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155 lines
4.7 KiB
Bash
Executable File
155 lines
4.7 KiB
Bash
Executable File
#!/bin/bash
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# Usage: ./stage3.sh <root dir>
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# Stage 3 of the bicrystal unit population program runs
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# post-processing analyses on completed LAMMPS runs located
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# under <root dir>.
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#
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#
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# Post-processing procedure:
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#
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# - Create initial and final state xyz files from .dump files.
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# - Create ecfg with atomic coordinates, energy, and pressure
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# - Create xmgrace-readable tables for each structure:
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# * atomic energy as function of x displacement
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# * atomic pressure as function of x displacement
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# * atomic stress xy component as function of x displacement
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# - Append info files with:
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# <num atoms> atoms
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# <formation energy> - <formation energy of pristine graphene>
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# <initial box dimensions>
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# <final box dimensions>
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# Coordinations
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# -------------
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# 4: # atoms
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# 3: # atoms
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# 2: # atoms
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# 1: # atoms
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#
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#
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# - Copy contents of all info files to file named "report" under
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# <root dir>.
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script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*/scripts\).*@\1@')
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bin_dir=$script_dir/../bin
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root_dir=$1
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source $script_dir/func/log_parsing.src
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source $script_dir/func/dump_parsing.src
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source $script_dir/func/utility.src
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pristine_form_energy="-7.956" # eV/atom, value obtained from SEDREBO
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# relaxation of pristine structure.
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# Find all info files, used as indicators of completed LAMMPS run.
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info_files=$(find $root_dir -name 'info')
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num_info_files=$(echo $info_files|wc -w)
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# Find and write formation energy difference and coordination histogram.
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echo -n "Analysing data, writing xyz files, creating tables, and "
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echo -ne "appending info files for $num_info_files structures.\n"
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sample_count=1
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count=0
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echo -n "0% complete."
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for info_file in $info_files; do
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# Locate files.
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proc_dir=$(dirname $info_file)
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initial_dump_file=$(find $proc_dir -name '*.dump'|sort -n|sed -n 1p)
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final_dump_file=$(find $proc_dir -name '*.dump'|sort -n -r|sed -n 1p)
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# Create initial and final state xyz files.
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$script_dir/conv/lammps_dump_to_xyz.sh $initial_dump_file $proc_dir/initial.xyz >> /dev/null
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$script_dir/conv/lammps_dump_to_xyz.sh $final_dump_file $proc_dir/final.xyz >> /dev/null
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#echo yo!
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# Create ecfg file with atomic energies and pressures.
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$script_dir/conv/lammps_dump_to_xyz_with_energy_and_pressure.sh $final_dump_file $proc_dir/final_wEP.xyz.tmp >> /dev/null
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$bin_dir/ylconv -sxyz:ecfg $proc_dir/final_wEP.xyz.tmp > $proc_dir/final.ecfg >> /dev/null 2> /dev/null
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# Create "minimized.input" for each final dump.
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$script_dir/conv/lammps_dump_to_input.sh $final_dump_file $proc_dir/minimized.input >> /dev/null
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# Create xmgrace-readable tables.
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energy_table_file="$proc_dir/energy_afo_x.xm"
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pressure_table_file="$proc_dir/pressure_afo_x.xm"
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stressxy_table_file="$proc_dir/stressxy_afo_x.xm"
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$script_dir/analysis/graph_energy_afo_x_displacement.sh $final_dump_file $energy_table_file >> /dev/null
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$script_dir/analysis/graph_pressure_afo_x_displacement.sh $final_dump_file $pressure_table_file >> /dev/null
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$script_dir/analysis/graph_stressxy_afo_x_displacement.sh $final_dump_file $stressxy_table_file >> /dev/null
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#echo here!
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# Gather info.
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energy=$(parse_final_energy $proc_dir/log.lmp)
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num_atoms=$(parse_num_atoms_from_dump $final_dump_file)
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form_energy=$(bc <<< "scale=10; $energy / $num_atoms")
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form_energy_diff=$(bc <<< "scale=10; $form_energy - $pristine_form_energy")
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box_xyz_initial=$(parse_box_dimensions_from_dump $initial_dump_file)
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box_xyz_final=$(parse_box_dimensions_from_dump $final_dump_file)
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#echo hello?
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# Write to info file.
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echo "$num_atoms atoms" >> $info_file
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echo $form_energy_diff >> $info_file
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echo $box_xyz_initial >> $info_file
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echo $box_xyz_final >> $info_file
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echo -e "Coordinations\n-------------" >> $info_file
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coordination_histogram=$(parse_coordinations $final_dump_file)
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for coordination_number in $(seq 0 9); do
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num_with_coordination=$(echo $coordination_histogram|cut -d' ' -f$((coordination_number +1)) )
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if [[ $num_with_coordination > 0 ]]; then
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echo -e "\t $coordination_number: $num_with_coordination" >> $info_file
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fi
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done
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#echo Hey!
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clean $proc_dir >> /dev/null
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(( count++ ))
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ratio=$(echo "
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scale=2
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count = $count
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num = $num_info_files
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count / num
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" | bc)
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percent=$(echo $ratio|sed 's/\.//')
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echo -ne "\r${percent}% complete."
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done
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echo -en "\n"
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# Compile info files to report.
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echo Compiling info files to report.
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report_file=$root_dir/report # $(date +%Y-%m-%d-%H:%M:%S)
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date > $report_file
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echo "" >> $report_file
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sorted_info_files=$(echo $info_files|sort)
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count=0
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echo -n "0% complete."
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for info_file in $sorted_info_files; do
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cat $info_file >> $report_file
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echo -en "\n\n" >> $report_file
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(( count++ ))
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ratio=$(echo "
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scale=2
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count = $count
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num = $num_info_files
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count / num
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" | bc)
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percent=$(echo $ratio|sed 's/\.//')
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echo -ne "\r${percent}% complete."
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done
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echo -en "\n"
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