Merge changes from main branch

openmmapi/include/openmm/internal/CMMotionRemoverImpl.h

@@ -49,7 +49,7 @@ public:
     const CMMotionRemover& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context);
+    void updateContextState(ContextImpl& context, bool& forcesInvalid);
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
         // This force doesn't apply forces to particles.
         return 0.0;

openmmapi/include/openmm/internal/ContextImpl.h

@@ -55,7 +55,8 @@ public:
     /**
      * Create an ContextImpl for a Context;
      */
-    ContextImpl(Context& owner, const System& system, Integrator& integrator, Platform* platform, const std::map<std::string, std::string>& properties);
+    ContextImpl(Context& owner, const System& system, Integrator& integrator, Platform* platform, const std::map<std::string, std::string>& properties,
+            ContextImpl* originalContext=NULL);
     ~ContextImpl();
     /**
      * Get the Context for which this is the implementation.
@@ -197,8 +198,11 @@ public:
     double calcForcesAndEnergy(bool includeForces, bool includeEnergy, int groups=0xFFFFFFFF);
     /**
      * Get the set of force group flags that were passed to the most recent call to calcForcesAndEnergy().
+     * 
+     * Note that this returns a reference, so it's possible to modify it.  Be very very cautious about
+     * doing that!  Only do it if you're also modifying forces stored inside the context.
      */
-    int getLastForceGroups() const;
+    int& getLastForceGroups();
     /**
      * Calculate the kinetic energy of the system (in kJ/mol).
      */
@@ -206,8 +210,11 @@ public:
     /**
      * This should be called at the start of each time step.  It calls updateContextState() on each
      * ForceImpl in the system, allowing them to modify the values of state variables.
+     * 
+     * @return true if the state was modified in any way that would cause the forces on particles
+     * to change, false otherwise
      */
-    void updateContextState();
+    bool updateContextState();
     /**
      * Get the list of ForceImpls belonging to this ContextImpl.
      */
@@ -261,8 +268,18 @@ public:
      * you should never call it.  It is exposed here because the same logic is useful to other classes too.
      */
     static std::vector<std::vector<int> > findMolecules(int numParticles, std::vector<std::vector<int> >& particleBonds);
+    /**
+     * Create a new Context based on this one.  The new context will use the same Platform, device, and property
+     * values as this one.  With the CUDA and OpenCL platforms, it also shares the same GPU context, allowing data
+     * to be transferred between them without leaving the GPU.
+     * 
+     * This method exists for very specialized purposes.  If you aren't certain whether you should use it, that probably
+     * means you shouldn't.
+     */
+    Context* createLinkedContext(const System& system, Integrator& integrator);
 private:
     friend class Context;
+    void initialize();
     Context& owner;
     const System& system;
     Integrator& integrator;

openmmapi/include/openmm/internal/CustomAngleForceImpl.h

@@ -53,7 +53,7 @@ public:
     const CustomAngleForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/CustomBondForceImpl.h

@@ -53,7 +53,7 @@ public:
     const CustomBondForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/CustomCVForceImpl.h

+#ifndef OPENMM_CUSTOMCVFORCEIMPL_H_
+#define OPENMM_CUSTOMCVFORCEIMPL_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * 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.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ForceImpl.h"
+#include "openmm/Context.h"
+#include "openmm/CustomCVForce.h"
+#include "openmm/Kernel.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include <map>
+#include <string>
+#include <vector>
+
+namespace OpenMM {
+
+/**
+ * This is the internal implementation of CustomCVForce.
+ */
+
+class OPENMM_EXPORT CustomCVForceImpl : public ForceImpl {
+public:
+    CustomCVForceImpl(const CustomCVForce& owner);
+    ~CustomCVForceImpl();
+    void initialize(ContextImpl& context);
+    const CustomCVForce& getOwner() const {
+        return owner;
+    }
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
+        // This force field doesn't update the state directly.
+    }
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
+    std::map<std::string, double> getDefaultParameters();
+    std::vector<std::string> getKernelNames();
+    void getCollectiveVariableValues(ContextImpl& context, std::vector<double>& values);
+    Context& getInnerContext();
+private:
+    const CustomCVForce& owner;
+    Kernel kernel;
+    System innerSystem;
+    VerletIntegrator innerIntegrator;
+    Context* innerContext;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUSTOMCVFORCEIMPL_H_*/

openmmapi/include/openmm/internal/CustomCentroidBondForceImpl.h

@@ -58,7 +58,7 @@ public:
     const CustomCentroidBondForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/CustomCompoundBondForceImpl.h

@@ -57,7 +57,7 @@ public:
     const CustomCompoundBondForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/CustomExternalForceImpl.h

@@ -53,7 +53,7 @@ public:
     const CustomExternalForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/CustomGBForceImpl.h

@@ -53,7 +53,7 @@ public:
     const CustomGBForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/CustomHbondForceImpl.h

@@ -57,7 +57,7 @@ public:
     const CustomHbondForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/CustomIntegratorUtilities.h

@@ -73,7 +73,7 @@ public:
      */
     static void analyzeComputations(const ContextImpl& context, const CustomIntegrator& integrator, std::vector<std::vector<Lepton::ParsedExpression> >& expressions,
             std::vector<Comparison>& comparisons, std::vector<int>& blockEnd, std::vector<bool>& invalidatesForces, std::vector<bool>& needsForces,
-            std::vector<bool>& needsEnergy, std::vector<bool>& computeBoth, std::vector<int>& forceGroup);
+            std::vector<bool>& needsEnergy, std::vector<bool>& computeBoth, std::vector<int>& forceGroup, const std::map<std::string, Lepton::CustomFunction*>& functions);
     /**
      * Determine whether an expression involves a particular variable.
      */

openmmapi/include/openmm/internal/CustomManyParticleForceImpl.h

@@ -57,7 +57,7 @@ public:
     const CustomManyParticleForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/CustomNonbondedForceImpl.h

@@ -54,7 +54,7 @@ public:
     const CustomNonbondedForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
@@ -69,7 +69,7 @@ public:
     static void calcLongRangeCorrection(const CustomNonbondedForce& force, const Context& context, double& coefficient, std::vector<double>& derivatives);
 private:
     static double integrateInteraction(Lepton::CompiledExpression& expression, const std::vector<double>& params1, const std::vector<double>& params2,
-            const CustomNonbondedForce& force, const Context& context);
+            const CustomNonbondedForce& force, const Context& context, const std::vector<std::string>& paramNames);
     const CustomNonbondedForce& owner;
     Kernel kernel;
 };

openmmapi/include/openmm/internal/CustomTorsionForceImpl.h

@@ -53,7 +53,7 @@ public:
     const CustomTorsionForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/ForceImpl.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "openmm/Context.h"
 #include "openmm/internal/windowsExport.h"
 #include <map>
 #include <string>
@@ -72,9 +73,16 @@ public:
      * to modify the state variables (positions, velocities, and parameters) stored in the
      * Context in arbitrary ways before integration is performed.
      * 
-     * @param context     the context in which the system is being simulated
+     * @param context        the context in which the system is being simulated
+     * @param forcesInvalid  if the state was modified in any way that might cause previously
+     *                       calculated forces to no longer be valid (such as modifying
+     *                       positions or parameters), the method should set this to true.
+     */
+    virtual void updateContextState(ContextImpl& context, bool& forcesInvalid);
+    /**
+     * @deprecated This version exists for backward compatibility.  Subclasses should implement the other version instead.
      */
-    virtual void updateContextState(ContextImpl& context) = 0;
+    virtual void updateContextState(ContextImpl& context);
     /**
      * Calculate the force on each particle generated by this ForceImpl and/or this ForceImpl's
      * contribution to the potential energy of the system.
@@ -104,6 +112,13 @@ public:
     virtual std::vector<std::pair<int, int> > getBondedParticles() const {
         return std::vector<std::pair<int, int> >(0);
     }
+protected:
+    /**
+     * Get the ContextImpl corresponding to a Context.
+     */
+    ContextImpl& getContextImpl(Context& context) {
+        return context.getImpl();
+    }
 };
 
 } // namespace OpenMM

openmmapi/include/openmm/internal/GBSAOBCForceImpl.h

@@ -50,7 +50,7 @@ public:
     const GBSAOBCForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/HarmonicAngleForceImpl.h

@@ -53,7 +53,7 @@ public:
     const HarmonicAngleForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/HarmonicBondForceImpl.h

@@ -53,7 +53,7 @@ public:
     const HarmonicBondForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);

openmmapi/include/openmm/internal/MonteCarloBarostatImpl.h

@@ -51,7 +51,7 @@ public:
     const MonteCarloBarostat& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context);
+    void updateContextState(ContextImpl& context, bool& forcesInvalid);
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
         // This force doesn't apply forces to particles.
         return 0.0;

openmmapi/include/openmm/internal/NonbondedForceImpl.h

@@ -55,7 +55,7 @@ public:
     const NonbondedForce& getOwner() const {
         return owner;
     }
-    void updateContextState(ContextImpl& context) {
+    void updateContextState(ContextImpl& context, bool& forcesInvalid) {
         // This force field doesn't update the state directly.
     }
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);