[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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