[QE-users] from rdiaghg : error # 452, S matrix not positive definite
Maxim Arsentev
arsentev at isc.nw.ru
Tue Mar 13 13:38:53 CET 2018
Dear Quantum-Espresso users and developers
I was trying to run NEB example and got following message:
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task # 0
from rdiaghg : error # 452
S matrix not positive definite
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Best wishes,
Maxim Arsent'ev, Ph.D. (Chemistry)
Laboratory of research of nanostructures
Institute of Silicate Chemistry of RAS
St-Petersburg, Russia
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Program NEB v.5.4.0 starts on 13Mar2018 at 16:50:51
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Parallel version (MPI), running on 4 processors
R & G space division: proc/nbgrp/npool/nimage = 4
parsing_file_name: H2+H.in
Reading input from pw_1.in
Warning: card &IONS ignored
Warning: card / ignored
Reading input from pw_2.in
Warning: card &IONS ignored
Warning: card / ignored
WARNING: atom 27 moved more than 1/2 alat from image 1 to image 2
You can set minimum_image to true to avoid jumps in the path
initial path length = 13.0096 bohr
initial inter-image distance = 6.5048 bohr
string_method = neb
restart_mode = from_scratch
opt_scheme = broyden
num_of_images = 3
nstep_path = 20
CI_scheme = auto
first_last_opt = F
use_freezing = F
ds = 2.0000 a.u.
k_max = 0.3000 a.u.
k_min = 0.2000 a.u.
suggested k_max = 0.1542 a.u.
suggested k_min = 0.1028 a.u.
path_thr = 0.1000 eV / A
------------------------------ iteration 1 ------------------------------
tcpu = 0.8 self-consistency for image 1
tcpu = 161.3 self-consistency for image 2
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine rdiaghg (452):
S matrix not positive definite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
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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 neb.x to calculate the"
$ECHO "minimum energy path (MEP) of the collinear proton transfer reaction:"
$ECHO " H2+H <==> H+H2, within the Born-Oppenheimer approximation."
$ECHO
$ECHO "!!! Beware: neb.x DOES NOT READ FROM STANDARD INPUT"
$ECHO "!!! run as 'neb.x -inp input_file_name > output_file_name'"
$ECHO
PREFIX=`cd /usr/share/doc/quantum-espresso ; pwd`
BIN_DIR=/home/mxm2/espresso-5.4.0/bin
PSEUDO_DIR=/home/mxm2/Documents/internal_and_full_opt/NEB_2
# Beware: everything in $TMP_DIR will be destroyed !
TMP_DIR=/home/mxm2/Documents/internal_and_full_opt/NEB_2/temp
# required executables and pseudopotentials
BIN_LIST="pw.x neb.x"
PSEUDO_LIST="Ti.pbe-spn-rrkjus_psl.0.3.1.UPF S.pbe-n-rrkjus_psl.0.1.UPF Mg.pbe-n-rrkjus_psl.0.3.0.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
$ECHO " done"
# how to run executables
NEB_COMMAND="$PARA_PREFIX mpirun -np 4 $BIN_DIR/neb.x $PARA_POSTFIX"
$ECHO
$ECHO " running Born-Oppenheimer NEB as: $NEB_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"
# NEB calculation. Automatic choice of the climbing image.
cat > H2+H.in << EOF
BEGIN
BEGIN_PATH_INPUT
&PATH
restart_mode = 'from_scratch'
string_method = 'neb',
nstep_path = 20,
ds = 2.D0,
opt_scheme = "broyden",
num_of_images = 3,
k_max = 0.3D0,
k_min = 0.2D0,
CI_scheme = "auto",
path_thr = 0.1D0,
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
prefix = "H2+H"
outdir = "$TMP_DIR",
pseudo_dir = "$PSEUDO_DIR",
/
&SYSTEM
ibrav = 0,
nat = 31,
ntyp = 3,
ecutwfc = 39.0, ecutrho = 300,
occupations ='smearing', smearing ='gaussian',
degauss=0.02,
celldm(1)=1.889726
/
&ELECTRONS
conv_thr = 1e-6,
mixing_beta=0.3,
electron_maxstep=500
/
&IONS
/
ATOMIC_SPECIES
Ti 47.86700 Ti.pbe-spn-rrkjus_psl.0.3.1.UPF
S 32.0660 S.pbe-n-rrkjus_psl.0.1.UPF
Mg 24.30 Mg.pbe-n-rrkjus_psl.0.3.0.UPF
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS { crystal }
Ti 0.348990000 0.691710000 0.327290000 1 1 1
Ti 0.308290000 0.651010000 0.672710000 1 1 1
Ti 0.997060000 0.981290000 0.327880000 1 1 1
Ti 0.018710000 0.002940000 0.672120000 1 1 1
Ti 0.636820000 0.325700000 0.328560000 1 1 1
Ti 0.674300000 0.363180000 0.671440000 1 1 1
Ti 0.832980000 0.167170000 0.829920000 1 1 1
Ti 0.832830000 0.167020000 0.170080000 1 1 1
S 0.909560000 0.579640000 0.246440000 1 1 1
S 0.420360000 0.090440000 0.753560000 1 1 1
S 0.244870000 0.251340000 0.583740000 1 1 1
S 0.748660000 0.755130000 0.416260000 1 1 1
S 0.752030000 0.751540000 0.084110000 1 1 1
S 0.248460000 0.247970000 0.915890000 1 1 1
S 0.248210000 0.251140000 0.247120000 1 1 1
S 0.748860000 0.751790000 0.752880000 1 1 1
S 0.585180000 0.912270000 0.590600000 1 1 1
S 0.087730000 0.414820000 0.409400000 1 1 1
S 0.079970000 0.412600000 0.081300000 1 1 1
S 0.587400000 0.920030000 0.918700000 1 1 1
S 0.577370000 0.913930000 0.244950000 1 1 1
S 0.086070000 0.422630000 0.755050000 1 1 1
S 0.916380000 0.574490000 0.583740000 1 1 1
S 0.425510000 0.083620000 0.416260000 1 1 1
S 0.417920000 0.085610000 0.084250000 1 1 1
S 0.914390000 0.582080000 0.915750000 1 1 1
Mg 0.172790000 0.827210000 0.500000000 1 1 1
Ti 0.662290000 0.337710000 0.000000000 1 1 1
Ti 0.332740000 0.667260000 0.000000000 1 1 1
Ti 0.006290000 0.993710000 0.000000000 0 0 0
Ti 0.510360000 0.489640000 0.500000000 1 1 1
LAST_IMAGE
ATOMIC_POSITIONS { crystal }
Ti 0.348990000 0.691710000 0.327290000
Ti 0.308290000 0.651010000 0.672710000
Ti 0.997060000 0.981290000 0.327880000
Ti 0.018710000 0.002940000 0.672120000
Ti 0.636820000 0.325700000 0.328560000
Ti 0.674300000 0.363180000 0.671440000
Ti 0.832980000 0.167170000 0.829920000
Ti 0.832830000 0.167020000 0.170080000
S 0.909560000 0.579640000 0.246440000
S 0.420360000 0.090440000 0.753560000
S 0.244870000 0.251340000 0.583740000
S 0.748660000 0.755130000 0.416260000
S 0.752030000 0.751540000 0.084110000
S 0.248460000 0.247970000 0.915890000
S 0.248210000 0.251140000 0.247120000
S 0.748860000 0.751790000 0.752880000
S 0.585180000 0.912270000 0.590600000
S 0.087730000 0.414820000 0.409400000
S 0.079970000 0.412600000 0.081300000
S 0.587400000 0.920030000 0.918700000
S 0.577370000 0.913930000 0.244950000
S 0.086070000 0.422630000 0.755050000
S 0.916380000 0.574490000 0.583740000
S 0.425510000 0.083620000 0.416260000
S 0.417920000 0.085610000 0.084250000
S 0.914390000 0.582080000 0.915750000
Mg 0.836455000 0.163545000 0.500000000
Ti 0.662290000 0.337710000 0.000000000
Ti 0.332740000 0.667260000 0.000000000
Ti 0.006290000 0.993710000 0.000000000
Ti 0.510360000 0.489640000 0.500000000
END_POSITIONS
K_POINTS { gamma }
CELL_PARAMETERS { alat }
5.9910000000 0.0000000000 0.0000000000
-2.9895576999 5.1917844484 0.0000000000
-3.0457945930 -5.2685034127 17.3162835891
END_ENGINE_INPUT
END
EOF
$ECHO " running Born-Oppenheimer NEB calculation for H2+H => H+H2...\c"
$NEB_COMMAND -inp H2+H.in > H2+H.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/pwscf*
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR: done"
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