[QE-users] Error in routine read_namelists (5010):, reading namelist system
Maxim Arsentev
arsentev at isc.nw.ru
Thu Nov 1 13:11:07 CET 2018
Dear QE users,
When I run my input with "space_group" variable activated, I got whis error:
Error in routine read_namelists (5010):
reading namelist system
--
Best wishes,
Maxim Arsent'ev, Ph.D. (Chemistry)
Laboratory of research of nanostructures
Institute of Silicate Chemistry of RAS
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#!/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
$ECHO
$ECHO "$EXAMPLE_DIR : starting"
$ECHO
$ECHO "This example shows how to use pw.x with vdw-DF functional. In the"
$ECHO "first part a cell relaxation of graphite will be calculated and"
$ECHO "then the energy of two water molecules far apart will be computed."
$ECHO "Optionally, at the end, you can see how to set up a force relaxation"
$ECHO "of an Argon dimer, not activated by default in the distribution."
PREFIX=`cd /usr/share/doc/quantum-espresso ; pwd`
BIN_DIR=/usr/bin
PSEUDO_DIR=/home/mxm222/Documents/internal_and_full_opt/AgBi2B5O11_internal_opt
# Beware: everything in $TMP_DIR will be destroyed !
TMP_DIR=/home/mxm222/Documents/internal_and_full_opt/AgBi2B5O11_internal_opt/temp
# required executables and pseudopotentials
BIN_LIST="pw.x generate_vdW_kernel_table.x"
PSEUDO_LIST="O.pbe-n-rrkjus_psl.0.1.UPF Bi.pbe-dn-rrkjus_psl.0.2.2.UPF Ag.pbe-dn-rrkjus_psl.0.1.UPF B.pbe-n-rrkjus_psl.0.1.UPF"
VDW_TABLE="vdW_kernel_table"
$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 "Downloading $FILE to $PSEUDO_DIR...\c"
$WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE 2> /dev/null
fi
if test $? != 0; 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 $PARA_POSTFIX"
GEN_COMMAND="$PARA_PREFIX $BIN_DIR/generate_vdW_kernel_table.x $PARA_POSTFIX"
PP_COMMAND="$PARA_PREFIX $BIN_DIR/pp.x $PARA_POSTFIX"
# check for vdw kernel table
if test ! -r $PSEUDO_DIR/$VDW_TABLE ; then
$ECHO " "
$ECHO " "
$ECHO " WARNING: $PSEUDO_DIR/$VDW_TABLE not existent or not readable"
$ECHO " WARNING: a new table will be generated, this process will"
$ECHO " WARNING: probably take about 20 mins (depending on your cpu"
$ECHO " WARNING: power and configuration)."
$ECHO
$ECHO " Generating $VDW_TABLE...\c"
if $GEN_COMMAND ; then
if test ! -r $VDW_TABLE ; then
$ECHO " ERROR: cannot generate vdW_kernel_table !!"
exit 1
fi
$ECHO "done ! Table moved to $PSEUDO_DIR"
mv $VDW_TABLE $PSEUDO_DIR
fi
fi
$ECHO " done"
# Print how we run executables
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO
#
# TiS3 cell relaxation
#
cat > TiS3.scf.in << EOF
&control
prefix='TiS3',
calculation = 'scf',
restart_mode = 'from_scratch'
pseudo_dir='$PSEUDO_DIR',
outdir = '$TMP_DIR',
forc_conv_thr = 1.0d-3 ,
!forc_conv_thr = 1.0d-2 ,
nstep = 99,
etot_conv_thr = 1.0d-4 ,
!etot_conv_thr = 2.0d-10 ,
/
&system
ibrav= 8,
A=24.98444525,
B=0.588411037,
C=1.372938916,
space_group=33,
nat= 38, ntyp= 4,
ecutwfc = 10.0, ecutrho = 100,
occupations ='smearing', smearing ='gaussian',
degauss=0.02,
/
&electrons
conv_thr = 1e-6,
mixing_beta=0.3,
electron_maxstep=500
/
&ions
/
&cell
cell_factor = 1.5
/
ATOMIC_SPECIES
O 15.999 O.pbe-n-rrkjus_psl.0.1.UPF
Bi 208.98038 Bi.pbe-dn-rrkjus_psl.0.2.2.UPF
Ag 107.8682 Ag.pbe-dn-rrkjus_psl.0.1.UPF
B 10.8110 B.pbe-n-rrkjus_psl.0.1.UPF
ATOMIC_POSITIONS crystal_sg
Bi 4d 0.60823 0.71538 0.40704
Bi 4d 0.3814 0.51722 0.32046
Bi 4d 0.1371 1.54083 0.617674
Bi 4d 0.36119 0.72986 0.527877
Ag 4d 0.38282 0.97648 0.32363
Ag 4d 0.367 0.50195 0.11175
O 4d 0.19 0.2643 0.3018
O 4d 0.4428 0.2554 0.6337
O 4d 0.3846 0.3118 0.7553
O 4d 0.1311 0.1801 0.1843
O 4d 0.2134 1.7414 0.5685
O 4d 0.0773 0.4428 0.375
O 4d 0.4583 0.7161 0.3729
O 4d 0.2679 0.203 0.6669
O 4d 0.0138 0.3018 0.2699
O 4d 0.2701 0.7065 0.2968
O 4d 0.566 0.5175 0.4876
O 4d 0.0593 0.1324 0.3757
O 4d 0.5685 0.2134 0.4887
O 4d 0.4532 0.5937 0.2181
O 4d 0.3143 0.2275 0.448
O 4d 0.3048 0.5294 0.4504
O 4d 0.5596 0.9124 0.4867
B 4d 0.0376 0.2555 0.1985
O 4d 0.2026 1.6029 0.7248
O 4d 0.3383 0.074 0.5606
O 4d 0.3117 0.9246 0.4494
B 4d 0.2061 0.1811 0.238
B 4d 0.2903 0.2373 0.7373
B 4d 0.4594 0.3262 0.7029
B 4d 0.5643 0.3685 0.4516
B 4d 0.0892 0.2858 0.3295
B 4d 0.3199 0.0755 0.4859
B 4d 0.3417 0.2258 0.606
B 4d 0.5693 1.0615 0.449
O 4d 0.311 0.3797 0.5627
O 4d -0.0233 0.2772 0.1399
B 4d 0.3098 0.3809 0.4877
K_POINTS {automatic}
1 1 1 0 0 0
EOF
$ECHO " running the graphite cell relaxation...\c"
$PW_COMMAND < TiS3.scf.in > TiS3.scf.out
check_failure $?
$ECHO " done"
# post-processing for charge density
cat > TiS3.pp_rho.in << EOF
&inputpp
prefix = 'TiS3'
outdir = '$TMP_DIR/'
filplot = 'TiS3charge'
plot_num= 0
/
&plot
nfile = 1
filepp(1) = 'TiS3charge'
weight(1) = 1.0
iflag = 3
output_format = 5
fileout = 'TiS3.xsf'
/
EOF
$ECHO " running pp.x to do a 2-d plot of the charge density...\c"
$PP_COMMAND < TiS3.pp_rho.in > TiS3.pp_rho.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/TiS3*
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/ar_vdw*
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR : done"
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