Initial commit

nle_cpp/scripts/gnuplot/make_gif_hex.plt

+#!/usr/bin/gnuplot
+
+#nx=500
+#ny=500
+
+#nt0=0
+#nt=100000
+#nts=100
+
+#prefix="data"
+#suffix=".dat"
+#title=""
+
+#sx=800
+#sy=800
+
+if (!exists("nt0")) nt0=0
+if (!exists("prefix")) prefix="data"
+if (!exists("suffix")) suffix=".dat"
+if (!exists("title")) title=""
+if (!exists("sx")) sx=800
+if (!exists("sy")) sy=800
+
+if (!exists("colorn")) colorn="yellow"
+if (!exists("colorl")) colorl="#b52000"
+if (!exists("colore")) colore="black"
+
+set terminal gif animate size sx,sy
+set termoption enhanced
+set output prefix.".gif"
+
+set xrange[-1:2*nx+1]
+set yrange[ny:-1]
+set cbrange[1:-1]
+unset colorbox
+set palette defined ( -1 colore, 0 colorl, 1 colorn )
+
+fmt=prefix."%08d".suffix
+
+do for [it=nt0:nt:nts] {
+  str=sprintf(fmt,it);
+  tit=sprintf("%s%08d",title,it)
+  set title tit
+  plot str binary array=(2*nx+1,ny) format="%d" with image
+}

nle_cpp/scripts/gnuplot/make_gif_sqr.plt

+#!/usr/bin/gnuplot
+
+#nx=500
+#ny=500
+
+#nt0=0
+#nt=100000
+#nts=100
+
+#prefix="data"
+#suffix=".dat"
+#title=""
+
+#sx=800
+#sy=800
+
+if (!exists("nt0")) nt0=0
+if (!exists("prefix")) prefix="data"
+if (!exists("suffix")) suffix=".dat"
+if (!exists("title")) title=""
+if (!exists("sx")) sx=800
+if (!exists("sy")) sy=800
+
+if (!exists("colorn")) colorn="yellow"
+if (!exists("colorl")) colorl="#b52000"
+if (!exists("colore")) colore="black"
+
+set terminal gif animate size sx,sy
+set termoption enhanced
+set output prefix.".gif"
+
+set xrange[-1:nx]
+set yrange[ny:-1]
+set cbrange[1:-1]
+unset colorbox
+set palette defined ( -1 colore, 0 colorl, 1 colorn )
+
+fmt=prefix."%08d".suffix
+
+do for [it=nt0:nt:nts] {
+  str=sprintf(fmt,it);
+  tit=sprintf("%s%08d",title,it)
+  set title tit
+  plot str binary array=(nx,ny) format="%d" with image
+}

nle_cpp/scripts/gnuplot/make_png_hex.plt

+#!/usr/bin/gnuplot
+
+#nx=500
+#ny=500
+
+#nt0=0
+#nt=100000
+#nts=100
+
+#prefix="data"
+#suffix=".dat"
+#title=""
+
+#sx=800
+#sy=800
+
+if (!exists("nt0")) nt0=0
+if (!exists("prefix")) prefix="data"
+if (!exists("suffix")) suffix=".dat"
+if (!exists("title")) title=""
+if (!exists("sx")) sx=800
+if (!exists("sy")) sy=800
+
+if (!exists("colorn")) colorn="yellow"
+if (!exists("colorl")) colorl="#b52000"
+if (!exists("colore")) colore="black"
+
+set terminal png size sx,sy
+set termoption enhanced
+
+set xrange[-1:2*nx+1]
+set yrange[ny:-1]
+set cbrange[1:-1]
+unset colorbox
+set palette defined ( -1 colore, 0 colorl, 1 colorn )
+
+fmt=prefix."%08d".suffix
+
+do for [it=nt0:nt:nts] {
+  str=sprintf(fmt,it);
+  set output str.".png"
+  tit=sprintf("%s%08d",title,it)
+  set title tit
+  plot str binary array=(2*nx+1,ny) format="%d" with image
+}

nle_cpp/scripts/gnuplot/make_png_sqr.plt

+#!/usr/bin/gnuplot
+
+#nx=500
+#ny=500
+
+#nt0=0
+#nt=100000
+#nts=100
+
+#prefix="data"
+#suffix=".dat"
+#title=""
+
+#sx=800
+#sy=800
+
+if (!exists("nt0")) nt0=0
+if (!exists("prefix")) prefix="data"
+if (!exists("suffix")) suffix=".dat"
+if (!exists("title")) title=""
+if (!exists("sx")) sx=800
+if (!exists("sy")) sy=800
+
+if (!exists("colorn")) colorn="yellow"
+if (!exists("colorl")) colorl="#b52000"
+if (!exists("colore")) colore="black"
+
+set terminal png size sx,sy
+set termoption enhanced
+
+set xrange[-1:nx]
+set yrange[ny:-1]
+set cbrange[1:-1]
+unset colorbox
+set palette defined ( -1 colore, 0 colorl, 1 colorn )
+
+fmt=prefix."%08d".suffix
+
+do for [it=nt0:nt:nts] {
+  str=sprintf(fmt,it);
+  set output str.".png"
+  tit=sprintf("%s%08d",title,it)
+  set title tit
+  plot str binary array=(nx,ny) format="%d" with image
+}

nle_cpp/scripts/run_multiple/do_all.sh

+#!/bin/bash
+
+source ./do_parameters.sh
+
+LC_NUMERIC="en_US.UTF-8"
+
+# Check if executable is present
+if [ ! -x $executable ]; then
+  echo "Error: executable file '${executable}' not found!"
+  echo "Please, run \"make clean ; make\" to built the executable."
+  exit
+fi
+
+if [ "$cell" != "hex" ]; then
+  cell="square"
+  script_png="$scripts_dir/make_png_sqr.plt"
+  script_gif="$scripts_dir/make_gif_sqr.plt"
+else
+  script_png="$scripts_dir/make_png_hex.plt"
+  script_gif="$scripts_dir/make_gif_hex.plt"
+fi
+
+for (( en100=${minn}; en100 <= ${maxn}; en100 += ${step} )); do
+  for (( enl100=${minnl}; enl100 < ${en100} && enl100 <= $maxnl; enl100 += ${step} )); do
+    for (( el100=${minl}; el100 < ${enl100} && el100 <= $maxl; el100 += ${step} )); do
+
+      en1=`echo "scale=2; ${en100}/100" | bc`
+      enl1=`echo "scale=2; ${enl100}/100" | bc`
+      el1=`echo "scale=2; ${el100}/100" | bc`
+
+      en=`printf "%04.2f" ${en1}`
+      enl=`printf "%04.2f" ${enl1}`
+      el=`printf "%04.2f" ${el1}`
+
+      name="en${en}_enl${enl}_el${el}"
+      title="e_n=${en} e_{nl}=${enl} e_l=${el} Step: "
+      echo ${name}
+
+      #continue
+
+      $executable -$cell -nsize $nsize -nx $nx -ny $ny -nt $nt -nts $nts -en $en -enl $enl -el $el -kt $kt -evap $evap -cond $cond -ipn $ipn -ipl $ipl -ipe $ipe -ofp $prefix -ofs $suffix -short | tee ${name}.txt
+      cat ${name}.txt >> output.txt
+
+      echo Making gif...
+      gnuplot -e "nx=${nx}; ny=${ny}; nt=${nt}; nts=${nts}; prefix=\"${prefix}\"; suffix=\"${suffix}\"; title=\"${title}\"" $script_gif
+      [ ! -d $gifdir ] && mkdir $gifdir
+      mv ${prefix}.gif $gifdir/${name}.gif
+
+      echo Making png...
+      gnuplot -e "nx=${nx}; ny=${ny}; nt=${nt}; nts=${nts}; prefix=\"${prefix}\"; suffix=\"${suffix}\"; title=\"${title}\"" $script_png
+      [ ! -d $pngdir ] && mkdir $pngdir
+      [ ! -d $pngdir/${name}_png ] && mkdir $pngdir/${name}_png
+      mv *.png $pngdir/${name}_png/
+      cd $pngdir
+      tar czf ${name}_png.tgz ${name}_png && rm -r ${name}_png
+      cd ..
+
+      echo Moving dat...
+      [ ! -d $datdir ] && mkdir $datdir
+      [ ! -d $datdir/${name}_dat ] && mkdir $datdir/${name}_dat
+      mv *.dat $datdir/${name}_dat/
+      cd $datdir
+      tar czf ${name}_dat.tgz ${name}_dat && rm -r ${name}_dat
+      cd ..
+
+    done
+  done
+done

nle_cpp/scripts/run_multiple/do_parameters.count.sh

+#!/bin/bash
+
+export cell=hex
+export nsize=3
+
+export nx=500
+export ny=500
+export nt=100000
+export nts=1000
+#export np=100
+
+#export en=2.0
+#export el=1.0
+#export enl=1.5
+export kt=1.0
+#export mu=-2.25
+export evap=0.0
+export cond=0.0
+
+# initial parts
+export ipn=0.4
+export ipl=0.6
+export ipe=0.0
+
+export prefix="data"
+export suffix=".dat"
+
+export min=0
+export max=500
+export step=20
+
+export minn=$min
+export maxn=$max
+export minnl=$min
+export maxnl=$max
+export minl=$min
+export maxl=$max
+
+export datdir="dat"
+export pngdir="png"
+export gifdir="gif"
+export datfindir="dat_$nt"
+export pngfindir="png_$nt"
+export png2ddir="png2d_$nt"
+export gif_sorted_dir="gif_sorted"
+export png_sorted_dir="png_sorted"
+
+export picsx=600
+export picsy=600
+
+#2d: pixels per picture
+export ppp=200

nle_cpp/scripts/run_multiple/do_parameters.sh

+#!/bin/bash
+
+export cell=hex
+export nsize=3
+
+export nx=100
+export ny=100
+export nt=1000
+export nts=100
+#export np=100
+
+#export en=2.0
+#export el=1.0
+#export enl=1.5
+export kt=1.0
+#export mu=-2.25
+export evap=0.0
+export cond=0.0
+
+# initial parts
+export ipn=0.4
+export ipl=0.6
+export ipe=0.0
+
+export prefix="data"
+export suffix=".dat"
+
+export min=0
+export max=100
+export step=20
+
+export minn=$min
+export maxn=$max
+export minnl=$min
+export maxnl=$max
+export minl=$min
+export maxl=$max
+
+export datdir="dat"
+export pngdir="png"
+export gifdir="gif"
+export datfindir="dat_$nt"
+export pngfindir="png_$nt"
+export png2ddir="png2d_$nt"
+export gif_sorted_dir="gif_sorted"
+export png_sorted_dir="png_sorted"
+
+export picsx=600
+export picsy=600
+
+#2d: pixels per picture
+export ppp=200
+
+export executable="../../src/nle"
+export scripts_dir="../gnuplot"

nle_cpp/scripts/run_multiple/do_parameters.small.sh

+#!/bin/bash
+
+export cell=hex
+export nsize=3
+
+export nx=100
+export ny=100
+export nt=1000
+export nts=100
+#export np=100
+
+#export en=2.0
+#export el=1.0
+#export enl=1.5
+export kt=1.0
+#export mu=-2.25
+export evap=0.0
+export cond=0.0
+
+# initial parts
+export ipn=0.4
+export ipl=0.6
+export ipe=0.0
+
+export prefix="data"
+export suffix=".dat"
+
+export min=0
+export max=100
+export step=20
+
+export minn=$min
+export maxn=$max
+export minnl=$min
+export maxnl=$max
+export minl=$min
+export maxl=$max
+
+export datdir="dat"
+export pngdir="png"
+export gifdir="gif"
+export datfindir="dat_$nt"
+export pngfindir="png_$nt"
+export png2ddir="png2d_$nt"
+export gif_sorted_dir="gif_sorted"
+export png_sorted_dir="png_sorted"
+
+export picsx=600
+export picsy=600
+
+#2d: pixels per picture
+export ppp=200

nle_cpp/scripts/run_single/load.sh

+#!/bin/bash
+
+initial_step=0
+
+if [ $# -lt 1 ]; then
+  echo "Usage: $0 <filename> [<initial_step_number>]"
+  exit
+fi
+
+file_to_load=$1
+if [ $# -gt 1 ]; then
+  initial_step=$2
+fi
+
+echo "File to load: $file_to_load   Initial step: ${initial_step}"
+
+source ./parameters.sh
+
+# Check if directory with the same name exist
+if [ -d $name ]; then
+  echo "Directory '$name' already exist!"
+  echo "Delete or rename it, or change the name in the top of the $0 file."
+  exit
+fi
+
+# Check if executable is present
+if [ ! -x $executable ]; then
+  echo "Error: executable file '${executable}' not found!"
+  echo "Please, run \"make clean ; make\" to built the executable."
+  exit
+fi
+
+# Set cell geometry
+if [ "$cell" != "hex" ]; then
+  cell="square"
+  script_png="$scripts_dir/make_png_sqr.plt"
+  script_gif="$scripts_dir/make_gif_sqr.plt"
+else
+  script_png="$scripts_dir/make_png_hex.plt"
+  script_gif="$scripts_dir/make_gif_hex.plt"
+fi
+
+echo "Name: ${name}"
+mkdir $name
+
+# Run simulation
+./${executable} -nx $nx -ny $ny -nt $nt -nts $nts -ntp $ntp -nsize $nsize -$cell \
+                -en $en -el $el -enl $enl -kt $kt -mu $mu -evap $evap -cond $cond \
+                -ipn $ipn -ipl $ipl -ipe $ipe \
+                -load $file_to_load -it $initial_step \
+                -ofp $prefix -ofs $suffix | tee ${name}/${name}.txt
+# check exit code
+[ ${PIPESTATUS[0]} -eq 0 ] || { rm -r $name ; exit ; }
+
+echo "Making gif..."
+gnuplot -e "nx=${nx}; ny=${ny}; nt=${initial_step}+${nt}; nts=${nts}; nt0=${initial_step};
+            prefix=\"${prefix}\"; suffix=\"${suffix}\"; 
+            title=\"${pic_title}\"; sx=${pic_size_x}; sy=${pic_size_y};
+            colorn=\"${colorN}\"; colorl=\"${colorL}\"; colore=\"${colorE}\"" ${script_gif}
+mv ${prefix}.gif ${name}/${name}.gif
+
+echo "Making png..."
+gnuplot -e "nx=${nx}; ny=${ny}; nt=${initial_step}+${nt}; nts=${nts}; nt0=${initial_step};
+            prefix=\"${prefix}\"; suffix=\"${suffix}\";
+            title=\"${pic_title}\"; sx=${pic_size_x}; sy=${pic_size_y};
+            colorn=\"${colorN}\"; colorl=\"${colorL}\"; colore=\"${colorE}\"" ${script_png}
+[ ! -d ${name}/png ] && mkdir ${name}/png
+mv *.png ${name}/png
+
+echo "Moving dat..."
+[ ! -d ${name}/dat ] && mkdir ${name}/dat
+mv *.dat ${name}/dat

nle_cpp/scripts/run_single/make_pics.sh

+#!/bin/bash
+
+initial_step=0
+
+if [ $# -gt 0 ]; then
+  initial_step=$1
+fi
+
+echo "Initial step: ${initial_step}"
+
+source ./parameters.sh
+
+# Check if directory with the same name exist
+if [ ! -d $name ]; then
+  echo "Directory '$name' does not exist!"
+  exit
+fi
+
+# Set cell geometry
+if [ "$cell" != "hex" ]; then
+  script_png="$scripts_dir/make_png_sqr.plt"
+  script_gif="$scripts_dir/make_gif_sqr.plt"
+else
+  script_png="$scripts_dir/make_png_hex.plt"
+  script_gif="$scripts_dir/make_gif_hex.plt"
+fi
+
+cd ${name}/dat
+
+echo "Making gif..."
+gnuplot -e "nx=${nx}; ny=${ny}; nt=${initial_step}+${nt}; nts=${nts}; nt0=${initial_step};
+            prefix=\"${prefix}\"; suffix=\"${suffix}\"; 
+            title=\"${pic_title}\"; sx=${pic_size_x}; sy=${pic_size_y};
+            colorn=\"${colorN}\"; colorl=\"${colorL}\"; colore=\"${colorE}\"" ../../${script_gif}
+mv -f ${prefix}.gif ../${name}.gif
+
+echo "Making png..."
+gnuplot -e "nx=${nx}; ny=${ny}; nt=${initial_step}+${nt}; nts=${nts}; nt0=${initial_step};
+            prefix=\"${prefix}\"; suffix=\"${suffix}\";
+            title=\"${pic_title}\"; sx=${pic_size_x}; sy=${pic_size_y};
+            colorn=\"${colorN}\"; colorl=\"${colorL}\"; colore=\"${colorE}\"" ../../${script_png}
+[ ! -d ../png ] && mkdir ../png
+mv -f *.png ../png
+
+cd ../..

nle_cpp/scripts/run_single/parameters.sh

+#!/bin/bash
+
+#------------------------------------------------------------
+# Simulation parameters
+#------------------------------------------------------------
+
+# Name of the run
+export name="run01"
+
+# Cell geometry: square/hex
+export cell=hex
+
+# Array sizes
+export nx=200
+export ny=200
+
+# Nanocrystal size
+export nsize=3
+
+# Number of simulation steps
+export nt=10000
+# Steps between saving to file
+export nts=100
+# Steps between printing output
+export ntp=100
+
+# Model parameters
+export en=4.6
+export el=1.0
+export enl=1.2
+export kt=1.0
+export mu=-2.25
+
+# Probabitity of evaporation and condensation
+export evap=0.0
+export cond=0.0
+
+# Initial fraction of N,L,E
+export ipn=0.4
+export ipl=0.6
+export ipe=0.0
+
+# Parts of the names of the output files
+export prefix="data"
+export suffix=".dat"
+
+# Picture sizes, pixels
+export pic_size_x=600
+export pic_size_y=600
+
+# Picture colors (https://www.google.ru/search?q=gnuplot+color+names)
+export colorN=yellow
+export colorL="#b52000"
+export colorE=black
+
+# Picture title
+export pic_title="e_l=${el} e_{nl}=${enl} e_n=${en} Step:"
+
+# directories
+export executable="../../src/nle"
+export scripts_dir="../gnuplot"

nle_cpp/scripts/run_single/run.sh

+#!/bin/bash
+
+source ./parameters.sh
+
+# Check if directory with the same name exist
+if [ -d $name ]; then
+  echo "Directory '$name' already exist!"
+  echo "Delete or rename it, or change the name in the top of the $0 file."
+  exit
+fi
+
+# Check if executable is present
+if [ ! -x $executable ]; then