Extended capabilities of time-dependent ELM transport model and neoclassical transport model; Added several fields to b2time.nc; Added and/or expanded several plotting scripts

doc/solps/b2.transport.inputfile.ELMs

@@ -0,0 +1,28 @@
+ &TRANSPORT
+ ndata(1, 1 , 1 )= 6 ,
+ tdata(1, 1 , 1 , 1 )= -4.00E-02 , tdata(2, 1 , 1 , 1 )= 1.30 , tdata(3, 1 , 1 , 1 )= 10.00 ,
+ tdata(1, 2 , 1 , 1 )= -1.50E-02 , tdata(2, 2 , 1 , 1 )= 1.30 , tdata(3, 2 , 1 , 1 )= 10.00 ,
+ tdata(1, 3 , 1 , 1 )= -1.40E-02 , tdata(2, 3 , 1 , 1 )= 0.05 , tdata(3, 3 , 1 , 1 )= 10.00 ,
+ tdata(1, 4 , 1 , 1 )=  5.00E-03 , tdata(2, 4 , 1 , 1 )= 0.05 , tdata(3, 4 , 1 , 1 )= 10.00 ,
+ tdata(1, 5 , 1 , 1 )=  5.50E-03 , tdata(2, 5 , 1 , 1 )= 1.30 , tdata(3, 5 , 1 , 1 )= 10.00 ,
+ tdata(1, 6 , 1 , 1 )=  2.50E-02 , tdata(2, 6 , 1 , 1 )= 1.30 , tdata(3, 6 , 1 , 1 )= 10.00 ,
+ ndata(1, 3 , 1 )= 6 ,
+ tdata(1, 1 , 3 , 1 )= -4.00E-02 , tdata(2, 1 , 3 , 1 )= 2.00 , tdata(3, 1 , 3 , 1 )= 10.00 ,
+ tdata(1, 2 , 3 , 1 )= -1.50E-02 , tdata(2, 2 , 3 , 1 )= 2.00 , tdata(3, 2 , 3 , 1 )= 10.00 ,
+ tdata(1, 3 , 3 , 1 )= -1.40E-02 , tdata(2, 3 , 3 , 1 )= 0.07 , tdata(3, 3 , 3 , 1 )= 10.00 ,
+ tdata(1, 4 , 3 , 1 )=  5.00E-03 , tdata(2, 4 , 3 , 1 )= 0.07 , tdata(3, 4 , 3 , 1 )= 10.00 ,
+ tdata(1, 5 , 3 , 1 )=  5.50E-03 , tdata(2, 5 , 3 , 1 )= 2.00 , tdata(3, 5 , 3 , 1 )= 10.00 ,
+ tdata(1, 6 , 3 , 1 )=  2.50E-02 , tdata(2, 6 , 3 , 1 )= 2.00 , tdata(3, 6 , 3 , 1 )= 10.00 ,
+ ndata(1, 4 , 1 )= 6 ,
+ tdata(1, 1 , 4 , 1 )= -4.00E-02 , tdata(2, 1 , 4 , 1 )= 2.00 , tdata(3, 1 , 4 , 1 )= 10.00 ,
+ tdata(1, 2 , 4 , 1 )= -1.50E-02 , tdata(2, 2 , 4 , 1 )= 2.00 , tdata(3, 2 , 4 , 1 )= 10.00 ,
+ tdata(1, 3 , 4 , 1 )= -1.40E-02 , tdata(2, 3 , 4 , 1 )= 0.07 , tdata(3, 3 , 4 , 1 )= 10.00 ,
+ tdata(1, 4 , 4 , 1 )=  5.00E-03 , tdata(2, 4 , 4 , 1 )= 0.07 , tdata(3, 4 , 4 , 1 )= 10.00 ,
+ tdata(1, 5 , 4 , 1 )=  5.50E-03 , tdata(2, 5 , 4 , 1 )= 2.00 , tdata(3, 5 , 4 , 1 )= 10.00 ,
+ tdata(1, 6 , 4 , 1 )=  2.50E-02 , tdata(2, 6 , 4 , 1 )= 2.00 , tdata(3, 6 , 4 , 1 )= 10.00 ,
+ ELM_TIME_PERIOD=0.001,
+ ELM_TIME_BEGIN=0.0002,
+ ELM_TIME_PLATEAU=0.0002,
+ ELM_TIME_RECOVERY=0.0006,
+ ELM_TIME_END=0.0006,
+ /

runs/Makefile

@@ -278,6 +278,7 @@ endif
 	-[ -s b2mn.exe.dir/b2time.nc ] && mv b2mn.exe.dir/b2time.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2batch.nc ] && mv b2mn.exe.dir/b2batch.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2wall.nc ] && mv b2mn.exe.dir/b2wall.nc . || echo > /dev/null
+	-[ -s b2mn.exe.dir/b2neo.nc ] && mv b2mn.exe.dir/b2neo.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2movies.nc ] && mv b2mn.exe.dir/b2movies.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/eirenemovies.nc ] && mv b2mn.exe.dir/eirenemovies.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2tallies.nc ] && mv b2mn.exe.dir/b2tallies.nc . || echo > /dev/null
@@ -378,6 +379,7 @@ endif
 	-[ -s b2mn.exe.dir/b2time.nc ] && mv b2mn.exe.dir/b2time.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2batch.nc ] && mv b2mn.exe.dir/b2batch.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2wall.nc ] && mv b2mn.exe.dir/b2wall.nc . || echo > /dev/null
+	-[ -s b2mn.exe.dir/b2neo.nc ] && mv b2mn.exe.dir/b2neo.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2movies.nc ] && mv b2mn.exe.dir/b2movies.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/eirenemovies.nc ] && mv b2mn.exe.dir/eirenemovies.nc . || echo > /dev/null
 	-[ -s b2mn.exe.dir/b2tallies.nc ] && mv b2mn.exe.dir/b2tallies.nc . || echo > /dev/null

scripts/2d

@@ -1,16 +1,24 @@
 #! /bin/csh -f
+
 if ("X$1" == "X-lx") then
   set lx="l"
   shift
 else
   set lx=""
 endif
+
 if ("X$1" == "X-ly") then
   set ly="l"
   shift
 else
   set ly=""
 endif
+
+if ( $#argv < 2 ) then
+    echo "Error: You must provide at least two arguments (2nd, 3rd, etc. arguments will be plotted vs. the 1st one)."
+    exit 1
+endif
+
 set x=$1
 shift
 set source=b2mn.exe.dir/b2time.nc
@@ -36,23 +44,92 @@ endif
 
 cp /dev/null ${tmpdir}gnuplot.data.tmp
 if ($no_nc2text == 1) then
-  ncdump $source -f f -v $x | \
-  awk 'BEGIN {ORS="";} /data:/{found1=1;next;} /$x/{if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}} END {print "\n";}' | \
-  sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+  if ("$x" =~ *[0-9]) then
+      # Multi-species quantities, called as $x = $name$is (e.g. $x = 'nasepm1')
+      echo "Error: Plotting multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+      exit 1
+  else
+      # Time, called as $x = 'timesa', or single species quantities, called as $x = $name (e.g. $x = 'nesepm')
+      ncdump $source -f f -v $x | \
+      awk 'BEGIN {ORS="";} /data:/{found1=1;next;} /$x/{if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}} END {print "\n";}' | \
+      sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+  endif
+else
+  if ("$x" =~ *[0-9]) then 
+      # Multi-species quantities, called as $x = $name$is (e.g. $x = 'nasepm1')
+      set is = `echo "$x" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+      set name = `echo "$x" | sed -E 's/([0-9]+)$//'`
+      @ is_plus_1 = $is + 1
+      echo `nc2text -n 9999999 $source "$name(:,$is_plus_1)"` >> ${tmpdir}gnuplot.data.tmp
+  else
+      # Time, called as $x = 'timesa', or single species quantities, called as $x = $name (e.g. $x = 'nesepm')
+      echo `nc2text -n 9999999 $source $x` >> ${tmpdir}gnuplot.data.tmp
+  endif
+endif
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
 else
-  echo `nc2text -n 9999999 $source $x` >> ${tmpdir}gnuplot.data.tmp
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
 endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_names = ()
+foreach name ($species_names)
+  set last_char = `echo "$name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+        set neutral_species_names = ($neutral_species_names $name)
+    endif
+end
+
 start:
   if ($no_nc2text == 1) then
-    ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}  END {print "\n";}' | \
-    sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+    if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        echo "Error: Plotting multi-species arrays from b2time.nc not yet implemented for $no_nc2text == 1."
+        exit 1
+    else
+        # Time, called as $1 = 'timesa', or single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        ncdump $source -f f -v $1 | awk -v string="$1" 'BEGIN {ORS="";} /data:/{found1=1;next;} $0 ~ string {if (found1==1) {if (found2==1) print $1; else {print $3;found2=1;}}}  END {print "\n";}' | \
+        sed 's/,/ /g' | sed 's/;//g' >> ${tmpdir}gnuplot.data.tmp
+    endif
   else
-    echo `nc2text -n 9999999 $source $1` >> ${tmpdir}gnuplot.data.tmp
+    if ("$1" =~ *[0-9]) then
+        # Multi-species quantities, called as $1 = $name$is (e.g. $1 = 'nasepm1')
+        set is = `echo "$1" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+        set name = `echo "$1" | sed -E 's/([0-9]+)$//'`
+        @ is_plus_1 = $is + 1
+        echo `nc2text -n 9999999 $source "$name(:,$is_plus_1)"` >> ${tmpdir}gnuplot.data.tmp
+    else
+        # Time, called as $1 = 'timesa', or single species quantities, called as $1 = $name (e.g. $1 = 'nesepm')
+        echo `nc2text -n 9999999 $source $1` >> ${tmpdir}gnuplot.data.tmp
+    endif
   endif
   shift
   if ("X$1X" != "XX") goto start
 
-awk.transpose < ${tmpdir}gnuplot.data.tmp | awk 'NR==1{saveNF=NF}NF==saveNF{print $0}' | plot ${lx}x${ly}yplot$nargs $args $x '' $PWD
+# Find species names, in case of multi-species array
+set args_plot=""
+set field_names = ( $args )
+foreach i ($field_names)
+  if ("$i" =~ *[0-9]) then
+      # Multi-species quantities, called as $i = $name$is (e.g. $i = 'nasepm1')
+      set is = `echo "$i" | sed -E 's/.*[^0-9]([0-9]+)$/\1/'`
+      set name = `echo "$i" | sed -E 's/([0-9]+)$//'`
+      @ is_plus_1 = $is + 1
+      if ("$name" =~ dab* || "$name" =~ dmb* || "$name" =~ tab* || "$name" =~ tmb*) then
+        setenv species_name $neutral_species_names[$is_plus_1]
+      else
+        setenv species_name $species_names[$is_plus_1]
+      endif
+      set args_plot="$args_plot $name($species_name)"
+  else
+      set args_plot="$args_plot $i"
+  endif
+end
+
+awk.transpose < ${tmpdir}gnuplot.data.tmp | awk 'NR==1{saveNF=NF}NF==saveNF{print $0}' | plot ${lx}x${ly}yplot$nargs $args_plot $x '' $PWD
 rm ${tmpdir}gnuplot.data.tmp
 
 if ($netcdf4 == 1) then

scripts/2d_plots

@@ -7,18 +7,31 @@ else
 endif
 setenv GNUPLOT_BATCH yes
 setenv GNUPLOT_POSTSCRIPT_OPTIONS 'color solid noenhanced'
-setenv PRINT_PLOT b2time2d.ps
+setenv PRINT_PLOT b2time2d_time_traces.ps
 rm -f ${tmpdir}GNUPLOT_COUNT ${tmpdir}gnuplot.cmd
 echo 0 > ${tmpdir}GNUPLOT_COUNT
 
+set source=b2mn.exe.dir/b2time.nc
+if (! -s $source) set source=b2time.nc
+set ns = `ncdump -h $source | grep -w "ns =" | sed -E 's/.*= *([0-9]+) *;.*/\1/'`
+
+set solps_fluids=`climb_and_look_for SOLPS_FLUIDS`
+if (-s $solps_fluids) then
+  setenv SOLPS_FLUIDS `cat $solps_fluids`
+else
+  setenv SOLPS_FLUIDS "`get_solps_fluids`"
+endif
+set species_names = ( $SOLPS_FLUIDS )
+set neutral_species_index = -1
+
 set nreg=`climb_and_look_for NREG`
 set nnreg=`pipe_run.log | grep -a ^nnreg | head -1`
 if (-s $nreg) then
   setenv NREG `cat $nreg`
-  echo Set NREG to $NREG "(based on $nreg)"
+  #echo Set NREG to $NREG "(based on $nreg)"
 else
   set NREG=$nnreg[2]
-  echo Set NREG to $NREG "(based on log file)"
+  #echo Set NREG to $NREG "(based on log file)"
 endif
 if (! $?NREG) set NREG = 4
 if ("X$nnreg" != "X") then
@@ -29,8 +42,110 @@ if ("X$nnreg" != "X") then
 endif
 
 2dt nesepm
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dabsepm if run with Eirene, nasepm if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dabsepm fields exist --> coupled run --> call dabsepm
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dabsepm$neutral_species_index "
+      else
+        # dabsepm fields do not exist --> standalone run --> call nasepm
+        set na_dens="$na_dens nasepm$is_minus_1 "
+      endif
+    else
+      # ion species: always call nasepm
+      set na_dens="$na_dens nasepm$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dt $group
+    @ offset = $end + 1
+end
 2dt tesepm tisepm
 2dt nesepi nemxip nesepa nemxap
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dabsepi if run with Eirene, nasepi if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dabsepi fields exist --> coupled run --> call dabsepi
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dabsepi$neutral_species_index "
+      else
+        # dabsepi fields do not exist --> standalone run --> call nasepi
+        set na_dens="$na_dens nasepi$is_minus_1 "
+      endif
+    else
+      # ion species: always call nasepi
+      set na_dens="$na_dens nasepi$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dt $group
+    @ offset = $end + 1
+end
+set na_dens=""
+set neutral_species_index = -1
+foreach is (`seq 1 $ns`)
+  @ is_minus_1 = $is - 1
+  setenv species_name $species_names[$is]
+  set last_char = `echo "$species_name" | awk '{print substr($0,length($0),1)}'`
+  set second_last_char = `echo "$species_name" | awk '{print substr($0,length($0)-1,1)}'`
+    if ("$last_char" == "0" && "$second_last_char" !~ [0-9]) then
+      # neutral species: call dabsepa if run with Eirene, nasepa if standalone run
+      if (`ncdump -h $source | grep -w dabsepm | wc -l` > 0) then
+        # dabsepa fields exist --> coupled run --> call dabsepa
+        @ neutral_species_index = $neutral_species_index + 1
+        set na_dens="$na_dens dabsepa$neutral_species_index "
+      else
+        # dabsepa fields do not exist --> standalone run --> call nasepa
+        set na_dens="$na_dens nasepa$is_minus_1 "
+      endif
+    else
+      # ion species: always call nasepa
+      set na_dens="$na_dens nasepa$is_minus_1 "
+    endif
+end
+set counts = (`groups_species`)
+set na_dens_list = (`echo $na_dens`)
+set offset = 1
+foreach c ($counts)
+    @ end = $offset + $c - 1
+    set group = ""
+    foreach i (`seq $offset $end`)
+        set group = "$group $na_dens_list[$i]"
+    end
+    2dt $group
+    @ offset = $end + 1
+end
 2dt tesepi temxip tesepa temxap
 2dt tisepi timxip tisepa timxap
 2dt fnixip fnixap