fixed multi-line stuff?

notes

@@ -5,6 +5,30 @@ look at paper from kirk's student and find the value of that parameter
 copy grids from thor
 
 
+this shows only the transition between 1s and 2p... where are the rest of the contributions?
+
+if indeed cloudy is meaning to print these out individually?
+
+this may not be true for hydrogen-like iron, but for H-alpha the three transitions should be included
+
+is this just sloppy notation in output file, or is this really accurate and then where is all the rest of it?
+
+
+
+
+save species line "species_lines" all
+save species labels "species_labels" all
+
+
+OR
+
+save species labels "species_labels"
+H[:]
+end 
+
+
+
+
 
 
 2017 grids needed

scripts/operations/package_tables.sh

@@ -29,66 +29,66 @@ cd fortfiles
 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)
+# inwTfortnums=$(grep 'InwT' fort.*|sed 's@^fort\.\([0-9]\+\):InwT.*@\1@'|sort -nr)
-echo "Computing 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 and shifting files:"
+# echo -n "Writing InwD tables to fortfiles and shifting files:"
-count=0
+# count=0
-for inwTnum in $(echo $inwTfortnums|sort -r)
+# for inwTnum in $(echo $inwTfortnums|sort -r)
-do
+# do
-    inwCnum=$(($inwTnum + 1))
+#     inwCnum=$(($inwTnum + 1))
-    inwDnum=$(($inwCnum + 1))
+#     inwDnum=$(($inwCnum + 1))
-    allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
+#     allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
-    fortnumstoproc=""
+#     fortnumstoproc=""
-    for fortnum in $allfortnums
+#     for fortnum in $allfortnums
-    do
+#     do
-        if (( $fortnum > $inwCnum ))
+#         if (( $fortnum > $inwCnum ))
-        then
+#         then
-            fortnumstoproc="$fortnum $fortnumstoproc"
+#             fortnumstoproc="$fortnum $fortnumstoproc"
-        fi
+#         fi
-    done
+#     done
-    # echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
+#     # echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
-    for fortnum in $fortnumstoproc
+#     for fortnum in $fortnumstoproc
-    do
+#     do
-        newnum=$(( $fortnum + 1 ))
+#         newnum=$(( $fortnum + 1 ))
-        mv fort.$fortnum fort.$newnum
+#         mv fort.$fortnum fort.$newnum
-    done
+#     done
-    #echo -n " $inwDnum"
+#     #echo -n " $inwDnum"
-    $bin_dir/subtract_fortfiles fort.$inwTnum fort.$inwCnum InwD > fort.$inwDnum
+#     $bin_dir/subtract_fortfiles fort.$inwTnum fort.$inwCnum InwD > fort.$inwDnum
-    echo -ne "\033[2K" ; printf "\r"
+#     echo -ne "\033[2K" ; printf "\r"
-    echo -n "Writing InwD tables to fortfiles and shifting files: $(( ++count ))"
+#     echo -n "Writing InwD tables to fortfiles and shifting files: $(( ++count ))"
-done
+# done
-echo ""
+# echo ""
-
+# 
-inwCfortnums=$(grep 'InwC' fort.*|sed 's@^fort\.\([0-9]\+\):InwC.*@\1@'|sort -nr)
+# 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 "Computing total diffuse tables for $(echo "$inwCfortnums"|wc -l) coordinates."
-echo -n "Writing nFnD tables to fortfiles and shifting files: 0"
+# echo -n "Writing nFnD tables to fortfiles and shifting files: 0"
-count=0
+# count=0
-for inwCnum in $(echo $inwCfortnums|sort -r)
+# for inwCnum in $(echo $inwCfortnums|sort -r)
-do
+# do
-    nFnunum=$(($inwCnum - 3))
+#     nFnunum=$(($inwCnum - 3))
-    nFnDnum=$(($inwCnum + 2))
+#     nFnDnum=$(($inwCnum + 2))
-    allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
+#     allfortnums=$(ls fort.*|sed 's@fort\.\([0-9]\+\)@\1@g'|sort -n)
-    fortnumstoproc=""
+#     fortnumstoproc=""
-    for fortnum in $allfortnums
+#     for fortnum in $allfortnums
-    do
+#     do
-        if (( $fortnum >= $nFnDnum ))
+#         if (( $fortnum >= $nFnDnum ))
-        then
+#         then
-            fortnumstoproc="$fortnum $fortnumstoproc"
+#             fortnumstoproc="$fortnum $fortnumstoproc"
-        fi
+#         fi
-    done
+#     done
-    # echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
+#     # echo "Shifting $( echo "$fortnumstoproc"|wc -w ) files."
-    for fortnum in $fortnumstoproc
+#     for fortnum in $fortnumstoproc
-    do
+#     do
-        newnum=$(( $fortnum + 1 ))
+#         newnum=$(( $fortnum + 1 ))
-        mv fort.$fortnum fort.$newnum
+#         mv fort.$fortnum fort.$newnum
-    done
+#     done
-    
+#     
-    #echo -n " $nFnDnum"
+#     #echo -n " $nFnDnum"
-    $bin_dir/subtract_fortfiles fort.$nFnunum fort.$inwCnum nFnD > fort.$nFnDnum
+#     $bin_dir/subtract_fortfiles fort.$nFnunum fort.$inwCnum nFnD > fort.$nFnDnum
-    echo -ne "\033[2K" ; printf "\r"
+#     echo -ne "\033[2K" ; printf "\r"
-    echo -n "Writing nFnD tables to fortfiles and shifting files: $(( ++count ))"
+#     echo -n "Writing nFnD tables to fortfiles and shifting files: $(( ++count ))"
-done
+# done
-echo ""
+# echo ""
 
 echo "Applying interpolative smoothing."
 $script_dir/operations/bulk_interpolation_fix.sh fort.* > interpolation_report

src/agn.hpp

@@ -17,7 +17,7 @@
 
 namespace agn {
 
-const bool debug = false;
+const bool debug = true;
 const bool line_debug = false;
 
 // General constants
@@ -159,8 +159,8 @@ std::ostream& agn::operator<< (std::ostream& outstream, cloudy_result output) {
 		<< std::setprecision(0)
 		<< output.colden
 		<< "): "
-		<< output.emergent_line_intensity.size()
+		<< output.intrinsic_line_intensity.size()
-		<< " emission lines, "
+		<< " intrinsic emission lines, "
 		<< output.cautions.size()
 		<< " cautions present.";
 	return outstream;
@@ -363,33 +363,44 @@ agn::cloudy_grid agn::read_cloudy_grid(std::ifstream& inputfile) {
 									eqwidthstr_len).c_str()
 							<< "\n";
 			}
-			if(point.emergent_line_intensity.count(label) == 0) {
+			if(point.intrinsic_line_intensity.count(label) == 0) {
 				data.has_duplicates = false;
-				point.emergent_line_intensity[label] = data;
+				point.intrinsic_line_intensity[label] = data;
 			}
 			else {
 				duplicate_labels.push_back(label);
-				data.has_duplicates = true;
+				std::stringstream zerolabel(label);
-				point.emergent_line_intensity[label].has_duplicates = true;
+				zerolabel << " j=0";
+				point.intrinsic_line_intensity[zerolabel.str()]
+					= point.intrinsic_line_intensity[label];
+				point.intrinsic_line_intensity[zerolabel.str()].has_duplicates = true;
+				point.intrinsic_line_intensity.erase(label);
 				int j=1;
+				data.has_duplicates = true;
 				while(true) {
 					std::stringstream newlabel;
 					newlabel << label;
 					newlabel << " j=" << j;
-					if(point.emergent_line_intensity.count(newlabel.str()) != 0) {
+					if(point.intrinsic_line_intensity.count(newlabel.str()) != 0) {
 						j++;
 						continue;
 					}
 					else {
-						point.emergent_line_intensity[newlabel.str()] = data;
+						point.intrinsic_line_intensity[newlabel.str()] = data;
 						break;
 					}
 				}
 			}
 			linetext_it++;
 		}
-		if(agn::debug) std::cout
+		if(agn::debug) {
-			<< " Grabbing footer.";
+			std::cout << " Duplicates found: ";
+			std::list<std::string>::iterator dup_it = duplicate_labels.begin();
+			while (dup_it != duplicate_labels.end() ) {
+				std::cout << *dup_it << " ";
+			}				
+			std::cout << " Grabbing footer.";
+		}
 		while (inputline == "")
 			getline(inputfile,inputline);
 		std::string footer="";

src/spectral_lines.hpp

@@ -157,8 +157,9 @@ std::string agn::format_eqwidth_table_slice(agn::eqwidth_table table,agn::iterat
 
 
 std::ostream& agn::operator<< (std::ostream& outstream, agn::eqwidth_table table) {
+    std::string header0_trimmed = table.header[0]; // need to setup a trim function for this
 	outstream
-		<< table.header[0]
+		<< header0_trimmed
 		<< std::endl
 		<< table.header[1]
 		<< std::endl;
@@ -222,6 +223,7 @@ agn::line_list agn::read_line_list(std::ifstream& inputfile) {
 std::list<agn::eqwidth_table> agn::compile_eqwidth_tables(agn::cloudy_grid grid,agn::line_list line_labels,double scale_factor) {
 	std::list<eqwidth_table> table_list_eq_width,table_list_radiated_energy;
 	agn::line_list::iterator line_label_it = line_labels.begin();
+    // Iterate over labels, creating table for each:
 	while (line_label_it != line_labels.end()) {
 		double x,y;
 		agn::cloudy_line_data data;
@@ -233,9 +235,8 @@ std::list<agn::eqwidth_table> agn::compile_eqwidth_tables(agn::cloudy_grid grid,
         std::stringstream header0;
         header0
             << *line_label_it
-            << "  relative to Inci 1215.00A scaled to "
+            << " relative to Inci 1215.00A scaled to "
-            << scale_factor
+            << 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();
@@ -243,12 +244,13 @@ std::list<agn::eqwidth_table> agn::compile_eqwidth_tables(agn::cloudy_grid grid,
 			x = result_it->first.first;
 			y = result_it->first.second;
 			std::string label = *line_label_it;
-			if ( result_it->second.emergent_line_intensity.count(label) == 0 ) {
+            // if no data exist under this label, initialize some:
+			if ( result_it->second.intrinsic_line_intensity.count(label) == 0 ) {
 				data.radiated_energy=-35.0;
 				data.eq_width=0.0;
 			}
 			else {
-				data = result_it->second.emergent_line_intensity[label];
+				data = result_it->second.intrinsic_line_intensity[label];
 				data.eq_width /= scale_factor;
 				if(agn::line_debug) std::cout
 					<< "Added  "