step9_soc.sh

#!/bin/bash

# Collecting data from excited states

out_file1="$1" # trans_st.out
out1_file1="$2" # original ORCA output
opt_soc="$3" # SOC option: default is 0 (S'=S), 1 (S'=S+1, including SOC) 

# Choosing the search spectra target
if (( $opt_soc == 1)); then
	# S'=S+1 and SOC evaluation option
	opt1="SOC CORRECTED COMBINED ELECTRIC DIPOLE + MAGNETIC DIPOLE + ELECTRIC QUADRUPOLE SPECTRUM (origin adjusted)"
        # Creating heads of temp_states_ts.tmp
	echo "STATE(root) coreMO->virtMO trans_probability ampt_coeff. fosc_soc_(D2+m2+Q2)" > temp_states_ts.tmp
else
	# S'=S
	opt1="  COMBINED ELECTRIC DIPOLE + MAGNETIC DIPOLE + ELECTRIC QUADRUPOLE SPECTRUM (origin adjusted)"
        # Creating heads of temp_states_ts.tmp
	echo "STATE(root) coreMO->virtMO trans_probability ampt_coeff. fosc_(D2+m2+Q2)" > temp_states_ts.tmp
fi

# Cleaning transition states file
sed -ne "/$opt1/,/^$/p" $out1_file1 > exc_fosc_corrected.tmp

st="0"


# opt_soc options generates the same trans_st.out but some format changes
if (( $opt_soc == 1)); then
        # Excited state is in position 2 (either from S'=S or S'=S+1) and 
	#  position 8 (that matches with the final target root from corrected spectra)
	# The following awk command has $3 (weight from either from S'=S or S'=S+1)
	#  and $5 (weight from SOC evaluation) both are multiplied
	awk -v st=$st '{if($1=="STATE") st=$8; else printf(" %s %s %s %s 0.0 0.0\n", st, $1, $3*$5, $4)}' ${out_file1} \
		| awk 'NF==6{if ($1>0 && $2!="Calculating") print $0}' >> temp_states_ts.tmp
else # Excited state is in position 2 from S'=S
	# awk command only has $3 (weight from S'=S)
	awk -v st=$st '{if($1=="STATE") st=$8; else printf(" %s %s %s %s 0.0 0.0\n", st, $1, $3, $4)}' ${out_file1} \
		| awk 'NF==6{if ($1>0 && $2!="Calculating") print $0}' >> temp_states_ts.tmp
fi

# External variable as passing argument to the awk command line;
#  depending on the soc_option, the column target is different
#  $col for the fosc_D2+m2+Q2 and $col_st for the State 
if (( $opt_soc == 1)); then
	col=$((8))
        col_st=$((2))
else
	col=$((7))
	col_st=$((1))
fi

for ii in $(awk '{print $1}' temp_states_ts.tmp | sort -nu | uniq)
do
	fosc_corr="$(awk -v st=$ii -v c=$col -v cs=$col_st '{if($(cs)==st) print $(c)}' exc_fosc_corrected.tmp)" 
	#fosc_edm
	#fosc_vdm="$(awk -v st=$ii '{if($1==st) print $4}' exc_fosc_velocity_dm.tmp)"
	awk -v fsc=$fosc_corr -v st=$ii \
		'{if($1==st && $1!="STATE"){ $5=fsc; print $0} else{ print $0}}' temp_states_ts.tmp > states_ts_fosc.tmp
	mv states_ts_fosc.tmp temp_states_ts.tmp
done

# Ordered list of core MO involved from all states
lst_coremo="$(awk '$2!="coreMO->virtMO"{print $2}' temp_states_ts.tmp | cut -d'-' -f1 | sort -nu | uniq)"
# Ordered list of virtual MO involved from all states
lst_virtmo="$(awk '$2!="coreMO->virtMO"{print $2}' temp_states_ts.tmp | cut -d'>' -f2 | sort -nu | uniq)"

echo "virt\core " $lst_coremo > corevirt_fosc_corr_matrix.tmp
echo "virt\core " $lst_coremo > corevirt_foscw_corr_matrix.tmp

for ii in $lst_virtmo
do

	row_val=$ii
	pos_val_e=""
	pos_val_we=""

	for jj in $lst_coremo
	do
		# Transition ocurrence number
		ts_num="$(grep -n "${jj}->${ii}" temp_states_ts.tmp | wc -l)"

		# Average weighted fosc (D2+m2+Q2)  (trans_probab.*fosc_elec_dm)
		ls_fosc_edm="$(grep -n "${jj}->${ii}" temp_states_ts.tmp | awk '{print $3*$5}')"
		# Sum of weights
		wij="$(grep -n "${jj}->${ii}" temp_states_ts.tmp | awk -v x=0 '{x=x+$3}END{print x}')" 
		
		if (( $ts_num > 0)); then
			# Weighted sum
			fs_e="$(echo $ls_fosc_edm | awk -v x=0 '{while (c++<=NF) x=x+$c; print x}')"
			# Weighted average
			fs_we="$(echo $ls_fosc_edm | awk -v x=0 -v y=$wij '{while (c++<=NF) x=x+$c; print x/y}')"
		else
			fs_e=0
			fs_we=0
		fi
		
		pos_val_e="$(echo "$pos_val_e $fs_e")"
		pos_val_we="$(echo "$pos_val_we $fs_we")"
		
	done

	echo "$row_val $pos_val_e" >> corevirt_fosc_corr_matrix.tmp
	echo "$row_val $pos_val_we" >> corevirt_foscw_corr_matrix.tmp
done

mv exc_fosc_corrected.tmp exc_fosc_corrected.out
mv corevirt_fosc_corr_matrix.tmp corevirt_fosc_corr_matrix.out
mv corevirt_foscw_corr_matrix.tmp corevirt_foscw_corr_matrix.out
mv temp_states_ts.tmp states_corevirtMO_fosc_table.out

sed -r 's/\s+/,/g' corevirt_fosc_corr_matrix.out > corevirt_fosc_corr_matrix.csv
sed -r 's/\s+/,/g' corevirt_foscw_corr_matrix.out > corevirt_foscw_corr_matrix.csv

#seven files as outputs from this script:
# (exc_fosc_elecdm.out, exc_fosc_veldm.out, corevirt_fosc_e_matrix.out, corevirt_fosc_v_matrix.out,
# states_corevirtMO_fosc_table.out, corevirt_fosc_e_matrix.csv, corevirt_fosc_v_matrix.csv)