Merge pull request #2122 from peastman/updatetable

Added CustomCVForce.updateParametersInContext()

olla/include/openmm/kernels.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2018 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -980,6 +980,13 @@ public:
      * @param innerContext   the context created by the CustomCVForce for computing collective variables
      */
     virtual void copyState(ContextImpl& context, ContextImpl& innerContext) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CustomCVForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CustomCVForce& force) = 0;
 };
 
 /**

openmmapi/include/openmm/CustomCVForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2017 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2018 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -255,6 +255,17 @@ public:
      * @return the inner Context used to evaluate the collective variables
      */
     Context& getInnerContext(Context& context);
+    /**
+     * Update the tabulated function parameters in a Context to match those stored in this Force object.  This method
+     * provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call getTabulatedFunction(index).setFunctionParameters() to modify this object's parameters, then call
+     * updateParametersInContext() to copy them over to the Context.
+     *
+     * This method is very limited.  The only information it updates is the parameters of tabulated functions.
+     * All other aspects of the Force (the energy expression, the set of collective variables, etc.) are unaffected and can
+     * only be changed by reinitializing the Context.
+     */
+    void updateParametersInContext(Context& context);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.

openmmapi/include/openmm/internal/CustomCVForceImpl.h

@@ -64,6 +64,7 @@ public:
     std::vector<std::string> getKernelNames();
     void getCollectiveVariableValues(ContextImpl& context, std::vector<double>& values);
     Context& getInnerContext();
+    void updateParametersInContext(ContextImpl& context);
 private:
     const CustomCVForce& owner;
     Kernel kernel;

openmmapi/src/CustomCVForce.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) 2008-2017 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2018 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -152,6 +152,10 @@ Context& CustomCVForce::getInnerContext(Context& context) {
     return dynamic_cast<CustomCVForceImpl&>(getImplInContext(context)).getInnerContext();
 }
 
+void CustomCVForce::updateParametersInContext(Context& context) {
+    dynamic_cast<CustomCVForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+}
+
 bool CustomCVForce::usesPeriodicBoundaryConditions() const {
     for (auto& variable : variables)
         if (variable.variable->usesPeriodicBoundaryConditions())

openmmapi/src/CustomCVForceImpl.cpp

@@ -111,3 +111,8 @@ void CustomCVForceImpl::getCollectiveVariableValues(ContextImpl& context, vector
 Context& CustomCVForceImpl::getInnerContext() {
     return *innerContext;
 }
+
+void CustomCVForceImpl::updateParametersInContext(ContextImpl& context) {
+    kernel.getAs<CalcCustomCVForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
+}

platforms/cuda/include/CudaKernels.h

@@ -1259,10 +1259,19 @@ public:
      * @param innerContext   the context created by the CustomCVForce for computing collective variables
      */
     void copyState(ContextImpl& context, ContextImpl& innerContext);
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CustomCVForce to copy the parameters from
+     */
+    void copyParametersToContext(ContextImpl& context, const CustomCVForce& force);
 private:
     class ReorderListener;
+    void rebuildExpressions(const OpenMM::CustomCVForce& force);
     CudaContext& cu;
     bool hasInitializedListeners;
+    std::string energyExpressionText;
     Lepton::ExpressionProgram energyExpression;
     std::vector<std::string> variableNames, paramDerivNames, globalParameterNames;
     std::vector<Lepton::ExpressionProgram> variableDerivExpressions;

platforms/cuda/src/CudaKernels.cpp

@@ -6588,33 +6588,15 @@ void CudaCalcCustomCVForceKernel::initialize(const System& system, const CustomC
     int numCVs = force.getNumCollectiveVariables();
     for (int i = 0; i < force.getNumGlobalParameters(); i++)
         globalParameterNames.push_back(force.getGlobalParameterName(i));
-    
-    // Create custom functions for the tabulated functions.
-
-    map<string, Lepton::CustomFunction*> functions;
-    for (int i = 0; i < (int) force.getNumTabulatedFunctions(); i++)
-        functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
-
-    // Create the expressions.
-
-    Lepton::ParsedExpression energyExpr = Lepton::Parser::parse(force.getEnergyFunction(), functions);
-    energyExpression = energyExpr.createProgram();
-    for (int i = 0; i < numCVs; i++) {
-        string name = force.getCollectiveVariableName(i);
-        variableNames.push_back(name);
-        variableDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
-    }
+    energyExpressionText = force.getEnergyFunction();
+    for (int i = 0; i < numCVs; i++)
+        variableNames.push_back(force.getCollectiveVariableName(i));
     for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
         string name = force.getEnergyParameterDerivativeName(i);
         paramDerivNames.push_back(name);
-        paramDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
         cu.addEnergyParameterDerivative(name);
     }
-
-    // Delete the custom functions.
-
-    for (auto& function : functions)
-        delete function.second;
+    rebuildExpressions(force);
         
     // Copy parameter derivatives from the inner context.
 
@@ -6730,6 +6712,34 @@ void CudaCalcCustomCVForceKernel::copyState(ContextImpl& context, ContextImpl& i
         innerContext.setParameter(param.first, context.getParameter(param.first));
 }
 
+void CudaCalcCustomCVForceKernel::copyParametersToContext(ContextImpl& context, const CustomCVForce& force) {
+    rebuildExpressions(force);
+}
+
+void CudaCalcCustomCVForceKernel::rebuildExpressions(const OpenMM::CustomCVForce& force) {
+    // Create custom functions for the tabulated functions.
+
+    map<string, Lepton::CustomFunction*> functions;
+    for (int i = 0; i < (int) force.getNumTabulatedFunctions(); i++)
+        functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
+
+    // Create the expressions.
+
+    Lepton::ParsedExpression energyExpr = Lepton::Parser::parse(energyExpressionText, functions);
+    energyExpression = energyExpr.createProgram();
+    variableDerivExpressions.clear();
+    for (auto& name : variableNames)
+        variableDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
+    paramDerivExpressions.clear();
+    for (auto& name : paramDerivNames)
+        paramDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
+
+    // Delete the custom functions.
+
+    for (auto& function : functions)
+        delete function.second;
+}
+
 class CudaCalcRMSDForceKernel::ForceInfo : public CudaForceInfo {
 public:
     ForceInfo(const RMSDForce& force) : force(force) {

platforms/opencl/include/OpenCLKernels.h

@@ -1235,10 +1235,19 @@ public:
      * @param innerContext   the context created by the CustomCVForce for computing collective variables
      */
     void copyState(ContextImpl& context, ContextImpl& innerContext);
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CustomCVForce to copy the parameters from
+     */
+    void copyParametersToContext(ContextImpl& context, const CustomCVForce& force);
 private:
     class ReorderListener;
+    void rebuildExpressions(const OpenMM::CustomCVForce& force);
     OpenCLContext& cl;
     bool hasInitializedKernels;
+    std::string energyExpressionText;
     Lepton::ExpressionProgram energyExpression;
     std::vector<std::string> variableNames, paramDerivNames, globalParameterNames;
     std::vector<Lepton::ExpressionProgram> variableDerivExpressions;

platforms/opencl/src/OpenCLKernels.cpp

@@ -6865,33 +6865,15 @@ void OpenCLCalcCustomCVForceKernel::initialize(const System& system, const Custo
     cl.addForce(new OpenCLForceInfo(1));
     for (int i = 0; i < force.getNumGlobalParameters(); i++)
         globalParameterNames.push_back(force.getGlobalParameterName(i));
-    
-    // Create custom functions for the tabulated functions.
-
-    map<string, Lepton::CustomFunction*> functions;
-    for (int i = 0; i < (int) force.getNumTabulatedFunctions(); i++)
-        functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
-
-    // Create the expressions.
-
-    Lepton::ParsedExpression energyExpr = Lepton::Parser::parse(force.getEnergyFunction(), functions);
-    energyExpression = energyExpr.createProgram();
-    for (int i = 0; i < numCVs; i++) {
-        string name = force.getCollectiveVariableName(i);
-        variableNames.push_back(name);
-        variableDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
-    }
+    energyExpressionText = force.getEnergyFunction();
+    for (int i = 0; i < numCVs; i++)
+        variableNames.push_back(force.getCollectiveVariableName(i));
     for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
         string name = force.getEnergyParameterDerivativeName(i);
         paramDerivNames.push_back(name);
-        paramDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
         cl.addEnergyParameterDerivative(name);
     }
-
-    // Delete the custom functions.
-
-    for (auto& function : functions)
-        delete function.second;
+    rebuildExpressions(force);
             
     // Copy parameter derivatives from the inner context.
 
@@ -7021,6 +7003,34 @@ void OpenCLCalcCustomCVForceKernel::copyState(ContextImpl& context, ContextImpl&
         innerContext.setParameter(param.first, context.getParameter(param.first));
 }
 
+void OpenCLCalcCustomCVForceKernel::copyParametersToContext(ContextImpl& context, const CustomCVForce& force) {
+    rebuildExpressions(force);
+}
+
+void OpenCLCalcCustomCVForceKernel::rebuildExpressions(const OpenMM::CustomCVForce& force) {
+    // Create custom functions for the tabulated functions.
+
+    map<string, Lepton::CustomFunction*> functions;
+    for (int i = 0; i < (int) force.getNumTabulatedFunctions(); i++)
+        functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
+
+    // Create the expressions.
+
+    Lepton::ParsedExpression energyExpr = Lepton::Parser::parse(energyExpressionText, functions);
+    energyExpression = energyExpr.createProgram();
+    variableDerivExpressions.clear();
+    for (auto& name : variableNames)
+        variableDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
+    paramDerivExpressions.clear();
+    for (auto& name : paramDerivNames)
+        paramDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
+
+    // Delete the custom functions.
+
+    for (auto& function : functions)
+        delete function.second;
+}
+
 class OpenCLCalcRMSDForceKernel::ForceInfo : public OpenCLForceInfo {
 public:
     ForceInfo(const RMSDForce& force) : OpenCLForceInfo(0), force(force) {

platforms/reference/include/ReferenceCustomCVForce.h

@@ -36,6 +36,7 @@ namespace OpenMM {
 
 class ReferenceCustomCVForce {
 private:
+    std::string energyExpressionText;
     Lepton::ExpressionProgram energyExpression;
     std::vector<std::string> variableNames, paramDerivNames;
     std::vector<Lepton::ExpressionProgram> variableDerivExpressions;
@@ -52,6 +53,13 @@ public:
      */
     ~ReferenceCustomCVForce();
 
+    /**
+     * Create the ExpressionPrograms.  This is called automatically when the object is
+     * created.  It can be called again to rebuild them if the user calls
+     * updateParametersInContext().
+     */
+    void rebuildExpressions(const OpenMM::CustomCVForce& force);
+
     /**
      * Calculate the interaction.
      * 

platforms/reference/include/ReferenceKernels.h

@@ -1037,6 +1037,13 @@ public:
      * @param innerContext   the context created by the CustomCVForce for computing collective variables
      */
     void copyState(ContextImpl& context, ContextImpl& innerContext);
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CustomCVForce to copy the parameters from
+     */
+    void copyParametersToContext(ContextImpl& context, const CustomCVForce& force);
 private:
     ReferenceCustomCVForce* ixn;
     std::vector<std::string> globalParameterNames, energyParamDerivNames;

platforms/reference/src/ReferenceKernels.cpp

@@ -1993,6 +1993,10 @@ void ReferenceCalcCustomCVForceKernel::copyState(ContextImpl& context, ContextIm
         innerContext.setParameter(param.first, context.getParameter(param.first));
 }
 
+void ReferenceCalcCustomCVForceKernel::copyParametersToContext(ContextImpl& context, const CustomCVForce& force) {
+    ixn->rebuildExpressions(force);
+}
+
 void ReferenceCalcRMSDForceKernel::initialize(const System& system, const RMSDForce& force) {
     particles = force.getParticles();
     if (particles.size() == 0)

platforms/reference/src/SimTKReference/ReferenceCustomCVForce.cpp

@@ -33,6 +33,15 @@ using namespace OpenMM;
 using namespace std;
 
 ReferenceCustomCVForce::ReferenceCustomCVForce(const CustomCVForce& force) {
+    energyExpressionText = force.getEnergyFunction();
+    for (int i = 0; i < force.getNumCollectiveVariables(); i++)
+        variableNames.push_back(force.getCollectiveVariableName(i));
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        paramDerivNames.push_back(force.getEnergyParameterDerivativeName(i));
+    rebuildExpressions(force);
+}
+
+void ReferenceCustomCVForce::rebuildExpressions(const OpenMM::CustomCVForce& force) {
     // Create custom functions for the tabulated functions.
 
     map<string, Lepton::CustomFunction*> functions;
@@ -41,18 +50,14 @@ ReferenceCustomCVForce::ReferenceCustomCVForce(const CustomCVForce& force) {
 
     // Create the expressions.
 
-    Lepton::ParsedExpression energyExpr = Lepton::Parser::parse(force.getEnergyFunction(), functions);
+    Lepton::ParsedExpression energyExpr = Lepton::Parser::parse(energyExpressionText, functions);
     energyExpression = energyExpr.createProgram();
-    for (int i = 0; i < force.getNumCollectiveVariables(); i++) {
-        string name = force.getCollectiveVariableName(i);
-        variableNames.push_back(name);
+    variableDerivExpressions.clear();
+    for (auto& name : variableNames)
         variableDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
-    }
-    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
-        string name = force.getEnergyParameterDerivativeName(i);
-        paramDerivNames.push_back(name);
+    paramDerivExpressions.clear();
+    for (auto& name : paramDerivNames)
         paramDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
-    }
 
     // Delete the custom functions.
 

tests/TestCustomCVForce.h

@@ -159,6 +159,8 @@ void testTabulatedFunction() {
     system.addForce(cv);
     Context context(system, integrator, platform);
     vector<Vec3> positions(1);
+    double scale = 1.0;
+    for (int i = 0; i < 2; i++) {
         for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
             for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
                 positions[0] = Vec3(x, y, 1.5);
@@ -168,14 +170,24 @@ void testTabulatedFunction() {
                 double energy = 1;
                 Vec3 force(0, 0, 0);
                 if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
-                energy = sin(0.25*x)*cos(0.33*y)+1;
-                force[0] = -0.25*cos(0.25*x)*cos(0.33*y);
-                force[1] = 0.3*sin(0.25*x)*sin(0.33*y);
+                    energy = scale*sin(0.25*x)*cos(0.33*y)+1;
+                    force[0] = -scale*0.25*cos(0.25*x)*cos(0.33*y);
+                    force[1] = scale*0.3*sin(0.25*x)*sin(0.33*y);
                 }
                 ASSERT_EQUAL_VEC(force, forces[0], 0.1);
                 ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
             }
         }
+        
+        // Now update the tabulated function, call updateParametersInContext(),
+        // and see if it's still correct.
+        
+        for (int i = 0; i < table.size(); i++)
+            table[i] *= 2;
+        dynamic_cast<Continuous2DFunction&>(cv->getTabulatedFunction(0)).setFunctionParameters(xsize, ysize, table, xmin, xmax, ymin, ymax);
+        cv->updateParametersInContext(context);
+        scale *= 2.0;
+    }
 }
 
 void testReordering() {