CustomIntegrator throws an exception if variable names are ambiguous

openmmapi/src/CustomIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2011-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,11 +36,11 @@
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/internal/OSRngSeed.h"
 #include "openmm/kernels.h"
+#include <set>
 #include <string>
 
 using namespace OpenMM;
-using std::string;
-using std::vector;
+using namespace std;
 
 CustomIntegrator::CustomIntegrator(double stepSize) : globalsAreCurrent(true), forcesAreValid(false) {
     setStepSize(stepSize);
@@ -52,6 +52,18 @@ CustomIntegrator::CustomIntegrator(double stepSize) : globalsAreCurrent(true), f
 void CustomIntegrator::initialize(ContextImpl& contextRef) {
     if (owner != NULL && &contextRef.getOwner() != owner)
         throw OpenMMException("This Integrator is already bound to a context");
+    vector<std::string> variableList;
+    set<std::string> variableSet;
+    variableList.insert(variableList.end(), globalNames.begin(), globalNames.end());
+    variableList.insert(variableList.end(), perDofNames.begin(), perDofNames.end());
+    for (int i = 0; i < (int) variableList.size(); i++) {
+        string& name = variableList[i];
+        if (variableSet.find(name) != variableSet.end())
+            throw OpenMMException("The Integrator defines two variables with the same name: "+name);
+        variableSet.insert(name);
+        if (contextRef.getParameters().find(name) != contextRef.getParameters().end())
+            throw OpenMMException("The Integrator defines a variable with the same name as a Context parameter: "+name);
+    }
     context = &contextRef;
     owner = &contextRef.getOwner();
     kernel = context->getPlatform().createKernel(IntegrateCustomStepKernel::Name(), contextRef);