Added Context::setState()

openmmapi/include/openmm/Context.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -129,6 +129,18 @@ public:
      * and energies.  Group i will be included if (groups&(1<<i)) != 0.  The default value includes all groups.
      */
     State getState(int types, bool enforcePeriodicBox=false, int groups=0xFFFFFFFF) const;
+    /**
+     * Copy information from a State object into this Context.  This restores the Context to
+     * approximately the same state it was in when the State was created.  If the State does not include
+     * a piece of information (e.g. positions or velocities), that aspect of the Context is
+     * left unchanged.
+     * 
+     * Even when all possible information is included in the State, the effect of calling this method
+     * is still less complete than loadCheckpoint().  For example, it does not restore the internal
+     * states of random number generators.  On the other hand, it has the advantage of not being hardware
+     * specific.
+     */
+    void setState(const State& state);
     /**
      * Set the current time of the simulation (in picoseconds).
      */

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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -146,6 +146,47 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
     return builder.getState();
 }
 
+void Context::setState(const State& state) {
+    // Determine what information the state contains.
+    
+    bool hasPositions = false, hasVelocities = false, hasParameters = false;
+    try {
+        state.getPositions();
+        hasPositions = true;
+    }
+    catch (OpenMMException& ex) {
+        // The State does not include positions.
+    }
+    try {
+        state.getVelocities();
+        hasVelocities = true;
+    }
+    catch (OpenMMException& ex) {
+        // The State does not include velocities.
+    }
+    try {
+        state.getParameters();
+        hasParameters = true;
+    }
+    catch (OpenMMException& ex) {
+        // The State does not include parameters.
+    }
+    
+    // Copy it over.
+    
+    setTime(state.getTime());
+    Vec3 a, b, c;
+    state.getPeriodicBoxVectors(a, b, c);
+    setPeriodicBoxVectors(a, b, c);
+    if (hasPositions)
+        setPositions(state.getPositions());
+    if (hasVelocities)
+        setVelocities(state.getVelocities());
+    if (hasParameters)
+        for (map<string, double>::const_iterator iter = state.getParameters().begin(); iter != state.getParameters().end(); ++iter)
+            setParameter(iter->first, iter->second);
+}
+
 void Context::setTime(double time) {
     impl->setTime(time);
 }

platforms/cuda/tests/TestCudaCheckpoints.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) 2012 Stanford University and the Authors.           *
+ * Portions copyright (c) 2012-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -159,11 +159,66 @@ void testCheckpoint() {
     compareStates(s6, s8);
 }
 
+void testSetState() {
+    const int numParticles = 10;
+    const double boxSize = 3.0;
+    const double temperature = 200.0;
+    System system;
+    system.addForce(new AndersenThermostat(0.0, 100.0));
+    NonbondedForce* nonbonded = new NonbondedForce();
+    system.addForce(nonbonded);
+    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
+        positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
+    }
+    VerletIntegrator integrator(0.001);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    context.setParameter(AndersenThermostat::Temperature(), temperature);
+    
+    // Run for a little while.
+    
+    integrator.step(100);
+    
+    // Record the current state.
+    
+    State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    
+    // Continue the simulation for a few more steps and record a partial state.
+    
+    integrator.step(10);
+    State s2 = context.getState(State::Positions);
+    
+    // Restore the original state and see if everything gets restored correctly.
+    
+    context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
+    context.setParameter(AndersenThermostat::Temperature(), temperature+10);
+    context.setState(s1);
+    State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    compareStates(s1, s3);
+    
+    // Set the partial state and see if the correct things were set.
+    
+    context.setState(s2);
+    State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    for (int i = 0; i < numParticles; i++) {
+        ASSERT_EQUAL_VEC(s2.getPositions()[i], s4.getPositions()[i], TOL);
+        ASSERT_EQUAL_VEC(s1.getVelocities()[i], s4.getVelocities()[i], TOL);
+    }
+}
+
 int main(int argc, char* argv[]) {
     try {
         if (argc > 1)
             platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
         testCheckpoint();
+        testSetState();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

platforms/opencl/tests/TestOpenCLCheckpoints.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) 2012 Stanford University and the Authors.           *
+ * Portions copyright (c) 2012-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -159,11 +159,66 @@ void testCheckpoint() {
     compareStates(s6, s8);
 }
 
+void testSetState() {
+    const int numParticles = 10;
+    const double boxSize = 3.0;
+    const double temperature = 200.0;
+    System system;
+    system.addForce(new AndersenThermostat(0.0, 100.0));
+    NonbondedForce* nonbonded = new NonbondedForce();
+    system.addForce(nonbonded);
+    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
+        positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
+    }
+    VerletIntegrator integrator(0.001);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    context.setParameter(AndersenThermostat::Temperature(), temperature);
+    
+    // Run for a little while.
+    
+    integrator.step(100);
+    
+    // Record the current state.
+    
+    State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    
+    // Continue the simulation for a few more steps and record a partial state.
+    
+    integrator.step(10);
+    State s2 = context.getState(State::Positions);
+    
+    // Restore the original state and see if everything gets restored correctly.
+    
+    context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
+    context.setParameter(AndersenThermostat::Temperature(), temperature+10);
+    context.setState(s1);
+    State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    compareStates(s1, s3);
+    
+    // Set the partial state and see if the correct things were set.
+    
+    context.setState(s2);
+    State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    for (int i = 0; i < numParticles; i++) {
+        ASSERT_EQUAL_VEC(s2.getPositions()[i], s4.getPositions()[i], TOL);
+        ASSERT_EQUAL_VEC(s1.getVelocities()[i], s4.getVelocities()[i], TOL);
+    }
+}
+
 int main(int argc, char* argv[]) {
     try {
         if (argc > 1)
             platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
         testCheckpoint();
+        testSetState();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

platforms/reference/tests/TestReferenceCheckpoints.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) 2012 Stanford University and the Authors.           *
+ * Portions copyright (c) 2012-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -121,9 +121,65 @@ void testCheckpoint() {
     compareStates(s2, s4);
 }
 
+void testSetState() {
+    const int numParticles = 10;
+    const double boxSize = 3.0;
+    const double temperature = 200.0;
+    ReferencePlatform platform;
+    System system;
+    system.addForce(new AndersenThermostat(0.0, 100.0));
+    NonbondedForce* nonbonded = new NonbondedForce();
+    system.addForce(nonbonded);
+    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
+        positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
+    }
+    VerletIntegrator integrator(0.001);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    context.setParameter(AndersenThermostat::Temperature(), temperature);
+    
+    // Run for a little while.
+    
+    integrator.step(100);
+    
+    // Record the current state.
+    
+    State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    
+    // Continue the simulation for a few more steps and record a partial state.
+    
+    integrator.step(10);
+    State s2 = context.getState(State::Positions);
+    
+    // Restore the original state and see if everything gets restored correctly.
+    
+    context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
+    context.setParameter(AndersenThermostat::Temperature(), temperature+10);
+    context.setState(s1);
+    State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    compareStates(s1, s3);
+    
+    // Set the partial state and see if the correct things were set.
+    
+    context.setState(s2);
+    State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    for (int i = 0; i < numParticles; i++) {
+        ASSERT_EQUAL_VEC(s2.getPositions()[i], s4.getPositions()[i], TOL);
+        ASSERT_EQUAL_VEC(s1.getVelocities()[i], s4.getVelocities()[i], TOL);
+    }
+}
+
 int main() {
     try {
         testCheckpoint();
+        testSetState();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;