mirror of
https://asciireactor.com/otho/lammps-graphene.git
synced 2024-11-22 05:15:07 +00:00
334 lines
8.8 KiB
Plaintext
334 lines
8.8 KiB
Plaintext
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# Return x, y, and/or z coordinate(s) for atom #
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# Usage: parse_coord [x][y][z] <LAMMPS dump file> <atom #>
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parse_coord() {
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x_on=$(echo $1|sed 's/^[^x]*x[^x]*$*/1/')
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y_on=$(echo $1|sed 's/^[^y]*y[^y]*$*/1/')
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z_on=$(echo $1|sed 's/^[^z]*z[^z]*$*/1/')
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##echo $x_on $y_on $z_on > /dev/stderr
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found_table="false"
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while read -r line_read; do
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line=$(echo $line_read|sed 's/^\s*//')
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if [[ $found_table == "true" ]]; then
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if [[ $(echo $line|cut -d' ' -f1) == $3 ]]; then
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x=$(echo $line|cut -d' ' -f$x_pos)
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y=$(echo $line|cut -d' ' -f$y_pos)
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z=$(echo $line|cut -d' ' -f$z_pos)
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##echo $x > /dev/stderr
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else continue
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fi
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if [[ $x_on == "1" ]]; then
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echo -n "$x "
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##echo "Hello" > /dev/stderr
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fi
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if [[ $y_on == "1" ]]; then
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echo -n "$y "
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fi
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if [[ $z_on == "1" ]]; then
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echo -n "$z "
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fi
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break
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fi
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if [[ $(echo $line|cut -f1,2 -d' ') == "ITEM: ATOMS" ]]; then
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i=3; words=$(echo $line|wc -w);
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while [[ "$i" -le "$words" ]]; do
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if [[ $(echo $line|cut -d' ' -f$i) == "x" ]]; then x_pos=$((i-2)); fi
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if [[ $(echo $line|cut -d' ' -f$i) == "y" ]]; then y_pos=$((i-2)); fi
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if [[ $(echo $line|cut -d' ' -f$i) == "z" ]]; then z_pos=$((i-2)); fi
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##echo $x_pos $y_pos $z_pos > /dev/stderr
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(( i++ ))
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done
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found_table="true"
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fi
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##echo "$found_table: $x $y $z" > /dev/stderr
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done < $2
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#echo -ne "\n"
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}
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# Function to return a particular atom's energy from a LAMMPS dump file.
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#
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# Usage: parse_atom_energy <LAMMPS dump file> <atom #>
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parse_atomic_energy() {
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found_table="false"
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energy=0
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energy_pos=0
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while read -r line_read; do
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line=$(echo $line_read|sed 's/^\s*//')
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if [[ $found_table == "true" ]]; then
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if [[ $(echo $line|cut -d' ' -f1) == $2 ]]; then
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energy=$(echo $line|cut -d' ' -f$energy_pos)
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else continue
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fi
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break
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fi
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if [[ $(echo $line|cut -f1,2 -d' ') == "ITEM: ATOMS" ]]; then
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i=3; words=$(echo $line|wc -w);
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while [[ "$i" -le "$words" ]]; do
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if [[ $(echo $line|cut -d' ' -f$i) == "c_atomic_energy" ]]; then
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energy_pos=$((i-2))
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fi
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(( i++ ))
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done
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found_table="true"
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fi
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done < $1
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echo $energy
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}
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# Function to return a particular atom's pressure from a LAMMPS dump file.
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# v_atomic_pressure is defined in a LAMMPS script, usually as
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# v_atomic_pressure = (stress[xx] + stress[yy])/2.
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#
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# Usage: parse_atomic_pressure <LAMMPS dump file> <atom #>
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parse_atomic_pressure() {
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found_table="false"
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pressure=0
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pressure_pos=0
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while read -r line_read; do
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line=$(echo $line_read|sed 's/^\s*//')
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if [[ $found_table == "true" ]]; then
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if [[ $(echo $line|cut -d' ' -f1) == $2 ]]; then
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pressure=$(echo $line|cut -d' ' -f$pressure_pos)
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else continue
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fi
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break
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fi
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if [[ $(echo $line|cut -f1,2 -d' ') == "ITEM: ATOMS" ]]; then
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i=3; words=$(echo $line|wc -w);
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while [[ "$i" -le "$words" ]]; do
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if [[ $(echo $line|cut -d' ' -f$i) == "v_atomic_pressure" ]]; then
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pressure_pos=$((i-2))
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fi
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(( i++ ))
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done
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found_table="true"
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fi
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done < $1
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echo $pressure
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}
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# Returns the average bond length for all bonds between the atom with ID
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# <atom #> and its neighbors.
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# Usage: parse_avg_bond_length <LAMMPS dump file> <atom #>
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parse_avg_bond_length() {
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LAMMPS_dump=$1
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atom_id=$atom_id
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cutoff_dist="1.7" #angstroms
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neb="0"
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r="0.0"
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#echo Hello? > /dev/stderr
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coords_ori=$(parse_coord xyz $LAMMPS_dump $atom_id)
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x_ori=$(echo $coords_ori|cut -d' ' -f1|sed 's/[eE]\+/\*10\^/')
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y_ori=$(echo $coords_ori|cut -d' ' -f2|sed 's/[eE]\+/\*10\^/')
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z_ori=$(echo $coords_ori|cut -d' ' -f3|sed 's/[eE]\+/\*10\^/')
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#echo Greetings. > /dev/stderr
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#x_ori=$(parse_coord x $LAMMPS_dump $atom_id|sed 's/[eE]\+/\*10\^/')
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#y_ori=$(parse_coord y $LAMMPS_dump $atom_id|sed 's/[eE]\+/\*10\^/')
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#z_ori=$(parse_coord z $LAMMPS_dump $atom_id|sed 's/[eE]\+/\*10\^/')
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#echo $x_ori $y_ori $z_ori > /dev/stderr
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found_table="false"
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while read -r line_read; do
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line=$(echo $line_read|sed 's/^\s*//')
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if [[ $found_table == "true" ]]; then
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remote_id=$(echo $line|cut -d' ' -f$id_pos)
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if [[ $remote_id == $atom_id ]]; then continue; fi
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#coords_rem=$(parse_coord xyz $LAMMPS_dump $remote_id )
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#x_rem=$(echo $coords_rem|cut -d' ' -f1|sed 's/[eE]\+/\*10\^/')
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#y_rem=$(echo $coords_rem|cut -d' ' -f2|sed 's/[eE]\+/\*10\^/')
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#z_rem=$(echo $coords_rem|cut -d' ' -f3|sed 's/[eE]\+/\*10\^/')
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x_rem=$(echo $line|cut -d' ' -f$x_pos|sed 's/[eE]\+/\*10\^/')
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y_rem=$(echo $line|cut -d' ' -f$y_pos|sed 's/[eE]\+/\*10\^/')
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z_rem=$(echo $line|cut -d' ' -f$z_pos|sed 's/[eE]\+/\*10\^/')
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#echo $x_ori - $x_rem > /dev/stderr
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#echo $y_ori - $y_rem > /dev/stderr
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#echo $z_ori - $z_rem > /dev/stderr
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dist=$(echo "scale=5
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x=$x_ori - $x_rem
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y=$y_ori - $y_rem
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z=$z_ori - $z_rem
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sqrt(x*x + y*y + z*z)
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"|bc)
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#dist="7"
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#echo $dist > /dev/stderr
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#echo $r
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if [[ $(bc <<< "$dist < $cutoff_dist") == "1" ]]; then
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(( neb++ ))
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r_tmp=$(bc <<< "$r + $dist")
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r=$r_tmp
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fi
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fi
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if [[ $(echo $line|cut -f1,2 -d' ') == "ITEM: ATOMS" ]]; then
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i=3; words=$(echo $line|wc -w);
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while [[ "$i" -le "$words" ]]; do
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if [[ $(echo $line|cut -d' ' -f$i) == "id" ]]; then id_pos=$((i-2)); fi
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if [[ $(echo $line|cut -d' ' -f$i) == "x" ]]; then x_pos=$((i-2)); fi
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if [[ $(echo $line|cut -d' ' -f$i) == "y" ]]; then y_pos=$((i-2)); fi
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if [[ $(echo $line|cut -d' ' -f$i) == "z" ]]; then z_pos=$((i-2)); fi
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#echo $x_pos $y_pos $z_pos > /dev/stderr
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(( i++ ))
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done
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found_table="true"
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fi
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done < $LAMMPS_dump
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echo $(bc <<< "scale=5; $r / $neb")
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#echo $(bc <<< "scale=5; $r")
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}
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# Function to return a particular atom's stress xy component from a LAMMPS
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# dump file. This is the stress [4] component according to LAMMPS.
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#
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# Usage: parse_atomic_stressxy <LAMMPS dump file> <atom #>
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parse_atomic_stressxy() {
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found_table="false"
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stressxy=0
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stressxy_pos=0
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while read -r line_read; do
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line=$(echo $line_read|sed 's/^\s*//')
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if [[ $found_table == "true" ]]; then
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if [[ $(echo $line|cut -d' ' -f1) == $2 ]]; then
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stressxy=$(echo $line|cut -d' ' -f$stressxy_pos)
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else continue
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fi
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break
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fi
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if [[ $(echo $line|cut -f1,2 -d' ') == "ITEM: ATOMS" ]]; then
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i=3; words=$(echo $line|wc -w);
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while [[ "$i" -le "$words" ]]; do
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if [[ $(echo $line|cut -d' ' -f$i) == "c_atomic_stress[4]" ]]; then
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stressxy_pos=$((i-2))
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fi
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(( i++ ))
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done
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found_table="true"
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fi
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done < $1
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echo $stressxy
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}
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# Return histrogram of atomic coordination from LAMMPS dump file. Bins are
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# 0-9. Output format is "# # # # # # # # # #".
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#
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# Usage: parse_coordinations <LAMMPS dump file>
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parse_coordinations() {
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num_0=0
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num_1=0
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num_2=0
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num_3=0
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num_4=0
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num_5=0
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num_6=0
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num_7=0
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num_8=0
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num_9=0
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coordination_col=8
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found_table="false"
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while read -r line_read; do
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line=$(echo $line_read|sed 's/^\s*//')
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num_fields=$(echo $line_read|wc -w)
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#echo $num_fields
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if [[ $found_table == "false" ]]; then
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if [[ $(echo $line|cut -d' ' -f1) == "ITEM:" && $(echo $line|cut -d' ' -f2) == "ATOMS" ]]; then
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found_table=true
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#echo Found it
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for field_num in $(seq 1 $num_fields); do
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if [[ $(echo $line|cut -d' ' -f$field_num) == "c_crd" ]]; then
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coordination_col=$((field_num - 2))
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break
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fi
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done
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fi
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continue
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fi
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#echo here
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#echo $coordination_col
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coordination_num=$(echo $line|cut -d' ' -f$coordination_col)
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case $coordination_num in
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0) (( num_0++ )) ;;
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1) (( num_1++ )) ;;
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2) (( num_2++ )) ;;
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3) (( num_3++ )) ;;
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4) (( num_4++ )) ;;
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5) (( num_5++ )) ;;
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6) (( num_6++ )) ;;
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7) (( num_7++ )) ;;
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8) (( num_8++ )) ;;
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9) (( num_9++ )) ;;
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esac
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done < $1
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echo $num_0 $num_1 $num_2 $num_3 $num_4 $num_5 $num_6 $num_7 $num_8 $num_9
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}
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# Return
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# Return number of atoms found in LAMMPS dump file.
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#
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# Usage: parse_num_atoms_from_dump <LAMMPS dump file>
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parse_num_atoms_from_dump() {
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num_atoms="0"
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while [[ $num_atoms == "0" ]]; do
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read -r line_read
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line=$(echo $line_read|sed 's/^\s*//')
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if [[ $line == "ITEM: NUMBER OF ATOMS" ]]; then
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read num_atoms anything_else
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break
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fi
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continue
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done < $1
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echo $num_atoms
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}
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# Return "$xlo $xhi $ylo $yhi $zlo $zhi" from <LAMMPS dump file> to stdout.
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#
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# Usage: parse_box_dimensions_from_dump <LAMMPS dump file>
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parse_box_dimensions_from_dump() {
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xlo=0
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xhi=0
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ylo=0
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yhi=0
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zlo=0
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zhi=0
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while read -r line_read ; do
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line=$(echo $line_read|sed 's/^\s*//')
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if [[ $(echo $line|cut -d' ' -f1-3) == "ITEM: BOX BOUNDS" ]]; then
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read xlo xhi
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read ylo yhi
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read zlo zhi
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break;
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fi
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done < $1
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echo "$xlo $xhi $ylo $yhi $zlo $zhi"
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}
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# Return Lx, Ly, and Lz from <LAMMPS dump file> to stdout. Format:
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# "Lx Ly Lz".
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#
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# Usage: parse_box_lengths_from_dump <LAMMPS dump file>
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parse_box_lengths_from_dump() {
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parse_box_dimensions_from_dump $1 > tmp.boxdims
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read xlo xhi ylo yhi zlo zhi < tmp.boxdims
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rm tmp.boxdims
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Lx=$(bc <<< "$xhi - $xlo")
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Ly=$(bc <<< "$yhi - $ylo")
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Lz=$(bc <<< "$zhi - $zlo")
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echo $Lx $Ly $Lz
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}
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