Created
March 23, 2016 13:17
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Shell scripts to generate Delta-SCF calculations with Gaussian & extract results; see http://jarvist.github.io/post/2016-03-17-delta-scf/
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#!/bin/sh | |
# delta_SCF_extract_values.sh - extract values from Delta-SCF Gaussian calculations | |
for i in *neutral.log | |
do | |
# Kohn-Sham HOMO/LUMO from the 'neutral' Gaussian calculation | |
HOMO=` grep "occ" "${i}" | tail -n 1 | awk '{print $NF*27.2114}' ` | |
LUMO=` grep "virt" "${i}" | head -n 1 | awk '{print $5*27.2114}' ` | |
KSGAP=` echo "${LUMO} - ${HOMO}" | bc -l ` | |
echo -n "${i} HOMO: ${HOMO} LUMO: ${LUMO} KSGAP: ${KSGAP} " | |
# These are the Delta-SCF total energies; from 'SCF Done' line in Gaussian output | |
neutral=` grep "SCF Done" "${i}" | awk '{print $5}' ` | |
cation=` grep "SCF Done" "${i/neutral/cation}" | awk '{print $5}' ` | |
anion=` grep "SCF Done" "${i/neutral/anion}" | awk '{print $5}' ` | |
# Calculate IP and EA with maths & scale to eV | |
IP=` echo "(${cation} - ${neutral} ) * 27.2114" | bc -l ` | |
EA=` echo "(${neutral} - ${anion} ) * 27.2114" | bc -l ` | |
echo -n "IonisationPotential: ${IP} ElectronAffinity: ${EA} " | |
echo -n "FundamentalGap: " | |
echo "${IP} - ${EA}" | bc -l | |
done |
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#!/bin/sh | |
# extract_list_geoms.sh | |
# give a list of Gaussian .logs; extract geoms to filename.xyz | |
for i | |
do | |
echo "${i}" | |
jkp_extract_geom.awk "${i}" > "${i%.*}.xyz" | |
done |
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#!/bin/sh | |
cat > HEADER <<EOF | |
%nprocshared=24 | |
#p sp b3lyp/6-31g* SCF(Tight,Conver=8) Integral(Grid=UltraFine) | |
Auto-Delta-SCF Job; via g09_xyz_to_delta_SCF_coms_standalone.sh | |
EOF | |
for i | |
do | |
echo "Conjuring ${i}..." | |
cat HEADER > "${i%.*}-neutral.com" | |
echo "0 1" >> "${i%.*}-neutral.com" | |
cat "${i}" >> "${i%.*}-neutral.com" | |
echo >> "${i%.*}-neutral.com" | |
cat HEADER > "${i%.*}-anion.com" | |
echo "-1 2" >> "${i%.*}-anion.com" | |
cat "${i}" >> "${i%.*}-anion.com" | |
echo >> "${i%.*}-anion.com" | |
cat HEADER > "${i%.*}-cation.com" | |
echo "+1 2" >> "${i%.*}-cation.com" | |
cat "${i}" >> "${i%.*}-cation.com" | |
echo >> "${i%.*}-cation.com" | |
done |
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#! /bin/awk -f | |
BEGIN{j=0 | |
at_symbol[0]="Bq" | |
at_symbol[1]="H" | |
at_symbol[2]="He" | |
at_symbol[3]="Li" | |
at_symbol[4]="Be" | |
at_symbol[5]="B" | |
at_symbol[6]="C" | |
at_symbol[7]="N" | |
at_symbol[8]="O" | |
at_symbol[9]="F" | |
at_symbol[10]="Ne" | |
at_symbol[11]="Na" | |
at_symbol[12]="Mg" | |
at_symbol[13]="Al" | |
at_symbol[14]="Si" | |
at_symbol[15]="P" | |
at_symbol[16]="S" | |
at_symbol[17]="Cl" | |
at_symbol[18]="Ar" | |
at_symbol[19]="K" | |
at_symbol[20]="Ca" | |
at_symbol[21]="Sc" | |
at_symbol[22]="Ti" | |
at_symbol[23]="V" | |
at_symbol[24]="Cr" | |
at_symbol[25]="Mn" | |
at_symbol[26]="Fe" | |
at_symbol[27]="Co" | |
at_symbol[28]="Ni" | |
at_symbol[29]="Cu" | |
at_symbol[30]="Zn" | |
at_symbol[31]="Ga" | |
at_symbol[32]="Ge" | |
at_symbol[33]="As" | |
at_symbol[34]="Se" | |
at_symbol[35]="Br" | |
at_symbol[36]="Kr" | |
at_symbol[46]="Pd" | |
at_symbol[47]="Ag" | |
at_symbol[48]="Cd" | |
at_symbol[50]="Sn" | |
at_symbol[51]="Sb" | |
at_symbol[53]="I" | |
at_symbol[54]="Xe" | |
at_symbol[78]="Pt" | |
at_symbol[79]="Au" | |
at_symbol[80]="Hg" | |
at_symbol[81]="Tl" | |
at_symbol[82]="Pb" | |
at_symbol[83]="Bi" | |
} | |
{ | |
if (($1=="Standard" && $2=="orientation:") || ($1 == "Z-Matrix" && $2 == "orientation:")) { | |
getline | |
getline | |
getline | |
getline | |
getline | |
i=0 | |
while (NF!=1) { | |
i++ | |
at[i]=$2 | |
if (NF==5) { | |
x[i]=$3 | |
y[i]=$4 | |
z[i]=$5 | |
} | |
else { | |
x[i]=$4 | |
y[i]=$5 | |
z[i]=$6 | |
} | |
getline | |
} | |
} | |
if ($1=="SCF" && $2=="Done:") { | |
energy=$5 | |
j++ | |
} | |
} | |
END{ | |
for (k=1;k<=i;k++) { | |
print at_symbol[at[k]], x[k], y[k], z[k] | |
} | |
} |
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