Merge pull request #2651 from peastman/checkpoint

CustomIntegrator variables are saved to checkpoints

openmmapi/include/openmm/CustomIntegrator.h

@@ -668,6 +668,16 @@ protected:
      * Get whether computeKineticEnergy() expects forces to have been computed.
      */
     bool kineticEnergyRequiresForce() const;
+    /**
+     * This is called while writing checkpoints.  It gives the integrator a chance to write
+     * its own data.
+     */
+    void createCheckpoint(std::ostream& stream) const;
+    /**
+     * This is called while loading a checkpoint.  The integrator should read in whatever
+     * data it wrote in createCheckpoint() and update its internal state accordingly.
+     */
+    void loadCheckpoint(std::istream& stream);
 private:
     class ComputationInfo;
     class FunctionInfo;

openmmapi/include/openmm/Integrator.h

@@ -34,6 +34,7 @@
 
 #include "State.h"
 #include "Vec3.h"
+#include <iosfwd>
 #include <map>
 #include <vector>
 #include "internal/windowsExport.h"
@@ -151,6 +152,18 @@ protected:
     virtual double getVelocityTimeOffset() const {
         return 0.0;
     }
+    /**
+     * This is called while writing checkpoints.  It gives the integrator a chance to write
+     * its own data.  The default implementation does nothing.
+     */
+    virtual void createCheckpoint(std::ostream& stream) const {
+    }
+    /**
+     * This is called while loading a checkpoint.  The integrator should read in whatever
+     * data it wrote in createCheckpoint() and update its internal state accordingly.
+     */
+    virtual void loadCheckpoint(std::istream& stream) {
+    }
 private:
     double stepSize, constraintTol;
 };

openmmapi/src/ContextImpl.cpp

@@ -454,6 +454,7 @@ void ContextImpl::createCheckpoint(ostream& stream) {
         stream.write((char*) &param.second, sizeof(double));
     }
     updateStateDataKernel.getAs<UpdateStateDataKernel>().createCheckpoint(*this, stream);
+    integrator.createCheckpoint(stream);
     stream.flush();
 }
 
@@ -480,6 +481,7 @@ void ContextImpl::loadCheckpoint(istream& stream) {
         parameters[name] = value;
     }
     updateStateDataKernel.getAs<UpdateStateDataKernel>().loadCheckpoint(*this, stream);
+    integrator.loadCheckpoint(stream);
     hasSetPositions = true;
     integrator.stateChanged(State::Positions);
     integrator.stateChanged(State::Velocities);

openmmapi/src/CustomIntegrator.cpp

@@ -114,6 +114,31 @@ bool CustomIntegrator::kineticEnergyRequiresForce() const {
     return keNeedsForce;
 }
 
+void CustomIntegrator::createCheckpoint(std::ostream& stream) const {
+    for (int i = 0; i < getNumGlobalVariables(); i++) {
+        double value = getGlobalVariable(i);
+        stream.write((char*) &value, sizeof(double));
+    }
+    vector<Vec3> values;
+    for (int i = 0; i < getNumPerDofVariables(); i++) {
+        getPerDofVariable(i, values);
+        stream.write((char*) values.data(), sizeof(Vec3)*values.size());
+    }
+}
+
+void CustomIntegrator::loadCheckpoint(std::istream& stream) {
+    double value;
+    for (int i = 0; i < getNumGlobalVariables(); i++) {
+        stream.read((char*) &value, sizeof(double));
+        setGlobalVariable(i, value);
+    }
+    vector<Vec3> values(context->getSystem().getNumParticles());
+    for (int i = 0; i < getNumPerDofVariables(); i++) {
+        stream.read((char*) values.data(), sizeof(Vec3)*values.size());
+        setPerDofVariable(i, values);
+    }
+}
+
 void CustomIntegrator::step(int steps) {
     if (context == NULL)
         throw OpenMMException("This Integrator is not bound to a context!");  

tests/TestCustomIntegrator.h

@@ -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) 2008-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -48,6 +48,7 @@
 #include <algorithm>
 #include <cmath>
 #include <iostream>
+#include <sstream>
 #include <vector>
 
 using namespace OpenMM;
@@ -1156,6 +1157,31 @@ void testInitialTemperature() {
     ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
 }
 
+void testCheckpoint() {
+    // Test that integrator variables get loaded correctly from checkpoints.
+    System system;
+    system.addParticle(1.0);
+    CustomIntegrator integrator(0.001);
+    integrator.addGlobalVariable("a", 1.0);
+    integrator.addPerDofVariable("b", 2.0);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(1, Vec3());
+    context.setPositions(positions);
+    integrator.setGlobalVariable(0, 5.0);
+    vector<Vec3> b1(1, Vec3(1, 2, 3));
+    integrator.setPerDofVariable(0, b1);
+    stringstream checkpoint; 
+    context.createCheckpoint(checkpoint);
+    integrator.setGlobalVariable(0, 10.0);
+    vector<Vec3> b2(1, Vec3(4, 5, 6));
+    integrator.setPerDofVariable(0, b2);
+    context.loadCheckpoint(checkpoint);
+    ASSERT_EQUAL(5.0, integrator.getGlobalVariable(0));
+    vector<Vec3> b3;
+    integrator.getPerDofVariable(0, b3);
+    ASSERT_EQUAL_VEC(b1[0], b3[0], 1e-6);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -1184,6 +1210,7 @@ int main(int argc, char* argv[]) {
         testVectorFunctions();
         testRecordEnergy();
         testInitialTemperature();
+        testCheckpoint();
         runPlatformTests();
     }
     catch(const exception& e) {