2017 runs finished

notes

@@ -23,15 +23,15 @@ Run grid with new SED, or at least a point, check values: how to find the approp
 
     ✓   run models for comparising: 10.5,19.5
 
-    □   Why so many Fe 2 lines?
+    ✓   Why so many Fe 2 lines?
 
-    □   check if blnds are sums of the expected multiplets
+    ✓   check if blnds are sums of the expected multiplets
 
     ✓   add in more levels to the H atom, unresolved, 20, also add some to paschen, maybe others -- check how much time is lost
 
     ✓   punch the paschen and balmer lines up to 18
 
-    □   Read Intrinsic Lines
+    ✓   Read Intrinsic Lines
 
     □   Smoothing algorithm using n-dimensional smoothing
 
@@ -39,9 +39,9 @@ Run grid with new SED, or at least a point, check values: how to find the approp
 
     ✓   Run Grids in c17
 
-    □   Email about order of lines
+    ✓   Email about order of lines
 
-    □   Find blend correlated names and update
+    ✓   Find blend correlated names and update
 
 
 

scripts/cloudy/magdziarz.mpi.in

@@ -52,7 +52,7 @@ set nend 5000
 //
 //      derived quantities added in Otho's program ~2017
 //  InwD = InwT - InwC = Inward Diffuse
-//  nFnD = nFnu - InwD = Total Diffuse
+//  nFnD = nFnu - InwC = Total Diffuse
 //
 // "print continuum" redundant with set nFnu in c17
 //

scripts/cloudy/magdziarz.mpi_grid.in

@@ -50,7 +50,7 @@ set nend 5000
 //
 //      derived quantities added in Otho's program ~2017
 //  InwD = InwT - InwC = Inward Diffuse
-//  nFnD = nFnu - InwD = Total Diffuse
+//  nFnD = nFnu - InwC = Total Diffuse
 //
 // "print continuum" redundant with set nFnu in c17
 //

scripts/cloudy/mehdipour.mpi.in

@@ -52,7 +52,7 @@ set nend 5000
 //
 //      derived quantities added in Otho's program ~2017
 //  InwD = InwT - InwC = Inward Diffuse
-//  nFnD = nFnu - InwD = Total Diffuse
+//  nFnD = nFnu - InwC = Total Diffuse
 //
 // "print continuum" redundant with set nFnu in c17
 //

scripts/cloudy/mehdipour.mpi_grid.in

@@ -50,7 +50,7 @@ set nend 5000
 //
 //      derived quantities added in Otho's program ~2017
 //  InwD = InwT - InwC = Inward Diffuse
-//  nFnD = nFnu - InwD = Total Diffuse
+//  nFnD = nFnu - InwC = Total Diffuse
 //
 // "print continuum" redundant with set nFnu in c17
 //

scripts/meta/process_gridoutputs.sh

@@ -7,7 +7,7 @@ script_dir=$(
 base_dir=`pwd`
 bin_dir="$script_dir/../bin"
 
-for dir in $(echo cldn*)
+for dir in $(find . -type 'd' -name 'cldn*')
 do
     echo "Processing ${dir}."
     $script_dir/operations/package_tables.sh $dir

scripts/operations/package_tables.sh

@@ -11,8 +11,8 @@ script_dir=$(
 base_dir=`pwd`
 bin_dir="$script_dir/../bin"
 
-cldndir=$1
+griddir=$1
-cd $cldndir
+cd $griddir
 mkdir -p fortfiles
 cd fortfiles
 # pwd
@@ -21,13 +21,14 @@ echo "Directory ready. Calling fort file creation."
 $bin_dir/create_fort_files ../mpi_grid.out $script_dir/../reference/linelist.c17
 
 inwTfortnums=$(grep 'InwT' fort.*|sed 's@^fort\.\([0-9]\+\):InwT.*@\1@'|sort -nr)
-echo "Generating inward diffuse tables for $(echo "$inwTfortnums"|wc -l) coordinates."
+echo "Computing inward diffuse tables for $(echo "$inwTfortnums"|wc -l) coordinates."
-echo -n "Writing InwD tables to fortfiles:"
+echo -n "Writing InwD tables to fortfiles and shifting files:"
+count=0
 for inwTnum in $(echo $inwTfortnums|sort -r)
 do
     inwCnum=$(($inwTnum + 1))
     inwDnum=$(($inwCnum + 1))
-    allfortnums=$(echo fort.*|sed 's@fort\.\([0-9]\+\)@\1@g')
+    allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
     fortnumstoproc=""
     for fortnum in $allfortnums
     do
@@ -42,14 +43,52 @@ do
         newnum=$(( $fortnum + 1 ))
         mv fort.$fortnum fort.$newnum
     done
-    echo -n " $inwDnum"
+    #echo -n " $inwDnum"
     $bin_dir/subtract_fortfiles fort.$inwTnum fort.$inwCnum InwD > fort.$inwDnum
+    echo -ne "\033[2K" ; printf "\r"
+    echo -n "Writing InwD tables to fortfiles and shifting files: $(( ++count ))"
+done
+echo ""
+
+inwCfortnums=$(grep 'InwC' fort.*|sed 's@^fort\.\([0-9]\+\):InwC.*@\1@'|sort -nr)
+echo "Computing total diffuse tables for $(echo "$inwCfortnums"|wc -l) coordinates."
+echo -n "Writing nFnD tables to fortfiles and shifting files: 0"
+count=0
+for inwCnum in $(echo $inwCfortnums|sort -r)
+do
+    nFnunum=$(($inwCnum - 3))
+    nFnDnum=$(($inwCnum + 2))
+    allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
+    fortnumstoproc=""
+    for fortnum in $allfortnums
+    do
+        if (( $fortnum >= $nFnDnum ))
+        then
+            fortnumstoproc="$fortnum $fortnumstoproc"
+        fi
+    done
+    # echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
+    for fortnum in $fortnumstoproc
+    do
+        newnum=$(( $fortnum + 1 ))
+        mv fort.$fortnum fort.$newnum
+    done
+    
+    #echo -n " $nFnDnum"
+    $bin_dir/subtract_fortfiles fort.$nFnunum fort.$inwCnum nFnD > fort.$nFnDnum
+    echo -ne "\033[2K" ; printf "\r"
+    echo -n "Writing nFnD tables to fortfiles and shifting files: $(( ++count ))"
 done
 echo ""
 
 echo "Applying interpolative smoothing."
 $script_dir/operations/bulk_interpolation_fix.sh fort.* > interpolation_report
 
-tar cf ngc5548_mehdipour_$(basename ${base_dir})_${cldndir}.tar *
+
-gzip ngc5548_mehdipour_$(basename ${base_dir})_${cldndir}.tar
+grid_id=$(echo ${griddir}|sed 's@^\.\/\(.*\)@\1@'|sed 's@.grids@@'|sed 's@\/@.@g')
-mv ngc5548_mehdipour_$(basename ${base_dir})_${cldndir}.tar.gz $base_dir
+echo "Saving $grid_id grid"
+tar cf fortfiles_${grid_id}.tar *
+gzip fortfiles_${grid_id}.tar
+mv fortfiles_${grid_id}.tar.gz $base_dir
+
+cd $base_dir

src/agn.hpp

@@ -335,14 +335,14 @@ agn::cloudy_grid agn::read_cloudy_grid(std::ifstream& inputfile) {
 			agn::cloudy_line_data data;
 			data.index = ++index;
 			//std::stringstream values;
-			//data.radiated_energy = atof((*linetext_it).substr(
+			data.radiated_energy = atof((*linetext_it).substr(
-			//	radiatedenergystr_pos,
+				radiatedenergystr_pos,
-			//	radiatedenergystr_len).c_str()
+				radiatedenergystr_len).c_str()
-			//);
+			);
-			//data.eq_width = atof((*linetext_it).substr(
+			data.eq_width = atof((*linetext_it).substr(
-			//	eqwidthstr_pos,
+				eqwidthstr_pos,
-			//	eqwidthstr_len).c_str()
+				eqwidthstr_len).c_str()
-			//);
+			);
 			if(line_debug) {
 				std::cout 
 							<< std::setprecision(5)
@@ -400,7 +400,7 @@ agn::cloudy_grid agn::read_cloudy_grid(std::ifstream& inputfile) {
 			getline(inputfile,inputline);
 		}
 		if(agn::debug) std::cout
-			<< "\nAdding point to grid (size "
+			<< "\nAdding point to grid ("
 			<< grid.size()
 			<< " of "
 			<< coordlist.size()

src/create_fort_files.cpp

@@ -37,6 +37,15 @@ int main(int argc, char const *argv[]) {
     int num_zeroes=0;
     while(table_it != tables.end()) {
         if(agn::is_zero(*table_it)) {
+            std::string linetype = table_it->header[0].substr(0,4);
+            if (linetype == "nFnu" ||
+                linetype == "nInu" ||
+                linetype == "InwT" ||
+                linetype == "InwC") {
+                table_it++;
+                continue;
+            }
+
             zeroreport << " "
                         << table_it->header[0]
                         << std::endl;