[Pw_forum] can't read wavefunction and coords

[Jonas Baltrusaitis]

Hi all,

I am following an example 9 in trying to setup a single input to:
1. optimize structure at gamma point
2. calculate scf
3. phonon calculation
4. IR cross section calculation

What's absolutely not clear from example 9 is how (why) the wavefunction and coords gets read from scf calculation part to latter parts. It just does. Whereas it does not into scf run  if I add optimization run before scf and start scf with restart directive. It simply disregards my restart command. I was pretty convinced that restart will read previous wavefunction but now I just don't know

I attached my input, would appreciate any suggestions

Jonas Baltrusaitis
University of Iowa

#!/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., tstress=.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 (angstrom)
Si      -0.117489394     -0.768144287      0.335809279
H       -0.211023980     -0.607144136      1.652050052
H       -1.814442124     -1.682247277     -0.460054024
H       -0.023954807      0.421221649     -0.250551950
H        0.963879018     -1.487802354      0.053153717
K_POINTS (gamma)
EOF
$ECHO "  running the geometry opt calculation for SiH4...\c"
$PW_COMMAND < sih4.opt.in > sih4.opt.out
check_failure $?
$ECHO " done"

# self-consistent calculation
cat > sih4.scf.in << EOF
&control
    calculation='scf'
    pseudo_dir = '$PSEUDO_DIR/',
    restart_mode = ’restart’,
    outdir='$TMP_DIR/'
    title='Test Silane SiH4 gamma only'
    prefix='sih4'
    tprnfor=.true., tstress=.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
/
ATOMIC_SPECIES
Si 28.086 Si.vbc.UPF
  H  1.008  H.vbc.UPF
ATOMIC_POSITIONS (angstrom)
Si      -0.117489394     -0.768144287      0.335809279
H       -0.211023980     -0.607144136      1.652050052
H       -1.814442124     -1.682247277     -0.460054024
H       -0.023954807      0.421221649     -0.250551950
H        0.963879018     -1.487802354      0.053153717
K_POINTS (gamma)
EOF
$ECHO "  running the scf calculation for SiH4...\c"
$PW_COMMAND < sih4.scf.in > sih4.scf.out
check_failure $?
$ECHO " done"

# 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
check_failure $?
$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
check_failure $?
$ECHO " done"


$ECHO
$ECHO "$EXAMPLE_DIR: done"