[Pw_forum] can't read wavefunction and coords
Jonas Baltrusaitis
jasius_1 at yahoo.com
Wed Apr 29 02:23:27 CEST 2009
Gabriele,
I am almost there. I appreciate you helping me
I added coordinates, read nicely. However when calculating DOS in produces empty dos2 and pdos output files with no error and doesn't generate fildos at all. I suspect it has problems reading guess
I am confused as I am following Example 8, thus should be pretty straightforward but it's not.
My latest input is below
Jonas
#!/bin/sh
# run from directory where this script is
cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
EXAMPLE_DIR=/home/jbaltrus/$PBS_JOBNAME
# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi
$ECHO
$ECHO "$EXAMPLE_DIR : starting"
$ECHO
$ECHO "This example shows how to use pw.x and phcg.x to calculate the normal"
$ECHO "modes of a molecule (SiH4) at Gamma."
$ECHO
$ECHO
# set the needed environment variables
PREFIX=`pwd`
BIN_DIR=/share/apps/espresso-4.0.4/bin
PSEUDO_DIR=/share/apps/espresso-4.0.4/pseudo
TMP_DIR=/share/apps/scratch
mkdir $EXAMPLE_DIR/results
PARA_PREFIX="mpiexec -n 8 -machinefile $PBS_NODEFILE"
PARA_POSTFIX="-rmpool 0 -nodes 2 -procs 4"
# required executables and pseudopotentials
BIN_LIST="pw.x phcg.x ph.x"
PSEUDO_LIST="Si.vbc.UPF H.vbc.UPF C.pz-rrkjus.UPF H.vbc.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 $PARA_POSTFIX"
PH_COMMAND="$PARA_PREFIX $BIN_DIR/ph.x $PARA_POSTFIX"
PHCG_COMMAND="$PARA_PREFIX $BIN_DIR/phcg.x $PARA_POSTFIX"
DYNMAT_COMMAND=" $BIN_DIR/dynmat.x"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO " running ph.x as: $PH_COMMAND"
$ECHO " running phcg.x as: $PHCG_COMMAND"
$ECHO " running dynmat.x as: $DYNMAT_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
# geometry optimization calculation
cat > sih4.opt.in << EOF
&control
calculation='relax'
pseudo_dir = '$PSEUDO_DIR/',
restart_mode = ’from_scratch’,
outdir='$TMP_DIR/'
title='Test Silane SiH4 gamma only'
prefix='sih4'
tprnfor=.true.
/
&system
ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2,
ecutwfc =16.0
/
&electrons
mixing_mode='plain'
mixing_beta = 0.7,
conv_thr = 1.0d-8
/
&IONS
/
ATOMIC_SPECIES
Si 28.086 Si.vbc.UPF
H 1.008 H.vbc.UPF
ATOMIC_POSITIONS (alat)
Si 0.000000000 0.000000000 0.000000000
H 0.128530744 0.128530744 0.128530744
H -0.128530744 -0.128530744 0.128530744
H -0.128530744 0.128530744 -0.128530744
H 0.128530744 -0.128530744 -0.148530744
K_POINTS (gamma)
EOF
$ECHO " running the geometry opt calculation for SiH4...\c"
$PW_COMMAND < sih4.opt.in > sih4.opt.out
$ECHO " done"
nat=5
grep -A$((nat+5)) CELL_PARAMETERS sih4.opt.out | tail -$((nat+1)) > atpos.tmp
# normal mode calculation for SiH4
cat > sih4.nm.in << EOF
normal modes for sih4
&inputph
tr2_ph=1.0d-14,
prefix='sih4',
amass(1)=28.086,
amass(2)=1.008,
outdir='$TMP_DIR/',
epsil=.true.,
trans=.true., asr=.true.
raman=.false.
fildyn='sih4.dyn'
/
0.0 0.0 0.0
EOF
$ECHO " running normal mode calculation for SiH4...\c"
$PHCG_COMMAND < sih4.nm.in > sih4.nm.out
$ECHO " done"
# IR cross sections for SiH4
cat > sih4.dyn.in << EOF
&input fildyn='sih4.dyn', asr='zero-dim' /
EOF
$ECHO " running IR cross section calculation for SiH4...\c"
$DYNMAT_COMMAND < sih4.dyn.in > sih4.dyn.out
$ECHO " done"
# DOS (SCF) calculation for sih4
cat > sih4.scf.in << EOF
&control
calculation='scf'
prefix='sih4',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2,
ecutwfc =16.0
/
&electrons
mixing_mode='plain'
mixing_beta = 0.7,
conv_thr = 1.0d-8
/
ATOMIC_SPECIES
Si 28.086 Si.vbc.UPF
H 1.008 H.vbc.UPF
K_POINTS {automatic}
12 12 12 0 0 0
EOF
cat atpos.tmp >> sih4.scf.in
$PW_COMMAND < sih4.scf.in > sih4.scf.out
# DOS calculation for sih4
cat > sih4.dos.in << EOF
&control
calculation='nscf'
prefix='sih4',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
/
&system
ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2,
ecutwfc =16.0
/
&electrons
mixing_mode='plain'
mixing_beta = 0.7,
conv_thr = 1.0d-8
/
ATOMIC_SPECIES
Si 28.086 Si.vbc.UPF
H 1.008 H.vbc.UPF
K_POINTS {automatic}
12 12 12 0 0 0
EOF
cat atpos.tmp >> sih4.dos.in
cat > sih4.dos2.in << EOF
&inputpp
outdir='$TMP_DIR/'
prefix='sih4'
fildos='sih4.dos',
Emin=5.0, Emax=25.0, DeltaE=0.1
/
EOF
$ECHO " running DOS calculation for sih4...\c"
$PW_COMMAND < sih4.dos.in > sih4.dos.out
$DOS_COMMAND < sih4.dos2.in > sih4.dos2.out
$ECHO " done"
cat > sih4.pdos.in << EOF
&inputpp
outdir='$TMP_DIR/'
prefix='sih4'
Emin=5.0, Emax=25.0, DeltaE=0.1
ngauss=1, degauss=0.02
/
EOF
$ECHO " running PDOS calculation for Ni...\c"
$PROJWFC_COMMAND < sih4.pdos.in > sih4.pdos.out
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR: done"
--- On Tue, 4/28/09, Gabriele Sclauzero <sclauzer at sissa.it> wrote:
> From: Gabriele Sclauzero <sclauzer at sissa.it>
> Subject: Re: [Pw_forum] can't read wavefunction and coords
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Tuesday, April 28, 2009, 12:05 AM
> Jonas Baltrusaitis wrote:
> > Gabriele et al,
> >
> > I rerun input with alat and, yes , it reads nicely. I
> assume it will read and convert
> > ansgtroms from geom opt to alat in the next step no
> prob.
> >
> > Last thing I want to add to my input (after or before
> normal modes calcs) is DOS calcs.
> > And this is where I got stuck as it wouldn't read
> last optimized coordinates (in fact
> > it would miss ATOMIC SPECIES field if I didn't add
> it in ncsf part in hope that guess
> > will get read). If I added ATOMIC SPECIES in ncsf it
> would use those instead of
> > converting them from the optimization run.
>
> Sorry I cannot follow your logic, it seems to me that you
> are confusing things a bit...
>
> You must always have ATOMIC_SPECIES card if you want to
> include any atom in your calcs.
>
> >
> > So my questions is how to combined DOS calcs so it
> uses optimized coordinates, so in
> > one input I can 1) optimize, 2) normal modes and
> crossections and 3) DOS and PDOS calcs
> > from optimized geometries
>
> I don't see any problem, apart from the fact that in
> version 4.0.4 ATOMIC_POSITIONS are
> read from input instead of being read from the .save
> directory (but now in the CVS the
> coords should be read from the scf restart files, as it
> seems more logical to me, since
> the charge density is read from there as well).
> Anyway what I suggest to do (since you want to do
> everything in a single script) is: first
> the relaxation, then grep the final atomic positions with
> something like this
>
> nat=5
> grep -A$((nat+5)) CELL_PARAMETERS | tail -$((nat+1)) >
> atpos.tmp
>
> then use the positions in this temp file to add them at the
> end of any successive input
> file which needs them (_after_ removing the old ones from
> the middle of the file, obviously)
>
> cat > sih4.dos.in << EOF
> &control
> calculation='nscf'
> prefix='sih4',
> pseudo_dir = '$PSEUDO_DIR/',
> outdir='$TMP_DIR/'
> /
> &system
> ibrav=2, celldm(1) =12.0, nat=5, ntyp= 2,
> ecutwfc =16.0
> /
> &electrons
> mixing_mode='plain'
> mixing_beta = 0.7,
> conv_thr = 1.0d-8
> /
> ATOMIC_SPECIES
> Si 28.086 Si.vbc.UPF
> H 1.008 H.vbc.UPF
> K_POINTS {automatic}
> 12 12 12 0 0 0
> EOF
>
> cat atpos.tmp >> sih4.dos.in
>
> for instance. In this way you don't have to care about
> the format of the positions. You
> can do the same to build an scf run before the nscf one, if
> you wish. Then you can
> calculate dos, pdos, ..., whatever needs scf charge density
> and/or wfcs from the relaxed
> configuration.
>
> >
> > I attached the input that succeded in nm calcls but
> failed in DOS calcs: didn;t read
> > coords and produced empty output files
>
> This seems another "problem", not related with
> atomic positions...
>
> Did it give you an error? Are you sure that the fildos file
> is not present? ...?
>
>
> GS
>
> >
> > thanks
> >
> > Jonas
> >
> --
>
>
> 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
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