# 	Return displacement (#.#) from a string where the string matches
# "<ANYTHING>.#.#". This is useful for returning the displacement
# from a LAMMPS logfile that is in the form "log.#.#". 
#
# Usage: parse_displacement <string>

parse_displacement() {
	num_periods=`echo $1|grep -o "\."|wc -l`
	loc_characteristic=$(( num_periods ))
	loc_mantissa=$(( num_periods +1 ))
	characteristic=`echo $1|cut -d. -f${loc_characteristic}`
	mantissa=`echo $1|cut -d. -f${loc_mantissa}`
	if [[ !"$characteristic =~ ^[0-9]*$" ]]; then
		characteristic=$mantissa
		mantissa=0
	fi
	echo ${characteristic}.${mantissa}
}


#	Reads a LAMMPS log and returns (final energy - initial energy)/(number of atoms),
# i.e. the change in energy per atom.

#	Usage: parse_delta_energy_per_atom <LAMMPS log> 

parse_delta_energy_per_atom() {
	found_table=false
	num_atoms=1
	TotEng_col=3
	final_energy="UNMEASURED"
	while read -r line_read; do
		line=$(echo $line_read|sed 's/^\s*//')
		num_fields=$(echo $line_read|wc -w)
		field1=$(echo $line|cut -d' ' -f1)
		if [[ $found_table == "false" ]]; then
			if [ "$field1" == "Step" ]; then
				found_table=true
				for count in $(seq 1 $num_fields); do
					if [[ $(echo $line|cut -d' ' -f$count) == "TotEng" ]]; then
						TotEng_col=$count
						break
					fi
				done
			fi	
			continue
		fi
		if [[ $field1 == "Loop" ]]; then
			num_atoms=$(echo $line|sed 's/.* with \([0-9]*\) atoms/\1/')
			break
		fi
		if [[ $final_energy == "UNMEASURED" ]]; then
			initial_energy=$(echo $line|cut -d' ' -f$TotEng_col)
		fi 
		final_energy=$(echo $line|cut -d' ' -f$TotEng_col)
		continue
	done < $1
	relative_energy=$(bc <<< "scale=10; $final_energy - $initial_energy")
	bc <<< "scale=10; $relative_energy / $num_atoms"
}

#	Reads a LAMMPS log and returns (final energy - initial energy), i.e.
# change in energy over the run.

#	Usage: parse_delta_energy <LAMMPS log> 

parse_delta_energy() {
	found_table=false
	TotEng_col=3
	final_energy="UNMEASURED"
	while read -r line_read; do
		line=$(echo $line_read|sed 's/^\s*//')
		num_fields=$(echo $line_read|wc -w)
		field1=$(echo $line|cut -d' ' -f1)
		if [[ $found_table == "false" ]]; then
			if [ "$field1" == "Step" ]; then
				found_table=true
				for count in $(seq 1 $num_fields); do
					if [[ $(echo $line|cut -d' ' -f$count) == "TotEng" ]]; then
						TotEng_col=$count
						break
					fi
				done
			fi	
			continue
		fi
		if [[ $field1 == "Loop" ]]; then break; fi
		if [[ $final_energy == "UNMEASURED" ]]; then
			initial_energy=$(echo $line|cut -d' ' -f$TotEng_col)
		fi 
		final_energy=$(echo $line|cut -d' ' -f$TotEng_col)
		continue
	done < $1
	bc <<< "scale=10; $final_energy - $initial_energy"
}


# Returns index of $2 in $1.

strindex() { 
  x="${1%%$2*}"
  [[ $x = $1 ]] && echo -1 || echo ${#x}
}



# Returns final energy from LAAMPS log.
#
# Usage: parse_final_energy <LAMMPS log>

parse_final_energy() {
	found_table=false
	TotEng_col=3
	final_energy="UNMEASURED"
	while read -r line_read; do
		line=$(echo $line_read|sed 's/^\s*//')
		num_fields=$(echo $line_read|wc -w)
		field1=$(echo $line|cut -d' ' -f1)
		if [[ $found_table == "false" ]]; then
			if [[ "$field1" == "Step" ]]; then
				found_table=true
				for count in $(seq 1 $num_fields); do
					if [[ $(echo $line|cut -d' ' -f$count) == "TotEng" ]]; then
						TotEng_col=$count
						break
					fi
				done
			fi	
			continue
		fi
		if [[ $field1 == "Loop" ]]; then break; fi
		final_energy=$(echo $line|cut -d' ' -f$TotEng_col)
		continue
	done < $1
	echo $final_energy
}


#	Return final system stress (-pressure) from LAMMPS log.
#
#	Usage: parse_final_system_stress <LAMMPS log>

parse_final_system_stress() {
	found_table=false
	Press_col=3
	final_stress="UNMEASURED"
	while read -r line_read; do
		line=$(echo $line_read|sed 's/^\s*//')
		num_fields=$(echo $line_read|wc -w)
		field1=$(echo $line|cut -d' ' -f1)
		if [[ $found_table == "false" ]]; then
			if [[ "$field1" == "Step" ]]; then
				found_table=true
				for count in $(seq 1 $num_fields); do
					if [[ $(echo $line|cut -d' ' -f$count) == "Press" ]]; then
						Press_col=$count
						break
					fi
				done
			fi	
			continue
		fi
		if [[ $field1 == "Loop" ]]; then break; fi
		final_press=$(echo $line|cut -d' ' -f$Press_col)
		continue
	done < $1
	final_stress=$(bc <<< "$final_press * -1")
	echo $final_stress
}


# Return number of atoms found in LAMMPS log.
#
# Usage: parse_num_atoms <LAMMPS log>

parse_num_atoms() {
	num_atoms="UNKNOWN"
	while [[ $num_atoms == "UNKNOWN" ]]; do
		read -r line_read
		line=$(echo $line_read|sed 's/^\s*//')
		if [[ $(echo $line|cut -d' ' -f2) == "atoms" ]]; then
			num_atoms=$(echo $line|cut -d' ' -f1)
		fi
		continue
	done < $1
	echo $num_atoms
}