- fix compilation dont crash on null geometry

- command line should not require req, and just take gnuplot from path
fbergmann · Apr 14, 2021 · 198f995 · 198f995
1 parent e1323b2
commit 198f995
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Showing 2 changed files with 4 additions and 9 deletions.
diff --git a/SpatialCL/main.cpp b/SpatialCL/main.cpp
@@ -46,18 +46,13 @@ int main(int argc, const char *argv[])
 
   cout << "SpatialPlugin: " << (doc->getModel()->getPlugin("spatial") != NULL ? "not null": "null") <<endl;
   cout << "spatial required: "<< (doc->getPkgRequired("spatial") ? "yes": "no") << endl;
-  cout << "req required: "<< (doc->getPkgRequired("req") ? "yes": "no") << endl;
 
   if (doc->getModel()->getPlugin("spatial") != NULL && 
-    doc->getPkgRequired("spatial") && 
-    doc->getPkgRequired("req")) {
+    doc->getPkgRequired("spatial")) {
       // probably a spatial simulation 
       SpatialSimulator sim(doc, 101, 101);
-#ifdef WIN32
-      sim.setGnuplotExecutable("C:/gnuplot/bin/gnuplot.exe");
-#else
+      // just pick gnuplot from the path
       sim.setGnuplotExecutable("gnuplot");
-#endif
       sim.run(1001, 0.01);
       //spatialSimulator(doc, argc, argv);
   } 

diff --git a/SpatialSBML/spatialsimulator.cpp b/SpatialSBML/spatialsimulator.cpp
@@ -500,7 +500,7 @@ void SpatialSimulator::initFromModel(SBMLDocument* doc, int xdim, int ydim, int
             }
             if (samVol == NULL) continue;
             unsigned int  uncomprLen = samField->getUncompressedLength();
-            int *uncompr = (int*)calloc(sizeof(int), uncomprLen);
+            double *uncompr = (double*)calloc(sizeof(double), uncomprLen);
             samField->getUncompressed(uncompr);
 
             GeometryInfo *geoInfo = new GeometryInfo;
@@ -1463,7 +1463,7 @@ void SpatialSimulator::performStep(double t, double dt)
     //diffusion
     for (size_t i = 0; i < numOfSpecies; ++i) {
       variableInfo *sInfo = searchInfoById(varInfoList, los->get(i)->getId().c_str());
-      if (sInfo == NULL) continue;
+      if (sInfo == NULL || sInfo->geoi == NULL) continue;
       //volume diffusion
       if (sInfo->diffCInfo != 0 && sInfo->geoi->isVol) {
         calcDiffusion(sInfo, deltaX, deltaY, deltaZ, Xindex, Yindex, Zindex, m, dt, dimension);