fixed bug in cmdsetreactionratemolcount

ssandrews · Feb 25, 2024 · 9bbb62a · 9bbb62a
1 parent bc392f2
commit 9bbb62a
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diff --git a/docs/Smoldyn/SmoldynCodeDoc.pdf b/docs/Smoldyn/SmoldynCodeDoc.pdf
diff --git a/docs/Smoldyn/SmoldynCodeDoc.tex b/docs/Smoldyn/SmoldynCodeDoc.tex
@@ -7062,9 +7062,10 @@ \subsection*{Modifications for version 2.72 (released 8/17/23)}
 
 \subsection*{Modifications for version 2.73 (not released yet)}
 \item Investigated diffusion coefficients in crowded systems. I now believe that the overlap method is better than the reflection method. This is discussed in the reactions chapter of the Smoldyn manual. I changed the default behavior to overlap method.
-\item Added a line to the CMake file. In the Python module section, edited a line to read \ttt{find\_package(Python3 3.10 EXACT COMPONENTS Interpreter Development REQUIRED)}, where the new portion is the Python 3.10 requirement. This prevents an error of \ttt{invalid command 'bdist\_wheel'} because it now uses the same Python version for everything.
+\item Added a line to the CMake file. In the Python module section, edited a line to read \ttt{find\_package(Python3 3.10 EXACT COMPONENTS Interpreter Development REQUIRED)}, where the new portion is the Python 3.10 requirement. This prevents an error of \ttt{invalid command 'bdist\_wheel'} because it now uses the same Python version for everything. ... This was reverted by someone. The below \ttt{PYTHON\_VERSION} update fixes this problem.
 \item Edited Smoldyn/source/pybind11/tests/requirements.txt to simplify the file and hopefully stop warnings from the gitHub dependabot.
-\item Added \ttt{SMOLDYN\_VERSION} as an option to the build, with new code in the master CMakeLists.txt file. Using this fixes the problem of building for one Python version and running a different one.
+\item Added \ttt{PYTHON\_VERSION} as an option to the build, with new code in the master CMakeLists.txt file. Using this fixes the problem of building for one Python version and running a different one.
+\item Fixed bug in cmdsetreactionratemolcount. It wasn't loading the species name correctly, leading to a non-functional command. I'm not sure why it wasn't caught earlier, but it wasn't.
 
 
 \end{itemize}

diff --git a/source/Smoldyn/smolcmd.c b/source/Smoldyn/smolcmd.c
@@ -4507,7 +4507,7 @@ enum CMDcode cmdsetreactionratemolcount(simptr sim,cmdptr cmd,char *line2) {
   while(line2) {
     itct=strmathsscanf(line2,"%mlg %s",Varnames,Varvalues,Nvar,&coeff,nm1);
     SCMDCHECK(itct==2,"missing coefficient and/or species parameters");
-		i=molstring2index1(sim,line2,&ms,&index);
+		i=molstring2index1(sim,nm1,&ms,&index);
 		SCMDCHECK(i!=-1,"species is missing or cannot be read");
 		SCMDCHECK(i!=-2,"mismatched or improper parentheses around molecule state");
 		SCMDCHECK(i!=-3,"cannot read molecule state value");