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RUN_lamaGOET_release_serial.sh
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RUN_lamaGOET_release_serial.sh
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#!/bin/bash
export LC_NUMERIC="en_US.UTF-8"
source job_options.txt
GAMESS_ELMODB_OLD_PDB(){
I=$[ $I + 1 ]
PDB=$( echo $CIF | awk -F "/" '{print $NF}' )
echo "title" > $JOBNAME.gamess.inp
echo "prova $JOBNAME - $BASISSETG - closed shell SCF" >> $JOBNAME.gamess.inp
echo "charge $CHARGE " >> $JOBNAME.gamess.inp
if [ "$MULTIPLICITY" != "1" ]; then
echo "multiplicity $MULTIPLICITY" >> $JOBNAME.gamess.inp
fi
echo "adapt off" >> $JOBNAME.gamess.inp
echo "nosym" >> $JOBNAME.gamess.inp
echo "geometry angstrom" >> $JOBNAME.gamess.inp
if [ "$I" = "1" ]; then
awk '$1 ~ /ATOM/ {printf "%f\t %f\t %f\t %s\t %s\n", $6, $7, $8, "carga", $3}' $CIF > atoms
else
awk 'NR > 2 {printf "%f\t %f\t %f\t %s\t %s\n", $2, $3, $4, "carga", $1}' $JOBNAME.xyz > atoms
fi
awk '{print $5}' atoms | gawk 'BEGIN { FS = "" } {print $1}' | awk '{ if ($1 == "N") print "7.0"; else if ($1 == "H") print "1.0"; else if ($1 == "O") print "8.0"; else if ($1 == "C") print "6.0"; else if ($1 == "S") print "16.0"; }' > atoms_Z
awk '{print $5}' atoms | gawk 'BEGIN { FS = "" } {print $1}' > atoms_names
awk 'FNR==NR{a[NR]=$1;next}{$4=a[FNR]}1' atoms_Z atoms > full
cp full atoms
awk 'FNR==NR{a[NR]=$1;next}{$5=a[FNR]}1' atoms_names atoms > full
awk '{printf "%f\t %f\t %f\t %s\t %s\n", $1, $2, $3, $4, $5}' full >> $JOBNAME.gamess.inp
rm atoms
rm atoms_Z
rm full
rm atoms_names
echo "end" >> $JOBNAME.gamess.inp
case "6-31g(d,p)" in
$BASISSETG ) echo "basis 6-31G**" >> $JOBNAME.gamess.inp;;
*) case "6-311g(d,p)" in
$BASISSETG ) echo "basis 6-311G**" >> $JOBNAME.gamess.inp;;
*) echo "basis $BASISSETG" >> $JOBNAME.gamess.inp;;
esac;;
esac
echo "runtype scf" >> $JOBNAME.gamess.inp
echo "scftype rhf" >> $JOBNAME.gamess.inp
echo "enter " >> $JOBNAME.gamess.inp
echo "Calculating overlap integrals with gamessus, cycle number $I"
$GAMESS < $JOBNAME.gamess.inp > $JOBNAME.gamess.out
echo "Gamess cycle number $I ended"
mkdir $I.$SCFCALCPROG.cycle.$JOBNAME
cp $JOBNAME.gamess.inp $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.gamess.inp
cp $JOBNAME.gamess.out $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.gamess.out
cp sao $I.$SCFCALCPROG.cycle.$JOBNAME/$I.sao
rm ed*
rm gamess_input*
if ! grep -q 'OVERLAP INTEGRALS WRITTEN ON FILE sao' "$JOBNAME.gamess.out"; then
echo "ERROR: Calculation of overlap integrals with gamessus finished with error, please check the $I.th gamess.out file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
else
echo "Calculation of overlap integrals with gamess done, writing elmodb input files"
if [[ ! -f "$( echo $SCFCALC_BIN | awk -F "/" '{print $NF}' )" ]]; then
cp $SCFCALC_BIN .
fi
if [ "$I" = "1" ]; then
BASISSETDIR=$( echo "$(dirname $BASISSETDIR)/" )
ELMOLIB=$( echo "$(dirname $ELMOLIB)/" )
#this is correct but until the elmo problem is solved I will keep it commented
# if [[ "$INITADP" == "true" ]];then
# echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' cif=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
# else
echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
# fi
# if [[ "$INITADP" == "true" ]];then
# echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' cif_file='$INITADPFILE' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
# else
echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
# fi
if [[ "$NTAIL" != "0" ]]; then
echo "$MANUALRESIDUE" >> $JOBNAME.elmodb.inp
fi
if [[ "$NSSBOND" != "0" ]]; then
echo "$SSBONDATOMS" >> $JOBNAME.elmodb.inp
fi
else
#there is a problem with the conversion from fractional to cartesian inside the elmodb program, saving example files in the aga folder 4cut and changing back to always use the xyz. The elmo cannot read the cartesian cif
# echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' cif=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. comp_sao=.false. "'$END'" " > $JOBNAME.elmodb.inp
echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' xyz=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. comp_sao=.false. "'$END'" " > $JOBNAME.elmodb.inp
echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' xyz_file='$JOBNAME.xyz' ntail=$NTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
if [[ "$NTAIL" != "0" ]]; then
echo "$MANUALRESIDUE" >> $JOBNAME.elmodb.inp
fi
if [[ "$NSSBOND" != "0" ]]; then
echo "$SSBONDATOMS" >> $JOBNAME.elmodb.inp
fi
fi
echo "Running elmodb"
./$( echo $SCFCALC_BIN | awk -F "/" '{print $NF}' ) < $JOBNAME.elmodb.inp > $JOBNAME.elmodb.out
if ! grep -q 'CONGRATULATIONS: THE ELMO-TRANSFERs ENDED GRACEFULLY!!!' "$JOBNAME.elmodb.out"; then
echo "ERROR: elmodb finished with error, please check the $I.th elmodb.out file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
else
echo "elmodb job finish correctly."
cp $JOBNAME.elmodb.out $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.out
cp $JOBNAME.elmodb.inp $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.inp
cp $JOBNAME.fchk $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.fchk
if [ "$I" != "1" ]; then
cp $JOBNAME.xyz $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.xyz
fi
fi
fi
}
ELMODB(){
I=$[ $I + 1 ]
if [[ ! -f "$( echo $SCFCALC_BIN | awk -F "/" '{print $NF}' )" ]]; then
cp $SCFCALC_BIN .
fi
if [ "$I" = "1" ]; then
BASISSETDIR=$( echo "$(dirname $BASISSETDIR)/" )
ELMOLIB=$( echo "$(dirname $ELMOLIB)/" )
#this is correct but until the elmo problem is solved I will keep it commented
# if [[ "$INITADP" == "true" ]];then
# echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' cif=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
# else
echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
# fi
# if [[ "$INITADP" == "true" ]];then
# echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' cif_file='$INITADPFILE' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
# else
echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
# fi
if [[ "$NTAIL" != "0" ]]; then
echo "$MANUALRESIDUE" >> $JOBNAME.elmodb.inp
fi
if [[ "$NSSBOND" != "0" ]]; then
echo "$SSBONDATOMS" >> $JOBNAME.elmodb.inp
fi
else
#there is a problem with the conversion from fractional to cartesian inside the elmodb program, saving example files in the aga folder 4cut and changing back to always use the xyz. The elmo cannot read the cartesian cif
# echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' cif=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' xyz=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
if [[ "$NTAIL" != "0" ]]; then
# echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' cif_file='$JOBNAME.fractional.cif1' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' xyz_file='$JOBNAME.xyz' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
echo "$MANUALRESIDUE" >> $JOBNAME.elmodb.inp
else
# echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' cif_file='$JOBNAME.fractional.cif1' nssbond=$NSSBOND "'$END'" " >>
echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' xyz_file='$JOBNAME.xyz' nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
fi
if [[ "$NSSBOND" != "0" ]]; then
echo "$SSBONDATOMS" >> $JOBNAME.elmodb.inp
fi
fi
echo "Running elmodb"
./$( echo $SCFCALC_BIN | awk -F "/" '{print $NF}' ) < $JOBNAME.elmodb.inp > $JOBNAME.elmodb.out
if ! grep -q 'CONGRATULATIONS: THE ELMO-TRANSFERs ENDED GRACEFULLY!!!' "$JOBNAME.elmodb.out"; then
echo "ERROR: elmodb finished with error, please check the $I.th elmodb.out file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
else
echo "elmodb job finish correctly."
mkdir $I.$SCFCALCPROG.cycle.$JOBNAME
cp $JOBNAME.elmodb.out $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.out
cp $JOBNAME.elmodb.inp $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.inp
cp $JOBNAME.fchk $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.fchk
if [ "$I" != "1" ]; then
cp $JOBNAME.xyz $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.xyz
fi
fi
}
TONTO_TO_ORCA(){
I=$[ $I + 1 ]
echo "Extracting XYZ for Orca cycle number $I"
if [ "$METHOD" = "rks" ]; then
echo "! blyp $BASISSETG" > $JOBNAME.inp
else
if [ "$METHOD" = "uks" ]; then
echo "! ublyp $BASISSETG" > $JOBNAME.inp
else
echo "! $METHOD $BASISSETG" > $JOBNAME.inp
fi
fi
echo "" >> $JOBNAME.inp
echo "%output" >> $JOBNAME.inp
echo " PrintLevel=Normal" >> $JOBNAME.inp
echo " Print[ P_Basis ] 2" >> $JOBNAME.inp
echo " Print[ P_GuessOrb ] 1" >> $JOBNAME.inp
echo " Print[ P_MOs ] 1" >> $JOBNAME.inp
echo " Print[ P_Density ] 1" >> $JOBNAME.inp
echo " Print[ P_SpinDensity ] 1" >> $JOBNAME.inp
echo "end" >> $JOBNAME.inp
echo "" >> $JOBNAME.inp
echo "* xyz $CHARGE $MULTIPLICITY" >> $JOBNAME.inp
awk 'NR>2' $JOBNAME.xyz >> $JOBNAME.inp
if [ "$SCCHARGES" = "true" ]; then
if [ ! -f gaussian-point-charges ]; then
echo "" > gaussian-point-charges
awk '/Cluster monopole charges and positions/{print p; f=1} {p=$0} /------------------------------------------------------------------------/{c=1} f; c--==0{f=0}' stdout >> gaussian-point-charges
fi
echo "" >> $JOBNAME.inp
awk '{a[NR]=$0}{b=12}/^------------------------------------------------------------------------/{c=NR}END{for(d=b;d<=c-1;++d)print a[d]}' gaussian-point-charges | awk '{printf "%s\t %s\t %s\t %s\t \n", $1, $2, $3, $4 }' >> $JOBNAME.inp
echo "" >> $JOBNAME.inp
# rm gaussian-point-charges
fi
echo "*" >> $JOBNAME.inp
echo "Running Orca, cycle number $I"
$SCFCALC_BIN $JOBNAME.inp > $JOBNAME.log
echo "Orca cycle number $I ended"
if ! grep -q '****ORCA TERMINATED NORMALLY****' "$JOBNAME.out"; then
echo "ERROR: Orca job finished with error, please check the $I.th out file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
fi
echo "Generation molden file for Orca cycle number $I"
orca_2mkl $JOBNAME -molden
echo "Orca cycle number $I, final energy is: $ENERGIA, RMSD is: $RMSD "
mkdir $I.$SCFCALCPROG.cycle.$JOBNAME
cp $JOBNAME.inp $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.inp
cp $JOBNAME.molden.input $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.molden.input
cp $JOBNAME.log $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.log
}
TONTO_HEADER(){
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!" > stdin
echo "!!! !!!" >> stdin
echo "!!! This stdin was written with lamaGOET !!!" >> stdin
echo "!!! !!!" >> stdin
echo "!!! script written by Lorraine Andrade Malaspina !!!" >> stdin
echo "!!! contact: [email protected] !!!" >> stdin
echo "!!! !!!" >> stdin
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!" >> stdin
echo "{ " >> stdin
echo "" >> stdin
echo " keyword_echo_on" >> stdin
echo "" >> stdin
}
READ_ELMO_FCHK(){
echo " name= $JOBNAME" >> stdin
echo "" >> stdin
echo " read_g09_fchk_file $JOBNAME.fchk" >> stdin
echo "" >> stdin
}
READ_GAUSSIAN_FCHK(){
echo " name= $JOBNAME" >> stdin
echo "" >> stdin
echo " read_g09_fchk_file $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.fchk" >> stdin
echo "" >> stdin
}
READ_ORCA_FCHK(){
echo " name= $JOBNAME" >> stdin
echo "" >> stdin
echo " read_molden_file $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.molden.input" >> stdin
echo "" >> stdin
}
DEFINE_JOB_NAME(){
echo " name= $JOBNAME" >> stdin
echo "" >> stdin
}
CHANGE_JOB_NAME(){
echo " name= $JOBNAME.XCW" >> stdin
echo "" >> stdin
}
PROCESS_CIF(){
echo " ! Process the CIF" >> stdin
echo " CIF= {" >> stdin
if [ $J = 0 ]; then
if [[ "$COMPLETESTRUCT" == "true" && "$SCFCALCPROG" != "Tonto" ]]; then
echo " file_name= $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.cartesian.cif2" >> stdin
else
echo " file_name= $CIF" >> stdin
fi
if [ "$XHALONG" = "true" ]; then
if [[ ! -z "$BHBOND" ]]; then
echo " BH_bond_length= $BHBOND angstrom" >> stdin
fi
if [[ ! -z "$CHBOND" ]]; then
echo " CH_bond_length= $CHBOND angstrom" >> stdin
fi
if [[ ! -z "$NHBOND" ]]; then
echo " NH_bond_length= $NHBOND angstrom" >> stdin
fi
if [[ ! -z "$OHBOND" ]]; then
echo " OH_bond_length= $OHBOND angstrom" >> stdin
fi
fi
elif [ $J = 1 ]; then
if [[ "$SCCHARGES" == "true" && ("$SCFCALCPROG" == "Gaussian" || "$SCFCALCPROG" == "Orca") ]]; then
# if [[ "$SCFCALCPROG" == "Gaussian" || "$SCFCALCPROG" == "Orca" ]]; then
if [[ "$COMPLETESTRUCT" == "true" ]]; then
echo " file_name= 0.tonto_cycle.$JOBNAME/0.$JOBNAME.cartesian.cif2" >> stdin
else
echo " file_name= $CIF" >> stdin
fi
else
echo " file_name= $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.cartesian.cif2" >> stdin
fi
else
echo " file_name= $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.cartesian.cif2" >> stdin
fi
echo " }" >> stdin
echo "" >> stdin
echo " process_CIF" >> stdin
echo "" >> stdin
}
TONTO_BASIS_SET(){
echo " basis_directory= $BASISSETDIR" >> stdin
echo " basis_name= $BASISSETT" >> stdin
echo "" >> stdin
}
DISPERSION_COEF(){
echo " dispersion_coefficients= {" >> stdin
echo " $(cat DISP_inst.txt)" >> stdin
echo " }" >> stdin
echo "" >> stdin
}
CHARGE_MULT(){
echo " charge= $CHARGE" >> stdin
echo " multiplicity= $MULTIPLICITY" >> stdin
echo "" >> stdin
}
TONTO_IAM_BLOCK(){
echo ""
echo " crystal= { " >> stdin
if [[ "$SCFCALCPROG" = "elmodb" && "$INITADP" == "false" ]]; then
echo " REDIRECT tonto.cell" >> stdin
fi
echo " xray_data= { " >> stdin
echo " optimise_extinction= false" >> stdin
echo " correct_dispersion= $DISP" >> stdin
echo " wavelength= $WAVE Angstrom" >> stdin
if [ "$REFANHARM" == "true" ]; then
if [[ "$THIRDORD" == "false" && "$FOURTHORD" == "true" ]]; then
echo " refine_4th_order_only= true " >> stdin
echo " refine_4th_order_for_atoms= { $ANHARMATOMS } " >> stdin
elif [[ "$THIRDORD" == "true" && "$FOURTHORD" == "true" ]]; then
echo " refine_4th_order_for_atoms= { $ANHARMATOMS } " >> stdin
elif [[ "$THIRDORD" == "true" && "$FOURTHORD" == "false" ]]; then
echo " refine_3rd_order_for_atoms= { $ANHARMATOMS } " >> stdin
else
echo "ERROR: Please select at least one of the anharmonic terms to refine" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
fi
fi
echo " REDIRECT $HKL" >> stdin
if [[ "$FCUT" != "0" ]]; then
echo " f_sigma_cutoff= $FCUT" >> stdin
fi
if [[ "$MINCORCOEF" != "" ]]; then
echo " min_correlation= $MINCORCOEF" >> stdin
fi
echo " tol_for_shift_on_esd= $CONVTOL" >> stdin
echo " refine_H_U_iso= yes" >> stdin
echo "" >> stdin
echo " show_fit_output= true" >> stdin
echo " show_fit_results= true" >> stdin
echo "" >> stdin
echo " } " >> stdin
echo " } " >> stdin
echo "" >> stdin
echo " ! Geometry " >> stdin
echo " put" >> stdin
echo "" >> stdin
echo " IAM_refinement" >> stdin
echo "" >> stdin
}
CRYSTAL_BLOCK(){
echo "" >> stdin
echo " crystal= { " >> stdin
if [[ "$SCFCALCPROG" == "elmodb" && $J == 0 && "$INITADP" == "false" ]]; then
echo " REDIRECT tonto.cell" >> stdin
fi
if [[ "$SCFCALCPROG" == "optgaussian" ]]; then
echo " REDIRECT tonto.cell" >> stdin
fi
if [[ "$SCFCALCPROG" != "optgaussian" ]]; then
echo " xray_data= { " >> stdin
echo " thermal_smearing_model= hirshfeld" >> stdin
echo " partition_model= mulliken" >> stdin
if [[ "$PLOT_TONTO" == "false" ]]; then
echo " optimise_extinction= false" >> stdin
echo " correct_dispersion= $DISP" >> stdin
echo " optimise_scale_factor= true" >> stdin
fi
echo " wavelength= $WAVE Angstrom" >> stdin
if [[ "$REFANHARM" == "true" && "$PLOT_TONTO" == "false" ]]; then
if [[ "$THIRDORD" == "false" && "$FOURTHORD" == "true" ]]; then
echo " refine_4th_order_only= true " >> stdin
echo " refine_4th_order_for_atoms= { $ANHARMATOMS } " >> stdin
elif [[ "$THIRDORD" == "true" && "$FOURTHORD" == "true" ]]; then
echo " refine_4th_order_for_atoms= { $ANHARMATOMS } " >> stdin
elif [[ "$THIRDORD" == "true" && "$FOURTHORD" == "false" ]]; then
echo " refine_3rd_order_for_atoms= { $ANHARMATOMS } " >> stdin
else
echo "ERROR: Please select at least one of the anharmonic terms to refine" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
fi
fi
echo " REDIRECT $HKL" >> stdin
if [[ "$FCUT" != "0" ]]; then
echo " f_sigma_cutoff= $FCUT" >> stdin
fi
if [[ "$PLOT_TONTO" == "false" ]]; then
if [ "$MINCORCOEF" != "" ]; then
echo " min_correlation= $MINCORCOEF" >> stdin
fi
echo " tol_for_shift_on_esd= $CONVTOL" >> stdin
echo " refine_H_U_iso= $HADP" >> stdin
if [[ "$SCFCALCPROG" = "Tonto" && "$IAMTONTO" = "true" ]]; then
echo "" >> stdin
echo " show_fit_output= false" >> stdin
echo " show_fit_results= false" >> stdin
fi
echo "" >> stdin
if [ "$SCFCALCPROG" != "Tonto" ]; then
echo " show_fit_output= TRUE" >> stdin
echo " show_fit_results= TRUE" >> stdin
echo "" >> stdin
fi
if [ "$POSONLY" = "true" ]; then
echo " refine_positions_only= $POSONLY" >> stdin
fi
if [ "$ADPSONLY" = "true" ]; then
echo " refine_ADPs_only= $ADPSONLY" >> stdin
fi
if [ "$REFHADP" = "false" ]; then
if [ "$ADPSONLY" != "true" ]; then
echo " refine_H_ADPs= $REFHADP" >> stdin
fi
fi
if [ "$REFHPOS" = "false" ]; then
if [ "$ADPSONLY" != "true" ]; then
echo " refine_H_positions= $REFHPOS" >> stdin
fi
fi
if [ "$REFNOTHING" = "true" ]; then
echo " refine_nothing_for_atoms= { $ATOMLIST }" >> stdin
fi
if [ "$REFUISO" = "true" ]; then
echo " refine_u_iso_for_atoms= { $ATOMUISOLIST }" >> stdin
fi
if [[ "$MAXLSCYCLE" != "" ]]; then
echo " max_iterations= $MAXLSCYCLE" >> stdin
fi
fi
echo " } " >> stdin
fi
echo " } " >> stdin
echo "" >> stdin
}
SET_H_ISO(){
echo " set_isotropic_h_adps" >> stdin
echo "" >> stdin
}
PUT_GEOM(){
echo " ! Geometry " >> stdin
echo " put" >> stdin
echo "" >> stdin
}
BECKE_GRID(){
echo " !Tight grid" >> stdin
echo " becke_grid = {" >> stdin
echo " set_defaults" >> stdin
echo " accuracy= $ACCURACY" >> stdin
echo " pruning_scheme= $BECKEPRUNINGSCHEME" >> stdin
echo " }" >> stdin
echo "" >> stdin
}
SCF_BLOCK_NOT_TONTO(){
if [[ "$SCCHARGES" == "true" && "$SCFCALCPROG" != "elmodb" ]]; then
echo " ! SC cluster charge SCF" >> stdin
echo " scfdata= {" >> stdin
echo " initial_MOs= restricted " >> stdin # Only for new tonto may 2020
# echo " initial_MOs= existing" >> stdin
if [[ "$METHOD" != "rks" && "$METHOD" != "rhf" && "$METHOD" != "uhf" && "$METHOD" != "uks" ]]; then
echo " kind= rks " >> stdin
echo " output= true " >> stdin
echo " dft_exchange_functional= b3lypgx" >> stdin
echo " dft_correlation_functional= b3lypgc" >> stdin
else
echo " kind= $METHOD" >> stdin
echo " output= true " >> stdin
fi
echo " use_SC_cluster_charges= TRUE" >> stdin
echo " cluster_radius= $SCCRADIUS angstrom" >> stdin
echo " defragment= $DEFRAG" >> stdin
echo " save_cluster_charges= true" >> stdin
echo " convergence= 0.001" >> stdin
echo " diis= { convergence_tolerance= 0.0002 }" >> stdin
echo " output= YES" >> stdin
echo " output_results= YES" >> stdin
echo " }" >> stdin
echo "" >> stdin
echo " make_scf_density_matrix" >> stdin
echo " make_hirshfeld_inputs" >> stdin
echo " make_fock_matrix" >> stdin
echo "" >> stdin
echo " ! SC cluster charge SCF" >> stdin
echo " scfdata= {" >> stdin
echo " initial_density= promolecule" >> stdin
echo " initial_MOs= restricted " >> stdin # Only for new tonto may 2020
# echo " initial_MOs= existing" >> stdin
if [[ "$METHOD" != "rks" && "$METHOD" != "rhf" && "$METHOD" != "uhf" && "$METHOD" != "uks" ]]; then
echo " kind= rks " >> stdin
echo " output= true " >> stdin
echo " dft_exchange_functional= b3lypgx" >> stdin
echo " dft_correlation_functional= b3lypgc" >> stdin
else
echo " kind= $METHOD" >> stdin
echo " output= true " >> stdin
fi
echo " use_SC_cluster_charges= TRUE" >> stdin
echo " cluster_radius= $SCCRADIUS angstrom" >> stdin
echo " defragment= $DEFRAG" >> stdin
echo " put_cluster" >> stdin
echo " put_cluster_charges" >> stdin
echo "" >> stdin
echo " }" >> stdin
echo "" >> stdin
if [[ "$SCFCALCPROG" != "optgaussian" && "$J" != "0" ]]; then
echo " ! Make Hirshfeld structure factors" >> stdin
echo " fit_hirshfeld_atoms" >> stdin
echo "" >> stdin
fi
echo " write_xyz_file" >> stdin
if [[ "$SCFCALCPROG" == "optgaussian" ]]; then
echo "" >> stdin
echo " put_grown_cif" >> stdin
fi
else
if [[ "$SCFCALCPROG" != "optgaussian" ]]; then
echo " ! Make Hirshfeld structure factors" >> stdin
echo " fit_hirshfeld_atoms" >> stdin
echo "" >> stdin
fi
echo " write_xyz_file" >> stdin
if [[ "$SCFCALCPROG" == "optgaussian" ]]; then
echo "" >> stdin
echo " put_grown_cif" >> stdin
fi
fi
}
SCF_BLOCK_PROM_TONTO(){
echo " ! Normal SCF" >> stdin
echo " scfdata= {" >> stdin
echo " initial_density= promolecule " >> stdin
echo " kind= rhf" >> stdin # this is the promolecule guess, should be always rhf
echo " output= true " >> stdin
echo " use_SC_cluster_charges= FALSE" >> stdin
echo " convergence= 0.001" >> stdin
echo " diis= { convergence_tolerance= 0.0002 }" >> stdin
echo " }" >> stdin
echo "" >> stdin
echo " scf" >> stdin
echo "" >> stdin
}
SCF_BLOCK_REST_TONTO(){
echo " ! SC cluster charge SCF" >> stdin
echo " scfdata= {" >> stdin
echo " initial_MOs= restricted" >> stdin
if [[ "$METHOD" == "b3lyp" || "$METHOD" == "rks" ]]; then
echo " kind= rks" >> stdin
echo " output= true " >> stdin
echo " dft_exchange_functional= b3lypgx" >> stdin
echo " dft_correlation_functional= b3lypgc" >> stdin
else
echo " kind= $METHOD" >> stdin
echo " output= true " >> stdin
fi
if [[ "$SCCHARGES" == "true" ]]; then
echo " use_SC_cluster_charges= TRUE" >> stdin
echo " cluster_radius= $SCCRADIUS angstrom" >> stdin
echo " defragment= $DEFRAG" >> stdin
else
echo " use_SC_cluster_charges= FALSE" >> stdin
fi
if [[ "$PLOT_TONTO" == "false" ]]; then
echo " convergence= 0.001" >> stdin
echo " diis= { convergence_tolerance= 0.0002 }" >> stdin
fi
echo " }" >> stdin
echo "" >> stdin
echo " scf" >> stdin
echo "" >> stdin
if [[ "$XCWONLY" != "true" && "$PLOT_TONTO" == "false" ]]; then
echo " ! Make Hirshfeld structure factors" >> stdin
echo " refine_hirshfeld_atoms" >> stdin
echo "" >> stdin
fi
}
SCF_TO_TONTO(){
TONTO_HEADER
if [ "$SCFCALCPROG" = "elmodb" ]; then
READ_ELMO_FCHK
fi
if [[ "$SCFCALCPROG" == "Gaussian" || "$SCFCALCPROG" == "optgaussian" ]]; then
READ_GAUSSIAN_FCHK
elif [ "$SCFCALCPROG" = "Orca" ]; then
READ_ORCA_FCHK
else
DEFINE_JOB_NAME
fi
echo "" >> stdin
if [[ "$SCFCALCPROG" != "elmodb" && "$SCFCALCPROG" != "optgaussian" ]]; then
PROCESS_CIF
DEFINE_JOB_NAME
fi
if [[ $J -gt 0 && "$SCFCALCPROG" == "elmodb" ]]; then
PROCESS_CIF
DEFINE_JOB_NAME
fi
if [[ $J -eq 0 && "$SCFCALCPROG" == "elmodb" && "$INITADP" == "true" ]]; then
echo " ! Process the CIF" >> stdin
echo " CIF= {" >> stdin
echo " file_name= $INITADPFILE" >> stdin
echo " }" >> stdin
echo "" >> stdin
echo " process_CIF" >> stdin
echo "" >> stdin
echo " name= $JOBNAME" >> stdin
echo "" >> stdin
fi
if [[ "$SCFCALCPROG" == "Tonto" ]]; then
TONTO_BASIS_SET
if [[ "$COMPLETESTRUCT" == "true" ]]; then
COMPLETECIFBLOCK
fi
fi
if [[ "$DISP" == "yes" ]]; then
DISPERSION_COEF
fi
CHARGE_MULT
if [[ $J == 0 && "$IAMTONTO" == "true" ]]; then
TONTO_IAM_BLOCK
fi
CRYSTAL_BLOCK
if [[ "$HADP" == "yes" ]]; then
SET_H_ISO
fi
PUT_GEOM
if [[ "$USEBECKE" == "true" ]]; then
BECKE_GRID
fi
if [[ "$SCFCALCPROG" != "Tonto" ]]; then
SCF_BLOCK_NOT_TONTO
fi
if [[ "$SCFCALCPROG" == "Tonto" ]]; then
SCF_BLOCK_PROM_TONTO
SCF_BLOCK_REST_TONTO
fi
echo "" >> stdin
echo "}" >> stdin
J=$[ $J + 1 ]
echo "Running Tonto, cycle number $J"
# if [[ "$NUMPROC" != "1" ]]; then
# mpirun -n $NUMPROC $TONTO
# else
$TONTO
# fi
if [[ "$SCFCALCPROG" == "Tonto" ]]; then
mkdir $J.tonto_cycle.$JOBNAME
sed -i '/# NOTE: Cartesian 9Nx9N covariance matrix in BOHR units/,/# ===========/d' $JOBNAME.cartesian.cif2
cp $JOBNAME'.cartesian.cif2' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.cartesian.cif2
cp $JOBNAME'.archive.cif' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.archive.cif
cp $JOBNAME'.archive.fco' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.archive.fco
cp $JOBNAME'.archive.fcf' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.archive.fcf
cp stdin $J.tonto_cycle.$JOBNAME/$J.stdin
cp stdout $J.tonto_cycle.$JOBNAME/$J.stdout
cp $JOBNAME.residual_density_map,cell.cube $J.tonto_cycle.$JOBNAME/$J.residual_density_map,cell.cube
fi
INITIALCHI=$(awk '{a[NR]=$0}/^Begin rigid-atom fit/{b=NR}END {print a[b+10]}' stdout | awk '{print $2}')
# MAXSHIFT=$(awk '{a[NR]=$0}/^Begin rigid-atom fit/{b=NR+10}/^Rigid-atom fit results/{c=NR-4}END {for(d=b;d<=c;++d)print a[d]}' stdout | awk -v max=0 '{if($5>max){shift=$5; atom=$6; param=$7; max=$5}}END{print shift}')
# MAXSHIFTATOM=$(awk '{a[NR]=$0}/^Begin rigid-atom fit/{b=NR+10}/^Rigid-atom fit results/{c=NR-4}END {for(d=b;d<=c;++d)print a[d]}' stdout | awk -v max=0 '{if($5>max){shift=$5; atom=$6; param=$7; max=$5}}END{print atom}')
# MAXSHIFTPARAM=$(awk '{a[NR]=$0}/^Begin rigid-atom fit/{b=NR+10}/^Rigid-atom fit results/{c=NR-4}END {for(d=b;d<=c;++d)print a[d]}' stdout | awk -v max=0 '{if($5>max){shift=$5; atom=$6; param=$7; max=$5}}END{print param}')
MAXSHIFT=$(awk '{a[NR]=$0}/^Begin rigid-atom fit/{b=NR+10}/^Rigid-atom fit results/{c=NR-4}END {for(d=b;d<=c;++d)print a[d]}' stdout | awk '{ gsub("-","",$0); print $0 }' | awk -v max=0 '{if($5>max){shift=$5; atom=$7; param=$8; max=$5}}END{print shift}')
MAXSHIFTATOM=$(awk '{a[NR]=$0}/^Begin rigid-atom fit/{b=NR+10}/^Rigid-atom fit results/{c=NR-4}END {for(d=b;d<=c;++d)print a[d]}' stdout | awk '{ gsub("-","",$0); print $0 }' | awk -v max=0 '{if($5>max){shift=$5; atom=$7; param=$8; max=$5}}END{print atom}')
MAXSHIFTPARAM=$(awk '{a[NR]=$0}/^Begin rigid-atom fit/{b=NR+10}/^Rigid-atom fit results/{c=NR-4}END {for(d=b;d<=c;++d)print a[d]}' stdout | awk '{ gsub("-","",$0); print $0 }' |awk -v max=0 '{if($5>max){shift=$5; atom=$7; param=$8; max=$5}}END{print param}')
if [[ "$SCFCALCPROG" != "Tonto" && "$SCFCALCPROG" != "elmodb" ]]; then
sed -i 's/(//g' $JOBNAME.xyz
sed -i 's/)//g' $JOBNAME.xyz
fi
echo "Tonto cycle number $J ended"
sed -i 's/D[0-9]/H(iso=2)/g' $JOBNAME.xyz
if ! grep -q 'Wall-clock time taken' "stdout"; then
echo "ERROR: problems in fit cycle, please check the $J.th stdout file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
fi
if [ $J = 1 ]; then
echo "====================" >> $JOBNAME.lst
echo "Begin rigid-atom fit" >> $JOBNAME.lst
echo "====================" >> $JOBNAME.lst
echo "" >> $JOBNAME.lst
echo "__________________________________________________________________________________________________________________________________________________________________" >> $JOBNAME.lst
echo "" >> $JOBNAME.lst
echo "Cycle Fit initial final R R_w Max. Max. No. of No. of Energy RMSD Delta " >> $JOBNAME.lst
echo " Iter chi2 chi2 Shift Shift params eig's at final at final Energy " >> $JOBNAME.lst
echo " /esd param near 0 Geom. Geom. " >> $JOBNAME.lst
echo "" >> $JOBNAME.lst
echo "__________________________________________________________________________________________________________________________________________________________________" >> $JOBNAME.lst
echo "" >> $JOBNAME.lst
fi
if [[ "$SCFCALCPROG" != "Gaussian" && "$SCFCALCPROG" != "Orca" ]]; then
echo -e " $J\t$(awk '{a[NR]=$0}/^Rigid-atom fit results/{b=NR}END {print a[b-4]}' stdout | awk '{print $1}' )\t$INITIALCHI\t$(awk '{a[NR]=$0}/^Rigid-atom fit results/{b=NR}END {print a[b-4]}' stdout | awk '{print $2"\t"$3"\t"$4"\t"}') $MAXSHIFT\t$MAXSHIFTATOM $MAXSHIFTPARAM $(awk '{a[NR]=$0}/^Rigid-atom fit results/{b=NR}END {print a[b-4]}' stdout | awk '{print "\t"" "$9" \t"$10 }' ) " >> $JOBNAME.lst
fi
if [[ "$SCFCALCPROG" != "Tonto" ]]; then
mkdir $J.tonto_cycle.$JOBNAME
cp $JOBNAME.xyz $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.xyz
cp stdin $J.tonto_cycle.$JOBNAME/$J.stdin
cp stdout $J.tonto_cycle.$JOBNAME/$J.stdout
if [[ "$SCFCALCPROG" != "optgaussian" ]]; then
if [ -f $JOBNAME.cartesian.cif2 ]; then
sed -i '/# NOTE: Cartesian 9Nx9N covariance matrix in BOHR units/,/# ===========/d' $JOBNAME.cartesian.cif2
cp $JOBNAME'.cartesian.cif2' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.cartesian.cif2
cp $JOBNAME'.archive.cif' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.archive.cif
cp $JOBNAME'.archive.fco' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.archive.fco
cp $JOBNAME'.archive.fcf' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.archive.fcf
fi
fi
if [[ "$SCFCALCPROG" != "elmodb" && "$SCCHARGES" == "true" ]]; then
cp cluster_charges $J.tonto_cycle.$JOBNAME/$J.cluster_charges
cp gaussian-point-charges $J.tonto_cycle.$JOBNAME/$J.gaussian-point-charges
fi
fi
}
TONTO_TO_GAUSSIAN(){
I=$[ $I + 1 ]
echo "Extracting XYZ for Gaussian cycle number $I"
echo "%rwf=./$JOBNAME.rwf" >> $JOBNAME.com
echo "%int=./$JOBNAME.int" >> $JOBNAME.com
echo "%NoSave" >> $JOBNAME.com
echo "%chk=./$JOBNAME.chk" > $JOBNAME.com
echo "%mem=$MEM" >> $JOBNAME.com
echo "%nprocshared=$NUMPROC" >> $JOBNAME.com
if [ "$METHOD" = "rks" ]; then
if [ "$SCCHARGES" = "true" ]; then
echo "#$OPT blyp/$BASISSETG Charge nosymm $EXTRAKEY output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
else
echo "#$OPT blyp/$BASISSETG nosymm $EXTRAKEY output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
fi
elif [ "$METHOD" = "uks" ]; then
if [ "$SCCHARGES" = "true" ]; then
echo "#$OPT ublyp/$BASISSETG Charge nosymm $EXTRAKEY output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
else
echo "#$OPT ublyp/$BASISSETG nosymm $EXTRAKEY output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
fi
elif [ "$METHOD" = "rhf" ]; then
if [ "$SCCHARGES" = "true" ]; then
echo "#$OPT rhf/$BASISSETG Charge nosymm $EXTRAKEY output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
else
echo "#$OPT rhf/$BASISSETG nosymm $EXTRAKEY output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
fi
else
if [ "$SCCHARGES" = "true" ]; then
echo "#$OPT $METHOD/$BASISSETG Charge nosymm $EXTRAKEY output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
else
echo "#$OPT $METHOD/$BASISSETG nosymm $EXTRAKEY output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
fi
fi
echo "" >> $JOBNAME.com
echo "$JOBNAME" >> $JOBNAME.com
echo "" >> $JOBNAME.com
echo "$CHARGE $MULTIPLICITY" >> $JOBNAME.com
awk 'NR>2' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.xyz >> $JOBNAME.com
if [ "$SCCHARGES" = "true" ]; then
if [ ! -f gaussian-point-charges ]; then
echo "" > gaussian-point-charges
awk '/Cluster monopole charges and positions/{print p; f=1} {p=$0} /------------------------------------------------------------------------/{c=1} f; c--==0{f=0}' stdout >> gaussian-point-charges
fi
echo "" >> $JOBNAME.com
awk '{a[NR]=$0}{b=12}/^------------------------------------------------------------------------/{c=NR}END{for(d=b;d<=c-1;++d)print a[d]}' gaussian-point-charges | awk '{printf "%s\t %s\t %s\t %s\t \n", $1, $2, $3, $4 }' >> $JOBNAME.com
echo "" >> $JOBNAME.com
# rm gaussian-point-charges
fi
if [ "$GAUSGEN" = "true" ]; then
cat basis_gen.txt >> $JOBNAME.com
echo "" >> $JOBNAME.com
fi
echo "./$JOBNAME.wfn" >> $JOBNAME.com
echo "" >> $JOBNAME.com
echo "Running Gaussian, cycle number $I"
$SCFCALC_BIN $JOBNAME.com
echo "Gaussian cycle number $I ended"
if ! grep -q 'Normal termination of Gaussian' "$JOBNAME.log"; then
echo "ERROR: Gaussian job finished with error, please check the $I.th log file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
fi
echo "Generation fcheck file for Gaussian cycle number $I"
mkdir $I.$SCFCALCPROG.cycle.$JOBNAME
cp $JOBNAME.com $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.com
cp Test.FChk $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.fchk
cp $JOBNAME.log $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.log
}
GET_FREQ(){
I=$[ $I + 1 ]
echo "Extrating XYZ for Gaussian cycle number $I"
echo "%rwf=./$JOBNAME.rwf" >> $JOBNAME.com
echo "%int=./$JOBNAME.int" >> $JOBNAME.com
echo "%NoSave" >> $JOBNAME.com
echo "%chk=./$JOBNAME.chk" > $JOBNAME.com
echo "%mem=$MEM" >> $JOBNAME.com
echo "%nprocshared=$NUMPROC" >> $JOBNAME.com
#echo "# rb3lyp/$BASISSETG output=wfn" >> $JOBNAME.com
if [ "$METHOD" = "rks" ]; then
if [ "$SCCHARGES" = "true" ]; then
echo "# $ONLY_ONE blyp/$BASISSETG freq=noraman Charge nosymm output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
else
echo "# $ONLY_ONE blyp/$BASISSETG freq=noraman nosymm output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
fi
elif [ "$METHOD" = "uks" ]; then
if [ "$SCCHARGES" = "true" ]; then
echo "# $ONLY_ONE ublyp/$BASISSETG freq=noraman Charge nosymm output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
else
echo "# $ONLY_ONE ublyp/$BASISSETG freq=noraman nosymm output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
fi
elif [ "$METHOD" = "rhf" ]; then
if [ "$SCCHARGES" = "true" ]; then
echo "# $ONLY_ONE rhf/$BASISSETG freq=noraman Charge nosymm output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
else
echo "# $ONLY_ONE rhf/$BASISSETG freq=noraman nosymm output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
fi
else
if [ "$SCCHARGES" = "true" ]; then
echo "# $ONLY_ONE $METHOD/$BASISSETG freq=noraman Charge nosymm output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
else
echo "# $ONLY_ONE $METHOD/$BASISSETG freq=noraman nosymm output=wfn 6D 10F Fchk $INT $GAUSSEMPDISPKEY" >> $JOBNAME.com
fi
fi
echo "" >> $JOBNAME.com
echo "$JOBNAME" >> $JOBNAME.com
echo "" >> $JOBNAME.com
echo "$CHARGE $MULTIPLICITY" >> $JOBNAME.com
awk 'NR>2' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.xyz >> $JOBNAME.com
if [ "$SCCHARGES" = "true" ]; then
if [ ! -f gaussian-point-charges ]; then
echo "" > gaussian-point-charges
awk '/Cluster monopole charges and positions/{print p; f=1} {p=$0} /------------------------------------------------------------------------/{c=1} f; c--==0{f=0}' stdout >> gaussian-point-charges
fi
echo "" >> $JOBNAME.com
awk '{a[NR]=$0}{b=12}/^------------------------------------------------------------------------/{c=NR}END{for(d=b;d<=c-1;++d)print a[d]}' gaussian-point-charges | awk '{printf "%s\t %s\t %s\t %s\t \n", $1, $2, $3, $4 }' >> $JOBNAME.com
echo "" >> $JOBNAME.com
# rm gaussian-point-charges
fi
if [ "$GAUSGEN" = "true" ]; then
cat basis_gen.txt >> $JOBNAME.com
echo "" >> $JOBNAME.com
fi
echo "./$JOBNAME.wfn" >> $JOBNAME.com
echo "" >> $JOBNAME.com
echo "Running Gaussian, cycle number $I"
$SCFCALC_BIN $JOBNAME.com
echo "Gaussian cycle number $I ended"
if ! grep -q 'Normal termination of Gaussian' "$JOBNAME.log"; then
echo "ERROR: Gaussian job finished with error, please check the $I.th log file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
fi
echo "Generation fcheck file for Gaussian cycle number $I"
mkdir $I.$SCFCALCPROG.cycle.$JOBNAME
cp $JOBNAME.com $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.com
cp Test.FChk $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.fchk
cp $JOBNAME.log $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.log
}
CHECK_ENERGY(){
if [[ "$SCFCALCPROG" == "Gaussian" || "$SCFCALCPROG" == "optgaussian" ]]; then
ENERGIA2=$(sed -n '/Population analysis/,/Writing a WFN file/p' $JOBNAME.log | sed 's/^ //' | sed ':begin;$!N;s/\n//;tbegin' | awk '!f && sub(/.*HF=/,""){f=1} f' | awk -F '\' '{ print $1}' | tr -d '\r')
RMSD2=$(sed -n '/Population analysis/,/Writing a WFN file/p' $JOBNAME.log | sed 's/^ //' | sed ':begin;$!N;s/\n//;tbegin' | awk '!f && sub(/.*RMSD=/,""){f=1} f' | awk -F '\' '{ print $1}' | tr -d '\r')
# ENERGIA2=$(sed 's/^ //' $JOBNAME.log | sed 'N;s/\n//' | sed 'N;s/\n//' | sed 'N;s/\n//' | sed 'N;s/\n//' | sed -n '/HF=/{N;p;}' | sed 's/^.*HF=//' | sed 'N;s/\n//' | sed '2d' | sed 's/RMSD=//g' | awk -F '\' '{ print $1}' | tr -d '\r')
# RMSD2=$(sed 's/^ //' $JOBNAME.log | sed 'N;s/\n//' | sed 'N;s/\n//' | sed 'N;s/\n//'| sed -n '/RMSD=/{N;p;}' | sed 's/^.*RMSD=//' | sed 'N;s/\n//' | sed '2d' | sed 's/RMSD=//g' | awk -F '\' '{ print $1}'| tr -d '\r')
echo "Gaussian cycle number $I, final energy is: $ENERGIA2, RMSD is: $RMSD2 "
elif [ "$SCFCALCPROG" = "Orca" ]; then
ENERGIA2=$(sed -n '/Total Energy :/p' $JOBNAME.log | awk '{print $4}' | tr -d '\r')
RMSD2=$(sed -n '/Last RMS-Density change/p' $JOBNAME.log | awk '{print $5}' | tr -d '\r')
echo "Orca cycle number $I, final energy is: $ENERGIA2, RMSD is: $RMSD2 "
fi
DE=$(awk "BEGIN {print $ENERGIA2 - $ENERGIA}")
DE=$(printf '%.12f' $DE)
echo -e " $J\t$(awk '{a[NR]=$0}/^Rigid-atom fit results/{b=NR}END {print a[b-4]}' stdout | awk '{print $1}' )\t$INITIALCHI\t$(awk '{a[NR]=$0}/^Rigid-atom fit results/{b=NR}END {print a[b-4]}' stdout | awk '{print $2"\t"$3"\t"$4"\t"}') $MAXSHIFT\t$MAXSHIFTATOM $MAXSHIFTPARAM $(awk '{a[NR]=$0}/^Rigid-atom fit results/{b=NR}END {print a[b-4]}' stdout | awk '{print " "$9" \t"$10 }' ) $ENERGIA2 $RMSD2 \t$DE" >> $JOBNAME.lst
ENERGIA=$ENERGIA2
RMSD=$RMSD2
echo "Delta E (cycle $I - $[ I - 1 ]): $DE "
}
CHECKCONV(){
FINALPARAMESD=$(awk '{a[NR]=$0}/^Begin rigid-atom fit/{b=NR}END {print a[b+10]}' stdout | awk '{print $5}')
}
GET_RESIDUALS(){
TONTO_HEADER
DEFINE_JOB_NAME
if [ "$SCFCALCPROG" = "elmodb" ]; then
READ_ELMO_FCHK
fi
if [ "$SCFCALCPROG" = "Gaussian" ]; then
READ_GAUSSIAN_FCHK
elif [ "$SCFCALCPROG" = "Orca" ]; then
READ_ORCA_FCHK
else
DEFINE_JOB_NAME
fi
echo "" >> stdin
PROCESS_CIF
DEFINE_JOB_NAME
if [ "$SCFCALCPROG" = "Tonto" ]; then
TONTO_BASIS_SET
fi
if [ "$DISP" = "yes" ]; then
DISPERSION_COEF
fi
CHARGE_MULT
CRYSTAL_BLOCK
echo " scfdata= {" >> stdin
echo " initial_MOs= restricted" >> stdin #Only for new tonto may 2020
# echo " initial_MOs= existing" >> stdin
if [[ "$METHOD" != "rks" && "$METHOD" != "rhf" && "$METHOD" != "uhf" && "$METHOD" != "uks" ]]; then
echo " kind= rks " >> stdin
echo " dft_exchange_functional= b3lypgx" >> stdin
echo " dft_correlation_functional= b3lypgc" >> stdin
else
echo " kind= $METHOD" >> stdin
fi
echo " use_SC_cluster_charges= $SCCHARGES" >> stdin
if [ "$SCCHARGES" == "true" ]; then
echo " cluster_radius= $SCCRADIUS angstrom" >> stdin
echo " defragment= $DEFRAG" >> stdin
echo " save_cluster_charges= true" >> stdin
fi
echo " convergence= 0.001" >> stdin
echo " diis= { convergence_tolerance= 0.0002 }" >> stdin
echo " }" >> stdin
echo "" >> stdin
echo " make_scf_density_matrix" >> stdin
echo " make_structure_factors" >> stdin
echo "" >> stdin
echo " put_minmax_residual_density" >> stdin
echo "" >> stdin
# echo " plot_grid= { " >> stdin
# echo "" >> stdin
# echo " kind= residual_density_map" >> stdin
# echo " use_unit_cell_as_bbox" >> stdin
# echo " desired_separation= 0.1 angstrom" >> stdin
# echo " plot_format= cell.cube" >> stdin
# echo " plot_units= angstrom^-3" >> stdin
# echo "" >> stdin
# echo " }" >> stdin
# echo "" >> stdin
# echo " plot" >> stdin
echo " put_fitting_plots" >> stdin
# echo " normal_mode_analysis" >> stdin
echo "" >> stdin
echo "}" >> stdin
echo "Calculating residual density at final geometry"
J=$[ $J + 1 ]
# if [[ "$NUMPROC" != "1" ]]; then
# mpirun -n $NUMPROC $TONTO
# else
$TONTO
# fi
mkdir $J.tonto_cycle.$JOBNAME
cp stdin $J.tonto_cycle.$JOBNAME/$J.stdin
cp stdout $J.tonto_cycle.$JOBNAME/$J.stdout
cp $JOBNAME'.cartesian.cif2' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.cartesian.cif2
cp $JOBNAME'.archive.cif' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.archive.cif
cp $JOBNAME'.archive.fcf' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.archive.fcf
cp $JOBNAME'.archive.fco' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.archive.fco
cp $JOBNAME'.residual_density_map,cell.cube' $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.residual_density_map,cell.cube
}
XCW_SCF_BLOCK(){
echo " ! More accuracy" >> stdin
echo " output_style_options= {" >> stdin
echo " real_precision= 8" >> stdin
echo " real_width= 20" >> stdin
echo " }" >> stdin
echo " " >> stdin
SCF_BLOCK_PROM_TONTO
# if [[ "$XCWONLY" == "false" ]]; then