Hi everyone,
I am calculating thermal properties using the QHA. However, I get the following
error output in the matdyn.out file:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine matdyn (5010):
reading input namelist
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
Could anyone help locate the problem. Input file is attached.
Henry Odhiambo Otunga
Department of Physics and Materials Science
Maseno University
Kenya
#!/bin/sh
####################################################################
# Copyright Eyvaz Isaev
#
#
# Department of Physics, Chemistry, and Biophysics (IFM),
# Linkoping University, Sweden
#
# Theoretical Physics Department,
# Moscow State Institute of Steel and Alloys, Russia
# (Technological University)
#
# [email protected], [email protected]
#
# set environment variables
#
. ../environment_variables
#
# As input parameters you have to specify (there are no default parameters):
#
# Mandatory parameters:
#
# Atoms - specify atoms involved in your calculations, you can specify Fe1, Fe1, Cr1,Cr2, etc.
# N.B.! in the same order as you did it in your self-consistent input file.
# delta_e - frequency step (in cm{-1})
#
# "Temperature" file which contains
# T_start, T_end, T_delta
# initial T, final T, and delta T for calculation of the phonon contribution (F_vib) to
# the free energy, the heat capacity (C_v), phonon entropy (S_vib), and phonon internal
# energy (E_int)
#
# T_list - list of temperatures for which the Debye temperature has to be calculated.
# For lower T (do not specify T<10K !!!) calculations require more computer time,
# starting from 10K is much faster
#
# Optional parameters:
# Sysname - specify your system name you have considered,
# required to see your system name in output files
# SysInfo - Any information on your system (volume, pressure, etc.) will be reflected in the head part
# of output file
#
# Input parameters for Quasiharonic calculations (fqha.in)
# PHDOS.out - Total phonon DOS, you might specify any partial phonon DOS name but only
# total phonon DOS is used for this purpose
# Sysname.QHA.out - Name of output file for QHA calculations
# T_start, T_end, T_step - starting T, the highest T used in QHA calculations, and T step
#
#
# To start Phonon DOS calculatons you have to edit matdin.init file (See below) to specify
# force constants matrix, and atomic masses
# You need also "ttrinp" file to show Brillouin Zone:
# See ttrinp file for explanation how you can manage it
# There are some ttrinp files for a number of popular (FCC, BCC, Simple Cubic, and HCP) latticies
# For these crystal structures you need no additional information and ttrinp file added
# automatically.
##############################################################################
##############################################################################
# Optional parameters, any information specific for the system studied
#
SysInfo='nickel'
# Mandatory parameters
# Specify SystemName and Force Constants matrix
Sysname='ni'
FC_file='ni444.fc'
#
# Specify lattice type (used to create ttrinp file). It should be the same as in scf.in file
# Specify atoms in the unit cell as they specified in scf.in file
# Specify atomic masses for these atoms in the same order as atoms in scf.in file
# Specify the frequency step (delta_e) as well, but 0.75 is a good choice
ibrav=2
atoms="Ni"
mass="58.69"
delta_e=0.75
# Edit ONLY amass parameters
# Please do not change flfrq='frequency' line
# leave asr (acoustic sum rule) and flfrc lines
cat >matdyn.init <<EOF
&input
asr='crystal',
amass(1)=58.69,
flfrc=$FC_file,
flfrq='frequency'
&end
EOF
#
# In most cases there is no need to edit files listed below, but if you like ...
#
# Temperature range for thermodynamic properties
# T_start, T_end, T_step for QHA calculations
cat > Temperature <<EOF
5 500 5
EOF
# Debye Temperature calculations
# Phonon DOS filename (total phonon DOS, not projected), leave it as PHDOS.out
# accuracy (limited 1.d-5, more accuracy is not required )
# Low_temp_start, Low_Temp_end, and Low_Temp_step for LT limit, up to 15-30K
# Hihg temperature and T_step for HT limit
cat >T_Debye.in <<EOF
PHDOS.out
0.0001
3 15 3
500 10
EOF
#############################################################################
#
# Copy appropriate tetrahedra file to ttrinp
#
case $ibrav in
0) echo "You should know about the symmetry of a system you study"
exit ;;
1) cp $QHA_DIR/tetrahedra/ttrinp_sc ./ttrinp ;;
2) cp $QHA_DIR/tetrahedra/ttrinp_fcc ./ttrinp ;;
3) cp $QHA_DIR/tetrahedra/ttrinp_bcc ./ttrinp ;;
4) c2a1=`head -1 $FC_file | cut -c 36-44`
c2a=`echo "scale=8;(1/$c2a1)/2" | bc -l`
sed 's/X/'$c2a'/g' $QHA_DIR/tetrahedra/ttrinp_hcp > ./ttrinp ;;
5) echo "Trigonal R: not implemented yet"
exit ;;
6) c2a1=`head -1 $FC_file | cut -c 36-44`
c2a=`echo "scale=8;(1/$c2a1)/2" | bc -l`
echo $c2a
sed 's/X/'$c2a'/g' $QHA_DIR/tetrahedra/ttrinp_stetra > ./ttrinp ;;
7) echo "Running script instruction:"
echo "See instructions in $QHA_DIR/tetrahedra/ttrinp_bct file to setup tetrahedra vertecies for c/a<1"
echo "Then comment exit line by #"
echo "And uncomment the next line"
exit;;
# cp $QHA_DIR/tetrahedra/ttrinp_bct ./ttrinp ;;
8) b2a1=`head -1 $FC_file | cut -c 25-33`
c2a1=`head -1 $FC_file | cut -c 36-44`
b2a=`echo "scale=8;(1/$b2a1)/2" |bc -l`
c2a=`echo "scale=8;(1/$c2a1)/2" |bc -l`
sed 's/YY/'$b2a'/g' $QHA_DIR/tetrahedra/ttrinp_ortho_simple > ttrinp1
sed 's/ZZ/'$c2a'/g' ttrinp1 > ./ttrinp
rm -f ttrinp1;;
9) echo "Orthorhombic base centered: not implemented yet"
exit ;;
10) echo "Orthorhombic face centered: not implemented yet"
exit ;;
11) echo "Orthorhombic body centered: not implemented yet"
exit ;;
12) echo "Monoclinic P: not implemented yet"
exit ;;
13) echo "Monoclinic base centered: not implemented yet"
exit ;;
14) echo "Triclinic: not implemented yet"
exit ;;
esac
############################################################################
# Below run commands
# Generate q-points
$QHA_DIR/bin/tetra.x
cp matdyn.init matdyn.init.tmp
cat kpts_out >> matdyn.init.tmp
echo EOF >>matdyn.init.tmp
mv matdyn.init.tmp matdyn.in
echo ' Recalculating omega(q) from C(R)'
$BIN_DIR/matdyn.x < matdyn.in > matdyn.out
nmodes=`head -1 frequency | cut -c 13-16 `
nkpt=`head -1 frequency | cut -c 23-26 `
natoms=`echo "scale=0; $nmodes/3" | bc -l`
#
cat >phdos1.in <<EOF
$nkpt $nmodes
$atoms
EOF
# Calculate partial phonon DOS
$QHA_DIR/bin/Partial_phonon_DOS.x < phdos1.in
#rm -f phdos1.in
cat >phdos.in <<EOF
$delta_e
$atoms
EOF
# Calculate total phonon DOS and atom projected phonon DOS
$QHA_DIR/bin/phonon_dos.x <frequency
#rm -f phdos.in
# Remove NaN from all phonon DOS files
cat >name <<EOF
PHDOS.out
EOF
cp PHDOS.out PHDOS.out.copy
$QHA_DIR/bin/Ghost_DOS.x <name >out
mv out PHDOS.out
#rm -f name
# Atomic related properties
cat >atom_info <<EOF
$natoms
$atoms
$mass
EOF
for Atom in $atoms
do
cat > atom_name <<EOF
$Atom
EOF
$QHA_DIR/bin/atom_info.x < atom_info > atom_mass
cat >name <<EOF
projected_DOS.$Atom
EOF
$QHA_DIR/bin/Ghost_DOS.x <name >out
mv out projected_DOS.$Atom
cp projected_DOS.$Atom projected.DOS
echo "# $Sysname $Atom $SysInfo" >>Thermodynamics.$Atom
$QHA_DIR/bin/Atom_projected_properties.x >>Thermodynamics.$Atom
#
# Mean Square Displacement calculations for each atoms
cat name Temperature atom_mass > displacement.in
$QHA_DIR/bin/Mean_square_displacement.x < displacement.in
mv Displacements Displacements.$Atom
done
# Debye Temperature calculations
$QHA_DIR/bin/Debye.x >> Theta_D
#rm -f T_Debey.in
# Finally, thermodynamic properties
#
# Parameters required for QHA calculations
# Total Phonon DOS file
# output file for C_V, S, Internal energy
#
cat >fqha.in <<EOF
PHDOS.out
$Sysname.QHA.out
EOF
cat Temperature >> fqha.in
$QHA_DIR/bin/F_QHA.x <fqha.in
#rm -f fqha.in
echo 'Phonon DOS and Quasiharmonic calculations have finished.'
echo 'Now you can analyse these data using Gnuplot or xmgrace'
echo 'Enjoy!'
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