scripts updated, scripts for windows added

nle_cpp/scripts/gnuplot/make_gif_hex.plt

@@ -40,7 +40,7 @@ unset colorbox
 
 fmt=prefix."%08d".suffix
 
-do for [it=nt0:nt:nts] {
+do for [it=nt0:nt0+nt:nts] {
   str=sprintf(fmt,it);
   tit=sprintf("%s%08d",title,it)
   set title tit

nle_cpp/scripts/gnuplot/make_gif_sqr.plt

@@ -39,7 +39,7 @@ unset colorbox
 
 fmt=prefix."%08d".suffix
 
-do for [it=nt0:nt:nts] {
+do for [it=nt0:nt0+nt:nts] {
   str=sprintf(fmt,it);
   tit=sprintf("%s%08d",title,it)
   set title tit

nle_cpp/scripts/gnuplot/make_png_hex.plt

@@ -43,7 +43,7 @@ if (exists("name")) {
   plot name binary array=(2*nx+1,ny) format="%d" with image
 } else {
   if (!exists("format")) { format=prefix."%08d".suffix }
-  do for [it=nt0:nt:nts] {
+  do for [it=nt0:nt0+nt:nts] {
     str=sprintf(format,it);
     set output str.".png"
     tit=sprintf("%s%08d",title,it)

nle_cpp/scripts/gnuplot/make_png_sqr.plt

@@ -42,7 +42,7 @@ if (exists("name")) {
   plot name binary array=(nx,ny) format="%d" with image
 } else {
   if (!exists("format")) { format=prefix."%08d".suffix }
-  do for [it=nt0:nt:nts] {
+  do for [it=nt0:nt0+nt:nts] {
     str=sprintf(format,it);
     set output str.".png"
     tit=sprintf("%s%08d",title,it)

nle_cpp/scripts/run_single/load.sh

 #!/bin/bash
 
-initial_step=0
-
+# Check command line parameters
 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
+initial_step=0
+if [ $# -gt 1 ]; then initial_step=$2; fi
 
 echo "File to load: $file_to_load   Initial step: ${initial_step}"
 
@@ -30,37 +28,31 @@ if [ ! -x $executable ]; then
   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
+cp ./parameters.sh $name/
+mv $file_to_load $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
+                -en $en -el $el -enl $enl -kt $kt -mu $mu -evap $evap -cond $cond -g $pgroup \
+                -ipn $ipn -ipl $ipl -ipe $ipe -ofp $prefix -ofs $suffix \
+                -load $name/$file_to_load -it $initial_step \
+                ${nle_args} | tee ${name}/${name}.txt
+
+
 # check exit code
-[ ${PIPESTATUS[0]} -eq 0 ] || { rm -r $name ; exit ; }
+[ ${PIPESTATUS[0]} -eq 0 ] || { mv $name/$file_to_load . ; rm -r $name ; exit ; }
 
 echo "Making gif..."
-gnuplot -e "nx=${nx}; ny=${ny}; nt=${initial_step}+${nt}; nts=${nts}; nt0=${initial_step};
+gnuplot -e "nx=${nx}; ny=${ny}; nt=${nt}; nts=${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};
+gnuplot -e "nx=${nx}; ny=${ny}; nt=${nt}; nts=${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}
@@ -70,3 +62,4 @@ mv *.png ${name}/png
 echo "Moving dat..."
 [ ! -d ${name}/dat ] && mkdir ${name}/dat
 mv *.dat ${name}/dat
+mv $name/$file_to_load .

nle_cpp/scripts/run_single/make_pics.sh

@@ -19,14 +19,14 @@ fi
 cd ${name}/dat
 
 echo "Making gif..."
-gnuplot -e "nx=${nx}; ny=${ny}; nt=${initial_step}+${nt}; nts=${nts}; nt0=${initial_step};
+gnuplot -e "nx=${nx}; ny=${ny}; nt=${nt}; nts=${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};
+gnuplot -e "nx=${nx}; ny=${ny}; nt=${nt}; nts=${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}

nle_cpp/scripts/run_single/make_pics_groups.sh

@@ -21,14 +21,14 @@ fi
 cd ${name}/dat
 
 echo "Making gif..."
-gnuplot -e "nx=${nx}; ny=${ny}; nt=${initial_step}+${nt}; nts=${nts}; nt0=${initial_step};
+gnuplot -e "nx=${nx}; ny=${ny}; nt=${nt}; nts=${nts}; nt0=${initial_step};
             prefix=\"${prefix}\"; suffix=\"${suffix}\"; 
             title=\"${pic_title}\"; sx=${pic_size_x}; sy=${pic_size_y};
             defaultpalette=1" ../../${script_gif}
 mv -f ${prefix}.gif ../${name}.group.gif
 
 echo "Making png..."
-gnuplot -e "nx=${nx}; ny=${ny}; nt=${initial_step}+${nt}; nts=${nts}; nt0=${initial_step};
+gnuplot -e "nx=${nx}; ny=${ny}; nt=${nt}; nts=${nts}; nt0=${initial_step};
             prefix=\"${prefix}\"; suffix=\"${suffix}\";
             title=\"${pic_title}\"; sx=${pic_size_x}; sy=${pic_size_y};
             defaultpalette=1" ../../${script_png}

nle_cpp/scripts/run_single/parameters.sh

@@ -5,7 +5,7 @@
 #------------------------------------------------------------
 
 # Additional program arguments
-#export nle_args="-sg -fd"
+#export nle_args="-gstlog gst.txt -gstmin 10"
 
 # Name of the run
 export name="run01"

nle_cpp/scripts/run_single/run_single.sh → nle_cpp/scripts/run_single/run.sh

@@ -5,7 +5,7 @@ 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."
+  echo "Delete or rename it, or change the name in the top of the 'parameters.sh' file."
   exit
 fi
 
@@ -17,13 +17,14 @@ if [ ! -x $executable ]; then
 fi
 
 echo "Name: ${name}"
-mkdir $name
+mkdir ${name}
+cp ./parameters.sh ${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 -g $pgroup \
-              -ipn $ipn -ipl $ipl -ipe $ipe -ofp $prefix -ofs $suffix \
-              ${nle_args} | tee ${name}/${name}.txt
+./${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 -g $pgroup \
+                -ipn $ipn -ipl $ipl -ipe $ipe -ofp $prefix -ofs $suffix \
+                ${nle_args} | tee ${name}/${name}.txt
 # check exit code
 [ ${PIPESTATUS[0]} -eq 0 ] || { rm -r $name ; exit ; }
 

nle_cpp/scripts_mingw64/build_nle.bat

+@call set_path.bat
+@set SRCDIR=../src
+@set TARGET=%SRCDIR%/nle.exe
+
+@g++ -std=c++17 -O3 -march=native -I%SRCDIR% -o %TARGET% %SRCDIR%/main.cpp %SRCDIR%/param.cpp
+
+@if exist %TARGET% ( echo Done! ) else ( echo Failed! )

nle_cpp/scripts_mingw64/run_single/load_run.bat

+@echo off
+
+rem Check command line parameters
+set cnt=0
+for %%a in (%*) do set /a cnt+=1
+if %cnt% lss 1 (
+  echo Usage: %0 ^<filename^> [^<initial_step_number^>]
+  exit
+)
+set file_to_load=%1
+set initial_step=0
+if %cnt% gtr 1 set initial_step=%2
+echo File to load: %file_to_load%   Initial step: %initial_step%
+
+call ../set_path.bat
+call parameters.bat
+
+rem Check if directory with the same name exist
+if exist %name% (
+  echo Directory '%name%' already exist!
+  echo Delete or rename it, or change the name in the 'parameters.bat' file.
+  exit
+)
+
+rem Check if executable is present
+if not exist %executable% (
+  echo Error: executable file '%executable%' not found!
+  echo Please, run \"../build_nle.bat\" to built the executable.
+  exit
+)
+
+echo Name: %name%
+mkdir %name%
+copy parameters.bat %name% >NUL
+move %file_to_load% %name%\ >NUL
+
+rem 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% -g %pgroup% ^
+             -ipn %ipn% -ipl %ipl% -ipe %ipe% -ofp %prefix% -ofs %suffix% ^
+             -load %name%/%file_to_load% -it %initial_step% ^
+             %nle_args%
+if %errorlevel% neq 0 (
+  move %name%/%file_to_load% %file_to_load%
+  echo Error!
+  exit
+)
+
+echo Making gif...
+gnuplot -e "nx=%nx%; ny=%ny%; nt=%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%
+move %prefix%.gif %name%/%name%.gif >NUL
+
+echo Making png...
+gnuplot -e "nx=%nx%; ny=%ny%; nt=%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%
+
+if not exist %name%\png mkdir %name%\png
+move *.png %name%/png >NUL
+
+echo Moving dat...
+if not exist %name%\dat mkdir %name%\dat
+move *.dat %name%\dat >NUL
+move %name%\%file_to_load% %file_to_load% >NUL

nle_cpp/scripts_mingw64/run_single/make_pics.bat

+@echo off
+
+rem Check command line parameters
+set cnt=0
+for %%a in (%*) do set /a cnt+=1
+set initial_step=0
+if %cnt% gtr 0 set initial_step=%1
+echo Initial step: %initial_step%
+
+call ../set_path.bat
+call parameters.bat
+
+rem Check if directory with the same name exist
+if not exist %name% (
+  echo Directory '%name%' does not exist!
+  exit
+)
+
+cd %name%\dat
+
+echo Making gif...
+gnuplot -e "nx=%nx%; ny=%ny%; nt=%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%
+move %prefix%.gif ..\%name%.gif >NUL
+
+echo Making png...
+gnuplot -e "nx=%nx%; ny=%ny%; nt=%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%
+if not exist ..\png mkdir ..\png
+move *.png ..\png >NUL
+
+cd ../..

nle_cpp/scripts_mingw64/run_single/make_pics_groups.bat

+@echo off
+
+rem Check command line parameters
+set cnt=0
+for %%a in (%*) do set /a cnt+=1
+set initial_step=0
+if %cnt% gtr 0 set initial_step=%1
+echo Initial step: %initial_step%
+
+call ../set_path.bat
+call parameters.bat
+set prefix=group
+set suffix=.dat
+
+rem Check if directory with the same name exist
+if not exist %name% (
+  echo Directory '%name%' does not exist!
+  exit
+)
+
+cd %name%\dat
+
+echo Making gif...
+gnuplot -e "nx=%nx%; ny=%ny%; nt=%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%\"; defaultpalette=1" ..\..\%script_gif%
+move %prefix%.gif ..\%name%.group.gif >NUL
+
+echo Making png...
+gnuplot -e "nx=%nx%; ny=%ny%; nt=%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%\"; defaultpalette=1" ..\..\%script_png%
+if not exist ..\png.group mkdir ..\png.group
+move *.png ..\png.group >NUL
+
+cd ../..

nle_cpp/scripts_mingw64/run_single/parameters.bat

+@echo off
+rem ------------------------------------------------------------
+rem Simulation parameters
+rem ------------------------------------------------------------
+
+rem Additional program arguments
+rem set nle_args=-gstlog gst.txt -gstmin 10
+
+rem Name of the run
+set name=run01
+
+rem Cell geometry: sqr4/sqr8/hex
+set cell=sqr8
+
+rem Nanocrystal size
+set nsize=3
+
+rem Array sizes
+set nx=300
+set ny=300
+
+rem Number of simulation steps
+set nt=10000
+rem Steps between saving to file
+set nts=100
+rem Steps between printing output
+set ntp=1000
+
+rem Model parameters
+set en=3.4
+set enl=3.4
+set el=2.8
+set kt=1.0
+set mu=-2.25
+
+rem Probabitity of evaporation and condensation
+set evap=0.0
+set cond=0.0
+
+rem Probability of group movement
+set pgroup=0.0
+
+rem Initial fraction of N,L,E
+set ipn=0.4
+set ipl=0.6
+set ipe=0.0
+
+rem Parts of the names of the output files
+set prefix=data
+set suffix=.dat
+
+rem Picture sizes, pixels
+set pic_size_x=698
+set pic_size_y=698
+
+rem Picture colors (https://www.google.ru/search?q=gnuplot+color+names)
+set colorN=yellow
+set colorL=#b52000
+set colorE=black
+
+rem Picture title
+set pic_title=e_n=%en% e_{nl}=%enl% e_l=%el% Step: 
+
+rem Directories
+set executable="../../src/nle.exe"
+set gnuplot_scripts_dir=../../scripts/gnuplot
+
+
+rem ###############################################################################
+
+if %cell% == hex6 set cell=hex
+
+if %cell% neq hex if %cell% neq sqr8 set cell=sqr4
+
+if %cell% == sqr4 (
+  set script_gif=%gnuplot_scripts_dir%/make_gif_sqr.plt
+  set script_png=%gnuplot_scripts_dir%/make_png_sqr.plt
+) else (
+  if %cell% == sqr8 (
+    set script_gif=%gnuplot_scripts_dir%/make_gif_sqr.plt
+    set script_png=%gnuplot_scripts_dir%/make_png_sqr.plt
+  ) else (
+    set script_gif=%gnuplot_scripts_dir%/make_gif_hex.plt
+    set script_png=%gnuplot_scripts_dir%/make_png_hex.plt
+  )
+)

nle_cpp/scripts_mingw64/run_single/run.bat

+@echo off
+call ../set_path.bat
+call parameters.bat
+
+rem Check if directory with the same name exist
+if exist %name% (
+  echo Directory '%name%' already exist!
+  echo Delete or rename it, or change the name in the 'parameters.bat' file.
+  exit
+)
+
+rem Check if executable is present
+if not exist %executable% (
+  echo Error: executable file '%executable%' not found!
+  echo Please, run \"../build_nle.bat\" to built the executable.
+  exit
+)
+
+echo Name: %name%
+mkdir %name%
+copy parameters.bat %name% >NUL
+
+rem 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% -g %pgroup% ^
+             -ipn %ipn% -ipl %ipl% -ipe %ipe% -ofp %prefix% -ofs %suffix% ^
+             %nle_args%
+if %errorlevel% neq 0 (
+  echo Error!
+  exit
+)
+
+echo Making gif...
+gnuplot -e "nx=%nx%; ny=%ny%; nt=%nt%; nts=%nts%; nt0=0; prefix=\"%prefix%\"; suffix=\"%suffix%\"; title=\"%pic_title%\"; sx=%pic_size_x%; sy=%pic_size_y%; colorn=\"%colorN%\"; colorl=\"%colorL%\"; colore=\"%colorE%\"" %script_gif%
+move %prefix%.gif %name%/%name%.gif >NUL
+
+echo Making png...
+gnuplot -e "nx=%nx%; ny=%ny%; nt=%nt%; nts=%nts%; nt0=0; prefix=\"%prefix%\"; suffix=\"%suffix%\"; title=\"%pic_title%\"; sx=%pic_size_x%; sy=%pic_size_y%; colorn=\"%colorN%\"; colorl=\"%colorL%\"; colore=\"%colorE%\"" %script_png%
+if not exist %name%\png mkdir %name%\png
+move *.png %name%/png >NUL
+
+echo Moving dat...
+if not exist %name%\dat mkdir %name%\dat
+move *.dat %name%\dat >NUL

nle_cpp/scripts_mingw64/set_path.bat

+@PATH=%PATH%;C:\mingw64\bin;C:\Program Files\gnuplot\bin