changing geometry now seems to work

src/G4System.cc

@@ -38,10 +38,8 @@ void G4System::init(ConstructionWrapper &CW){
   //
   
   detConstruction = new B4::DetectorConstruction(&CW);
-
-  runManager->SetUserInitialization(detConstruction);
-
   if(first_init){
+     runManager->SetUserInitialization(detConstruction);
      auto physicsList = new FTFP_BERT;
      runManager->SetUserInitialization(physicsList);
 
@@ -52,7 +50,8 @@ void G4System::init(ConstructionWrapper &CW){
     actionInitialization->setDetectorConstruction(detConstruction);
 
     G4RunManager::GetRunManager()->GeometryHasBeenModified();
-    G4RunManager::GetRunManager()->ReinitializeGeometry();
+    G4RunManager::GetRunManager()->ReinitializeGeometry(true);
+    //runManager->SetUserInitialization(detConstruction);
   }
 
   if(visManager == nullptr){
@@ -134,6 +133,7 @@ void G4System::run_gui(){
 }
 
 void G4System::run_batch(int nEvents,const std::string& partSpecies, double minEnergy, double maxEnergy){
+  check();
     G4String partSpec = partSpecies;
     G4cout << "running with particle species " << partSpec << G4endl;
     UImanager->ApplyCommand("/run/initialize");