From b58d187c904b484994c201c85e8b7519546bd5bc Mon Sep 17 00:00:00 2001
From: caes <caes>
Date: Tue, 11 Jul 2017 05:53:30 -0400
Subject: [PATCH] update

---
 reference/linelist.c17 | 13 +++++++------
 src/agn.hpp            | 15 +++++++++++++++
 src/spectral_lines.hpp | 14 ++++++++++----
 3 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/reference/linelist.c17 b/reference/linelist.c17
index 9ac68bf..7e8561d 100644
--- a/reference/linelist.c17
+++ b/reference/linelist.c17
@@ -157,11 +157,12 @@ C  2      2326.93A      Stout, 2 4
 
 Blnd      1335.00A      Blend: "C  2      1334.53A"+"C  2      1335.66A"+"C  2      1335.71A"+"C 2R      1335.00A"
 # no inwd
-#C  2      1334.53A      Stout, 1 7
-#C  2      1335.66A      Stout, 2 7
-#C  2      1335.71A      Stout, 2 6
+C  2      1334.53A      Stout, 1 7
+C  2      1335.66A      Stout, 2 7
+C  2      1335.71A      Stout, 2 6
 
 Blnd      977.000A      Blend: "C  3      977.020A"+"C 3R      977.000A"
+# no inwd
 C  3      977.020A      Stout, 1 5
 
 Blnd      1909.00A      Blend: "C  3      1908.73A"+"C  3      1906.68A"+"C 3R      1909.00A"+"C 3H      1909.00A"
@@ -236,9 +237,9 @@ O  1      1306.03A
 
 Blnd      8446.00A              Blend: "O  1      8446.25A"+"O  1      8446.36A"+"O  1      8446.76A"
 # no inwd
-#O  1      8446.25A
-#O  1      8446.36A
-#O  1      8446.76A
+O  1      8446.25A
+O  1      8446.36A
+O  1      8446.76A
 
 Blnd      1666.00A              Blend: "O  3      1666.15A"+"O  3      1660.81A"+"O 3H      1665.00A"+"O 3A      1665.00A"
 # no inwd
diff --git a/src/agn.hpp b/src/agn.hpp
index 6881a38..0523688 100644
--- a/src/agn.hpp
+++ b/src/agn.hpp
@@ -281,22 +281,37 @@ agn::cloudy_grid agn::read_cloudy_grid(std::ifstream& inputfile) {
 	agn::gridcoordlist::iterator coords = coordlist.begin();
 
 	while(grid.size() < coordlist.size()) {
+		bool failmode = false;
 		agn::cloudy_result point;
 		point.hden = coords->first;
 		point.phi = coords->second;
 		seek_string = "Intrinsic line intensities";
+		std::string fail_string = "PROBLEM DISASTER";
 		if(agn::debug) std::cout
 			<< "Grabbing header and cautions.";
 		std::string header="";
 		std::list<std::string> cautions;
 		while (inputline.find(seek_string) == std::string::npos) {
 			getline(inputfile,inputline);
+			if (inputline.find(fail_string) != std::string::npos) {
+				if(agn::debug) std::cout
+					<< " Found broken model.";
+				failmode = true;
+				break;
+			}
 			header.append(inputline);
 			header.append("\n");
 			if((inputline[1] == 'C' && inputline[2] == '-')
 					|| (inputline[1] == ' ' && inputline[2] == '!' ))
 				cautions.push_back(inputline);
 		}
+		if (failmode) {
+			grid[*coords] = point;
+			coords++;
+			//agn::seek_to("c ======================",inputfile);
+			//agn::seek_to("c ======================",inputfile);
+			continue; 
+		}
 		point.header = header;
 		point.cautions = cautions;
 		std::stringstream headerstr;
diff --git a/src/spectral_lines.hpp b/src/spectral_lines.hpp
index 908c389..d5e07df 100644
--- a/src/spectral_lines.hpp
+++ b/src/spectral_lines.hpp
@@ -283,6 +283,9 @@ std::ostream& agn::operator<< ( std::ostream& outstream,
 
 agn::line_list agn::read_line_list(std::ifstream& inputfile) {
 	line_list list;
+    line_list nfnulist;
+    line_list inwtlist;
+    line_list inwclist;
 	inputfile.clear();
 	inputfile.seekg(0);
 	std::string line,label;
@@ -301,16 +304,19 @@ agn::line_list agn::read_line_list(std::ifstream& inputfile) {
 			<< " to capture list.\n";
         std::string applabel = label.substr(4);
         if (label.substr(0,4).compare(std::string("nFnu")) == 0) {
-            list.push_back(std::string("nFnu").append(applabel));
+            nfnulist.push_back(std::string("nFnu").append(applabel));
             //list.push_back(std::string("nInu").append(applabel));
-            list.push_back(std::string("InwT").append(applabel));
-            list.push_back(std::string("InwC").append(applabel));
+            inwtlist.push_back(std::string("InwT").append(applabel));
+            inwclist.push_back(std::string("InwC").append(applabel));
             continue;
         }
 		list.push_back(label);
         //if (label.substr(0,4) != "Inci" && applabel != "            0 ")
         //    list.push_back(std::string("Inwd").append(applabel));
 	}
+    list.insert(list.end(),nfnulist.begin(),nfnulist.end());
+    list.insert(list.end(),inwtlist.begin(),inwtlist.end());
+    list.insert(list.end(),inwclist.begin(),inwclist.end());
 	return list;
 }
 
@@ -388,7 +394,7 @@ std::list<agn::eqwidth_table> agn::compile_eqwidth_tables(agn::cloudy_grid grid,
                 label == "Blnd      2326.00A" ||
                 label == "Blnd      2798.00A" ||
                 label == "Blnd      1335.00A" ||
-                label == "C  3      977.000A" ||
+                label == "Blnd      977.000A" ||
                 label == "Blnd      1909.00A" ||
                 label == "Blnd      1176.00A" ||
                 label == "Blnd      2141.00A" ||