Initial commit of the monolayer analysis code.

Contains the code to extract 2d rdf functions as well as face and film statistics using the planar geometry submodule

CMakeLists.txt

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+cmake_minimum_required(VERSION 3.10)
+project(monolayer_film_tools)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED TRUE)
+
+# Include GROMACS libraries
+message(STATUS "Locating GROMACS package...")
+if (WIN32)
+else ()
+    find_package(GROMACS 2021 REQUIRED)
+    gromacs_check_compiler(CXX)
+    message(STATUS "GROMACS package at:${GROMACS_INCLUDE_DIRS}")
+endif ()
+
+# To build, we need gromacs. For some trajectory analysis functions, we require headers only available in the submodule
+include_directories(${GROMACS_INCLUDE_DIRS} submodules/gromacs/src/)
+
+#Include OpenMP capabilities
+find_package(OpenMP)
+
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/../lib)
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/../lib)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/../planar_bin)
+
+set(EXECUTABLE_OUTPUT_PATH "${CMAKE_BINARY_DIR}/../planar_bin")
+
+add_subdirectory(src)

run/2d_rdf/extract_distribution

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+#!/bin/bash
+
+
+echo "Trajectories should be put in subdirectories 'film_trajectories/<T>K_<pairs>A'"
+
+temperatures=( 200 250 300 350 400)
+il_pair_counts=(54 54 54 154 154)
+alu_count=(14592 14952 14952 58368 58368)
+oxy_count=(20736 20736 20736 82944 82944)
+ohy_count=(2304 2304 2304 9216 9216)
+
+bin_counts=(201 201 201 401 401)
+
+
+# IL type: C2Mim NTF2
+cation_atoms=19
+anion_atoms=15
+
+# distance in nanometer for particles to be considered touching
+cutoff_distance=6
+# minimal number of vertices a hole needs to have to be considered a hole and not a face of the film
+minimal_hole_vertex_count=6
+
+for i in "${!temperatures[@]}"
+do
+	temperature=${temperatures[i]}
+	il_pair_count=${il_pair_counts[i]}
+	bin_count=${bin_counts[i]}
+
+	indir=film_trajectories/${temperature}K_${il_pair_count}A
+	partialsdir=${indir}/partial/
+
+	trajectory_src=${indir}/nvt.xtc
+	period_out=${partialsdir}/pbc.period
+	cation_partial_xtc=${partialsdir}/cation_com.xtc
+	cation_partial_traj=${partialsdir}/cation_com.traj
+	anion_partial_xtc=${partialsdir}/anion_com.xtc
+	anion_partial_traj=${partialsdir}/anion_com.traj
+
+
+	echo "Processing trajectories in ${indir} and outputting to ${output_dir} ..."
+
+	output_dir="./results/2d_rdf/${temperature}K_${il_pair_count}A/"
+	mkdir -p ${output_dir}
+
+
+	# Calcualte 2d distribution of anions with respect to cation
+	./planar_bin/extractPlanarDistribution ${cation_partial_xtc} ${anion_partial_xtc} ${output_dir}/cation_anion_ ${il_pair_count} ${il_pair_count} 0 0 -b ${bin_count}
+
+	# Calcualte 2d distribution of anions with respect to cation
+	./planar_bin/extractPlanarDistribution ${cation_partial_xtc} ${cation_partial_xtc} ${output_dir}/cation_cation_ ${il_pair_count} ${il_pair_count} 0 0 -s 1 -b ${bin_count}
+done
+
+exit 0

run/2d_rdf/plot_distribution

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+#!/bin/bash
+
+echo "Trajectories should be put in subdirectories 'film_trajectories/<T>K_<pairs>A'"
+
+temperatures=(200 250 300 350 400)
+il_pair_counts=(54 54 54 154 154)
+alu_count=(14592 14952 14952 58368 58368)
+oxy_count=(20736 20736 20736 82944 82944)
+ohy_count=(2304 2304 2304 9216 9216)
+
+max_scale_adjusts=(0.34 0.34 0.34 0.16 0.16)
+rescale_adjusts=(0.31 0.295 0.335 0.32 0.40)
+grid_sizes=(60 60 51 51 51)
+vmaxs=(0.4 0.4 0.4 0.5 0.6)
+
+# IL type: C2Mim NTF2
+cation_atoms=19
+anion_atoms=15
+
+# distance in nanometer for particles to be considered touching
+cutoff_distance=6
+# minimal number of vertices a hole needs to have to be considered a hole and not a face of the film
+minimal_hole_vertex_count=6
+
+for i in "${!temperatures[@]}"; do
+	temperature=${temperatures[i]}
+	il_pair_count=${il_pair_counts[i]}
+	max_scale_adjust=${max_scale_adjusts[i]}
+	rescale_adjust=${rescale_adjusts[i]}
+	grid_size=${grid_sizes[i]}
+	vmax=${vmaxs[i]}
+
+	indir=film_trajectories/${temperature}K_${il_pair_count}A
+	partialsdir=${indir}/partial/
+
+	trajectory_src=${indir}/nvt.xtc
+	period_out=${partialsdir}/pbc.period
+	cation_partial_xtc=${partialsdir}/cation_com.xtc
+	cation_partial_traj=${partialsdir}/cation_com.traj
+	anion_partial_xtc=${partialsdir}/anion_com.xtc
+	anion_partial_traj=${partialsdir}/anion_com.traj
+
+	output_dir="./results/2d_rdf/${temperature}K_${il_pair_count}A/"
+
+	echo "Processing 2d distributions in ${output_dir} ..."
+
+	# Calcualte 2d distribution of anions with respect to cation
+	./scripts/film/plot_2d_distribution_colored.py -i ${output_dir}/cation_cation_ -i ${output_dir}/cation_anion_ -o ${output_dir} -cx ${max_scale_adjust} -cy ${max_scale_adjust} -g ${grid_size} -rx ${rescale_adjust} -a -m ${vmax}
+done
+
+exit 0

run/Readme.md

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+# The run script directory
+
+This directory contains certain bash scripts to perform analysis and create plots for various systems
+
+# 2d_rdf
+
+Has sample scripts to extract 2d relative density distribution functions from a trajectory
+
+
+# morphology
+
+Has sample scripts to area, perimeter and face statistics from the 2d planar graph being constructed from a trajectory

run/morphology/extract_area_perimeter

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+#!/bin/bash
+
+echo "Trajectories should be put in subdirectories 'film_trajectories/<T>K_<pairs>A'"
+
+temperatures=(200 250 300 350 400)
+il_pair_counts=(54 54 54 154 154)
+alu_count=(14592 14952 14952 58368 58368)
+oxy_count=(20736 20736 20736 82944 82944)
+ohy_count=(2304 2304 2304 9216 9216)
+
+# IL type: C2Mim NTF2
+cation_atoms=19
+anion_atoms=15
+
+# distance in nanometer for particles to be considered touching
+cutoff_distance=1.3
+# minimal number of vertices a hole needs to have to be considered a hole and not a face of the film
+minimal_hole_vertex_count=5
+
+for i in "${!temperatures[@]}"; do
+	temperature=${temperatures[i]}
+	il_pair_count=${il_pair_counts[i]}
+
+	indir=film_trajectories/${temperature}K_${il_pair_count}A
+	partialsdir=${indir}/partial/
+
+	trajectory_src=${indir}/nvt.xtc
+	period_out=${partialsdir}/pbc.period
+	cation_partial_xtc=${partialsdir}/cation_com.xtc
+	cation_partial_traj=${partialsdir}/cation_com.traj
+	anion_partial_xtc=${partialsdir}/anion_com.xtc
+	anion_partial_traj=${partialsdir}/anion_com.traj
+
+	output_dir="./results/morphology/${temperature}K_${il_pair_count}A/"
+	mkdir -p ${output_dir}
+
+	echo "Processing trajectories in ${indir} and outputting to ${output_dir} ..."
+
+	# Calcualte area and perimeter statistics of the film
+	./planar_bin/extractFilmParams -i1 ${cation_partial_xtc} -i2 ${anion_partial_xtc} -o ${output_dir}/film_ -c ${cutoff_distance} -hl ${minimal_hole_vertex_count} &
+done
+
+exit 0

run/morphology/extract_graph

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+echo "Trajectories should be put in subdirectories 'film_trajectories/<T>K_<pairs>A'"
+
+temperatures=(200 250 300 350 400)
+il_pair_counts=(54 54 54 154 154)
+alu_count=(14592 14952 14952 58368 58368)
+oxy_count=(20736 20736 20736 82944 82944)
+ohy_count=(2304 2304 2304 9216 9216)
+frame_indices=(0 1500 0 0 0)
+
+# IL type: C2Mim NTF2
+cation_atoms=19
+anion_atoms=15
+
+# distance in nanometer for particles to be considered touching
+cutoff_distance=1.3
+# minimal number of vertices a hole needs to have to be considered a hole and not a face of the film
+minimal_hole_vertex_count=5
+
+for i in "${!temperatures[@]}"; do
+	temperature=${temperatures[i]}
+	il_pair_count=${il_pair_counts[i]}
+	frame_index=${frame_indices[i]}
+
+	indir=film_trajectories/${temperature}K_${il_pair_count}A
+	partialsdir=${indir}/partial/
+
+	trajectory_src=${indir}/nvt.xtc
+	period_out=${partialsdir}/pbc.period
+	cation_partial_xtc=${partialsdir}/cation_com.xtc
+	cation_partial_traj=${partialsdir}/cation_com.traj
+	anion_partial_xtc=${partialsdir}/anion_com.xtc
+	anion_partial_traj=${partialsdir}/anion_com.traj
+
+	output_dir="./results/morphology/${temperature}K_${il_pair_count}A/"
+	mkdir -p ${output_dir}
+
+	echo "Processing trajectories in ${indir} and outputting dumped graphs to ${output_dir} ..."
+
+	# Calcualte area and perimeter statistics of the film
+	./planar_bin/extractFilmParams -i1 ${cation_partial_xtc} -i2 ${anion_partial_xtc} -o ${output_dir}/film_ -c ${cutoff_distance} -hl ${minimal_hole_vertex_count} -d 1 -df ${frame_index} &
+done
+
+exit 0

run/morphology/extract_line_surface_tension

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+temperatures=(200 250 300 350 400)
+il_pair_counts=(54 54 54 154 154)
+alu_count=(14592 14952 14952 58368 58368)
+oxy_count=(20736 20736 20736 82944 82944)
+ohy_count=(2304 2304 2304 9216 9216)
+
+# IL type: C2Mim NTF2
+cation_atoms=19
+anion_atoms=15
+
+# distance in nanometer for particles to be considered touching
+cutoff_distance=2
+# minimal number of vertices a hole needs to have to be considered a hole and not a face of the film
+minimal_hole_vertex_count=6
+
+morph_dir="./results/morphology"
+
+SYSTEM_AGGR_OPTS=(-og "${morph_dir}/")
+
+for i in "${!temperatures[@]}"; do
+	temperature=${temperatures[i]}
+	il_pair_count=${il_pair_counts[i]}
+
+	indir=film_trajectories/${temperature}K_${il_pair_count}A
+	partialsdir=${indir}/partial/
+
+	output_dir="${morph_dir}/${temperature}K_${il_pair_count}A/"
+
+    SYSTEM_AGGR_OPTS+=(-i ${output_dir}/film_outline_area.dat -ie ${indir}/nvt_fee.xvg -n "T=${temperature}K")
+    SYSTEM_AGGR_OPTS+=(-m ${il_pair_count} -o ${output_dir}/)
+done
+
+echo "Running: ./scripts/film/extract_line_surface_tension.py ${SYSTEM_AGGR_OPTS[@]}"
+./scripts/film/extract_line_surface_tension.py "${SYSTEM_AGGR_OPTS[@]}"
+exit 0

run/morphology/plot_face_statistics

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+echo "Trajectories should be put in subdirectories 'film_trajectories/<T>K_<pairs>A'"
+
+temperatures=(200 250 300 350 400)
+il_pair_counts=(54 54 54 154 154)
+alu_count=(14592 14952 14952 58368 58368)
+oxy_count=(20736 20736 20736 82944 82944)
+ohy_count=(2304 2304 2304 9216 9216)
+
+# IL type: C2Mim NTF2
+cation_atoms=19
+anion_atoms=15
+
+# distance in nanometer for particles to be considered touching
+cutoff_distance=2
+# minimal number of vertices a hole needs to have to be considered a hole and not a face of the film
+minimal_hole_vertex_count=3
+
+morph_dir="./results/morphology"
+
+SYSTEM_AGGR_OPTS=(-og "${morph_dir}/" -c ${minimal_hole_vertex_count})
+
+for i in "${!temperatures[@]}"; do
+	temperature=${temperatures[i]}
+	il_pair_count=${il_pair_counts[i]}
+
+	indir=film_trajectories/${temperature}K_${il_pair_count}A
+	partialsdir=${indir}/partial/
+
+	output_dir="${morph_dir}/${temperature}K_${il_pair_count}A/"
+
+    SYSTEM_AGGR_OPTS+=(-i ${output_dir}/film_face_statistics.dat -n "T=${temperature}K")
+    SYSTEM_AGGR_OPTS+=(-m ${il_pair_count} -o ${output_dir}/)
+done
+
+echo "Running: ./scripts/film/plot_hole_statistics_comparison.py ${SYSTEM_AGGR_OPTS[@]}"
+./scripts/film/plot_hole_statistics_comparison.py "${SYSTEM_AGGR_OPTS[@]}"
+exit 0

run/morphology/plot_hole_statistics

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+#!/bin/bash
+
+echo "Trajectories should be put in subdirectories 'film_trajectories/<T>K_<pairs>A'"
+
+temperatures=(200 250 300 350 400)
+il_pair_counts=(54 54 54 154 154)
+alu_count=(14592 14952 14952 58368 58368)
+oxy_count=(20736 20736 20736 82944 82944)
+ohy_count=(2304 2304 2304 9216 9216)
+
+# IL type: C2Mim NTF2
+cation_atoms=19
+anion_atoms=15
+
+# distance in nanometer for particles to be considered touching
+cutoff_distance=2
+# minimal number of vertices a hole needs to have to be considered a hole and not a face of the film
+minimal_hole_vertex_count=5
+
+morph_dir="./results/morphology"
+
+SYSTEM_AGGR_OPTS=(-og "${morph_dir}/" -c ${minimal_hole_vertex_count})
+
+for i in "${!temperatures[@]}"; do
+	temperature=${temperatures[i]}
+	il_pair_count=${il_pair_counts[i]}
+
+	indir=film_trajectories/${temperature}K_${il_pair_count}A
+	partialsdir=${indir}/partial/
+
+	output_dir="${morph_dir}/${temperature}K_${il_pair_count}A/"
+
+    SYSTEM_AGGR_OPTS+=(-i ${output_dir}/film_holes_statistics.dat -n "T=${temperature}K")
+    SYSTEM_AGGR_OPTS+=(-m ${il_pair_count} -o ${output_dir}/)
+done
+
+echo "Running: ./scripts/film/plot_hole_morphology.py ${SYSTEM_AGGR_OPTS[@]}"
+./scripts/film/plot_hole_morphology.py "${SYSTEM_AGGR_OPTS[@]}"
+exit 0

src/CMakeLists.txt

@@ -0,0 +1 @@
+add_subdirectory(monolayer)

src/monolayer/CMakeLists.txt

@@ -0,0 +1,20 @@
+
+include_directories(.)
+
+add_library(planar_geometry STATIC GraphConstructor.cpp PlanarGeometry.cpp Utils.cpp)
+
+# Executable to get area and perimeter statistics of film
+add_executable(extractFilmParams extractFilmParams.cpp)
+target_link_libraries(extractFilmParams PUBLIC planar_geometry OpenMP::OpenMP_CXX ${GROMACS_LIBRARIES})
+
+# Executable to get 2Drdf distribution from one trajectory with both kinds of particles
+add_executable(extractPlanarDistribution extractPlanarDistribution.cpp)
+target_link_libraries(extractPlanarDistribution PUBLIC planar_geometry OpenMP::OpenMP_CXX ${GROMACS_LIBRARIES})
+
+# Test for the graph2d library
+add_executable(GraphTest GraphTest.cpp)
+target_link_libraries(GraphTest PUBLIC planar_geometry OpenMP::OpenMP_CXX)
+
+# Test for the graph2d library with 400K data
+add_executable(GraphTest400K GraphTest400K.cpp)
+target_link_libraries(GraphTest400K PUBLIC planar_geometry OpenMP::OpenMP_CXX)