API changes to support variable time step integrators

platforms/reference/src/ReferenceKernels.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "ReferencePlatform.h"
 #include "openmm/kernels.h"
 #include "SimTKUtilities/SimTKOpenMMRealType.h"
 #include "SimTKReference/ReferenceNeighborList.h"
@@ -67,6 +68,35 @@ public:
     void execute(OpenMMContextImpl& context);
 };
 
+/**
+ * This kernel is invoked to get or set the current time.
+ */
+class ReferenceUpdateTimeKernel : public UpdateTimeKernel {
+public:
+    ReferenceUpdateTimeKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : UpdateTimeKernel(name, platform), data(data) {
+    }
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     */
+    void initialize(const System& system);
+    /**
+     * Get the current time (in picoseconds).
+     *
+     * @param context    the context in which to execute this kernel
+     */
+    double getTime(const OpenMMContextImpl& context) const;
+    /**
+     * Set the current time (in picoseconds).
+     *
+     * @param context    the context in which to execute this kernel
+     */
+    void setTime(OpenMMContextImpl& context, double time);
+private:
+    ReferencePlatform::PlatformData& data;
+};
+
 /**
  * This kernel is invoked by HarmonicBondForce to calculate the forces acting on the system and the energy of the system.
  */

platforms/reference/src/ReferencePlatform.cpp

@@ -32,6 +32,7 @@
 #include "ReferencePlatform.h"
 #include "ReferenceKernelFactory.h"
 #include "ReferenceKernels.h"
+#include "openmm/internal/OpenMMContextImpl.h"
 #include "SimTKUtilities/SimTKOpenMMRealType.h"
 
 using namespace OpenMM;
@@ -39,6 +40,7 @@ using namespace OpenMM;
 ReferencePlatform::ReferencePlatform() {
     ReferenceKernelFactory* factory = new ReferenceKernelFactory();
     registerKernelFactory(InitializeForcesKernel::Name(), factory);
+    registerKernelFactory(UpdateTimeKernel::Name(), factory);
     registerKernelFactory(CalcHarmonicBondForceKernel::Name(), factory);
     registerKernelFactory(CalcHarmonicAngleForceKernel::Name(), factory);
     registerKernelFactory(CalcPeriodicTorsionForceKernel::Name(), factory);
@@ -61,3 +63,12 @@ bool ReferencePlatform::supportsDoublePrecision() const {
 const StreamFactory& ReferencePlatform::getDefaultStreamFactory() const {
     return defaultStreamFactory;
 }
+
+void ReferencePlatform::contextCreated(OpenMMContextImpl& context) const {
+    context.setPlatformData(new PlatformData());
+}
+
+void ReferencePlatform::contextDestroyed(OpenMMContextImpl& context) const {
+    PlatformData* data = reinterpret_cast<PlatformData*>(context.getPlatformData());
+    delete data;
+}