[Pw_forum] can't read wavefunction and coords
Jonas Baltrusaitis
jasius_1 at yahoo.com
Thu Apr 30 04:23:33 CEST 2009
OK, this time I have a tricky one. Fixed bash issues (my mistake). Now my fil.dos and all PDOS files have only one line:
# E (eV) dos(E) Int dos(E)
Seems like it all starts with .dos2. file which is not complete, either. No crash error is produced
thanks
Jonas
Program POST-PROC v.4.0.4 starts ...
Today is 29Apr2009 at 21:15:46
Parallel version (MPI)
Number of processors in use: 8
R & G space division: proc/pool = 8
Planes per process (thick) : nr3 = 24 npp = 3 ncplane = 576
Proc/ planes cols G planes cols G columns G
Pool (dense grid) (smooth grid) (wavefct grid)
1 3 39 464 3 39 464 14 95
2 3 39 464 3 39 464 14 95
3 3 39 465 3 39 465 14 95
4 3 39 465 3 39 465 13 92
5 3 39 465 3 39 465 13 92
6 3 39 465 3 39 465 13 92
7 3 39 465 3 39 465 14 94
8 3 40 466 3 40 466 14 94
tot 24 313 3719 24 313 3719 109 749
Gaussian broadening (read from input): ngauss,degauss= 1 0.020000
INput:
#!/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
$ECHO
# set the needed environment variables
PREFIX=`pwd`
BIN_DIR=/share/apps/espresso-4.0.4/bin
PSEUDO_DIR=/share/apps/espresso-4.0.4/pseudo
TMP_DIR=/share/apps/scratch/$PBS_JOBNAME
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 dos.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=" $BIN_DIR/dynmat.x"
DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX"
PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX"
$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"
$ECHO
# geometry optimization calculation
cat > sih4.opt.in << EOF
&control
calculation='relax'
pseudo_dir = '$PSEUDO_DIR/',
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,
ngauss=1, degauss=0.02
/
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"
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