have a working packaging meta script, now

reference/linelist

@@ -2,8 +2,8 @@
 # Lines appear in approximate order they appear in Cloudy standard output file.
 
 #two incident continuum points
-inci 1215.00A
-inci 4860.00A
+Inci 1215.00A
+Inci 4860.00A
 
 #Lyman Lines:
 TOTL 1215.68A
@@ -264,4 +264,4 @@ nFnu 1.48022m
 nFnu 1.64313m
 nFnu 2.32440m
 nFnu 4.11370m 
-nFnu 122.400m
+nFnu 122.400m

scripts/operations/package_tables.sh

@@ -18,38 +18,38 @@ cd fortfiles
 # pwd
 
 echo "Directory ready. Calling fort file creation."
-# $bin_dir/create_fort_files ../mpi_grid.out $script_dir/../reference/linelist
+$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@')
+inwTfortnums=$(grep 'InwT' fort.*|sed 's@^fort\.\([0-9]\+\):InwT.*@\1@'|sort -nr)
 echo "Generating inward diffuse tables for $(echo "$inwTfortnums"|wc -l) coordinates."
-for inwTnum in $inwTfortnums
+echo -n "Writing InwD tables to fortfiles:"
+for inwTnum in $(echo $inwTfortnums|sort -r)
 do
     inwCnum=$(($inwTnum + 1))
     inwDnum=$(($inwCnum + 1))
+    allfortnums=$(echo fort.*|sed 's@fort\.\([0-9]\+\)@\1@g')
     fortnumstoproc=""
     for fortnum in $allfortnums
     do
-        if [[ $fortnum > $inwCnum ]]
+        if (( $fortnum > $inwCnum ))
         then
             fortnumstoproc="$fortnum $fortnumstoproc"
         fi
     done
-    echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
+    # 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
+    echo -n " $inwDnum"
+    $bin_dir/subtract_fortfiles fort.$inwTnum fort.$inwCnum InwD > fort.$inwDnum
 done
+echo ""
 
 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 $base_dir/..
-
-
+tar cf ngc5548_mehdipour_$(basename ${base_dir})_${cldndir}.tar *
+gzip ngc5548_mehdipour_$(basename ${base_dir})_${cldndir}.tar
+mv ngc5548_mehdipour_$(basename ${base_dir})_${cldndir}.tar.gz $base_dir

src/agn.hpp

@@ -212,7 +212,7 @@ agn::cloudy_grid agn::read_cloudy_grid(std::ifstream& inputfile) {
 		}
 		else {
 			getline(inputfile,inputline);
-			while (inputline.find(seek_string) == std::string::npos) 
+			while (inputline.find(seek_string) == std::string::npos)
 				getline(inputfile,inputline);
 		}
 	}

src/create_fort_files.cpp

@@ -25,11 +25,39 @@ int main(int argc, char const *argv[]) {
 		<< " emission lines.\n";
 	std::list<agn::eqwidth_table> tables = agn::compile_eqwidth_tables(grid,lines_to_print,1215.00);
 
+
+    // Remove any tables that are zero.
+    std::list<agn::eqwidth_table>::iterator table_it = tables.begin();
+    std::ofstream zeroreport;
+    zeroreport.open("zero_report");
+    zeroreport << "These headers were pulled from tables"
+                << " that returned minimum values."
+                << std::endl;
+    int zeroes=0;
+    while(table_it != tables.end()) {
+        if(agn::is_zero(*table_it)) {
+            zeroreport << " "
+                        << table_it->header[0]
+                        << std::endl;
+            zeroes++;
+            table_it = tables.erase(table_it);
+            continue;
+        }
+
+    table_it++;
+    }
+    std::cout << "Removed "
+            << zeroes
+            << " tables from the list because"
+            << " they had zero value."
+            << std::endl;
+
+    // Write the tables to the fortfile stack.
 	std::cout
 		<< "Printing "
 		<< tables.size()
 		<< " tables to fortfiles.\n";
-	std::list<agn::eqwidth_table>::iterator table_it = tables.begin();
+    table_it = tables.begin();
 	int fortfilenum=11;
 	while(table_it != tables.end()) {
 		std::ofstream outfile;

src/spectral_lines.hpp

@@ -21,6 +21,7 @@ struct eqwidth_table {
 	std::string header[2];
 	table2d value;
 };
+bool is_zero(const eqwidth_table&);
 eqwidth_table read_eqwidth_table(std::ifstream& table_file);
 std::string format_eqwidth_table(eqwidth_table table);
 std::string format_eqwidth_table_slice(eqwidth_table table,iterator2d x);
@@ -64,11 +65,24 @@ std::ostream& operator<< (std::ostream&,eqwidth_table);
 
 
 
-
 
 
 // Definitions
 
+bool agn::is_zero(const eqwidth_table& table_to_check) {
+    agn::table2d::const_iterator x_it = table_to_check.value.begin();
+    while (x_it != table_to_check.value.end()) {
+        agn::table1d::const_iterator y_it= x_it->second.begin();
+        while (y_it != x_it->second.end()) {
+            if (y_it->second != EQWIDTH_MIN_VAL)
+                return false;
+                y_it++;
+        }
+        x_it++;
+    }
+    return true;
+}
+
 
 agn::eqwidth_table agn::read_eqwidth_table(std::ifstream& table_file) {
     agn::eqwidth_table resultant;

src/subtract_fortfiles.cpp

@@ -68,7 +68,8 @@ int main(int argc, char const *argv[])
     std::cout
             << first_line
             << std::endl
-            << "HDen   Phi(H)  ScaInten"
+            //<< "HDen   Phi(H)  ScaInten"
+            << second_line
             << std::endl;
 
     for (int i=0; i<table_entries; i++) {
@@ -85,5 +86,7 @@ int main(int argc, char const *argv[])
             << std::endl;
     }
 
+    table1.close();
+    table2.close();
     return 0;
 }