Merged fork with latest original master

serialization/tests/TestSerializeCustomCompoundBondForce.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -67,6 +67,7 @@ void testSerialization() {
     for (int i = 0; i < 10; i++)
         values[i] = sin((double) i);
     force.addTabulatedFunction("f", new Continuous1DFunction(values, 0.5, 1.5));
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -88,6 +89,7 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
     for (int i = 0; i < force.getNumBonds(); i++) {
         vector<int> particles1, particles2;

serialization/tests/TestSerializeCustomTorsionForce.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -53,6 +53,7 @@ void testSerialization() {
     force.addTorsion(4, 0, 1, 5, params);
     params[0] = 2.1;
     force.addTorsion(3, 7, 6, 8, params);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -73,6 +74,7 @@ void testSerialization() {
         ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
         ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
     }
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int a1, a2, b1, b2, c1, c2, d1, d2;

serialization/tests/TestSerializeHarmonicAngleForce.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -47,6 +47,7 @@ void testSerialization() {
     force.addAngle(0, 2, 3, 2.0, 2.1);
     force.addAngle(2, 3, 4, 3.0, 2.2);
     force.addAngle(5, 1, 2, 4.0, 2.3);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -58,6 +59,7 @@ void testSerialization() {
 
     HarmonicAngleForce& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumAngles(), force2.getNumAngles());
     for (int i = 0; i < force.getNumAngles(); i++) {
         int a1, a2, a3, b1, b2, b3;

serialization/tests/TestSerializeHarmonicBondForce.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -47,6 +47,7 @@ void testSerialization() {
     force.addBond(0, 2, 2.0, 2.1);
     force.addBond(2, 3, 3.0, 2.2);
     force.addBond(5, 1, 4.0, 2.3);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -58,6 +59,7 @@ void testSerialization() {
 
     HarmonicBondForce& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
     for (int i = 0; i < force.getNumBonds(); i++) {
         int a1, a2, b1, b2;

serialization/tests/TestSerializeMonteCarloAnisotropicBarostat.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -56,7 +56,7 @@ void testSerialization() {
     MonteCarloAnisotropicBarostat& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL_VEC(force.getDefaultPressure(), force2.getDefaultPressure(), 0.0);
-    ASSERT_EQUAL(force.getTemperature(), force2.getTemperature());
+    ASSERT_EQUAL(force.getDefaultTemperature(), force2.getDefaultTemperature());
     ASSERT_EQUAL(force.getScaleX(), force2.getScaleX());
     ASSERT_EQUAL(force.getScaleY(), force2.getScaleY());
     ASSERT_EQUAL(force.getScaleZ(), force2.getScaleZ());

serialization/tests/TestSerializeMonteCarloBarostat.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -56,7 +56,7 @@ void testSerialization() {
     MonteCarloBarostat& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getDefaultPressure(), force2.getDefaultPressure());
-    ASSERT_EQUAL(force.getTemperature(), force2.getTemperature());
+    ASSERT_EQUAL(force.getDefaultTemperature(), force2.getDefaultTemperature());
     ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
     ASSERT_EQUAL(force.getRandomNumberSeed(), force2.getRandomNumberSeed());
 }

serialization/tests/TestSerializeMonteCarloMembraneBarostat.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -57,7 +57,7 @@ void testSerialization() {
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force.getDefaultPressure(), force2.getDefaultPressure());
     ASSERT_EQUAL(force.getDefaultSurfaceTension(), force2.getDefaultSurfaceTension());
-    ASSERT_EQUAL(force.getTemperature(), force2.getTemperature());
+    ASSERT_EQUAL(force.getDefaultTemperature(), force2.getDefaultTemperature());
     ASSERT_EQUAL(force.getXYMode(), force2.getXYMode());
     ASSERT_EQUAL(force.getZMode(), force2.getZMode());
     ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());

serialization/tests/TestSerializePeriodicTorsionForce.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -47,6 +47,7 @@ void testSerialization() {
     force.addTorsion(0, 2, 3, 4, 2, 2.0, 2.1);
     force.addTorsion(2, 3, 4, 7, 1, 3.0, 2.2);
     force.addTorsion(5, 1, 2, 3, 3, 4.0, 2.3);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -58,6 +59,7 @@ void testSerialization() {
 
     PeriodicTorsionForce& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int a1, a2, a3, a4, b1, b2, b3, b4, perioda, periodb;

serialization/tests/TestSerializeRBTorsionForce.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -46,6 +46,7 @@ void testSerialization() {
     force.addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
     force.addTorsion(0, 2, 3, 4, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7);
     force.addTorsion(2, 3, 4, 7, -1, -2, -3, 1.1, 2.2, 3.3);
+    force.setUsesPeriodicBoundaryConditions(true);
 
     // Serialize and then deserialize it.
 
@@ -57,6 +58,7 @@ void testSerialization() {
 
     RBTorsionForce& force2 = *copy;
     ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
     ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
     for (int i = 0; i < force.getNumTorsions(); i++) {
         int a1, a2, a3, a4, b1, b2, b3, b4;

tests/TestCMAPTorsionForce.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) 2010-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -158,6 +158,61 @@ void testChangingParameters() {
     ASSERT_EQUAL_TOL(2-20*sin(M_PI/4), energy, 1e-5);
 }
 
+void testPeriodic() {
+    const int mapSize = 36;
+
+    // Create two systems that use periodic boundary conditions: one with a pair
+    // of periodic torsions, and one with a CMAP torsion that approximates the same force.
+
+    System system1;
+    for (int i = 0; i < 5; i++)
+        system1.addParticle(1.0);
+    PeriodicTorsionForce* periodic = new PeriodicTorsionForce();
+    periodic->addTorsion(0, 1, 2, 3, 2, M_PI/4, 1.5);
+    periodic->addTorsion(1, 2, 3, 4, 3, M_PI/3, 2.0);
+    periodic->setUsesPeriodicBoundaryConditions(true);
+    system1.addForce(periodic);
+    System system2;
+    for (int i = 0; i < 5; i++)
+        system2.addParticle(1.0);
+    CMAPTorsionForce* cmap = new CMAPTorsionForce();
+    vector<double> mapEnergy(mapSize*mapSize);
+    for (int i = 0; i < mapSize; i++) {
+        double angle1 = i*2*M_PI/mapSize;
+        double energy1 = 1.5*(1+cos(2*angle1-M_PI/4));
+        for (int j = 0; j < mapSize; j++) {
+            double angle2 = j*2*M_PI/mapSize;
+            double energy2 = 2.0*(1+cos(3*angle2-M_PI/3));
+            mapEnergy[i+j*mapSize] = energy1+energy2;
+        }
+    }
+    cmap->addMap(mapSize, mapEnergy);
+    cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4);
+    cmap->setUsesPeriodicBoundaryConditions(true);
+    system2.addForce(cmap);
+
+    // Set the atoms in various positions, and verify that both systems give equal forces and energy.
+
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<Vec3> positions(5);
+    VerletIntegrator integrator1(0.01);
+    VerletIntegrator integrator2(0.01);
+    Context c1(system1, integrator1, platform);
+    Context c2(system2, integrator2, platform);
+    for (int i = 0; i < 50; i++) {
+        for (int j = 0; j < (int) positions.size(); j++)
+            positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
+        c1.setPositions(positions);
+        c2.setPositions(positions);
+        State s1 = c1.getState(State::Forces | State::Energy);
+        State s2 = c2.getState(State::Forces | State::Energy);
+        for (int i = 0; i < system1.getNumParticles(); i++)
+            ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 0.05);
+        ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-3);
+    }
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -165,6 +220,7 @@ int main(int argc, char* argv[]) {
         initializeTests(argc, argv);
         testCMAPTorsions();
         testChangingParameters();
+        testPeriodic();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestCustomAngleForce.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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,6 +29,9 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#ifdef WIN32
+  #define _USE_MATH_DEFINES // Needed to get M_PI
+#endif
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "openmm/CustomAngleForce.h"
@@ -145,6 +148,39 @@ void testIllegalVariable() {
     ASSERT(threwException);
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+    
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 1.5, 0), Vec3(0, 0, 3));
+    VerletIntegrator integrator(0.01);
+    CustomAngleForce* angles = new CustomAngleForce("0.5*k*(theta-theta0)^2");
+    angles->addPerAngleParameter("theta0");
+    angles->addPerAngleParameter("k");
+    vector<double> parameters(2);
+    parameters[0] = M_PI/3;
+    parameters[1] = 1.1;
+    angles->addAngle(0, 1, 2, parameters);
+    angles->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(angles);
+    angles->setUsesPeriodicBoundaryConditions(true);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(3);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(1, 0, 0);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    const vector<Vec3>& forces = state.getForces();
+    double torque = 1.1*M_PI/6;
+    ASSERT_EQUAL_VEC(Vec3(2*torque, 0, 0), forces[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, -torque, 0), forces[2], TOL);
+    ASSERT_EQUAL_TOL(0.5*1.1*(M_PI/6)*(M_PI/6), state.getPotentialEnergy(), TOL);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -152,6 +188,7 @@ int main(int argc, char* argv[]) {
         initializeTests(argc, argv);
         testAngles();
         testIllegalVariable();
+        testPeriodic();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestCustomBondForce.h

@@ -148,6 +148,36 @@ void testIllegalVariable() {
     ASSERT(threwException);
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+    
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    VerletIntegrator integrator(0.01);
+    CustomBondForce* forceField = new CustomBondForce("scale*k*(r-r0)^2");
+    forceField->addPerBondParameter("r0");
+    forceField->addPerBondParameter("k");
+    forceField->addGlobalParameter("scale", 0.5);
+    vector<double> parameters(2);
+    parameters[0] = 1.9;
+    parameters[1] = 0.8;
+    forceField->addBond(0, 1, parameters);
+    forceField->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 2, 0);
+    positions[1] = Vec3(0, 0, 0);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    const vector<Vec3>& forces = state.getForces();
+    ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.9, 0), forces[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, 0.8*0.9, 0), forces[1], TOL);
+    ASSERT_EQUAL_TOL(0.5*0.8*0.9*0.9, state.getPotentialEnergy(), TOL);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -156,6 +186,7 @@ int main(int argc, char* argv[]) {
         testBonds();
         testManyParameters();
         testIllegalVariable();
+        testPeriodic();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestCustomCentroidBondForce.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) 2015 Stanford University and the Authors.           *
+ * Portions copyright (c) 2015-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -277,6 +277,62 @@ void testIllegalVariable() {
     ASSERT(threwException);
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+    
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(2.0);
+    system.addParticle(3.0);
+    system.addParticle(4.0);
+    system.addParticle(5.0);
+    system.setDefaultPeriodicBoxVectors(Vec3(2, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "k*distance(g1,g2)^2");
+    force->addPerBondParameter("k");
+    vector<int> particles1;
+    particles1.push_back(0);
+    particles1.push_back(1);
+    vector<int> particles2;
+    particles2.push_back(2);
+    particles2.push_back(3);
+    particles2.push_back(4);
+    force->addGroup(particles1);
+    force->addGroup(particles2);
+    vector<int> groups;
+    groups.push_back(0);
+    groups.push_back(1);
+    vector<double> parameters;
+    parameters.push_back(1.0);
+    force->addBond(groups, parameters);
+    force->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(force);
+
+    // The center of mass of group 0 is (1.5, 0, 0).
+
+    vector<Vec3> positions(5);
+    positions[0] = Vec3(2.5, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+
+    // The center of mass of group 1 is (-1, 0, 0).
+
+    positions[2] = Vec3(-6, 0, 0);
+    positions[3] = Vec3(-1, 0, 0);
+    positions[4] = Vec3(2, 0, 0);
+
+    // Check the forces and energy.
+
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(0.5*0.5, state.getPotentialEnergy(), TOL);
+    ASSERT_EQUAL_VEC(Vec3(-2*0.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(-2*0.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
+    ASSERT_EQUAL_VEC(Vec3(2*0.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
+    ASSERT_EQUAL_VEC(Vec3(2*0.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
+    ASSERT_EQUAL_VEC(Vec3(2*0.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -286,6 +342,7 @@ int main(int argc, char* argv[]) {
         testComplexFunction();
         testCustomWeights();
         testIllegalVariable();
+        testPeriodic();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestCustomCompoundBondForce.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) 2012-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2012-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -171,7 +171,7 @@ void testContinuous2DFunction() {
     const double xmin = 0.4;
     const double xmax = 1.1;
     const double ymin = 0.0;
-    const double ymax = 0.9;
+    const double ymax = 0.95;
     System system;
     system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
@@ -215,10 +215,10 @@ void testContinuous3DFunction() {
     const int zsize = 12;
     const double xmin = 0.4;
     const double xmax = 1.1;
-    const double ymin = 0.0;
-    const double ymax = 0.9;
+    const double ymin = 2.0;
+    const double ymax = 2.9;
     const double zmin = 0.2;
-    const double zmax = 1.3;
+    const double zmax = 1.35;
     System system;
     system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
@@ -330,6 +330,82 @@ void testIllegalVariable() {
     ASSERT(threwException);
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+
+    System customSystem;
+    customSystem.addParticle(1.0);
+    customSystem.addParticle(1.0);
+    customSystem.addParticle(1.0);
+    customSystem.addParticle(1.0);
+    customSystem.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    CustomCompoundBondForce* custom = new CustomCompoundBondForce(4, "0.5*kb*((distance(p1,p2)-b0)^2+(distance(p2,p3)-b0)^2)+0.5*ka*(angle(p2,p3,p4)-a0)^2+kt*(1+cos(dihedral(p1,p2,p3,p4)-t0))");
+    custom->addPerBondParameter("kb");
+    custom->addPerBondParameter("ka");
+    custom->addPerBondParameter("kt");
+    custom->addPerBondParameter("b0");
+    custom->addPerBondParameter("a0");
+    custom->addPerBondParameter("t0");
+    vector<int> particles(4);
+    particles[0] = 0;
+    particles[1] = 1;
+    particles[2] = 3;
+    particles[3] = 2;
+    vector<double> parameters(6);
+    parameters[0] = 1.5;
+    parameters[1] = 0.8;
+    parameters[2] = 0.6;
+    parameters[3] = 1.1;
+    parameters[4] = 2.9;
+    parameters[5] = 1.3;
+    custom->addBond(particles, parameters);
+    custom->setUsesPeriodicBoundaryConditions(true);
+    customSystem.addForce(custom);
+
+    // Create an identical system using standard forces.
+
+    System standardSystem;
+    standardSystem.addParticle(1.0);
+    standardSystem.addParticle(1.0);
+    standardSystem.addParticle(1.0);
+    standardSystem.addParticle(1.0);
+    standardSystem.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    bonds->addBond(0, 1, 1.1, 1.5);
+    bonds->addBond(1, 3, 1.1, 1.5);
+    bonds->setUsesPeriodicBoundaryConditions(true);
+    standardSystem.addForce(bonds);
+    HarmonicAngleForce* angles = new HarmonicAngleForce();
+    angles->addAngle(1, 3, 2, 2.9, 0.8);
+    angles->setUsesPeriodicBoundaryConditions(true);
+    standardSystem.addForce(angles);
+    PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
+    torsions->addTorsion(0, 1, 3, 2, 1, 1.3, 0.6);
+    torsions->setUsesPeriodicBoundaryConditions(true);
+    standardSystem.addForce(torsions);
+
+    // Set the atoms in various positions, and verify that both systems give identical forces and energy.
+
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    VerletIntegrator integrator1(0.01);
+    VerletIntegrator integrator2(0.01);
+    Context c1(customSystem, integrator1, platform);
+    Context c2(standardSystem, integrator2, platform);
+    vector<Vec3> positions(4);
+    for (int i = 0; i < 10; i++) {
+        for (int j = 0; j < (int) positions.size(); j++)
+            positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
+        c1.setPositions(positions);
+        c2.setPositions(positions);
+        State s1 = c1.getState(State::Forces | State::Energy);
+        State s2 = c2.getState(State::Forces | State::Energy);
+        for (int i = 0; i < customSystem.getNumParticles(); i++)
+            ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
+        ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
+    }
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -341,6 +417,7 @@ int main(int argc, char* argv[]) {
         testContinuous3DFunction();
         testMultipleBonds();
         testIllegalVariable();
+        testPeriodic();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestCustomIntegrator.h

@@ -391,18 +391,21 @@ void testSum() {
     }
     CustomIntegrator integrator(0.005);
     integrator.addGlobalVariable("ke", 0);
+    integrator.addGlobalVariable("temp", 0);
     integrator.addComputePerDof("v", "v+dt*f/m");
     integrator.addComputePerDof("x", "x+dt*v");
     integrator.addComputeSum("ke", "m*v*v/2");
+    integrator.addComputeGlobal("temp", "ke+dt");
     Context context(system, integrator, platform);
     context.setPositions(positions);
     
     // See if the sum is being computed correctly.
     
     for (int i = 0; i < 100; ++i) {
+        integrator.step(1);
         State state = context.getState(State::Energy);
         ASSERT_EQUAL_TOL(state.getKineticEnergy(), integrator.getGlobalVariable(0), 1e-5);
-        integrator.step(1);
+        ASSERT_EQUAL_TOL(integrator.getGlobalVariable(0)+integrator.getStepSize(), integrator.getGlobalVariable(1), 1e-5);
     }
 }
 

tests/TestCustomNonbondedForce.h

@@ -937,6 +937,37 @@ void testInteractionGroupLongRangeCorrection() {
     ASSERT_EQUAL_TOL(expected, energy2-energy1, 1e-4);
 }
 
+void testInteractionGroupTabulatedFunction() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r-1)+1");
+    set<int> set1, set2;
+    set1.insert(0);
+    set2.insert(1);
+    forceField->addInteractionGroup(set1, set2);
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table;
+    for (int i = 0; i < 21; i++)
+        table.push_back(sin(0.25*i));
+    forceField->addTabulatedFunction("fn", new Discrete1DFunction(table));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (int i = 0; i < (int) table.size(); i++) {
+        positions[1] = Vec3(i+1, 0, 0);
+        context.setPositions(positions);
+        State state = context.getState(State::Forces | State::Energy);
+        const vector<Vec3>& forces = state.getForces();
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
+        ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
+    }
+}
+
 void testMultipleCutoffs() {
     System system;
     system.addParticle(1.0);
@@ -1033,6 +1064,7 @@ int main(int argc, char* argv[]) {
         testInteractionGroups();
         testLargeInteractionGroup();
         testInteractionGroupLongRangeCorrection();
+        testInteractionGroupTabulatedFunction();
         testMultipleCutoffs();
         testIllegalVariable();
         runPlatformTests();

tests/TestCustomTorsionForce.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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -186,6 +186,42 @@ void testIllegalVariable() {
     ASSERT(threwException);
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+    
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    VerletIntegrator integrator(0.01);
+    CustomTorsionForce* torsions = new CustomTorsionForce("k*(1+cos(n*theta-theta0))");
+    torsions->addPerTorsionParameter("theta0");
+    torsions->addPerTorsionParameter("n");
+    torsions->addGlobalParameter("k", 1.1);
+    vector<double> parameters(2);
+    parameters[0] = M_PI/3;
+    parameters[1] = 2;
+    torsions->addTorsion(0, 1, 2, 3, parameters);
+    torsions->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(torsions);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(4);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(1, 0, 0);
+    positions[3] = Vec3(1, 0, 2);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    const vector<Vec3>& forces = state.getForces();
+    double torque = -2*1.1*std::sin(2*M_PI/3);
+    ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, -torque, 0), forces[3], TOL);
+    ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
+    ASSERT_EQUAL_TOL(1.1*(1+std::cos(2*M_PI/3)), state.getPotentialEnergy(), TOL);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -194,6 +230,7 @@ int main(int argc, char* argv[]) {
         testTorsions();
         testRange();
         testIllegalVariable();
+        testPeriodic();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestEwald.h

@@ -270,6 +270,49 @@ void testTriclinic() {
     ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-4);
 }
 
+void testTriclinic2() {
+    // Create a triclinic box containing a large molecule made up of randomly positioned particles and make sure the
+    // results match the reference platform.
+
+    if (platform.getName() == "Reference")
+        return;
+    const int numParticles = 1000;
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(3.2, 0, 0), Vec3(-1.1, 3.1, 0), Vec3(-1.1, -1.5, 2.7));
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    NonbondedForce* force = new NonbondedForce();
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        force->addParticle(i%2 == 0 ? -1.0 : 1.0, 1.0, 0.0);
+        positions[i] = Vec3(10*genrand_real2(sfmt)-2, 10*genrand_real2(sfmt)-2, 10*genrand_real2(sfmt)-2);
+        if (i > 0) {
+            Vec3 delta = positions[i-1]-positions[i];
+            system.addConstraint(i-1, i, sqrt(delta.dot(delta)));
+        }
+    }
+    system.addForce(force);
+    force->setNonbondedMethod(NonbondedForce::PME);
+    force->setCutoffDistance(1.0);
+    force->setReciprocalSpaceForceGroup(1);
+    force->setPMEParameters(2.62826, 27, 25, 24);
+
+    // Compute the forces and energy.
+
+    VerletIntegrator integ1(0.001);
+    Context context1(system, integ1, platform);
+    context1.setPositions(positions);
+    VerletIntegrator integ2(0.001);
+    Context context2(system, integ2, Platform::getPlatformByName("Reference"));
+    context2.setPositions(positions);
+    State state1 = context1.getState(State::Forces | State::Energy, false, 2);
+    State state2 = context2.getState(State::Forces | State::Energy, false, 2);
+    ASSERT_EQUAL_TOL(state2.getPotentialEnergy(), state1.getPotentialEnergy(), 1e-4);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(state2.getForces()[i], state1.getForces()[i], 1e-4);
+}
+
 void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
     // Create a cloud of random point charges.
 
@@ -391,6 +434,7 @@ int main(int argc, char* argv[]) {
         testEwaldPME(false);
         testEwaldPME(true);
         testTriclinic();
+        testTriclinic2();
         testErrorTolerance(NonbondedForce::Ewald);
         testErrorTolerance(NonbondedForce::PME);
         testPMEParameters();

tests/TestHarmonicAngleForce.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) 2008-2015 Stanford University and the Authors.s      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.s      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -93,12 +93,40 @@ void testAngles() {
     }
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+    
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 1.5, 0), Vec3(0, 0, 3));
+    VerletIntegrator integrator(0.01);
+    HarmonicAngleForce* angles = new HarmonicAngleForce();
+    angles->addAngle(0, 1, 2, PI_M/3, 1.1);
+    system.addForce(angles);
+    angles->setUsesPeriodicBoundaryConditions(true);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(3);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(1, 0, 0);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    const vector<Vec3>& forces = state.getForces();
+    double torque = 1.1*PI_M/6;
+    ASSERT_EQUAL_VEC(Vec3(2*torque, 0, 0), forces[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, -torque, 0), forces[2], TOL);
+    ASSERT_EQUAL_TOL(0.5*1.1*(PI_M/6)*(PI_M/6), state.getPotentialEnergy(), TOL);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
     try {
         initializeTests(argc, argv);
         testAngles();
+        testPeriodic();
         runPlatformTests();
     }
     catch(const exception& e) {

tests/TestHarmonicBondForce.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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -82,12 +82,37 @@ void testBonds() {
     }
 }
 
+void testPeriodic() {
+    // Create a force that uses periodic boundary conditions.
+    
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
+    VerletIntegrator integrator(0.01);
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    bonds->addBond(0, 1, 1.2, 0.8);
+    bonds->setUsesPeriodicBoundaryConditions(true);
+    system.addForce(bonds);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 2, 0);
+    positions[1] = Vec3(0, 0, 0);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    const vector<Vec3>& forces = state.getForces();
+    ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.2, 0), forces[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, 0.8*0.2, 0), forces[1], TOL);
+    ASSERT_EQUAL_TOL(0.5*0.8*0.2*0.2, state.getPotentialEnergy(), TOL);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
     try {
         initializeTests(argc, argv);
         testBonds();
+        testPeriodic();
         runPlatformTests();
     }
     catch(const exception& e) {