setting up complete automation of fortfile packaging

scripts/meta/bulk_interpolation_fix.sh

@@ -1,26 +0,0 @@
-#!/bin/bash
-
-script_dir=$( cd $(dirname $0) ; pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@')
-basedir=`pwd`
-
-if [[ -x $script_dir/../bin/interpolation_fix ]]
-then
-    echo "Binary available. Proceeding."
-else
-    echo "Binary unavailable. Exiting."
-    exit 9
-fi
-
-for fortfile in $@
-do
-    if [[ -e $(basename $fortfile) ]]
-    then
-        mkdir -p uninterpolated
-        mv $fortfile uninterpolated
-        $script_dir/../bin/interpolation_fix uninterpolated/$(basename $fortfile) $fortfile
-    else
-        $script_dir/../bin/interpolation_fix $fortfile $(basename $fortfile)
-    fi
-    echo ""
-done
-exit 0

scripts/operations/package_tables.sh

@@ -1,11 +1,55 @@
-cldn=$1
-cd cldn${cldn}
+#!/usr/local/bin/bash
+
+# This still isn't really generalized. Need to go to a
+# specific directory of runs to run this. Feed it a list
+# of column densities.
+
+script_dir=$(
+    cd $(dirname $0) ;
+    pwd -P |sed 's@^\(.*\)/scripts.*@\1/scripts@'
+    )
+base_dir=`pwd`
+bin_dir="$script_dir/../bin"
+
+cldndir=$1
+cd $cldndir
 mkdir -p fortfiles
 cd fortfiles
 # pwd
-../../../../../bin/create_fort_files ../mpi_grid.out ../../../../../reference/linelist
-tar cf ngc5548_mehdipour_4thdexgrid_cldn${cldn}.tar *
-gzip ngc5548_mehdipour_4thdexgrid_cldn${cldn}.tar
-mv ngc5548_mehdipour_4thdexgrid_cldn${cldn}.tar.gz ../..
 
- 
+echo "Directory ready. Calling fort file creation."
+# $bin_dir/create_fort_files ../mpi_grid.out $script_dir/../reference/linelist
+
+allfortnums=$(echo fort.*|sed 's@fort\.\([0-9]\+\)@\1@g')
+inwTfortnums=$(grep 'InwT' fort.*|sed 's@^fort\.\([0-9]\+\):InwT.*@\1@')
+echo "Generating inward diffuse tables for $(echo "$inwTfortnums"|wc -l) coordinates."
+for inwTnum in $inwTfortnums
+do
+    inwCnum=$(($inwTnum + 1))
+    inwDnum=$(($inwCnum + 1))
+    fortnumstoproc=""
+    for fortnum in $allfortnums
+    do
+        if [[ $fortnum > $inwCnum ]]
+        then
+            fortnumstoproc="$fortnum $fortnumstoproc"
+        fi
+    done
+    echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
+    for fortnum in $fortnumstoproc
+    do
+        newnum=$(( $fortnum + 1 ))
+        mv fort.$fortnum fort.$newnum
+    done
+    echo "Writing inwD table to fort.$inwDnum"
+    $bin_dir/subtract_fortfiles fort.$inwTnum fort.$inwCnum > fort.$inwDnum
+done
+
+echo "Applying interpolative smoothing."
+$script_dir/operations/bulk_interpolation_fix.sh fort.* > interpolation_report
+
+tar cf ngc5548_mehdipour_4thdexgrid_${cldndir}.tar *
+gzip ngc5548_mehdipour_4thdexgrid_${cldndir}.tar
+mv ngc5548_mehdipour_4thdexgrid_${cldndir}.tar.gz $base_dir/..
+
+

src/agn.hpp

@@ -184,15 +184,15 @@ agn::cloudy_grid agn::read_cloudy_grid(std::ifstream& inputfile) {
 		pos = inputline.find(seek_string);
 		if (pos != std::string::npos) break;
 	}
-	if(agn::debug) std::cout 
-		<< "Collecting grid meta data starting on line " 
-		<< line_num 
+	if(agn::debug) std::cout
+		<< "Collecting grid meta data starting on line "
+		<< line_num
 		<< std::endl;
 	agn::gridcoordlist coordlist;
 	std::pair<double,double> xy (0,0);
 	seek_string="**************************************************";
 	while(!inputfile.eof()) {
-		while (inputline.find(seek_string) == std::string::npos) 
+		while (inputline.find(seek_string) == std::string::npos)
 			getline(inputfile,inputline);
 		while(inputfile.peek() == ' ') inputfile.get(); // Skip blank space
 		// Break for first grid

src/spectral_lines.hpp

@@ -215,8 +215,13 @@ std::list<agn::eqwidth_table> agn::compile_eqwidth_tables(agn::cloudy_grid grid,
             << "Processing label "
             << *line_label_it
             << std::endl;
-		new_table.header[0] = *line_label_it;
-		new_table.header[0].append("  relative to Inci 1215.00A scaled to 1215.00A");
+        std::stringstream header0;
+        header0
+            << *line_label_it
+            << "  relative to Inci 1215.00A scaled to "
+            << scale_factor
+            << "A.";
+        new_table.header[0] = header0.str();
 		new_table.header[1] = "Hden   Phi(H)  Eq_Width (A)";
 		agn::cloudy_grid::iterator result_it = grid.begin();
 		while (result_it != grid.end()) {

src/subtract_fortfiles.cpp

@@ -59,22 +59,22 @@ int main(int argc, char const *argv[])
         table2 >> hden2 >> phi2 >> magnitude2;
         resultant_magnitude[i] = magnitude1[i] - magnitude2;
         }
-        if ( resultant_magnitude[i] < 1e-10 ) 
+        if ( resultant_magnitude[i] < 1e-10 )
             resultant_magnitude[i]=1e-10;
     }
 
 
 
-    std::cout 
+    std::cout
             << first_line
             << std::endl
             << "HDen   Phi(H)  ScaInten"
             << std::endl;
 
     for (int i=0; i<table_entries; i++) {
-        std::cout 
-            << std::fixed 
-            << std::setprecision(3) 
+        std::cout
+            << std::fixed
+            << std::setprecision(3)
             << hden1[i]
             << "  "
             << phi1[i]