Beginnings of support for derivatives with respect to parameters

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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -172,6 +172,12 @@ public:
      * @param forces  on exit, this contains the forces
      */
     virtual void getForces(ContextImpl& context, std::vector<Vec3>& forces) = 0;
+    /**
+     * Get the current derivatives of the energy with respect to context parameters.
+     *
+     * @param derivs  on exit, this contains the derivatives
+     */
+    virtual void getEnergyParameterDerivatives(ContextImpl& context, std::map<std::string, double>& derivs) = 0;
     /**
      * Get the current periodic box vectors.
      *

openmmapi/include/openmm/CustomBondForce.h

@@ -64,6 +64,10 @@ namespace OpenMM {
  * force->addPerBondParameter("r0");
  * </pre></tt>
  * 
+ * This class also has the ability to compute derivatives of the potential energy with respect to global parameters.
+ * Call addEnergyParameterDerivative() to request that the derivative with respect to a particular parameter be
+ * computed.  You can then query its value in a Context by calling getState() on it.
+ *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
  * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
@@ -97,6 +101,13 @@ public:
     int getNumGlobalParameters() const {
         return globalParameters.size();
     }
+    /**
+     * Get the number of global parameters with respect to which the derivative of the energy
+     * should be computed.
+     */
+    int getNumEnergyParameterDerivatives() const {
+        return energyParameterDerivatives.size();
+    }
     /**
      * Get the algebraic expression that gives the interaction energy for each bond
      */
@@ -162,6 +173,21 @@ public:
      * @param defaultValue   the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
+    /**
+     * Request that this Force compute the derivative of its energy with respect to a global parameter.
+     * The parameter must have already been added with addGlobalParameter().
+     *
+     * @param name             the name of the parameter
+     */
+    void addEnergyParameterDerivative(const std::string& name);
+    /**
+     * Get the name of a global parameter with respect to which this Force should compute the
+     * derivative of the energy.
+     *
+     * @param index     the index of the parameter derivative, between 0 and getNumEnergyParameterDerivatives()
+     * @return the parameter name
+     */
+    const std::string& getEnergyParameterDerivativeName(int index) const;
     /**
      * Add a bond term to the force field.
      *
@@ -222,6 +248,7 @@ private:
     std::vector<BondParameterInfo> parameters;
     std::vector<GlobalParameterInfo> globalParameters;
     std::vector<BondInfo> bonds;
+    std::vector<int> energyParameterDerivatives;
     bool usePeriodic;
 };
 

openmmapi/include/openmm/State.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -58,7 +58,7 @@ public:
      * This is an enumeration of the types of data which may be stored in a State.  When you create
      * a State, use these values to specify which data types it should contain.
      */
-    enum DataType {Positions=1, Velocities=2, Forces=4, Energy=8, Parameters=16};
+    enum DataType {Positions=1, Velocities=2, Forces=4, Energy=8, Parameters=16, ParameterDerivatives=32};
     /**
      * Construct an empty State containing no data.  This exists so State objects can be used in STL containers.
      */
@@ -108,6 +108,17 @@ public:
      * Get a map containing the values of all parameters.  If this State does not contain parameters, this will throw an exception.
      */
     const std::map<std::string, double>& getParameters() const;
+    /**
+     * Get a map containing derivatives of the potential energy with respect to context parameters.
+     * In most cases derivatives are only calculated if the corresponding Force objects have been
+     * specifically told to compute them.  Otherwise, the values in the map will be zero.  Likewise,
+     * if multiple Forces depend on the same parameter but only some have been told to compute
+     * derivatives with respect to it, the returned value will include only the contributions from
+     * the Forces that were told to compute it.
+     * 
+     * If this State does not contain parameter derivatives, this will throw an exception.
+     */
+    const std::map<std::string, double>& getEnergyParameterDerivatives() const;
     /**
      * Get which data types are stored in this State.  The return value is a sum of DataType flags.
      */
@@ -118,6 +129,7 @@ private:
     void setVelocities(const std::vector<Vec3>& vel);
     void setForces(const std::vector<Vec3>& force);
     void setParameters(const std::map<std::string, double>& params);
+    void setEnergyParameterDerivatives(const std::map<std::string, double>& derivs);
     void setEnergy(double ke, double pe);
     void setPeriodicBoxVectors(const Vec3& a, const Vec3& b, const Vec3& c);
     int types;
@@ -126,7 +138,7 @@ private:
     std::vector<Vec3> velocities;
     std::vector<Vec3> forces;
     Vec3 periodicBoxVectors[3];
-    std::map<std::string, double> parameters;
+    std::map<std::string, double> parameters, energyParameterDerivatives;
 };
 
 /**
@@ -142,6 +154,7 @@ public:
     void setVelocities(const std::vector<Vec3>& vel);
     void setForces(const std::vector<Vec3>& force);
     void setParameters(const std::map<std::string, double>& params);
+    void setEnergyParameterDerivatives(const std::map<std::string, double>& params);
     void setEnergy(double ke, double pe);
     void setPeriodicBoxVectors(const Vec3& a, const Vec3& b, const Vec3& c);
 private:

openmmapi/include/openmm/internal/ContextImpl.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) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -138,6 +138,10 @@ public:
      * @param value the value of the parameter
      */
     void setParameter(std::string name, double value);
+    /**
+     * Get the derivatives of the energy with respect to parameters.
+     */
+    void getEnergyParameterDerivatives(std::map<std::string, double>& derivs);
     /**
      * Get the vectors defining the axes of the periodic box (measured in nm).  They will affect
      * any Force that uses periodic boundary conditions.

openmmapi/src/Context.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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -84,8 +84,9 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
     builder.setPeriodicBoxVectors(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2]);
     bool includeForces = types&State::Forces;
     bool includeEnergy = types&State::Energy;
-    if (includeForces || includeEnergy) {
-        double energy = impl->calcForcesAndEnergy(includeForces || includeEnergy, includeEnergy, groups);
+    bool includeParameterDerivs = types&State::ParameterDerivatives;
+    if (includeForces || includeEnergy || includeParameterDerivs) {
+        double energy = impl->calcForcesAndEnergy(includeForces || includeEnergy || includeParameterDerivs, includeEnergy, groups);
         if (includeEnergy)
             builder.setEnergy(impl->calcKineticEnergy(), energy);
         if (includeForces) {
@@ -100,6 +101,11 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
             params[iter->first] = iter->second;
         builder.setParameters(params);
     }
+    if (types&State::ParameterDerivatives) {
+        map<string, double> derivs;
+        impl->getEnergyParameterDerivatives(derivs);
+        builder.setEnergyParameterDerivatives(derivs);
+    }
     if (types&State::Positions) {
         vector<Vec3> positions;
         impl->getPositions(positions);

openmmapi/src/ContextImpl.cpp

@@ -240,6 +240,10 @@ void ContextImpl::setParameter(std::string name, double value) {
     integrator.stateChanged(State::Parameters);
 }
 
+void ContextImpl::getEnergyParameterDerivatives(std::map<std::string, double>& derivs) {
+    updateStateDataKernel.getAs<UpdateStateDataKernel>().getEnergyParameterDerivatives(*this, derivs);
+}
+
 void ContextImpl::getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) {
     updateStateDataKernel.getAs<UpdateStateDataKernel>().getPeriodicBoxVectors(*this, a, b, c);
 }

openmmapi/src/CustomBondForce.cpp

@@ -95,6 +95,20 @@ void CustomBondForce::setGlobalParameterDefaultValue(int index, double defaultVa
     globalParameters[index].defaultValue = defaultValue;
 }
 
+void CustomBondForce::addEnergyParameterDerivative(const string& name) {
+    for (int i = 0; i < globalParameters.size(); i++)
+        if (name == globalParameters[i].name) {
+            energyParameterDerivatives.push_back(i);
+            return;
+        }
+    throw OpenMMException(string("addEnergyParameterDerivative: Unknown global parameter '"+name+"'"));
+}
+
+const string& CustomBondForce::getEnergyParameterDerivativeName(int index) const {
+    ASSERT_VALID_INDEX(index, energyParameterDerivatives);
+    return globalParameters[energyParameterDerivatives[index]].name;
+}
+
 int CustomBondForce::addBond(int particle1, int particle2, const vector<double>& parameters) {
     bonds.push_back(BondInfo(particle1, particle2, parameters));
     return bonds.size()-1;

openmmapi/src/State.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -76,6 +76,11 @@ const map<string, double>& State::getParameters() const {
         throw OpenMMException("Invoked getParameters() on a State which does not contain parameters.");
     return parameters;
 }
+const map<string, double>& State::getEnergyParameterDerivatives() const {
+    if ((types&ParameterDerivatives) == 0)
+        throw OpenMMException("Invoked getEnergyParameterDerivatives() on a State which does not contain parameter derivatives.");
+    return energyParameterDerivatives;
+}
 int State::getDataTypes() const {
     return types;
 }
@@ -103,6 +108,11 @@ void State::setParameters(const std::map<std::string, double>& params) {
     types |= Parameters;
 }
 
+void State::setEnergyParameterDerivatives(const std::map<std::string, double>& derivs) {
+    energyParameterDerivatives = derivs;
+    types |= ParameterDerivatives;
+}
+
 void State::setEnergy(double kinetic, double potential) {
     ke = kinetic;
     pe = potential;
@@ -138,6 +148,10 @@ void State::StateBuilder::setParameters(const std::map<std::string, double>& par
     state.setParameters(params);
 }
 
+void State::StateBuilder::setEnergyParameterDerivatives(const std::map<std::string, double>& derivs) {
+    state.setEnergyParameterDerivatives(derivs);
+}
+
 void State::StateBuilder::setEnergy(double ke, double pe) {
     state.setEnergy(ke, pe);
 }

platforms/cpu/src/CpuBondForce.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) 2014 Stanford University and the Authors.           *
+ * Portions copyright (c) 2014-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -196,7 +196,7 @@ void CpuBondForce::calculateForce(vector<RealVec>& atomCoordinates, RealOpenMM**
     
     for (int i = 0; i < extraBonds.size(); i++) {
         int bond = extraBonds[i];
-        referenceBondIxn.calculateBondIxn(bondAtoms[bond], atomCoordinates, parameters[bond], forces, totalEnergy);
+        referenceBondIxn.calculateBondIxn(bondAtoms[bond], atomCoordinates, parameters[bond], forces, totalEnergy, NULL);
     }
 
     // Compute the total energy.
@@ -212,6 +212,6 @@ void CpuBondForce::threadComputeForce(ThreadPool& threads, int threadIndex, vect
     int numBonds = bonds.size();
     for (int i = 0; i < numBonds; i++) {
         int bond = bonds[i];
-        referenceBondIxn.calculateBondIxn(bondAtoms[bond], atomCoordinates, parameters[bond], forces, totalEnergy);
+        referenceBondIxn.calculateBondIxn(bondAtoms[bond], atomCoordinates, parameters[bond], forces, totalEnergy, NULL);
     }
 }
\ No newline at end of file

platforms/cuda/include/CudaKernels.h

@@ -163,6 +163,12 @@ public:
      * @param forces  on exit, this contains the forces
      */
     void getForces(ContextImpl& context, std::vector<Vec3>& forces);
+    /**
+     * Get the current derivatives of the energy with respect to context parameters.
+     *
+     * @param derivs  on exit, this contains the derivatives
+     */
+    void getEnergyParameterDerivatives(ContextImpl& context, std::map<std::string, double>& derivs);
     /**
      * Get the current periodic box vectors.
      *

platforms/cuda/src/CudaKernels.cpp

@@ -339,6 +339,10 @@ void CudaUpdateStateDataKernel::getForces(ContextImpl& context, vector<Vec3>& fo
         forces[order[i]] = Vec3(scale*force[i], scale*force[i+paddedNumParticles], scale*force[i+paddedNumParticles*2]);
 }
 
+void CudaUpdateStateDataKernel::getEnergyParameterDerivatives(ContextImpl& context, map<string, double>& derivs) {
+    
+}
+
 void CudaUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const {
     cu.getPeriodicBoxVectors(a, b, c);
 }

platforms/opencl/include/OpenCLKernels.h

@@ -141,6 +141,12 @@ public:
      * @param forces  on exit, this contains the forces
      */
     void getForces(ContextImpl& context, std::vector<Vec3>& forces);
+    /**
+     * Get the current derivatives of the energy with respect to context parameters.
+     *
+     * @param derivs  on exit, this contains the derivatives
+     */
+    void getEnergyParameterDerivatives(ContextImpl& context, std::map<std::string, double>& derivs);
     /**
      * Get the current periodic box vectors.
      *

platforms/opencl/src/OpenCLKernels.cpp

@@ -368,6 +368,10 @@ void OpenCLUpdateStateDataKernel::getForces(ContextImpl& context, vector<Vec3>&
     }
 }
 
+void OpenCLUpdateStateDataKernel::getEnergyParameterDerivatives(ContextImpl& context, map<string, double>& derivs) {
+    
+}
+
 void OpenCLUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const {
     cl.getPeriodicBoxVectors(a, b, c);
 }

platforms/reference/include/ReferenceAngleBondIxn.h

 
-/* Portions copyright (c) 2006 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -94,7 +94,7 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
       
       void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
                             RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
-                            RealOpenMM* totalEnergy) const;
+                            RealOpenMM* totalEnergy, double* energyParamDerivs);
       
 
 };

platforms/reference/include/ReferenceBondIxn.h

 
-/* Portions copyright (c) 2006 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -67,7 +67,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
       
       virtual void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
                                     RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
-                                    RealOpenMM* totalEnergy) const;
+                                    RealOpenMM* totalEnergy, double* energyParamDerivs);
       
       /**---------------------------------------------------------------------------------------
       

platforms/reference/include/ReferenceCMAPTorsionIxn.h

 
-/* Portions copyright (c) 2010 Stanford University and Simbios.
+/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -97,7 +97,7 @@ public:
 
     void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
                          RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
-                         RealOpenMM* totalEnergy) const;
+                         RealOpenMM* totalEnergy, double* energyParamDerivs);
 
 // ---------------------------------------------------------------------------------------
 

platforms/reference/include/ReferenceCustomAngleIxn.h

@@ -85,7 +85,7 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
 
       void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
                             RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
-                            RealOpenMM* totalEnergy) const;
+                            RealOpenMM* totalEnergy, double* energyParamDerivs);
 
 
 };

platforms/reference/include/ReferenceCustomBondIxn.h

@@ -26,6 +26,7 @@
 #define __ReferenceCustomBondIxn_H__
 
 #include "ReferenceBondIxn.h"
+#include "openmm/internal/CompiledExpressionSet.h"
 #include "lepton/CompiledExpression.h"
 
 namespace OpenMM {
@@ -35,10 +36,10 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
    private:
       Lepton::CompiledExpression energyExpression;
       Lepton::CompiledExpression forceExpression;
-      std::vector<double*> energyParams;
-      std::vector<double*> forceParams;
-      double* energyR;
-      double* forceR;
+      std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
+      CompiledExpressionSet expressionSet;
+      std::vector<int> bondParamIndex;
+      int rIndex;
       int numParameters;
       bool usePeriodic;
       RealVec boxVectors[3];
@@ -52,7 +53,8 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
          --------------------------------------------------------------------------------------- */
 
        ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
-                              const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
+                              const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters,
+                              const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions);
 
       /**---------------------------------------------------------------------------------------
 
@@ -86,7 +88,7 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
 
       void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
                             RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
-                            RealOpenMM* totalEnergy) const;
+                            RealOpenMM* totalEnergy, double* energyParamDerivs);
 
 
 };

platforms/reference/include/ReferenceCustomTorsionIxn.h

@@ -85,7 +85,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
 
       void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
                             RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
-                            RealOpenMM* totalEnergy) const;
+                            RealOpenMM* totalEnergy, double* energyParamDerivs);
 
 
 };

platforms/reference/include/ReferenceHarmonicBondIxn.h

@@ -79,7 +79,7 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
       
       void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
                             RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
-                            RealOpenMM* totalEnergy) const;
+                            RealOpenMM* totalEnergy, double* energyParamDerivs);
 
 };