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quantum-espresso/PW/examples/RISM_example/run_example_ESM-RISM

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#!/bin/sh
###############################################################################
##
## ESM-RISM EXAMPLE
##
###############################################################################
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 Laue-RISM calculation"
$ECHO "3) Vacuum/Li(100)/EtOH,"
$ECHO "4) Vacuum/Al(111)/NaCl(aq,5.0M) where slab of Al is charged., and"
$ECHO "5) NaCl(aq,1.0M)/Cl-/NaCl(aq,1.0M)."
$ECHO
# set the needed environment variables
. ../../../environment_variables
# required executables, pseudopotentials and molecules
BIN_LIST="pw.x pprism.x"
PSEUDO_LIST="Li.pbe-n-van.UPF Al.pbe-n-van.UPF Cl.pbe-n-van.UPF"
MOL_LIST="H2O.spc.MOL Na+.aq.MOL Cl-.aq.MOL Ethanol.oplsua.MOL"
$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"
# check for molecules
for FILE in $MOL_LIST ; do
if test ! -r $PSEUDO_DIR/$FILE ; then
$ECHO
$ECHO "Copy $FILE to $PSEUDO_DIR...\c"
cp $EXAMPLE_DIR/MOL/$FILE $PSEUDO_DIR 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 $PARA_POSTFIX"
PP_COMMAND="$PARA_PREFIX $BIN_DIR/pprism.x $PARA_POSTFIX"
$ECHO
$ECHO " running pw.x as: $PW_COMMAND"
$ECHO " running pprism.x as: $PP_COMMAND"
$ECHO
# ESM-RISM calculation for Li(100) with ethanol
cat > Li-EtOH.in << EOF
&control
calculation = 'scf'
prefix = 'Li-EtOH'
pseudo_dir = '$PSEUDO_DIR/'
outdir = '$TMP_DIR/'
trism = .true.
/
&system
ibrav = 0
ntyp = 1
nat = 5
ecutwfc = 25.0
ecutrho = 225.0
occupations = 'smearing'
smearing = 'gauss'
degauss = 0.01
! ESM
assume_isolated = 'esm'
esm_bc = 'bc1'
/
&electrons
diagonalization = 'rmm-davidson'
mixing_beta = 0.4
/
&rism
nsolv = 1
closure = 'kh'
tempv = 300.0 ! Kelvin
ecutsolv = 144.0 ! Rydberg
! Lennard-Jones
solute_lj(1) = 'uff'
! Laue-RISM
laue_expand_right = 50.00 ! bohr
laue_starting_right = 3.24 ! bohr
laue_buffer_right = 2.00 ! bohr
/
ATOMIC_SPECIES
Li -1.0 Li.pbe-n-van.UPF
CELL_PARAMETERS (angstrom)
3.430000067 0.000000000 0.000000000
0.000000000 3.430000067 0.000000000
0.000000000 0.000000000 26.860000179
ATOMIC_POSITIONS (angstrom)
Li 0.0000000000 0.0000000000 -3.4300000895
Li 0.0000000000 0.0000000000 0.0000000005
Li 0.0000000000 0.0000000000 3.4300000895
Li 1.7150000330 1.7150000330 -1.7150000445
Li 1.7150000330 1.7150000330 1.7149998915
K_POINTS {automatic}
2 2 1 0 0 0
SOLVENTS {mol/L}
EtOH -1.0 Ethanol.oplsua.MOL
EOF
$ECHO " running the ESM-RISM calculation for Li(100) with ethanol...\c"
$PW_COMMAND < Li-EtOH.in > Li-EtOH.out
check_failure $?
cp -f $TMP_DIR/Li-EtOH.1drism ./
cp -f $TMP_DIR/Li-EtOH.rism1 ./
cp -f $TMP_DIR/Li-EtOH.esm1 ./
cp -f $TMP_DIR/Li-EtOH.xml ./
$ECHO " done"
# plot solvent distribution
cat > Li-EtOH.post.in << EOF
&inputpp
prefix = 'Li-EtOH'
outdir = '$TMP_DIR/'
lpunch = .true.
/
&plot
iflag = 3 ! 3D plot
output_format = 6 ! Gaussian's CUBE
/
EOF
$ECHO " running the postprocessing to plot solvent...\c"
$PP_COMMAND < Li-EtOH.post.in > Li-EtOH.post.out
check_failure $?
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/Li-EtOH*
$ECHO " done"
# ESM-RISM calculation for charged Al(111) with NaCl(aq)/5.0M
cat > Al-NaCl_aq.in << EOF
&control
calculation = 'scf'
prefix = 'Al-NaCl_aq'
pseudo_dir = '$PSEUDO_DIR/'
outdir = '$TMP_DIR/'
trism = .true.
forc_conv_thr = 2.0e-3
/
&system
ibrav = 0
ntyp = 1
nat = 3
ecutwfc = 25.0
ecutrho = 225.0
occupations = 'smearing'
smearing = 'gauss'
degauss = 0.01
! Charged
tot_charge = +0.1
! ESM
assume_isolated = 'esm'
esm_bc = 'bc1'
/
&electrons
diagonalization = 'rmm-davidson'
mixing_beta = 0.2
/
&ions
ion_dynamics = 'bfgs'
/
&rism
nsolv = 3
closure = 'kh'
tempv = 300.0 ! Kelvin
ecutsolv = 100.0 ! Rydberg
! Lennard-Jones
solute_lj(1) = 'uff'
! Laue-RISM
laue_expand_right = 50.00 ! bohr
laue_starting_right = 0.00 ! bohr
/
ATOMIC_SPECIES
Al -1.0 Al.pbe-n-van.UPF
CELL_PARAMETERS (angstrom)
2.863782644 0.000000000 0.000000000
1.431891322 2.480108521 0.000000000
0.000000000 0.000000000 24.676537653
ATOMIC_POSITIONS (angstrom)
Al 0.0000000000 0.0000000000 -2.3382688265
Al 2.8637827300 1.6534057300 2.3382688265
Al 1.4318913650 0.8267028650 0.0000000005
K_POINTS {automatic}
2 2 1 0 0 0
SOLVENTS {mol/L}
H2O -1.0 H2O.spc.MOL
Na+ 5.0 Na+.aq.MOL
Cl- 5.0 Cl-.aq.MOL
EOF
$ECHO " running the ESM-RISM calculation for charged Al(111) with NaCl(aq)/5.0M...\c"
$PW_COMMAND < Al-NaCl_aq.in > Al-NaCl_aq.out
check_failure $?
cp -f $TMP_DIR/Al-NaCl_aq.1drism ./
cp -f $TMP_DIR/Al-NaCl_aq.rism1 ./
cp -f $TMP_DIR/Al-NaCl_aq.esm1 ./
cp -f $TMP_DIR/Al-NaCl_aq.xml ./
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/Al-NaCl_aq*
$ECHO " done"
# ESM-RISM calculation for Cl- in NaCl(aq)/1.0M
cat > Cl-_NaCl_aq.in << EOF
&control
calculation = 'scf'
prefix = 'Cl-_NaCl_aq'
pseudo_dir = '$PSEUDO_DIR/'
outdir = '$TMP_DIR/'
trism = .true.
/
&system
ibrav = 0
ntyp = 1
nat = 1
ecutwfc = 25.0
ecutrho = 225.0
occupations = 'smearing'
smearing = 'gauss'
degauss = 0.01
! Charged
tot_charge = -1.0
! ESM
assume_isolated = 'esm'
esm_bc = 'bc1'
/
&electrons
diagonalization = 'rmm-davidson'
mixing_beta = 0.2
/
&ions
ion_dynamics = 'bfgs'
/
&rism
nsolv = 3
closure = 'kh'
tempv = 300.0 ! Kelvin
ecutsolv = 100.0 ! Rydberg
! Lennard-Jones
solute_lj(1) = 'uff'
! Laue-RISM
laue_expand_right = 50.00 ! bohr
laue_expand_left = 50.00 ! bohr
/
ATOMIC_SPECIES
Cl -1.0 Cl.pbe-n-van.UPF
CELL_PARAMETERS (angstrom)
10.000000000 0.000000000 0.000000000
0.000000000 10.000000000 0.000000000
0.000000000 0.000000000 10.000000000
ATOMIC_POSITIONS (angstrom)
Cl 5.0000000000 5.0000000000 0.0000000000
K_POINTS {gamma}
SOLVENTS {mol/L}
H2O -1.0 H2O.spc.MOL
Na+ 1.0 Na+.aq.MOL
Cl- 1.0 Cl-.aq.MOL
EOF
$ECHO " running the ESM-RISM calculation for Cl- in NaCl(aq)/1.0M...\c"
$PW_COMMAND < Cl-_NaCl_aq.in > Cl-_NaCl_aq.out
check_failure $?
cp -f $TMP_DIR/Cl-_NaCl_aq.1drism ./
cp -f $TMP_DIR/Cl-_NaCl_aq.rism1 ./
cp -f $TMP_DIR/Cl-_NaCl_aq.esm1 ./
cp -f $TMP_DIR/Cl-_NaCl_aq.xml ./
$ECHO " done"
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/Cl-_NaCl_aq*
$ECHO " done"
$ECHO
$ECHO "run_example_ESM-RISM: done"
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