-7,
> mixing_beta = 0.3D0,
> /
> &IONS
> ion_dynamics = "damp",
> pot_extrapolation = "second_order",
> wfc_extrapolation = "second_order",
> /
> ATOMIC_SPECIES
> Ag 1.D0 Al_pbe-d-rrkusj.UPF
> O 1.0 O.pbe-rrkjus.PUF
> ATOMIC_POSITIONS {bohr}
> Ag ?0.0000????? 0.00000?????? 30.5759
> Ag? 7.7290????? 0.00000?????? 30.5759
> Ag? 0.0000????? 7.72900?????? 30.5759
> Ag? 3.8645????? 3.86450?????? 30.5759
> Ag? 3.8645???? 11.5935??????? 30.5759
> Ag? 7.7290????? 7.72900?????? 30.5759
> Ag? 11.5935??? 3.8645???????? 30.5759
> Ag? 11.5935?? 11.5935??????? 30.5759
> Ag? 0.0000???? 3.8645???????? 34.4404
> Ag? 0.0000??? 11.5935??????? 34.4404
> Ag? 3.8645?? ?0.0000????????? 34.4404
> Ag? 11.5935? ?0.0000???????? 34.4404
> Ag? 7.729???? 3.8645????????? 34.4404
> Ag? 7.729??? 11.5935???????? 34.4404
> Ag? 3.8645??? 7.7290???????? 34.4404
> Ag? 11.5935?? 7.7290??????? 34.4404
> Ag? 0.0000??? 0.000?????????? 38.3049
> Ag? 7.7290?? ?0.000?????????? 38.3049
> Ag? 0.0000??? 7.729?????????? 38.3049
> Ag? 3.8645??? 3.8645???????? 38.3049
> Ag? 3.8645?? 11.5935??????? 38.3049
> Ag? 7.7290???? 7.7290??????? 38.3049
> Ag? 11.5935??? 3.8645???????38.3049
> Ag? 11.5935?? 11.5935??????38.3049
> Ag? 0.00000??? 3.864500???? 26.7114
> Ag? 0.00000?? 11.59350????? 26.7114
> Ag? 3.86450?? 0.0000000??? 26.7114
> Ag? 11.5935? ?0.0?????????????? 26.7114
> Ag? 7.729????? 3.8645????????? 26.7114
> Ag? 7.729???? 11.5935???????? 26.7114
> Ag? 3.8645??? 7.729??????????? 26.7114
> Ag? 11.5935? ?7.729???????????26.7114
> Ag? 0.0000??? 0.00000??????????? 22.8469
> Ag? 7.7290??? 0.00000??????????? 22.8469
> Ag? 0.0000??? 7.72900??????????? 22.8469
> Ag? 3.8645??? 3.86450??????????? 22.8469
> Ag? 3.8645??? 11.5935??????????? 22.8469
> Ag? 7.7290???? 7.72900?????????? 22.8469
> Ag? 11.5935??? 3.8645??????????? 22.8469
> Ag? 11.5935?? 11.5935?????????? 22.8469
> O?? 3.8645??? 3.86450??????????? 40.3049
> O?? 3.8645??? 11.5935??????????? 40.3049
> O?? 11.5935??? 3.8645??????????? 40.3049
> O?? 11.5935?? 11.5935???????????40.3049
> O?? 3.8645????? 3.86450????????? 20.8469
> O?? 3.8645????? 11.5935????????? 20.8469
> O?? 11.5935???? 3.8645?????????? 20.8469
> O?? 11.5935??? 11.5935???????? ?20.8469
> K_POINTS automatic
> 4 4 1
> ?
> ?
> ?
> thanks
> fereydoon Kh.
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
> ?
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
From wangqj1 at 126.com Sun Nov 30 11:01:56 2008
From: wangqj1 at 126.com (wangqj1)
Date: Sun, 30 Nov 2008 18:01:56 +0800 (CST)
Subject: [Pw_forum] relax
Message-ID: <19778204.397231228039316587.JavaMail.coremail@bj126app26.126.com>
Dear all
When relax ,which algorithm is better ? Bfgs or damp ? I use bfgs,but find it very slow . Anybody who know about this ,please give some advice ,thank you .
Q J Wang
XiangTan University
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From akohlmey at cmm.chem.upenn.edu Sun Nov 30 12:56:45 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 30 Nov 2008 12:56:45 +0100
Subject: [Pw_forum] relax
In-Reply-To: <19778204.397231228039316587.JavaMail.coremail@bj126app26.126.com>
References: <19778204.397231228039316587.JavaMail.coremail@bj126app26.126.com>
Message-ID: <7b6913e90811300356i3d3a82a8kd829a3af4e199437@mail.gmail.com>
On 11/30/08, wangqj1 <wangqj1 at 126.com> wrote:
>
> Dear all
dear wang,
> When relax ,which algorithm is better ? Bfgs or damp ? I use bfgs,but
the better algorithm is the one that works better for your system.
there is no "golden" algorithm that is always the best. sometimes
even algorithms considered the worst can be the best choice.
please note, that many algorithms have adjustable parameters
that can make all the difference. to begin with, you first have to
define what is "best" (fastest convergence, not getting stuck in local
minima easily, efficient handling of shallow or highly asymmetric
potential surfaces).
...and on top of that, it is quite likely that a combination of algorithms
(i.e. start with one that "gets you down" fast, and then switching to
one that can find a minimum fast) would be the "best" solution for
many scenarios.
> find it very slow . Anybody who know about this ,please give some advice
you'll have to define "slow" as well. you always have to see this
in relation to the problem you are studying...
cheers,
axel.
> ,thank you .
>
>
>
> Q J Wang
> XiangTan University
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From akohlmey at cmm.chem.upenn.edu Sun Nov 30 13:08:07 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 30 Nov 2008 13:08:07 +0100
Subject: [Pw_forum] slab
In-Reply-To: <88705.84554.qm@web30102.mail.mud.yahoo.com>
References: <88705.84554.qm@web30102.mail.mud.yahoo.com>
Message-ID: <7b6913e90811300408s2dcf0407v602b16f5ad8c6248@mail.gmail.com>
On 11/29/08, fereydoon khazali <frnkhzi at yahoo.com> wrote:
> Dear All
> Is this input file correct for 5-layer slab of Ag(001)? vacuum thickness
> about 8.18 ang. & surface geometry is (2*2)
dear fereydoon,
please note that you are asking a not overly smart question:
a) if you care whether your input is syntactically correct, you
can just run pw.x (well, you didn't even state that it was for pw.x)
on it, and see if it gives the correct result.
b) if you care whether the output is acceptable, you have to verify
this for yourself as well. if you want to publish this in a paper, do
you think "some guy on the pw_forum mailing list wrote this is ok"
is a good justification of the choice of input?
so while everybody here understands, that it is not always easy
to trust your own choice of parameters, there is no substitute for
teaching yourself how to find out. there are many examples in the
literature (including text books) on how to do this kind of calculation
and perhaps you should start with a very simple system that has
been studied a lot and is thus well documented, so you can check
the impact of your choices of parameters. not only will this solve
the currently pending question, but all similar ones in the future.
if you give this a little bit of thought, you'll understand that this
will be a much more reliable way than doing a poll amongst forum
members whether an input is good or bad.
for example, the fact, that you write to have an oxygen attached to your
surface makes all my neck hairs stand up and remind me of all
the problems one can have with the spin states of molecular oxygen.
...and thus i would not trust anything without careful testing (it may
be harmless, but i never studied this kind of system).
cheers,
axel.
[...]
>
> thanks
> fereydoon Kh.
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From akohlmey at cmm.chem.upenn.edu Sun Nov 30 13:08:07 2008
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 30 Nov 2008 13:08:07 +0100
Subject: [Pw_forum] slab
In-Reply-To: <88705.84554.qm@web30102.mail.mud.yahoo.com>
References: <88705.84554.qm@web30102.mail.mud.yahoo.com>
Message-ID: <7b6913e90811300408s2dcf0407v602b16f5ad8c6248@mail.gmail.com>
On 11/29/08, fereydoon khazali <frnkhzi at yahoo.com> wrote:
> Dear All
> Is this input file correct for 5-layer slab of Ag(001)? vacuum thickness
> about 8.18 ang. & surface geometry is (2*2)
dear fereydoon,
please note that you are asking a not overly smart question:
a) if you care whether your input is syntactically correct, you
can just run pw.x (well, you didn't even state that it was for pw.x)
on it, and see if it gives the correct result.
b) if you care whether the output is acceptable, you have to verify
this for yourself as well. if you want to publish this in a paper, do
you think "some guy on the pw_forum mailing list wrote this is ok"
is a good justification of the choice of input?
so while everybody here understands, that it is not always easy
to trust your own choice of parameters, there is no substitute for
teaching yourself how to find out. there are many examples in the
literature (including text books) on how to do this kind of calculation
and perhaps you should start with a very simple system that has
been studied a lot and is thus well documented, so you can check
the impact of your choices of parameters. not only will this solve
the currently pending question, but all similar ones in the future.
if you give this a little bit of thought, you'll understand that this
will be a much more reliable way than doing a poll amongst forum
members whether an input is good or bad.
for example, the fact, that you write to have an oxygen attached to your
surface makes all my neck hairs stand up and remind me of all
the problems one can have with the spin states of molecular oxygen.
...and thus i would not trust anything without careful testing (it may
be harmless, but i never studied this kind of system).
cheers,
axel.
[...]
>
> thanks
> fereydoon Kh.
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
From manoj at phys.ufl.edu Sun Nov 30 20:53:06 2008
From: manoj at phys.ufl.edu (Manoj Srivastava)
Date: Sun, 30 Nov 2008 14:53:06 -0500 (EST)
Subject: [Pw_forum] complex band
In-Reply-To: <200811280859.46256.smogunov@sissa.it>
Message-ID: <Pine.GSO.4.21.0811301437520.27070-100000@neptune.phys.ufl.edu>
Dear Alexander,
Thank you very much for your answer. It has started making sense, but
unfortunately not a whole lot. I think I need to have complete
understanding of this subroutine in order to have the bigger picture. In
the other e-mail, copied and pasted as below -
> the expression -
> norm2=(((il+xyk(1,ik))*bg(1,1)+(jl+xyk(2,ik))*bg(1,2))**2+ &
> ((il+xyk(1,ik))*bg(2,1)+(jl+xyk(2,ik))*bg(2,2))**2)* &
>
> i believe is |G+k|^2. How do you get above expression in the code for
> this?
norm2 is indeed |G_perp+k_perp|^2, where G_perp=il*b_1+jl*b_2 and 2d
vector
k_perp=xyk(1,ik)*b_1+xyk(2,ik)*b_2 and you indeed select out those
G_perp+k_perp which satisfy (G_perp+k_perp)^2<Ecut2d.
Why is K_perp in terms of b_1 and b_2? You can ofcourse take it
like that but is there any specific reason to do that? If we look at the
Fourier transform of wavefunction psi(r)=sum_{G}\psi(G)exp(i(K+G).r).
here in this expression do we always take K in terms of G. I dont think
so, K can be a label, which might be in terms of G vectors but not
necessarily. What do you think?
In the input file where we enter k_x and k_y, do we enter these in
terms of b1 and b2? or somewhere later in the code it gets multiplied with
b1 and b2, if yes where? I am having tough time figuring it out :(
Thanks for help.
Regards,
Manoj Srivastava
Department of Physics,
University of Florida, Gainesville
On Fri, 28 Nov 2008,
Alexander wrote:
> Dear Manoj
> Ngper is the total number of g_perp=G_perp+k_perp with |g_perp|^2<E_cut
> which are arranged into the shells. Each shell contains g_perp having the same
> norm which is very useful because many calculations with g_perp depend only
> on their norms. The number of shells is ngpsh. gnsh(ngpsh) is the norm for
> each shell, ninsh(ngpsh) is the number of g_perp in the shell.
> The array nshell is the auxiliary array used further to arrange the g_perp
> vectors in the shells.
>
> Hope this helps you,
> regards, Alexander
>
> and ngpsh is the number of shells
>
> On Thursday 27 November 2008 00:26, Manoj Srivastava wrote:
> > Dear Alexander, PWSCF users and developers,
> > I have a technical question in one of the subroutines used to calculate
> > complex band. The subroutine 'init_gper.f90' under PWCOND directory is
> > used to calculate number of G perpendicular vectors within the energy
> > cutoff by using [k_{\perp}+G_{\perp}]^2.le.E_{cut}. I understand the
> > counting of Gper, but i dont understand how do they construct the Gper
> > vectors. For example what is 'ngpsh'? It is defined as 'no. of shells for
> > G', but i really dont understand what this is. I dont understand after
> > line 50 of the code in init_gper.f90. Mainly what does the following
> > piece of code do
> >
> > do i=1,nrx
> > do j=1,nry
> > icount=0
> > do iw=1, ngpsh
> > if (abs(norm2-gnorm2(iw)).gt.eps) then
> > icount=icount+1
> > else
> > nshell(i,j)=iw
> > endif
> > enddo
> > if (icount.eq.ngpsh) then
> > ngpsh=ngpsh+1
> > gnorm2(ngpsh)=norm2
> > nshell(i,j)=ngpsh
> > endif
> > endif
> > enddo
> > enddo
> > I understand it is not a good way of asking question, but I am completely
> > lost. Any help will be appreciated.
> >
> > Regards,
> > Manoj
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
From bogus@does.not.exist.com Wed Nov 19 23:20:46 2008
From: bogus@does.not.exist.com ()
Date: Wed, 19 Nov 2008 22:20:46 -0000
Subject: No subject
Message-ID: <mailman.2.1229877822.15649.pw_forum@pwscf.org>
The Latin term ab initio means from the beginning and is used in several co=
ntexts:
=20
in science: A calculation is said to be "ab initio" (or "from first princip=
les") if it relies on basic and established laws of nature without addition=
al assumptions or special models.
For example, an ab initio calculation of the properties of liquid water mig=
ht start with the properties of the constituent hydrogen and oxygen atoms a=
nd the laws of electrodynamics. From these basics, the properties of isolat=
ed individual water molecules would be derived, followed by computations of=
the interactions of larger and larger groups of water molecules, until the=
bulk properties of water had been determined.
In our computational materials Science we use only atomic numbers (and expe=
rimental atomic positions which are not necessarily required) and=20
quantum-mechanics laws that make our calculations "ab initio" or "from firs=
t principles".
And no one can explain "ab initio" results "from first principles". as the=
y are the same, no difference between them except that "ab initio" refers t=
o Latin, and "from first principles" is in English.
Bests,
Eyvaz.
-------------------------------------------------------------------
Prof. Eyvaz Isaev,=20
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, R=
ussia,=20
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, =
Sweden=20
Condensed Matter Theory Group, Uppsala University, Sweden=20
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
--- On Sun, 12/21/08, Hongsheng Zhao <zhaohscas at yahoo.com.cn> wrote:
> From: Hongsheng Zhao <zhaohscas at yahoo.com.cn>
> Subject: [Pw_forum] ab initio vs. first principles.
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Sunday, December 21, 2008, 2:49 PM
> Hi all,
>=20
> Some times we say ab initio, sometimes first principles.=20
> Actually,
> I find in many case people use them to explain one another.
> But the fact may be not the case, who can give some hints
> on the differences between ab initio and first principles?=20
>=20
> Regards,
> --=20
> Hongsheng Zhao <zhaohscas at yahoo.com.cn>=20
> Xinjiang Technical Institute of Physics and Chemistry
> Chinese Academy of Sciences=20
> GnuPG DSA: 0xD108493
> 2008-12-21
>=20
> __________________________________________________
> =E8=B5=B6=E5=BF=AB=E6=B3=A8=E5=86=8C=E9=9B=85=E8=99=8E=E8=B6=85=E5=A4=A7=
=E5=AE=B9=E9=87=8F=E5=85=8D=E8=B4=B9=E9=82=AE=E7=AE=B1?
> http://cn.mail.yahoo.com
>=20
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum=0A=0A=0A
From bogus@does.not.exist.com Wed Nov 19 23:20:46 2008
From: bogus@does.not.exist.com ()
Date: Wed, 19 Nov 2008 22:20:46 -0000
Subject: No subject
Message-ID: <mailman.3.1230910461.15649.pw_forum@pwscf.org>
total stress (Ry/bohr**3) (kbar) P= -0.32
-0.00000219 0.00000000 0.00000000 -0.32 0.00 0.00
0.00000000 -0.00000219 -0.00000000 0.00 -0.32 -0.00
0.00000000 -0.00000000 -0.00000219 0.00 -0.00 -0.32
bfgs converged in 9 scf cycles and 2 bfgs steps
End of BFGS Geometry Optimization
Final enthalpy = -290.2578578224 Ry
new unit-cell volume = 341.40915 a.u.^3 ( 50.59162 Ang^3 )
CELL_PARAMETERS (alat)
-0.499531821 -0.000000000 0.499531821
0.000000000 0.499531821 0.499531821
-0.499531821 0.499531821 -0.000000000
ATOMIC_POSITIONS (crystal)
Sc 0.000000000 0.000000000 -0.000000000
Sb 0.500000000 0.500000000 0.500000000
and then i made the second input file (scsb.vc-relax1.out).
So just suggest me how to prepare the second input file?
regards
Bipul
On 1/2/09, Lorenzo Paulatto <> wrote:
> On Fri, 02 Jan 2009 14:52:10 +0100, Bipul Rakshit <bipulrr at gmail.com> wrote:
>> getting relaxed cell volume, CELL_PARAMETER AND relaxed atomic position
>> ...
>> But this is not the case. The pressure changes to some other value
>> (-10.38 kbar).
>
> Dear Bipul,
> if you had not used ibrav=0 in the initial input file, reconstructiong input
> cell parameters from the output can be a bit tricky, please double check it.
> Otherwise provide more detail so we can take a more educated guess.
>
> regards
>
>
> --
> Lorenzo Paulatto
> SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www: http://people.sissa.it/~paulatto/
>
> *** save italian brains ***
> http://saveitalianbrains.wordpress.com/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Bipul Rakshit
PhD Student,
Barkatullah University,
Bhopal 462026,
MP, India
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------=_Part_173840_14143949.1230910456144--
