scripts updated

nle_cpp/scripts/run_multiple/do_datfin2png2d.sh

+#!/bin/bash
+
+source ./do_parameters.sh
+
+fromdir="dat_${nt}"
+todir="png2d_${nt}"
+
+[ ! -d ${fromdir} ] && { echo "Directory ${fromdir} does not exist!" ; exit ; }
+[ -d ${todir} ] && { echo "Terget directory ${todir} already exist!" ; exit ; }
+mkdir ${todir}
+
+LC_NUMERIC="en_US.UTF-8"
+
+count=0
+for (( en100=${minn}; en100 <= ${maxn}; en100 += ${step} )); do
+  en1=`echo "scale=2; ${en100}/100" | bc`
+  en=`printf "%04.2f" ${en1}`
+  val[$count]=$en
+  count=$((count + 1))
+done
+
+for inn in `seq 0 $((count - 1))`; do
+  echo "en:" ${val[$inn]}
+  enn=${val[$inn]}
+
+  inls=`seq 0 $inn`
+  nls=`for i in $inls; do echo -n "${val[$i]} "; done`
+
+  ills=`seq 0 $inn`
+  lls=`for i in $ills; do echo -n "${val[$i]} "; done`
+
+  target="${todir}/en${enn}_enl_el"
+
+  #echo "  nls: ${nls[*]}"
+  #echo "  lls: ${lls[*]}"
+
+  gnuplot -e "name=\"${target}\"; nx=${nx}; ny=${ny}; ppp=${ppp}; \
+              rows=\"${nls}\"; cols=\"${lls}\"; rlabel=\"e_{nl}=\"; clabel=\"e_{l}=\"; \
+              format=\"${fromdir}/en${enn}_enl%s_el%s${suffix}\";" $script_png2d
+
+#  [ ! -d ${todir} ] && mkdir ${todir}
+#  mv ${name}.png ${todir}/
+
+done
+
+for inl in `seq 0 $((count - 1))`; do
+  echo "enl:" ${val[$inl]}
+  enl=${val[$inl]}
+
+  inns=`seq $inl $((count - 1))`
+  nns=`for i in $inns; do echo -n "${val[$i]} "; done`
+
+  ills=`seq 0 $inl`
+  lls=`for i in $ills; do echo -n "${val[$i]} "; done`
+
+  target="${todir}/en_enl${enl}_el"
+
+  #echo "  nns: ${nns[*]}"
+  #echo "  lls: ${lls[*]}"
+
+  gnuplot -e "name=\"${target}\"; nx=${nx}; ny=${ny}; ppp=${ppp}; \
+              rows=\"${nns}\"; cols=\"${lls}\"; rlabel=\"e_{n}=\"; clabel=\"e_{l}=\"; \
+              format=\"${fromdir}/en%s_enl${enl}_el%s${suffix}\";" $script_png2d
+
+#  [ ! -d ${todir} ] && mkdir ${todir}
+#  mv ${name}.png ${todir}/
+done
+
+for ill in `seq 0 $((count - 1))`; do
+  echo "el:" ${val[$ill]}
+  ell=${val[$ill]}
+
+  inls=`seq $ill $((count - 1))`
+  nls=`for i in $inls; do echo -n "${val[$i]} "; done`
+
+  inns=`seq $ill $((count - 1))`
+  nns=`for i in $inns; do echo -n "${val[$i]} "; done`
+
+  target="${todir}/en_enl_el${ell}"
+
+  #echo "  nns: ${nns[*]}"
+  #echo "  nls: ${nls[*]}"
+
+  gnuplot -e "name=\"${target}\"; nx=${nx}; ny=${ny}; ppp=${ppp}; \
+              rows=\"${nns}\"; cols=\"${nls}\"; rlabel=\"e_{n}=\"; clabel=\"e_{nl}=\"; \
+              format=\"${fromdir}/en%s_enl%s_el${ell}${suffix}\";" $script_png2d
+
+#  [ ! -d ${todir} ] && mkdir ${todir}
+#  mv ${name}.png ${todir}/
+done

nle_cpp/scripts/run_multiple/do_datgz2datfin.sh

+#!/bin/bash
+
+source ./do_parameters.sh
+
+renew=1
+
+fromdir=${rootdir}/${datdir}
+todir="dat_${nt}"
+
+[ ! -d ${fromdir} ] && { echo "Directory ${fromdir} does not exist!" ; exit ; }
+
+if [ $renew -ne 0 ]; then 
+  [ -d ${todir} ] || mkdir ${todir}
+else
+  [ -d ${todir} ] && { echo "Terget directory ${todir} already exist!" ; exit ; }
+  mkdir ${todir}
+fi
+
+tmpdir=$(mktemp -d)
+echo $tmpdir
+trap "rm -r $tmpdir" SIGINT SIGTERM
+
+echo "Extracting $suffix files..."
+
+init_iteration
+while next_iteration; do
+  name=$(get_name)
+  datname=${name}_dat
+  dattgzfile=${fromdir}/$datname.tgz
+  target=$todir/${name}${suffix}
+  if [[ -f $dattgzfile ]]; then
+    [[ $renew -ne 0 && -f $target ]] && continue
+    filename=`printf "%s%08d%s" ${prefix} ${nt} ${suffix}`
+    tmpdatname=${datname}/${filename}
+    #echo "|$name|$datname|$dattgzfile|$filename|$tmpdatname|"
+    #echo "tar -C $tmpdir -xzf $dattgzfile $tmpdatname"
+    #echo "Extract file $tmpdatname from $dattgzfile to $tmpdir"
+    tar -C $tmpdir -xzf $dattgzfile $tmpdatname || { echo "tar -C $tmpdir -xzf $dattgzfile $tmpdatname : failed!"; exit; }
+    #echo "mv $tmpdir/$tmpdatname  ->  $target"
+    mv $tmpdir/$tmpdatname $target
+    rmdir $tmpdir/$datname
+  fi
+done
+
+rm -r $tmpdir

nle_cpp/scripts/run_multiple/do_datgz2pngfin.sh

+#!/bin/bash
+
+source ./do_parameters.sh
+
+renew=1
+
+#nt=6400
+
+fromdir=${rootdir}/${datdir}
+todir=${rootdir}/png_${nt}
+
+[ ! -d ${fromdir} ] && { echo "Directory ${fromdir} does not exist!" ; exit ; }
+[ ! -d ${todir} ] && mkdir ${todir}
+
+filename=`printf "%s%08d%s" ${prefix} ${nt} ${suffix}`
+
+tmpdir=$(mktemp -d)
+
+init_iteration
+while next_iteration; do
+
+  name=$(get_name)
+  datname=${name}_dat
+  dattgzfile=${fromdir}/${datname}.tgz
+  tmpdatname=${datname}/${filename}
+  targetfile=${todir}/${datname}.png
+
+  if [[ -f $dattgzfile && ( $renew == 1 || !( -f $targetfile ) ) ]]; then
+
+    echo $name
+    title=$(get_title)
+
+    tar -C $tmpdir -xzf $dattgzfile ${tmpdatname} || { echo "tar -C $tmpdir -xzf $dattgzfile ${tmpdir}/${tmpdatname} : failed!"; exit; }
+    #mv ${tmpdatname} $targetfile
+
+    gnuplot -e "nx=${nx}; ny=${ny}; nt=${nt}; nts=${nts};
+                name=\"${tmpdir}/${tmpdatname}\";
+                title=\"${title}\"; sx=${pic_size_x}; sy=${pic_size_y};
+                colorn=\"${colorN}\"; colorl=\"${colorL}\"; colore=\"${colorE}\"" ${script_png}
+
+#                name=\"${fromdir}/${datname}\";
+
+    mv -f ${tmpdir}/${tmpdatname}.png $targetfile
+    rm ${tmpdir}/${tmpdatname}
+    rmdir ${tmpdir}/${datname}
+  fi
+
+done
+rmdir $tmpdir

nle_cpp/scripts/run_multiple/do_parameters.sh

@@ -6,15 +6,15 @@
 
 #export nle_args="-mgslog mgs.txt -sg"
 
-# Cell geometry: square/hex
-export cell=square
+# Cell geometry: sqr4/sqr8/hex
+export cell="sqr8"
 
 # Nanocrystal size
 export nsize=3
 
 # Array sizes
-export nx=500
-export ny=500
+export nx=400
+export ny=400
 
 # Number of simulation steps
 export nt=100000
@@ -72,34 +72,34 @@ export pngfindir="png_${nt}"
 export executable="../../src/nle"
 export gnuplot_scripts_dir="../gnuplot"
 
-export mindl=20
-export maxdl=480
-export mindn=20
-export maxdn=480
+#export mindl=20
+#export maxdl=480
+#export mindn=20
+#export maxdn=480
 
 export step=20
 
-#export min=0
-#export max=500
+export min=0
+export max=500
 
-#export minl=20
-#export maxl=20
-#export minnl=60
-#export maxnl=60
-#export minn=239
-#export maxn=239
+export minl=${min}
+export maxl=${max}
+export minnl=${min}
+export maxnl=${max}
+export minn=${min}
+export maxn=${max}
 
 #pixels per picture (for 2D) 500x500 : 251
-export ppp=251
+export ppp=201
 
 ################################################################################
 LC_NUMERIC="en_US.UTF-8"
 
-#get_name() { echo "en${en}_enl${enl}_el${el}"; }
-#get_title() { echo "e_n=${en} e_{nl}=${enl} e_l=${el} Step: "; }
+get_name() { echo "en${en}_enl${enl}_el${el}"; }
+get_title() { echo "e_n=${en} e_{nl}=${enl} e_l=${el} Step: "; }
 
-get_name() { echo "dn${dn}_dl${dl}"; }
-get_title() { echo "e_n-e_{nl}=${dn} e_{nl}-e_l=${dl} Step: "; }
+#get_name() { echo "dn${dn}_dl${dl}"; }
+#get_title() { echo "e_n-e_{nl}=${dn} e_{nl}-e_l=${dl} Step: "; }
 post_run() { true; }
 
 #get_name() { echo "en${en}_enl${enl}_el${el}_ipn${ipn}"; }
@@ -120,46 +120,55 @@ loop3_check() { (( el100 <= maxl )); return $?; }
 loop3_next()  { (( el100 += step )); }
 
 
-loop_ipn_init()  { (( ipn100 = min )); }
-loop_ipn_check() { (( ipn100 <= max )); return $?; }
-loop_ipn_next()  { (( ipn100 += step )); }
+#loop_ipn_init()  { (( ipn100 = min )); }
+#loop_ipn_check() { (( ipn100 <= max )); return $?; }
+#loop_ipn_next()  { (( ipn100 += step )); }
 
 
-loop1_dnl_init()  { (( dn100 = mindn )); loop2_dnl_init; }
-loop1_dnl_check() { loop2_dnl_check; (( !$? && dn100 <= maxdn )); return $?; }
-loop1_dnl_next()  { loop2_dnl_next; if !(loop2_dnl_check); then (( dn100 += step )); loop2_dnl_init; fi; }
+#loop1_dnl_init()  { (( dn100 = mindn )); loop2_dnl_init; }
+#loop1_dnl_check() { loop2_dnl_check; (( !$? && dn100 <= maxdn )); return $?; }
+#loop1_dnl_next()  { loop2_dnl_next; if !(loop2_dnl_check); then (( dn100 += step )); loop2_dnl_init; fi; }
 
-loop2_dnl_init()  { (( dl100 = mindl )); }
-loop2_dnl_check() { (( dl100 <= maxdl )); return $?; }
-loop2_dnl_next()  { (( dl100 += step )); }
+#loop2_dnl_init()  { (( dl100 = mindl )); }
+#loop2_dnl_check() { (( dl100 <= maxdl )); return $?; }
+#loop2_dnl_next()  { (( dl100 += step )); }
 
 
+check_iteration() { (( el100 <= enl100 && enl100 <= en100 )); return $?; }
 #check_iteration() { (( el100 < enl100 && enl100 < en100 )); return $?; }
-check_iteration() { return 0; }
-init_iteration() { loop1_dnl_init; first_iteration=1; }
+#check_iteration() { return 0; }
+init_iteration() { loop1_init; first_iteration=1; }
 next_iteration() {
   if (( !first_iteration )); then
-    loop1_dnl_next
+    loop1_next
   else
     first_iteration=0
   fi
-  if !(loop1_dnl_check); then return 1; fi
+  if !(loop1_check); then return 1; fi
   while !(check_iteration); do
-    loop1_dnl_next
-    if !(loop1_dnl_check); then return 1; fi
+    loop1_next
+    if !(loop1_check); then return 1; fi
   done
   LC_NUMERIC="en_US.UTF-8"
-  local dl1=`echo "scale=2; ${dl100}/100" | bc`
-  local dn1=`echo "scale=2; ${dn100}/100" | bc`
-  dl=`printf "%04.2f" ${dl1}`
-  dn=`printf "%04.2f" ${dn1}`
-  el100=0
+#  local dl1=`echo "scale=2; ${dl100}/100" | bc`
+#  local dn1=`echo "scale=2; ${dn100}/100" | bc`
+#  dl=`printf "%04.2f" ${dl1}`
+#  dn=`printf "%04.2f" ${dn1}`
+#  el100=0
+#  local el1=`echo "scale=2; ${el100}/100" | bc`
+#  local enl1=`echo "scale=2;(${el100}+${dl100})/100" | bc`
+#  local en1=`echo "scale=2; (${el100}+${dl100}+${dn100})/100" | bc`
+#  en=`printf "%04.2f" ${en1}`
+#  enl=`printf "%04.2f" ${enl1}`
+#  el=`printf "%04.2f" ${el1}`
+
+  local en1=`echo "scale=2; ${en100}/100" | bc`
+  local enl1=`echo "scale=2; ${enl100}/100" | bc`
   local el1=`echo "scale=2; ${el100}/100" | bc`
-  local enl1=`echo "scale=2;(${el100}+${dl100})/100" | bc`
-  local en1=`echo "scale=2; (${el100}+${dl100}+${dn100})/100" | bc`
   en=`printf "%04.2f" ${en1}`
   enl=`printf "%04.2f" ${enl1}`
   el=`printf "%04.2f" ${el1}`
+
 #  local ipn1=`echo "scale=2; ${ipn100}/100" | bc`
 #  local ipl1=`echo "scale=2; (100-${ipn100})/100" | bc`
 #  ipn=`printf "%04.2f" ${ipn1}`
@@ -169,8 +178,11 @@ next_iteration() {
 
 ################################################################################
 
-if [ "$cell" != "hex" ]; then
-  cell="square"
+if [[ "$cell" != "hex" ]] && [[ "$cell" != "sqr8" ]]; then
+  cell="sqr4"
+fi
+
+if [[ "$cell" == "sqr4" ]] || [[ "$cell" == "sqr8" ]]; then
   script_gif="${gnuplot_scripts_dir}/make_gif_sqr.plt"
   script_png="${gnuplot_scripts_dir}/make_png_sqr.plt"
   script_png2d="${gnuplot_scripts_dir}/make_png2d_sqr.plt"

nle_cpp/scripts/run_multiple/do_run.sh

@@ -17,9 +17,12 @@ while next_iteration; do
   name=$(get_name)
   namepng=${name}_png
   namedat=${name}_dat
+  namedattgz=${namedat}.tgz
   title=$(get_title)
   echo ${name}
 
+  [ -f $datdir/${namedattgz} ] && continue
+
   #continue
 
   # Run simulation
@@ -60,7 +63,7 @@ while next_iteration; do
   [ ! -d $datdir/${namedat} ] && mkdir $datdir/${namedat}
   mv ${prefix}*${suffix} $datdir/${namedat}/
   cd $datdir
-  tar czf ${namedat}.tgz ${namedat} && rm -r ${namedat}
+  tar czf ${namedattgz} ${namedat} && rm -r ${namedat}
   cd ..
 
   # Check if group data exists

nle_cpp/src/nle_ca.h

 #include "ca2d.h"
 
 // TODO: check what parameter values are set (use LOG to print in constructors, setData(), etc.)
-#define LOG 1
+#define LOG 0
 
 #define logfn(C,X) if (LOG) fprintf(stderr,"%s::%s(%s)\n",C,__FUNCTION__,X)
 
@@ -1501,7 +1501,7 @@ class NLE_hex_CA : public NLE_CA_base<hood_hex> {
       count[1] = snl;
       count[2] = sll;
     }
-  
+
     virtual double count_dH_move_NL(int bx,int by,int dir) {
       double dH = 0;
       for (int i=0;i<st[dir].size();i++) {