Merge branch '452-optimize-column-density-fails-for-molecules' into 'master'

Resolve "Optimize column density fails for molecules"

Closes #452

See merge request !32

docs/latex/hazy1/optimize.tex

@@ -181,13 +181,17 @@ to match.
 
 \subsection{Optimize column density}
 
-This specifies a set of column densities.
-A series of column densities,
+This specifies a set of column densities to be optimized.
+A series of species and constraints are read,
 ending with a line with the keyword \cdCommand{end} in columns 1 to 3,
 will be read
 in from subsequent lines.
-One column density is entered per line and there is no limit to
+One species is entered per line and there is no limit to
 the number of entries.
+
+The species can be specified in one of two ways:
+
+\cdTerm{Atomic ions:}
 Columns 1 to 4 of the column density lines must
 contain the first four characters of the name of the element spelled as
 in the output from the zone results.
@@ -211,34 +215,36 @@ silicon 3 14.6 # The Si+2 column density
 end of column densities
 \end{verbatim}
 
-\cdTerm{Molecular and level column densities:  how this command works:}
-The label
-and ion that are parsed from the lines giving the column densities
+\cdTerm{Molecular and level column densities:}
+The species is specified as a quoted, case-sensitive string, and no ionization
+stage is specified.  (This is different from previous
+versions of Cloudy, where the species did not need to be quoted, but
+only the first 4 characters were used, and an ionization stage
+of 0 had to be specified.)
+The species names which are parsed from the lines giving the column density
+constraints
 are simply
 passed to routine \cdTerm{cdColm}.
 That routine is described in Part 2 of \Hazy.
 This optimization command accepts any species that
 \cdTerm{cdColm} recognizes.
 Column densities of molecules and excited states of some ions
-can be specified by entering an ion stage of zero and one of the strings
-that is described where \cdTerm{cdColm} is described.
-The first four characters
-of the label given on the input line must agree with those listed there.
+can be specified by special syntax, and one of the cases
+that is described where \cdTerm{cdColm} is shown in the example below.
 
 The following shows some examples of optimizing molecular and state column
 densities:
 \begin{verbatim}
 optimize column densities
-H-   0  < 17 # The H- column density is a limit
-H2   0 17.4 error =.001 # Match the H_2 column density exactly
-H2+  0 14.6 # The H2+ molecular ion
-O11* 0  16.3 # This is an excited level within the O^0 ground term
+"H-"      < 17 # The H- column density is a limit
+"H2"      17.4 error =.001 # Match the total H_2 column density exactly
+"H2+"     14.6 # The H2+ molecular ion
+"O11*"    16.3 # This is an excited level within the O^0 ground term
+"He+[2]"  16.3 # This selects just one level from the He+ ion
+"CO[2]"   16.3 # This is a level in the CO molecule
+"CO[1:3]" 18.3 # This is the sum of levels 1,2,3 in the CO molecule
 end of column densities
 \end{verbatim}
-Note that extra spaces were placed after the labels for the molecules to
-pad out the needed four-character label.
-The ion, the first number after
-the four-character label, is always zero
 
 \subsection{Optimize, [intensity, luminosity]=36.425 [error =0.1]}
 

docs/latex/hazy2/TestSuite.tex

@@ -84,19 +84,25 @@ announce it.
 Table \ref{tab:AutoSimulationList} lists the simulations in the 
 \cdFilename{auto} test directory.
 
-\begin{table}
-\centering
-\caption{
-The simulations in the auto test suite.}
-\begin{tabular}{ c c  }
+%\begin{longtable}{>{\centering}p{0.2\textwidth}>{\centering}p{0.7\textwidth}}
+\begin{longtable}{cp{0.7\textwidth}}
+\caption{The simulations in the auto test suite.}\\
 \hline
-Class & Function \\
+Class & Function\\
 \hline
-\input{../../../tsuite/auto/doc_tsuite.txt}
+\endfirsthead
+\caption{(continued)}\\
 \hline
+Class & Function\\
+\hline
+\endhead
+\hline\multicolumn{2}{r}{\textit{Continued on next page}}
+\endfoot
+\hline
+\endlastfoot
+\input{../../../tsuite/auto/doc_tsuite.txt}
 \label{tab:AutoSimulationList}
-\end{tabular}
-\end{table}
+\end{longtable}
 
 \includepdf[pages=-]{../../../tsuite/auto/doc_tsuite.pdf}
 
@@ -105,19 +111,24 @@ Class & Function \\
 Table \ref{tab:SlowSimulationList} lists the simulations in the
 \cdFilename{slow} test directory.
 
-\begin{table}
-\centering
-\caption{
-The simulations in the slow test suite.}
-\begin{tabular}{ c c  }
+\begin{longtable}{cp{0.7\textwidth}}
+\caption{The simulations in the slow test suite.}\\
 \hline
-Class & Function \\
+Class & Function\\
 \hline
-\input{../../../tsuite/slow/doc_tsuite.txt}
+\endfirsthead
+\caption{(continued)}\\
 \hline
+Class & Function\\
+\hline
+\endhead
+\hline\multicolumn{2}{r}{\textit{Continued on next page}}
+\endfoot
+\hline
+\endlastfoot
+\input{../../../tsuite/slow/doc_tsuite.txt}
 \label{tab:SlowSimulationList}
-\end{tabular}
-\end{table}
+\end{longtable}
 
 \includepdf[pages=-]{../../../tsuite/slow/doc_tsuite.pdf}
 

docs/latex/head_info.tex

@@ -54,6 +54,11 @@ top=2.5cm,bottom=2.5cm]{geometry}
 
 % allow external files to be included verbatim
 \usepackage{moreverb}
+
+% allow tables to wrap over pages
+\usepackage{longtable}
+
+
 % set the default tabsize
 \def\verbatimtabsize{4\relax}
 

source/optimize_func.cpp

@@ -154,8 +154,18 @@ chi2_type optimize_func(const realnum param[],
 		cdWarnings(ioQQQ);
 
 		/* print header before any of the individual chi2 values are printed */
+		int wlab = 4;
+		for( i=0; i < long(optimize.chTempLab.size()); i++ )
+		{
+			wlab = max(wlab,optimize.chTempLab[i].size());
+		}
+		for( i=0; i < long(optimize.chColDen_label.size()); i++ )
+		{
+			wlab = max(wlab,optimize.chColDen_label[i].size());
+		}
 		if( optimize.lgOptimize )
-			fprintf( ioQQQ, "  ID                    Model       Observed    error      chi**2     Type\n" );
+			fprintf( ioQQQ, " %*.*s%7s%12.12s%12.12s%12.12s%12.12s Type\n",
+						wlab,wlab,"ID","","Model","Observed","error","chi**2");
 		else
 			ASSERT( grid.lgGrid );
 
@@ -251,7 +261,8 @@ chi2_type optimize_func(const realnum param[],
 			nobs_cat[cat]++;
 			chi2_cat[cat] += chi1;
 
-			fprintf( ioQQQ, " %4.4s%7ld%12.4e%12.4e%12.5f%12.2e Temperature\n",
+			fprintf( ioQQQ, " %*.*s%7ld%12.4e%12.4e%12.5f%12.2e Temperature\n",
+						wlab, wlab,
 				 optimize.chTempLab[i].c_str(), optimize.ionTemp[i], temp_theory,
 				 optimize.temp_obs[i], optimize.temp_error[i], chi1 );
 		}
@@ -272,8 +283,9 @@ chi2_type optimize_func(const realnum param[],
 			cat = 1;
 			nobs_cat[cat]++;
 			chi2_cat[cat] += chi1;
-
-			fprintf( ioQQQ, " %4.4s%7ld%12.4e%12.4e%12.5f%12.2e Column density\n", 
+			
+			fprintf( ioQQQ, " %*.*s%7ld%12.4e%12.4e%12.5f%12.2e Column density\n",
+						wlab,wlab,
 				 optimize.chColDen_label[i].c_str(), optimize.ion_ColDen[i], theocl, 
 				 optimize.ColDen_Obs[i], optimize.ColDen_error[i], chi1 );
 		}

source/parse_optimize.cpp

@@ -304,31 +304,48 @@ STATIC void GetOptColDen(Parser &p )
 
 	while( !p.m_lgEOF )
 	{
-		/* order on line is element label (col 1-4), ionization stage, column density, err */
-		/* copy cap'd version of first 4 char of chCard to chColDen_label */
-		optimize.chColDen_label.push_back(elementnames.chElementNameShort[p.getElement()]);
-
-		/* now get the ion stage, this should be 1 for atom, up to element
-		 * number plus one */
-		long ion = nint(p.FFmtRead());
-		if( p.lgEOL() )
+		string chLabel;
+		if ( p.GetQuote( chLabel ) == 0 )
 		{
-			p.PrintLine( ioQQQ );
-			fprintf( ioQQQ, " The ionization stage MUST appear on this line.  Sorry.\n" );
-			cdEXIT(EXIT_FAILURE);
+			// Read a quote-delimited string, which will be interpreted
+			// by cdColm as a generic species label.  It would be better
+			// to do the lookup earlier, to validate the input and save
+			// repeated effort.
+			
+			/* order on line is species, column density, err */
+			optimize.chColDen_label.push_back(chLabel);
+			optimize.ion_ColDen.push_back(0);
 		}
-
-		/* the ion must be 1 or greater unless requesting a special,
-		 * like a molecule or excited state population, in which
-		 * case ion = 0
-		 * can't check on upper limit yet since have not resolved element name */
-		if( ion < 0 )
+		else
 		{
-			p.PrintLine( ioQQQ );
-			fprintf( ioQQQ, " An ionization stage of %ld does not make sense.  Sorry.\n", ion );
-			cdEXIT(EXIT_FAILURE);
+			/* order on line is element name (at least 4 characters), ionization stage, column density, err */
+			/* copy cap'd version of first 4 char of chCard to chColDen_label */
+			// The other branch can handle also ions, with the 'chemical'
+			// syntax '"H+"' (in quotes), rather than 'HYDR 2' below
+			optimize.chColDen_label.push_back(elementnames.chElementNameShort[p.getElement()]);
+			
+			/* now get the ion stage, this should be 1 for atom, up to element
+			 * number plus one */
+			long ion = nint(p.FFmtRead());
+			if( p.lgEOL() )
+			{
+				p.PrintLine( ioQQQ );
+				fprintf( ioQQQ, " The ionization stage MUST appear on this line.  Sorry.\n" );
+				cdEXIT(EXIT_FAILURE);
+			}
+			
+			/* the ion must be 1 or greater unless requesting a special,
+			 * like a molecule or excited state population, in which
+			 * case ion = 0
+			 * can't check on upper limit yet since have not resolved element name */
+			if( ion < 0 )
+			{
+				p.PrintLine( ioQQQ );
+				fprintf( ioQQQ, " An ionization stage of %ld does not make sense.  Sorry.\n", ion );
+				cdEXIT(EXIT_FAILURE);
+			}
+			optimize.ion_ColDen.push_back(ion);
 		}
-		optimize.ion_ColDen.push_back(ion);
 
 		optimize.ColDen_Obs.push_back( realnum(exp10(p.FFmtRead())) );
 		if( p.lgEOL() )