Continuing to refactor tests

CMakeLists.txt

@@ -340,6 +340,7 @@ ELSE(DL_LIBRARY)
 ENDIF(DL_LIBRARY)
 
 IF(BUILD_TESTING)
+    INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/tests)
     ADD_SUBDIRECTORY(platforms/reference/tests)
 ENDIF(BUILD_TESTING)
 

platforms/cpu/tests/CpuTests.h

@@ -34,4 +34,4 @@
 OpenMM::CpuPlatform platform;
 
 void initializeTests(int argc, char* argv[]) {
-}
+}
\ No newline at end of file

platforms/cuda/tests/CudaTests.h

@@ -37,4 +37,4 @@ OpenMM::CudaPlatform platform;
 void initializeTests(int argc, char* argv[]) {
     if (argc > 1)
         platform.setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
-}
+}
\ No newline at end of file

platforms/cuda/tests/TestCudaCustomAngleForce.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) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,107 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CUDA implementation of CustomAngleForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CudaPlatform.h"
-#include "openmm/CustomAngleForce.h"
-#include "openmm/HarmonicAngleForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-CudaPlatform platform;
-
-void testAngles() {
-    // Create a system using a CustomAngleForce.
-
-    System customSystem;
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    CustomAngleForce* custom = new CustomAngleForce("scale*k*(theta-theta0)^2");
-    custom->addPerAngleParameter("theta0");
-    custom->addPerAngleParameter("k");
-    custom->addGlobalParameter("scale", 0.5);
-    vector<double> parameters(2);
-    parameters[0] = 1.5;
-    parameters[1] = 0.8;
-    custom->addAngle(0, 1, 2, parameters);
-    parameters[0] = 2.0;
-    parameters[1] = 0.5;
-    custom->addAngle(1, 2, 3, parameters);
-    customSystem.addForce(custom);
-
-    // Create an identical system using a HarmonicAngleForce.
-
-    System harmonicSystem;
-    harmonicSystem.addParticle(1.0);
-    harmonicSystem.addParticle(1.0);
-    harmonicSystem.addParticle(1.0);
-    harmonicSystem.addParticle(1.0);
-    HarmonicAngleForce* harmonic = new HarmonicAngleForce();
-    harmonic->addAngle(0, 1, 2, 1.5, 0.8);
-    harmonic->addAngle(1, 2, 3, 2.0, 0.5);
-    harmonicSystem.addForce(harmonic);
-
-    // 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);
-
-    vector<Vec3> positions(4);
-    VerletIntegrator integrator1(0.01);
-    VerletIntegrator integrator2(0.01);
-    Context c1(customSystem, integrator1, platform);
-    Context c2(harmonicSystem, integrator2, platform);
-    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);
-    }
-    
-    // Try changing the angle parameters and make sure it's still correct.
-    
-    parameters[0] = 1.6;
-    parameters[1] = 0.9;
-    custom->setAngleParameters(0, 0, 1, 2, parameters);
-    parameters[0] = 2.1;
-    parameters[1] = 0.6;
-    custom->setAngleParameters(1, 1, 2, 3, parameters);
-    custom->updateParametersInContext(c1);
-    harmonic->setAngleParameters(0, 0, 1, 2, 1.6, 0.9);
-    harmonic->setAngleParameters(1, 1, 2, 3, 2.1, 0.6);
-    harmonic->updateParametersInContext(c2);
-    {
-        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);
-    }
-}
+#include "CudaTests.h"
+#include "TestCustomAngleForce.h"
 
 void testParallelComputation() {
     System system;
@@ -160,17 +61,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
-        testAngles();
-        testParallelComputation();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }

platforms/cuda/tests/TestCudaCustomBondForce.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) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,111 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CUDA implementation of CustomBondForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CudaPlatform.h"
-#include "openmm/CustomBondForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "SimTKOpenMMRealType.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-CudaPlatform platform;
-
-void testBonds() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    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] = 1.5;
-    parameters[1] = 0.8;
-    forceField->addBond(0, 1, parameters);
-    parameters[0] = 1.2;
-    parameters[1] = 0.7;
-    forceField->addBond(1, 2, parameters);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(3);
-    positions[0] = Vec3(0, 2, 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();
-        ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
-        ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
-        ASSERT_EQUAL_TOL(0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
-    }
-    
-    // Try changing the bond parameters and make sure it's still correct.
-    
-    parameters[0] = 1.6;
-    parameters[1] = 0.9;
-    forceField->setBondParameters(0, 0, 1, parameters);
-    parameters[0] = 1.3;
-    parameters[1] = 0.8;
-    forceField->setBondParameters(1, 1, 2, parameters);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(0, -0.9*0.4, 0), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0.8*0.3, 0, 0), forces[2], TOL);
-        ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
-        ASSERT_EQUAL_TOL(0.5*0.9*0.4*0.4 + 0.5*0.8*0.3*0.3, state.getPotentialEnergy(), TOL);
-    }
-}
-
-void testManyParameters() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomBondForce* forceField = new CustomBondForce("(a+b+c+d+e+f+g+h+i)*r");
-    forceField->addPerBondParameter("a");
-    forceField->addPerBondParameter("b");
-    forceField->addPerBondParameter("c");
-    forceField->addPerBondParameter("d");
-    forceField->addPerBondParameter("e");
-    forceField->addPerBondParameter("f");
-    forceField->addPerBondParameter("g");
-    forceField->addPerBondParameter("h");
-    forceField->addPerBondParameter("i");
-    vector<double> parameters(forceField->getNumPerBondParameters());
-    for (int i = 0; i < parameters.size(); i++)
-        parameters[i] = i;
-    forceField->addBond(0, 1, parameters);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, 2.5, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-    double f = 1+2+3+4+5+6+7+8;
-    ASSERT_EQUAL_VEC(Vec3(0, f, 0), forces[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, -f, 0), forces[1], TOL);
-    ASSERT_EQUAL_TOL(f*2.5, state.getPotentialEnergy(), TOL);
-}
+#include "CudaTests.h"
+#include "TestCustomBondForce.h"
 
 void testParallelComputation() {
     System system;
@@ -164,18 +61,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
-        testBonds();
-        testManyParameters();
-        testParallelComputation();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }

platforms/cuda/tests/TestCudaCustomCentroidBondForce.cpp

@@ -29,247 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the reference implementation of CustomCompoundBondForce.
- */
+#include "CudaTests.h"
+#include "TestCustomCentroidBondForce.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CudaPlatform.h"
-#include "openmm/CustomCentroidBondForce.h"
-#include "openmm/CustomCompoundBondForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-CudaPlatform platform;
-
-const double TOL = 1e-5;
-
-void testHarmonicBond() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(2.0);
-    system.addParticle(3.0);
-    system.addParticle(4.0);
-    system.addParticle(5.0);
-    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);
-    system.addForce(force);
-    ASSERT(!system.usesPeriodicBoundaryConditions());
-
-    // 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(2.5*2.5, state.getPotentialEnergy(), TOL);
-    ASSERT_EQUAL_VEC(Vec3(-2*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(-2*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
-    ASSERT_EQUAL_VEC(Vec3(2*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
-    ASSERT_EQUAL_VEC(Vec3(2*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
-    ASSERT_EQUAL_VEC(Vec3(2*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
-
-    // Update the per-bond parameter and see if the results change.
-
-    parameters[0] = 2.0;
-    force->setBondParameters(0, groups, parameters);
-    force->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(2*2.5*2.5, state.getPotentialEnergy(), TOL);
-    ASSERT_EQUAL_VEC(Vec3(-4*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(-4*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
-    ASSERT_EQUAL_VEC(Vec3(4*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
-    ASSERT_EQUAL_VEC(Vec3(4*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
-    ASSERT_EQUAL_VEC(Vec3(4*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
-    
-    // All the particles should be treated as a single molecule.
-    
-    vector<std::vector<int> > molecules = context.getMolecules();
-    ASSERT_EQUAL(1, molecules.size());
-    ASSERT_EQUAL(5, molecules[0].size());
-}
-
-void testComplexFunction() {
-    int numParticles = 5;
-    System system;
-    for (int i = 0; i < numParticles; i++)
-        system.addParticle(2.0);
-    vector<double> table(20);
-    for (int i = 0; i < 20; i++)
-        table[i] = sin(0.11*i);
-
-    // When every group contains only one particle, a CustomCentroidBondForce is identical to a
-    // CustomCompoundBondForce.  Use that to test a complicated energy function with lots of terms.
-
-    CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+fn(distance(p1,p2))*angle(p3,p2,p4)+scale*dihedral(p2,p1,p4,p3)");
-    CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+fn(distance(g1,g2))*angle(g3,g2,g4)+scale*dihedral(g2,g1,g4,g3)");
-    compound->addGlobalParameter("scale", 0.5);
-    centroid->addGlobalParameter("scale", 0.5);
-    compound->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
-    centroid->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
-
-    // Add two bonds to the CustomCompoundBondForce.
-
-    vector<int> particles(4);
-    vector<double> parameters;
-    particles[0] = 0;
-    particles[1] = 1;
-    particles[2] = 2;
-    particles[3] = 3;
-    compound->addBond(particles, parameters);
-    particles[0] = 2;
-    particles[1] = 4;
-    particles[2] = 3;
-    particles[3] = 1;
-    compound->addBond(particles, parameters);
-
-    // Add identical bonds to the CustomCentroidBondForce.  As a stronger test, make sure that
-    // group number is different from particle number.
-
-    vector<int> groupMembers(1);
-    groupMembers[0] = 3;
-    centroid->addGroup(groupMembers);
-    groupMembers[0] = 0;
-    centroid->addGroup(groupMembers);
-    groupMembers[0] = 1;
-    centroid->addGroup(groupMembers);
-    groupMembers[0] = 2;
-    centroid->addGroup(groupMembers);
-    groupMembers[0] = 4;
-    centroid->addGroup(groupMembers);
-    vector<int> groups(4);
-    groups[0] = 1;
-    groups[1] = 2;
-    groups[2] = 3;
-    groups[3] = 0;
-    centroid->addBond(groups, parameters);
-    groups[0] = 3;
-    groups[1] = 4;
-    groups[2] = 0;
-    groups[3] = 2;
-    centroid->addBond(groups, parameters);
-
-    // Add both forces as different force groups, and create a context.
-
-    centroid->setForceGroup(1);
-    system.addForce(compound);
-    system.addForce(centroid);
-    VerletIntegrator integrator(0.01);
-    Context context(system, integrator, platform);
-
-    // Evaluate the force and energy for various positions and see if they match.
-
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    vector<Vec3> positions(numParticles);
-    for (int i = 0; i < 10; i++) {
-        for (int j = 0; j < numParticles; j++)
-            positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
-        context.setPositions(positions);
-        State state1 = context.getState(State::Forces | State::Energy, false, 1<<0);
-        State state2 = context.getState(State::Forces | State::Energy, false, 1<<1);
-        ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), TOL);
-        for (int i = 0; i < numParticles; i++)
-            ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], TOL);
-    }
-}
-
-void testCustomWeights() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(2.0);
-    system.addParticle(3.0);
-    system.addParticle(4.0);
-    CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "distance(g1,g2)^2");
-    vector<int> particles(2);
-    vector<double> weights(2);
-    particles[0] = 0;
-    particles[1] = 1;
-    weights[0] = 0.5;
-    weights[1] = 1.5;
-    force->addGroup(particles, weights);
-    particles[0] = 2;
-    particles[1] = 3;
-    weights[0] = 2.0;
-    weights[1] = 1.0;
-    force->addGroup(particles, weights);
-    vector<int> groups;
-    groups.push_back(0);
-    groups.push_back(1);
-    vector<double> parameters;
-    force->addBond(groups, parameters);
-    system.addForce(force);
-
-    // The center of mass of group 0 is (0, 1, 0).
-
-    vector<Vec3> positions(4);
-    positions[0] = Vec3(0, 4, 0);
-    positions[1] = Vec3(0, 0, 0);
-
-    // The center of mass of group 1 is (0, 10, 0).
-
-    positions[2] = Vec3(0, 9, 0);
-    positions[3] = Vec3(0, 12, 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(9.0*9.0, state.getPotentialEnergy(), TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, 2*9*(0.5/2.0), 0), state.getForces()[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, 2*9*(1.5/2.0), 0), state.getForces()[1], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, -2*9*(2.0/3.0), 0), state.getForces()[2], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, -2*9*(1.0/3.0), 0), state.getForces()[3], TOL);
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
-        testHarmonicBond();
-        testComplexFunction();
-        testCustomWeights();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }

platforms/cuda/tests/TestCudaCustomCompoundBondForce.cpp

@@ -29,145 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CUDA implementation of CustomCompoundBondForce.
- */
-
-#ifdef WIN32
-  #define _USE_MATH_DEFINES // Needed to get M_PI
-#endif
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CudaPlatform.h"
-#include "openmm/CustomCompoundBondForce.h"
-#include "openmm/HarmonicAngleForce.h"
-#include "openmm/HarmonicBondForce.h"
-#include "openmm/PeriodicTorsionForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-CudaPlatform platform;
-
-void testBond() {
-    // Create a system using a CustomCompoundBondForce.
-
-    System customSystem;
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    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);
-    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);
-    HarmonicBondForce* bonds = new HarmonicBondForce();
-    bonds->addBond(0, 1, 1.1, 1.5);
-    bonds->addBond(1, 3, 1.1, 1.5);
-    standardSystem.addForce(bonds);
-    HarmonicAngleForce* angles = new HarmonicAngleForce();
-    angles->addAngle(1, 3, 2, 2.9, 0.8);
-    standardSystem.addForce(angles);
-    PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
-    torsions->addTorsion(0, 1, 3, 2, 1, 1.3, 0.6);
-    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);
-    }
-    
-    // Try changing the bond parameters and make sure it's still correct.
-    
-    parameters[0] = 1.6;
-    parameters[3] = 1.3;
-    custom->setBondParameters(0, particles, parameters);
-    custom->updateParametersInContext(c1);
-    bonds->setBondParameters(0, 0, 1, 1.3, 1.6);
-    bonds->setBondParameters(1, 1, 3, 1.3, 1.6);
-    bonds->updateParametersInContext(c2);
-    {
-        State s1 = c1.getState(State::Forces | State::Energy);
-        State s2 = c2.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = s1.getForces();
-        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 testPositionDependence() {
-    System customSystem;
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    CustomCompoundBondForce* custom = new CustomCompoundBondForce(2, "scale1*distance(p1,p2)+scale2*x1+2*y2");
-    custom->addGlobalParameter("scale1", 0.3);
-    custom->addGlobalParameter("scale2", 0.2);
-    vector<int> particles(2);
-    particles[0] = 1;
-    particles[1] = 0;
-    vector<double> parameters;
-    custom->addBond(particles, parameters);
-    customSystem.addForce(custom);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(1.5, 1, 0);
-    positions[1] = Vec3(0.5, 1, 0);
-    VerletIntegrator integrator(0.01);
-    Context context(customSystem, integrator, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(0.3*1.0+0.2*0.5+2*1, state.getPotentialEnergy(), 1e-5);
-    ASSERT_EQUAL_VEC(Vec3(-0.3, -2, 0), state.getForces()[0], 1e-5);
-    ASSERT_EQUAL_VEC(Vec3(0.3-0.2, 0, 0), state.getForces()[1], 1e-5);
-}
+#include "CudaTests.h"
+#include "TestCustomCompoundBondForce.h"
 
 void testParallelComputation() {
     System system;
@@ -202,165 +65,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-void testContinuous2DFunction() {
-    const int xsize = 10;
-    const int ysize = 11;
-    const double xmin = 0.4;
-    const double xmax = 1.1;
-    const double ymin = 0.0;
-    const double ymax = 0.9;
-    System system;
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1)+1");
-    vector<int> particles(1, 0);
-    forceField->addBond(particles, vector<double>());
-    vector<double> table(xsize*ysize);
-    for (int i = 0; i < xsize; i++) {
-        for (int j = 0; j < ysize; j++) {
-            double x = xmin + i*(xmax-xmin)/xsize;
-            double y = ymin + j*(ymax-ymin)/ysize;
-            table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
-        }
-    }
-    forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
-        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
-            positions[0] = Vec3(x, y, 1.5);
-            context.setPositions(positions);
-            State state = context.getState(State::Forces | State::Energy);
-            const vector<Vec3>& forces = state.getForces();
-            double energy = 1;
-            Vec3 force(0, 0, 0);
-            if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
-                energy = sin(0.25*x)*cos(0.33*y)+1;
-                force[0] = -0.25*cos(0.25*x)*cos(0.33*y);
-                force[1] = 0.3*sin(0.25*x)*sin(0.33*y);
-            }
-            ASSERT_EQUAL_VEC(force, forces[0], 0.1);
-            ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
-        }
-    }
-}
-
-void testContinuous3DFunction() {
-    const int xsize = 10;
-    const int ysize = 11;
-    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 zmin = 0.2;
-    const double zmax = 1.3;
-    System system;
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1,z1)+1");
-    vector<int> particles(1, 0);
-    forceField->addBond(particles, vector<double>());
-    vector<double> table(xsize*ysize*zsize);
-    for (int i = 0; i < xsize; i++) {
-        for (int j = 0; j < ysize; j++) {
-            for (int k = 0; k < zsize; k++) {
-                double x = xmin + i*(xmax-xmin)/xsize;
-                double y = ymin + j*(ymax-ymin)/ysize;
-                double z = zmin + k*(zmax-zmin)/zsize;
-                table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
-            }
-        }
-    }
-    forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
-        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
-            for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
-                positions[0] = Vec3(x, y, z);
-                context.setPositions(positions);
-                State state = context.getState(State::Forces | State::Energy);
-                const vector<Vec3>& forces = state.getForces();
-                double energy = 1;
-                Vec3 force(0, 0, 0);
-                if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
-                    energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1;
-                    force[0] = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
-                    force[1] = 0.3*sin(0.25*x)*sin(0.33*y)*(1.0+z);
-                    force[2] = -sin(0.25*x)*cos(0.33*y);
-                }
-                ASSERT_EQUAL_VEC(force, forces[0], 0.1);
-                ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
-            }
-        }
-    }
-}
-
-void testMultipleBonds() {
-    // Two compound bonds using Urey-Bradley example from API doc
-    System customSystem;
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    CustomCompoundBondForce* custom = new CustomCompoundBondForce(3,
-            "0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");
-    custom->addPerBondParameter("kangle");
-    custom->addPerBondParameter("kbond");
-    custom->addPerBondParameter("theta0");
-    custom->addPerBondParameter("r0");
-    vector<double> parameters(4);
-    parameters[0] = 1.0;
-    parameters[1] = 1.0;
-    parameters[2] = 2 * M_PI / 3;
-    parameters[3] = sqrt(3.0) / 2;
-    vector<int> particles0(3);
-    particles0[0] = 0;
-    particles0[1] = 1;
-    particles0[2] = 2;
-    vector<int> particles1(3);
-    particles1[0] = 1;
-    particles1[1] = 2;
-    particles1[2] = 3;
-    custom->addBond(particles0, parameters);
-    custom->addBond(particles1, parameters);
-    customSystem.addForce(custom);
-
-    vector<Vec3> positions(4);
-    positions[0] = Vec3(0, 0.5, 0);
-    positions[1] = Vec3(0, 0, 0);
-    positions[2] = Vec3(0.5, 0, 0);
-    positions[3] = Vec3(0.6, 0, 0.4);
-    VerletIntegrator integrator(0.01);
-    Context context(customSystem, integrator, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(0.199, state.getPotentialEnergy(), 1e-3);
-    vector<Vec3> forces(state.getForces());
-    ASSERT_EQUAL_VEC(Vec3(-1.160, 0.112, 0.0), forces[0], 1e-3);
-    ASSERT_EQUAL_VEC(Vec3(0.927, 1.047, -0.638), forces[1], 1e-3);
-    ASSERT_EQUAL_VEC(Vec3(-0.543, -1.160, 0.721), forces[2], 1e-3);
-    ASSERT_EQUAL_VEC(Vec3(0.776, 0.0, -0.084), forces[3], 1e-3);
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
-        testBond();
-        testPositionDependence();
-        testParallelComputation();
-        testContinuous2DFunction();
-        testContinuous3DFunction();
-        testMultipleBonds();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }

platforms/cuda/tests/TestCudaCustomExternalForce.cpp

@@ -29,106 +29,9 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CUDA implementation of CustomExternalForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CudaPlatform.h"
-#include "openmm/CustomExternalForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "SimTKOpenMMRealType.h"
+#include "CudaTests.h"
+#include "TestCustomExternalForce.h"
 #include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-CudaPlatform platform;
-
-void testForce() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomExternalForce* forceField = new CustomExternalForce("scale*(x+yscale*(y-y0)^2)");
-    forceField->addPerParticleParameter("y0");
-    forceField->addPerParticleParameter("yscale");
-    forceField->addGlobalParameter("scale", 0.5);
-    vector<double> parameters(2);
-    parameters[0] = 0.5;
-    parameters[1] = 2.0;
-    forceField->addParticle(0, parameters);
-    parameters[0] = 1.5;
-    parameters[1] = 3.0;
-    forceField->addParticle(2, parameters);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(3);
-    positions[0] = Vec3(0, 2, 0);
-    positions[1] = Vec3(0, 0, 1);
-    positions[2] = Vec3(1, 0, 1);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
-        ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
-        ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.getPotentialEnergy(), TOL);
-    }
-    
-    // Try changing the parameters and make sure it's still correct.
-    
-    parameters[0] = 1.4;
-    parameters[1] = 3.5;
-    forceField->setParticleParameters(1, 2, parameters);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
-        ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.5*2.0*1.4, 0), forces[2], TOL);
-        ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.5*1.4*1.4), state.getPotentialEnergy(), TOL);
-    }
-}
-
-void testManyParameters() {
-    System system;
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomExternalForce* forceField = new CustomExternalForce("xscale*(x-x0)^2+yscale*(y-y0)^2+zscale*(z-z0)^2");
-    forceField->addPerParticleParameter("x0");
-    forceField->addPerParticleParameter("y0");
-    forceField->addPerParticleParameter("z0");
-    forceField->addPerParticleParameter("xscale");
-    forceField->addPerParticleParameter("yscale");
-    forceField->addPerParticleParameter("zscale");
-    vector<double> parameters(6);
-    parameters[0] = 1.0;
-    parameters[1] = 2.0;
-    parameters[2] = 3.0;
-    parameters[3] = 0.1;
-    parameters[4] = 0.2;
-    parameters[5] = 0.3;
-    forceField->addParticle(0, parameters);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, -1, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-    ASSERT_EQUAL_VEC(Vec3(2*0.1*1.0, 2*0.2*3.0, 2*0.3*3.0), forces[0], TOL);
-    ASSERT_EQUAL_TOL(0.1*1*1 + 0.2*3*3 + 0.3*3*3, state.getPotentialEnergy(), TOL);
-}
 
 void testParallelComputation() {
     System system;
@@ -161,60 +64,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-void testPeriodic() {
-    Vec3 vx(5, 0, 0);
-    Vec3 vy(0, 6, 0);
-    Vec3 vz(1, 2, 7);
-    double x0 = 51, y0 = -17, z0 = 11.2;
-    System system;
-    system.setDefaultPeriodicBoxVectors(vx, vy, vz);
-    system.addParticle(1.0);
-    CustomExternalForce* force = new CustomExternalForce("periodicdistance(x, y, z, x0, y0, z0)^2");
-    force->addPerParticleParameter("x0");
-    force->addPerParticleParameter("y0");
-    force->addPerParticleParameter("z0");
-    vector<double> params(3);
-    params[0] = x0;
-    params[1] = y0;
-    params[2] = z0;
-    force->addParticle(0, params);
-    system.addForce(force);
-    VerletIntegrator integrator(0.01);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, 2, 0);
-    context.setPositions(positions);
-    for (int i = 0; i < 100; i++) {
-        State state = context.getState(State::Positions | State::Forces | State::Energy);
-
-        // Apply periodic boundary conditions to the difference between the two positions.
-
-        Vec3 delta = Vec3(x0, y0, z0)-state.getPositions()[0];
-        delta -= vz*floor(delta[2]/vz[2]+0.5);
-        delta -= vy*floor(delta[1]/vy[1]+0.5);
-        delta -= vx*floor(delta[0]/vx[0]+0.5);
-
-        // Verify that the force and energy are correct.
-
-        ASSERT_EQUAL_VEC(delta*2, state.getForces()[0], 1e-5);
-        ASSERT_EQUAL_TOL(delta.dot(delta), state.getPotentialEnergy(), 1e-5);
-        integrator.step(1);
-    }
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
-        testForce();
-        testManyParameters();
-        testParallelComputation();
-        testPeriodic();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }

platforms/cuda/tests/TestCudaCustomGBForce.cpp

-
 /* -------------------------------------------------------------------------- *
  *                                   OpenMM                                   *
  * -------------------------------------------------------------------------- *
@@ -7,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -30,453 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CUDA implementation of CustomGBForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "sfmt/SFMT.h"
-#include "openmm/Context.h"
-#include "CudaPlatform.h"
-#include "openmm/CustomGBForce.h"
-#include "openmm/GBSAOBCForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-CudaPlatform platform;
-
-void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMethod customMethod) {
-    const int numMolecules = 70;
-    const int numParticles = numMolecules*2;
-    const double boxSize = 10.0;
-    const double cutoff = 2.0;
-
-    // Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
-
-    System standardSystem;
-    System customSystem;
-    for (int i = 0; i < numParticles; i++) {
-        standardSystem.addParticle(1.0);
-        customSystem.addParticle(1.0);
-    }
-    standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
-    customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
-    GBSAOBCForce* obc = new GBSAOBCForce();
-    CustomGBForce* custom = new CustomGBForce();
-    obc->setCutoffDistance(cutoff);
-    custom->setCutoffDistance(cutoff);
-    custom->addPerParticleParameter("q");
-    custom->addPerParticleParameter("radius");
-    custom->addPerParticleParameter("scale");
-    custom->addGlobalParameter("solventDielectric", obc->getSolventDielectric());
-    custom->addGlobalParameter("soluteDielectric", obc->getSoluteDielectric());
-    custom->addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
-                                  "U=r+sr2;"
-                                  "C=2*(1/or1-1/L)*step(sr2-r-or1);"
-                                  "L=max(or1, D);"
-                                  "D=abs(r-sr2);"
-                                  "sr2 = scale2*or2;"
-                                  "or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
-    custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
-                                  "psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
-    custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
-    string invCutoffString = "";
-    if (obcMethod != GBSAOBCForce::NoCutoff) {
-        stringstream s;
-        s<<(1.0/cutoff);
-        invCutoffString = s.str();
-    }
-    custom->addEnergyTerm("138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*("+invCutoffString+"-1/f);"
-                          "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
-    vector<Vec3> positions(numParticles);
-    vector<Vec3> velocities(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    vector<double> params(3);
-    for (int i = 0; i < numMolecules; i++) {
-        if (i < numMolecules/2) {
-            obc->addParticle(1.0, 0.2, 0.5);
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.5;
-            custom->addParticle(params);
-            obc->addParticle(-1.0, 0.1, 0.5);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        else {
-            obc->addParticle(1.0, 0.2, 0.8);
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.8;
-            custom->addParticle(params);
-            obc->addParticle(-1.0, 0.1, 0.8);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
-        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
-        velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-    }
-    obc->setNonbondedMethod(obcMethod);
-    custom->setNonbondedMethod(customMethod);
-    standardSystem.addForce(obc);
-    customSystem.addForce(custom);
-    VerletIntegrator integrator1(0.01);
-    VerletIntegrator integrator2(0.01);
-    Context context1(standardSystem, integrator1, platform);
-    context1.setPositions(positions);
-    context1.setVelocities(velocities);
-    State state1 = context1.getState(State::Forces | State::Energy);
-    Context context2(customSystem, integrator2, platform);
-    context2.setPositions(positions);
-    context2.setVelocities(velocities);
-    State state2 = context2.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
-    for (int i = 0; i < numParticles; i++) {
-        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
-    }
-    
-    // Try changing the particle parameters and make sure it's still correct.
-    
-    for (int i = 0; i < numMolecules/2; i++) {
-        obc->setParticleParameters(2*i, 1.1, 0.3, 0.6);
-        params[0] = 1.1;
-        params[1] = 0.3;
-        params[2] = 0.6;
-        custom->setParticleParameters(2*i, params);
-        obc->setParticleParameters(2*i+1, -1.1, 0.2, 0.4);
-        params[0] = -1.1;
-        params[1] = 0.2;
-        params[2] = 0.4;
-        custom->setParticleParameters(2*i+1, params);
-    }
-    obc->updateParametersInContext(context1);
-    custom->updateParametersInContext(context2);
-    state1 = context1.getState(State::Forces | State::Energy);
-    state2 = context2.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
-    for (int i = 0; i < numParticles; i++) {
-        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
-    }
-}
-
-void testMembrane() {
-    const int numMolecules = 70;
-    const int numParticles = numMolecules*2;
-    const double boxSize = 10.0;
-
-    // Create a system with an implicit membrane.
-
-    System system;
-    for (int i = 0; i < numParticles; i++) {
-        system.addParticle(1.0);
-    }
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
-    CustomGBForce* custom = new CustomGBForce();
-    custom->setCutoffDistance(2.0);
-    custom->addPerParticleParameter("q");
-    custom->addPerParticleParameter("radius");
-    custom->addPerParticleParameter("scale");
-    custom->addGlobalParameter("thickness", 3);
-    custom->addGlobalParameter("solventDielectric", 78.3);
-    custom->addGlobalParameter("soluteDielectric", 1);
-    custom->addComputedValue("Imol", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
-                             "U=r+sr2;"
-                             "C=2*(1/or1-1/L)*step(sr2-r-or1);"
-                             "L=max(or1, D);"
-                             "D=abs(r-sr2);"
-                             "sr2 = scale2*or2;"
-                             "or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
-    custom->addComputedValue("Imem", "(1/radius+2*log(2)/thickness)/(1+exp(7.2*(abs(z)+radius-0.5*thickness)))", CustomGBForce::SingleParticle);
-    custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
-                             "psi=max(Imol,Imem)*or; or=radius-0.009", CustomGBForce::SingleParticle);
-    custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
-    custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
-                          "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
-    vector<Vec3> positions(numParticles);
-    vector<Vec3> velocities(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    vector<double> params(3);
-    for (int i = 0; i < numMolecules; i++) {
-        if (i < numMolecules/2) {
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.5;
-            custom->addParticle(params);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        else {
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.8;
-            custom->addParticle(params);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
-        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
-        velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-    }
-    system.addForce(custom);
-    VerletIntegrator integrator(0.01);
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    context.setVelocities(velocities);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-
-    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-    double norm = 0.0;
-    for (int i = 0; i < (int) forces.size(); ++i)
-        norm += forces[i].dot(forces[i]);
-    norm = std::sqrt(norm);
-    const double stepSize = 1e-2;
-    double step = 0.5*stepSize/norm;
-    vector<Vec3> positions2(numParticles), positions3(numParticles);
-    for (int i = 0; i < (int) positions.size(); ++i) {
-        Vec3 p = positions[i];
-        Vec3 f = forces[i];
-        positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-        positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
-    }
-    context.setPositions(positions2);
-    State state2 = context.getState(State::Energy);
-    context.setPositions(positions3);
-    State state3 = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
-}
-
-void testTabulatedFunction() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomGBForce* force = new CustomGBForce();
-    force->addComputedValue("a", "0", CustomGBForce::ParticlePair);
-    force->addEnergyTerm("fn(r)+1", CustomGBForce::ParticlePair);
-    force->addParticle(vector<double>());
-    force->addParticle(vector<double>());
-    vector<double> table;
-    for (int i = 0; i < 21; i++)
-        table.push_back(std::sin(0.25*i));
-    force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
-    system.addForce(force);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (int i = 1; i < 30; i++) {
-        double x = (7.0/30.0)*i;
-        positions[1] = Vec3(x, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        double force = (x < 1.0 || x > 6.0 ? 0.0 : -std::cos(x-1.0));
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
-        ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
-        ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
-    }
-    for (int i = 1; i < 20; i++) {
-        double x = 0.25*i+1.0;
-        positions[1] = Vec3(x, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Energy);
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
-    }
-}
-
-void testMultipleChainRules() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomGBForce* force = new CustomGBForce();
-    force->addComputedValue("a", "2*r", CustomGBForce::ParticlePair);
-    force->addComputedValue("b", "a+1", CustomGBForce::SingleParticle);
-    force->addComputedValue("c", "2*b+a", CustomGBForce::SingleParticle);
-    force->addEnergyTerm("0.1*a+1*b+10*c", CustomGBForce::SingleParticle); // 0.1*(2*r) + 2*r+1 + 10*(3*a+2) = 0.2*r + 2*r+1 + 40*r+20+20*r = 62.2*r+21
-    force->addParticle(vector<double>());
-    force->addParticle(vector<double>());
-    system.addForce(force);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (int i = 1; i < 5; i++) {
-        positions[1] = Vec3(i, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(124.4, 0, 0), forces[0], 1e-4);
-        ASSERT_EQUAL_VEC(Vec3(-124.4, 0, 0), forces[1], 1e-4);
-        ASSERT_EQUAL_TOL(2*(62.2*i+21), state.getPotentialEnergy(), 0.02);
-    }
-}
-
-void testPositionDependence() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomGBForce* force = new CustomGBForce();
-    force->addComputedValue("a", "r", CustomGBForce::ParticlePair);
-    force->addComputedValue("b", "a+x*y", CustomGBForce::SingleParticle);
-    force->addEnergyTerm("b*z", CustomGBForce::SingleParticle);
-    force->addEnergyTerm("b1+b2", CustomGBForce::ParticlePair); // = 2*r+x1*y1+x2*y2
-    force->addParticle(vector<double>());
-    force->addParticle(vector<double>());
-    system.addForce(force);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    vector<Vec3> forces(2);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    for (int i = 0; i < 5; i++) {
-        positions[0] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        positions[1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        Vec3 delta = positions[0]-positions[1];
-        double r = sqrt(delta.dot(delta));
-        double energy = 2*r+positions[0][0]*positions[0][1]+positions[1][0]*positions[1][1];
-        for (int j = 0; j < 2; j++)
-            energy += positions[j][2]*(r+positions[j][0]*positions[j][1]);
-        Vec3 force1(-(1+positions[0][2])*delta[0]/r-(1+positions[0][2])*positions[0][1]-(1+positions[1][2])*delta[0]/r,
-                    -(1+positions[0][2])*delta[1]/r-(1+positions[0][2])*positions[0][0]-(1+positions[1][2])*delta[1]/r,
-                    -(1+positions[0][2])*delta[2]/r-(r+positions[0][0]*positions[0][1])-(1+positions[1][2])*delta[2]/r);
-        Vec3 force2((1+positions[0][2])*delta[0]/r+(1+positions[1][2])*delta[0]/r-(1+positions[1][2])*positions[1][1],
-                    (1+positions[0][2])*delta[1]/r+(1+positions[1][2])*delta[1]/r-(1+positions[1][2])*positions[1][0],
-                    (1+positions[0][2])*delta[2]/r+(1+positions[1][2])*delta[2]/r-(r+positions[1][0]*positions[1][1]));
-        ASSERT_EQUAL_VEC(force1, forces[0], 1e-4);
-        ASSERT_EQUAL_VEC(force2, forces[1], 1e-4);
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
-
-        // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-        double norm = 0.0;
-        for (int i = 0; i < (int) forces.size(); ++i)
-            norm += forces[i].dot(forces[i]);
-        norm = std::sqrt(norm);
-        const double stepSize = 1e-3;
-        double step = 0.5*stepSize/norm;
-        vector<Vec3> positions2(2), positions3(2);
-        for (int i = 0; i < (int) positions.size(); ++i) {
-            Vec3 p = positions[i];
-            Vec3 f = forces[i];
-            positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-            positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
-        }
-        context.setPositions(positions2);
-        State state2 = context.getState(State::Energy);
-        context.setPositions(positions3);
-        State state3 = context.getState(State::Energy);
-        ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
-    }
-}
-
-void testExclusions() {
-    for (int i = 0; i < 4; i++) {
-        System system;
-        system.addParticle(1.0);
-        system.addParticle(1.0);
-        VerletIntegrator integrator(0.01);
-        CustomGBForce* force = new CustomGBForce();
-        force->addComputedValue("a", "r", i < 2 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
-        force->addEnergyTerm("a", CustomGBForce::SingleParticle);
-        force->addEnergyTerm("(1+a1+a2)*r", i%2 == 0 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
-        force->addParticle(vector<double>());
-        force->addParticle(vector<double>());
-        force->addExclusion(0, 1);
-        system.addForce(force);
-        Context context(system, integrator, platform);
-        vector<Vec3> positions(2);
-        positions[0] = Vec3(0, 0, 0);
-        positions[1] = Vec3(1, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        double f, energy;
-        switch (i)
-        {
-            case 0: // e = 0
-                f = 0;
-                energy = 0;
-                break;
-            case 1: // e = r
-                f = 1;
-                energy = 1;
-                break;
-            case 2: // e = 2r
-                f = 2;
-                energy = 2;
-                break;
-            case 3: // e = 3r + 2r^2
-                f = 7;
-                energy = 5;
-                break;
-            default:
-                ASSERT(false);
-        }
-        ASSERT_EQUAL_VEC(Vec3(f, 0, 0), forces[0], 1e-4);
-        ASSERT_EQUAL_VEC(Vec3(-f, 0, 0), forces[1], 1e-4);
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
-
-        // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-        double norm = 0.0;
-        for (int i = 0; i < (int) forces.size(); ++i)
-            norm += forces[i].dot(forces[i]);
-        norm = std::sqrt(norm);
-        const double stepSize = 1e-3;
-        double step = stepSize/norm;
-        for (int i = 0; i < (int) positions.size(); ++i) {
-            Vec3 p = positions[i];
-            Vec3 f = forces[i];
-            positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-        }
-        context.setPositions(positions);
-        State state2 = context.getState(State::Energy);
-        ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/stepSize, 1e-3*abs(state.getPotentialEnergy()));
-    }
-}
+#include "CudaTests.h"
+#include "TestCustomGBForce.h"
 
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
-        testOBC(GBSAOBCForce::NoCutoff, CustomGBForce::NoCutoff);
-        testOBC(GBSAOBCForce::CutoffNonPeriodic, CustomGBForce::CutoffNonPeriodic);
-        testOBC(GBSAOBCForce::CutoffPeriodic, CustomGBForce::CutoffPeriodic);
-        testMembrane();
-        testTabulatedFunction();
-        testMultipleChainRules();
-        testPositionDependence();
-        testExclusions();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }

platforms/cuda/tests/TestCudaPeriodicTorsionForce.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) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,69 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CUDA implementation of PeriodicTorsionForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CudaPlatform.h"
-#include "openmm/PeriodicTorsionForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "SimTKOpenMMRealType.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-CudaPlatform platform;
-
-const double TOL = 1e-5;
-
-void testPeriodicTorsions() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    PeriodicTorsionForce* forceField = new PeriodicTorsionForce();
-    forceField->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
-    system.addForce(forceField);
-    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*PI_M/3);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0.5*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*PI_M/3)), state.getPotentialEnergy(), TOL);
-    }
-    
-    // Try changing the torsion parameters and make sure it's still correct.
-    
-    forceField->setTorsionParameters(0, 0, 1, 2, 3, 3, PI_M/3.2, 1.3);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        double dtheta = (3*PI_M/2)-(PI_M/3.2);
-        double torque = -3*1.3*std::sin(dtheta);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0.5*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(1.3*(1+std::cos(dtheta)), state.getPotentialEnergy(), TOL);
-    }
-}
+#include "CudaTests.h"
+#include "TestPeriodicTorsionForce.h"
 
 void testParallelComputation() {
     System system;
@@ -121,18 +60,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
-        testPeriodicTorsions();
-        testParallelComputation();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }
-

platforms/cuda/tests/TestCudaRBTorsionForce.cpp

@@ -29,88 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CUDA implementation of RBTorsionForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CudaPlatform.h"
-#include "openmm/RBTorsionForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "SimTKOpenMMRealType.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-CudaPlatform platform;
-
-const double TOL = 1e-5;
-
-void testRBTorsions() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    RBTorsionForce* forceField = new RBTorsionForce();
-    forceField->addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
-    system.addForce(forceField);
-    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, 1, 1);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        double psi = 0.25*PI_M - PI_M;
-        double torque = 0.0;
-        for (int i = 1; i < 6; ++i) {
-            double c = 0.1*(i+1);
-            torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
-        }
-        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, -0.5*torque), 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);
-        double energy = 0.0;
-        for (int i = 0; i < 6; ++i) {
-            double c = 0.1*(i+1);
-            energy += c*std::pow(std::cos(psi), i);
-        }
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
-    }
-    
-    // Try changing the torsion parameters and make sure it's still correct.
-    
-    forceField->setTorsionParameters(0, 0, 1, 2, 3, 0.11, 0.22, 0.33, 0.44, 0.55, 0.66);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        double psi = 0.25*PI_M - PI_M;
-        double torque = 0.0;
-        for (int i = 1; i < 6; ++i) {
-            double c = 0.11*(i+1);
-            torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
-        }
-        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, -0.5*torque), 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);
-        double energy = 0.0;
-        for (int i = 0; i < 6; ++i) {
-            double c = 0.11*(i+1);
-            energy += c*std::pow(std::cos(psi), i);
-        }
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
-    }
-}
+#include "CudaTests.h"
+#include "TestRBTorsionForce.h"
 
 void testParallelComputation() {
     System system;
@@ -140,18 +60,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
-        testRBTorsions();
-        testParallelComputation();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }
-

platforms/opencl/tests/OpenCLTests.h

@@ -37,4 +37,4 @@ OpenMM::OpenCLPlatform platform;
 void initializeTests(int argc, char* argv[]) {
     if (argc > 1)
         platform.setPropertyDefaultValue("OpenCLPrecision", std::string(argv[1]));
-}
+}
\ No newline at end of file

platforms/opencl/tests/TestOpenCLCustomAngleForce.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) 2008-2010 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,109 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the OpenCL implementation of CustomAngleForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "OpenCLPlatform.h"
-#include "openmm/CustomAngleForce.h"
-#include "openmm/HarmonicAngleForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-static OpenCLPlatform platform;
-
-void testAngles() {
-    // Create a system using a CustomAngleForce.
-
-    System customSystem;
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    CustomAngleForce* custom = new CustomAngleForce("scale*k*(theta-theta0)^2");
-    custom->addPerAngleParameter("theta0");
-    custom->addPerAngleParameter("k");
-    custom->addGlobalParameter("scale", 0.5);
-    vector<double> parameters(2);
-    parameters[0] = 1.5;
-    parameters[1] = 0.8;
-    custom->addAngle(0, 1, 2, parameters);
-    parameters[0] = 2.0;
-    parameters[1] = 0.5;
-    custom->addAngle(1, 2, 3, parameters);
-    customSystem.addForce(custom);
-
-    // Create an identical system using a HarmonicAngleForce.
-
-    System harmonicSystem;
-    harmonicSystem.addParticle(1.0);
-    harmonicSystem.addParticle(1.0);
-    harmonicSystem.addParticle(1.0);
-    harmonicSystem.addParticle(1.0);
-    HarmonicAngleForce* harmonic = new HarmonicAngleForce();
-    harmonic->addAngle(0, 1, 2, 1.5, 0.8);
-    harmonic->addAngle(1, 2, 3, 2.0, 0.5);
-    harmonicSystem.addForce(harmonic);
-
-    // 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);
-
-    vector<Vec3> positions(4);
-    VerletIntegrator integrator1(0.01);
-    VerletIntegrator integrator2(0.01);
-    Context c1(customSystem, integrator1, platform);
-    Context c2(harmonicSystem, integrator2, platform);
-    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);
-        const vector<Vec3>& forces = s1.getForces();
-        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);
-    }
-    
-    // Try changing the angle parameters and make sure it's still correct.
-    
-    parameters[0] = 1.6;
-    parameters[1] = 0.9;
-    custom->setAngleParameters(0, 0, 1, 2, parameters);
-    parameters[0] = 2.1;
-    parameters[1] = 0.6;
-    custom->setAngleParameters(1, 1, 2, 3, parameters);
-    custom->updateParametersInContext(c1);
-    harmonic->setAngleParameters(0, 0, 1, 2, 1.6, 0.9);
-    harmonic->setAngleParameters(1, 1, 2, 3, 2.1, 0.6);
-    harmonic->updateParametersInContext(c2);
-    {
-        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);
-        const vector<Vec3>& forces = s1.getForces();
-        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);
-    }
-}
+#include "OpenCLTests.h"
+#include "TestCustomAngleForce.h"
 
 void testParallelComputation() {
     System system;
@@ -162,20 +61,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
-        testAngles();
-        testParallelComputation();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }
-
-
-

platforms/opencl/tests/TestOpenCLCustomBondForce.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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,111 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the OpenCL implementation of CustomBondForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "OpenCLPlatform.h"
-#include "openmm/CustomBondForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "SimTKOpenMMRealType.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-static OpenCLPlatform platform;
-
-const double TOL = 1e-5;
-
-void testBonds() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    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] = 1.5;
-    parameters[1] = 0.8;
-    forceField->addBond(0, 1, parameters);
-    parameters[0] = 1.2;
-    parameters[1] = 0.7;
-    forceField->addBond(1, 2, parameters);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(3);
-    positions[0] = Vec3(0, 2, 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();
-        ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
-        ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
-        ASSERT_EQUAL_TOL(0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
-    }
-    
-    // Try changing the bond parameters and make sure it's still correct.
-    
-    parameters[0] = 1.6;
-    parameters[1] = 0.9;
-    forceField->setBondParameters(0, 0, 1, parameters);
-    parameters[0] = 1.3;
-    parameters[1] = 0.8;
-    forceField->setBondParameters(1, 1, 2, parameters);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(0, -0.9*0.4, 0), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0.8*0.3, 0, 0), forces[2], TOL);
-        ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
-        ASSERT_EQUAL_TOL(0.5*0.9*0.4*0.4 + 0.5*0.8*0.3*0.3, state.getPotentialEnergy(), TOL);
-    }
-}
-
-void testManyParameters() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomBondForce* forceField = new CustomBondForce("(a+b+c+d+e+f+g+h+i)*r");
-    forceField->addPerBondParameter("a");
-    forceField->addPerBondParameter("b");
-    forceField->addPerBondParameter("c");
-    forceField->addPerBondParameter("d");
-    forceField->addPerBondParameter("e");
-    forceField->addPerBondParameter("f");
-    forceField->addPerBondParameter("g");
-    forceField->addPerBondParameter("h");
-    forceField->addPerBondParameter("i");
-    vector<double> parameters(forceField->getNumPerBondParameters());
-    for (int i = 0; i < (int) parameters.size(); i++)
-        parameters[i] = i;
-    forceField->addBond(0, 1, parameters);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, 2.5, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-    double f = 1+2+3+4+5+6+7+8;
-    ASSERT_EQUAL_VEC(Vec3(0, f, 0), forces[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, -f, 0), forces[1], TOL);
-    ASSERT_EQUAL_TOL(f*2.5, state.getPotentialEnergy(), TOL);
-}
+#include "OpenCLTests.h"
+#include "TestCustomBondForce.h"
 
 void testParallelComputation() {
     System system;
@@ -164,19 +61,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
-        testBonds();
-        testManyParameters();
-        testParallelComputation();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }
-

platforms/opencl/tests/TestOpenCLCustomCentroidBondForce.cpp

@@ -29,247 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the reference implementation of CustomCompoundBondForce.
- */
+#include "OpenCLTests.h"
+#include "TestCustomCentroidBondForce.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "OpenCLPlatform.h"
-#include "openmm/CustomCentroidBondForce.h"
-#include "openmm/CustomCompoundBondForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-OpenCLPlatform platform;
-
-const double TOL = 1e-5;
-
-void testHarmonicBond() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(2.0);
-    system.addParticle(3.0);
-    system.addParticle(4.0);
-    system.addParticle(5.0);
-    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);
-    system.addForce(force);
-    ASSERT(!system.usesPeriodicBoundaryConditions());
-
-    // 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(2.5*2.5, state.getPotentialEnergy(), TOL);
-    ASSERT_EQUAL_VEC(Vec3(-2*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(-2*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
-    ASSERT_EQUAL_VEC(Vec3(2*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
-    ASSERT_EQUAL_VEC(Vec3(2*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
-    ASSERT_EQUAL_VEC(Vec3(2*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
-
-    // Update the per-bond parameter and see if the results change.
-
-    parameters[0] = 2.0;
-    force->setBondParameters(0, groups, parameters);
-    force->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(2*2.5*2.5, state.getPotentialEnergy(), TOL);
-    ASSERT_EQUAL_VEC(Vec3(-4*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(-4*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
-    ASSERT_EQUAL_VEC(Vec3(4*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
-    ASSERT_EQUAL_VEC(Vec3(4*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
-    ASSERT_EQUAL_VEC(Vec3(4*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
-    
-    // All the particles should be treated as a single molecule.
-    
-    vector<std::vector<int> > molecules = context.getMolecules();
-    ASSERT_EQUAL(1, molecules.size());
-    ASSERT_EQUAL(5, molecules[0].size());
-}
-
-void testComplexFunction() {
-    int numParticles = 5;
-    System system;
-    for (int i = 0; i < numParticles; i++)
-        system.addParticle(2.0);
-    vector<double> table(20);
-    for (int i = 0; i < 20; i++)
-        table[i] = sin(0.11*i);
-
-    // When every group contains only one particle, a CustomCentroidBondForce is identical to a
-    // CustomCompoundBondForce.  Use that to test a complicated energy function with lots of terms.
-
-    CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+fn(distance(p1,p2))*angle(p3,p2,p4)+scale*dihedral(p2,p1,p4,p3)");
-    CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+fn(distance(g1,g2))*angle(g3,g2,g4)+scale*dihedral(g2,g1,g4,g3)");
-    compound->addGlobalParameter("scale", 0.5);
-    centroid->addGlobalParameter("scale", 0.5);
-    compound->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
-    centroid->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
-
-    // Add two bonds to the CustomCompoundBondForce.
-
-    vector<int> particles(4);
-    vector<double> parameters;
-    particles[0] = 0;
-    particles[1] = 1;
-    particles[2] = 2;
-    particles[3] = 3;
-    compound->addBond(particles, parameters);
-    particles[0] = 2;
-    particles[1] = 4;
-    particles[2] = 3;
-    particles[3] = 1;
-    compound->addBond(particles, parameters);
-
-    // Add identical bonds to the CustomCentroidBondForce.  As a stronger test, make sure that
-    // group number is different from particle number.
-
-    vector<int> groupMembers(1);
-    groupMembers[0] = 3;
-    centroid->addGroup(groupMembers);
-    groupMembers[0] = 0;
-    centroid->addGroup(groupMembers);
-    groupMembers[0] = 1;
-    centroid->addGroup(groupMembers);
-    groupMembers[0] = 2;
-    centroid->addGroup(groupMembers);
-    groupMembers[0] = 4;
-    centroid->addGroup(groupMembers);
-    vector<int> groups(4);
-    groups[0] = 1;
-    groups[1] = 2;
-    groups[2] = 3;
-    groups[3] = 0;
-    centroid->addBond(groups, parameters);
-    groups[0] = 3;
-    groups[1] = 4;
-    groups[2] = 0;
-    groups[3] = 2;
-    centroid->addBond(groups, parameters);
-
-    // Add both forces as different force groups, and create a context.
-
-    centroid->setForceGroup(1);
-    system.addForce(compound);
-    system.addForce(centroid);
-    VerletIntegrator integrator(0.01);
-    Context context(system, integrator, platform);
-
-    // Evaluate the force and energy for various positions and see if they match.
-
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    vector<Vec3> positions(numParticles);
-    for (int i = 0; i < 10; i++) {
-        for (int j = 0; j < numParticles; j++)
-            positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
-        context.setPositions(positions);
-        State state1 = context.getState(State::Forces | State::Energy, false, 1<<0);
-        State state2 = context.getState(State::Forces | State::Energy, false, 1<<1);
-        ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), TOL);
-        for (int i = 0; i < numParticles; i++)
-            ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], TOL);
-    }
-}
-
-void testCustomWeights() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(2.0);
-    system.addParticle(3.0);
-    system.addParticle(4.0);
-    CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "distance(g1,g2)^2");
-    vector<int> particles(2);
-    vector<double> weights(2);
-    particles[0] = 0;
-    particles[1] = 1;
-    weights[0] = 0.5;
-    weights[1] = 1.5;
-    force->addGroup(particles, weights);
-    particles[0] = 2;
-    particles[1] = 3;
-    weights[0] = 2.0;
-    weights[1] = 1.0;
-    force->addGroup(particles, weights);
-    vector<int> groups;
-    groups.push_back(0);
-    groups.push_back(1);
-    vector<double> parameters;
-    force->addBond(groups, parameters);
-    system.addForce(force);
-
-    // The center of mass of group 0 is (0, 1, 0).
-
-    vector<Vec3> positions(4);
-    positions[0] = Vec3(0, 4, 0);
-    positions[1] = Vec3(0, 0, 0);
-
-    // The center of mass of group 1 is (0, 10, 0).
-
-    positions[2] = Vec3(0, 9, 0);
-    positions[3] = Vec3(0, 12, 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(9.0*9.0, state.getPotentialEnergy(), TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, 2*9*(0.5/2.0), 0), state.getForces()[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, 2*9*(1.5/2.0), 0), state.getForces()[1], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, -2*9*(2.0/3.0), 0), state.getForces()[2], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, -2*9*(1.0/3.0), 0), state.getForces()[3], TOL);
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
-        testHarmonicBond();
-        testComplexFunction();
-        testCustomWeights();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }

platforms/opencl/tests/TestOpenCLCustomCompoundBondForce.cpp

@@ -29,145 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the OpenCL implementation of CustomCompoundBondForce.
- */
-
-#ifdef WIN32
-  #define _USE_MATH_DEFINES // Needed to get M_PI
-#endif
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "OpenCLPlatform.h"
-#include "openmm/CustomCompoundBondForce.h"
-#include "openmm/HarmonicAngleForce.h"
-#include "openmm/HarmonicBondForce.h"
-#include "openmm/PeriodicTorsionForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-static OpenCLPlatform platform;
-
-const double TOL = 1e-5;
-
-void testBond() {
-    // Create a system using a CustomCompoundBondForce.
-
-    System customSystem;
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    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);
-    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);
-    HarmonicBondForce* bonds = new HarmonicBondForce();
-    bonds->addBond(0, 1, 1.1, 1.5);
-    bonds->addBond(1, 3, 1.1, 1.5);
-    standardSystem.addForce(bonds);
-    HarmonicAngleForce* angles = new HarmonicAngleForce();
-    angles->addAngle(1, 3, 2, 2.9, 0.8);
-    standardSystem.addForce(angles);
-    PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
-    torsions->addTorsion(0, 1, 3, 2, 1, 1.3, 0.6);
-    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);
-    }
-    
-    // Try changing the bond parameters and make sure it's still correct.
-    
-    parameters[0] = 1.6;
-    parameters[3] = 1.3;
-    custom->setBondParameters(0, particles, parameters);
-    custom->updateParametersInContext(c1);
-    bonds->setBondParameters(0, 0, 1, 1.3, 1.6);
-    bonds->setBondParameters(1, 1, 3, 1.3, 1.6);
-    bonds->updateParametersInContext(c2);
-    {
-        State s1 = c1.getState(State::Forces | State::Energy);
-        State s2 = c2.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = s1.getForces();
-        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 testPositionDependence() {
-    System customSystem;
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    CustomCompoundBondForce* custom = new CustomCompoundBondForce(2, "scale1*distance(p1,p2)+scale2*x1+2*y2");
-    custom->addGlobalParameter("scale1", 0.3);
-    custom->addGlobalParameter("scale2", 0.2);
-    vector<int> particles(2);
-    particles[0] = 1;
-    particles[1] = 0;
-    vector<double> parameters;
-    custom->addBond(particles, parameters);
-    customSystem.addForce(custom);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(1.5, 1, 0);
-    positions[1] = Vec3(0.5, 1, 0);
-    VerletIntegrator integrator(0.01);
-    Context context(customSystem, integrator, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(0.3*1.0+0.2*0.5+2*1, state.getPotentialEnergy(), 1e-5);
-    ASSERT_EQUAL_VEC(Vec3(-0.3, -2, 0), state.getForces()[0], 1e-5);
-    ASSERT_EQUAL_VEC(Vec3(0.3-0.2, 0, 0), state.getForces()[1], 1e-5);
-}
+#include "OpenCLTests.h"
+#include "TestCustomCompoundBondForce.h"
 
 void testParallelComputation() {
     System system;
@@ -202,165 +65,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-void testContinuous2DFunction() {
-    const int xsize = 10;
-    const int ysize = 11;
-    const double xmin = 0.4;
-    const double xmax = 1.1;
-    const double ymin = 0.0;
-    const double ymax = 0.9;
-    System system;
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1)+1");
-    vector<int> particles(1, 0);
-    forceField->addBond(particles, vector<double>());
-    vector<double> table(xsize*ysize);
-    for (int i = 0; i < xsize; i++) {
-        for (int j = 0; j < ysize; j++) {
-            double x = xmin + i*(xmax-xmin)/xsize;
-            double y = ymin + j*(ymax-ymin)/ysize;
-            table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
-        }
-    }
-    forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
-        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
-            positions[0] = Vec3(x, y, 1.5);
-            context.setPositions(positions);
-            State state = context.getState(State::Forces | State::Energy);
-            const vector<Vec3>& forces = state.getForces();
-            double energy = 1;
-            Vec3 force(0, 0, 0);
-            if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
-                energy = sin(0.25*x)*cos(0.33*y)+1;
-                force[0] = -0.25*cos(0.25*x)*cos(0.33*y);
-                force[1] = 0.3*sin(0.25*x)*sin(0.33*y);
-            }
-            ASSERT_EQUAL_VEC(force, forces[0], 0.1);
-            ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
-        }
-    }
-}
-
-void testContinuous3DFunction() {
-    const int xsize = 10;
-    const int ysize = 11;
-    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 zmin = 0.2;
-    const double zmax = 1.3;
-    System system;
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1,z1)+1");
-    vector<int> particles(1, 0);
-    forceField->addBond(particles, vector<double>());
-    vector<double> table(xsize*ysize*zsize);
-    for (int i = 0; i < xsize; i++) {
-        for (int j = 0; j < ysize; j++) {
-            for (int k = 0; k < zsize; k++) {
-                double x = xmin + i*(xmax-xmin)/xsize;
-                double y = ymin + j*(ymax-ymin)/ysize;
-                double z = zmin + k*(zmax-zmin)/zsize;
-                table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
-            }
-        }
-    }
-    forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
-        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
-            for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
-                positions[0] = Vec3(x, y, z);
-                context.setPositions(positions);
-                State state = context.getState(State::Forces | State::Energy);
-                const vector<Vec3>& forces = state.getForces();
-                double energy = 1;
-                Vec3 force(0, 0, 0);
-                if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
-                    energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1;
-                    force[0] = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
-                    force[1] = 0.3*sin(0.25*x)*sin(0.33*y)*(1.0+z);
-                    force[2] = -sin(0.25*x)*cos(0.33*y);
-                }
-                ASSERT_EQUAL_VEC(force, forces[0], 0.1);
-                ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
-            }
-        }
-    }
-}
-
-void testMultipleBonds() {
-    // Two compound bonds using Urey-Bradley example from API doc
-    System customSystem;
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    customSystem.addParticle(1.0);
-    CustomCompoundBondForce* custom = new CustomCompoundBondForce(3,
-            "0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");
-    custom->addPerBondParameter("kangle");
-    custom->addPerBondParameter("kbond");
-    custom->addPerBondParameter("theta0");
-    custom->addPerBondParameter("r0");
-    vector<double> parameters(4);
-    parameters[0] = 1.0;
-    parameters[1] = 1.0;
-    parameters[2] = 2 * M_PI / 3;
-    parameters[3] = sqrt(3.0) / 2;
-    vector<int> particles0(3);
-    particles0[0] = 0;
-    particles0[1] = 1;
-    particles0[2] = 2;
-    vector<int> particles1(3);
-    particles1[0] = 1;
-    particles1[1] = 2;
-    particles1[2] = 3;
-    custom->addBond(particles0, parameters);
-    custom->addBond(particles1, parameters);
-    customSystem.addForce(custom);
-
-    vector<Vec3> positions(4);
-    positions[0] = Vec3(0, 0.5, 0);
-    positions[1] = Vec3(0, 0, 0);
-    positions[2] = Vec3(0.5, 0, 0);
-    positions[3] = Vec3(0.6, 0, 0.4);
-    VerletIntegrator integrator(0.01);
-    Context context(customSystem, integrator, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(0.199, state.getPotentialEnergy(), 1e-3);
-    vector<Vec3> forces(state.getForces());
-    ASSERT_EQUAL_VEC(Vec3(-1.160, 0.112, 0.0), forces[0], 1e-3);
-    ASSERT_EQUAL_VEC(Vec3(0.927, 1.047, -0.638), forces[1], 1e-3);
-    ASSERT_EQUAL_VEC(Vec3(-0.543, -1.160, 0.721), forces[2], 1e-3);
-    ASSERT_EQUAL_VEC(Vec3(0.776, 0.0, -0.084), forces[3], 1e-3);
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
-        testBond();
-        testPositionDependence();
-        testParallelComputation();
-        testContinuous2DFunction();
-        testContinuous3DFunction();
-        testMultipleBonds();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }

platforms/opencl/tests/TestOpenCLCustomExternalForce.cpp

@@ -29,106 +29,9 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the OpenCL implementation of CustomExternalForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "OpenCLPlatform.h"
-#include "openmm/CustomExternalForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "SimTKOpenMMRealType.h"
+#include "OpenCLTests.h"
+#include "TestCustomExternalForce.h"
 #include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-static OpenCLPlatform platform;
-
-const double TOL = 1e-5;
-
-void testForce() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomExternalForce* forceField = new CustomExternalForce("scale*(x+yscale*(y-y0)^2)");
-    forceField->addPerParticleParameter("y0");
-    forceField->addPerParticleParameter("yscale");
-    forceField->addGlobalParameter("scale", 0.5);
-    vector<double> parameters(2);
-    parameters[0] = 0.5;
-    parameters[1] = 2.0;
-    forceField->addParticle(0, parameters);
-    parameters[0] = 1.5;
-    parameters[1] = 3.0;
-    forceField->addParticle(2, parameters);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(3);
-    positions[0] = Vec3(0, 2, 0);
-    positions[1] = Vec3(0, 0, 1);
-    positions[2] = Vec3(1, 0, 1);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
-        ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
-        ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.getPotentialEnergy(), TOL);
-    }
-    
-    // Try changing the parameters and make sure it's still correct.
-    
-    parameters[0] = 1.4;
-    parameters[1] = 3.5;
-    forceField->setParticleParameters(1, 2, parameters);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
-        ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.5*2.0*1.4, 0), forces[2], TOL);
-        ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.5*1.4*1.4), state.getPotentialEnergy(), TOL);
-    }
-}
-
-void testManyParameters() {
-    System system;
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomExternalForce* forceField = new CustomExternalForce("xscale*(x-x0)^2+yscale*(y-y0)^2+zscale*(z-z0)^2");
-    forceField->addPerParticleParameter("x0");
-    forceField->addPerParticleParameter("y0");
-    forceField->addPerParticleParameter("z0");
-    forceField->addPerParticleParameter("xscale");
-    forceField->addPerParticleParameter("yscale");
-    forceField->addPerParticleParameter("zscale");
-    vector<double> parameters(6);
-    parameters[0] = 1.0;
-    parameters[1] = 2.0;
-    parameters[2] = 3.0;
-    parameters[3] = 0.1;
-    parameters[4] = 0.2;
-    parameters[5] = 0.3;
-    forceField->addParticle(0, parameters);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, -1, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-    ASSERT_EQUAL_VEC(Vec3(2*0.1*1.0, 2*0.2*3.0, 2*0.3*3.0), forces[0], TOL);
-    ASSERT_EQUAL_TOL(0.1*1*1 + 0.2*3*3 + 0.3*3*3, state.getPotentialEnergy(), TOL);
-}
 
 void testParallelComputation() {
     System system;
@@ -161,63 +64,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-void testPeriodic() {
-    Vec3 vx(5, 0, 0);
-    Vec3 vy(0, 6, 0);
-    Vec3 vz(1, 2, 7);
-    double x0 = 51, y0 = -17, z0 = 11.2;
-    System system;
-    system.setDefaultPeriodicBoxVectors(vx, vy, vz);
-    system.addParticle(1.0);
-    CustomExternalForce* force = new CustomExternalForce("periodicdistance(x, y, z, x0, y0, z0)^2");
-    force->addPerParticleParameter("x0");
-    force->addPerParticleParameter("y0");
-    force->addPerParticleParameter("z0");
-    vector<double> params(3);
-    params[0] = x0;
-    params[1] = y0;
-    params[2] = z0;
-    force->addParticle(0, params);
-    system.addForce(force);
-    VerletIntegrator integrator(0.01);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, 2, 0);
-    context.setPositions(positions);
-    for (int i = 0; i < 100; i++) {
-        State state = context.getState(State::Positions | State::Forces | State::Energy);
-
-        // Apply periodic boundary conditions to the difference between the two positions.
-
-        Vec3 delta = Vec3(x0, y0, z0)-state.getPositions()[0];
-        delta -= vz*floor(delta[2]/vz[2]+0.5);
-        delta -= vy*floor(delta[1]/vy[1]+0.5);
-        delta -= vx*floor(delta[0]/vx[0]+0.5);
-
-        // Verify that the force and energy are correct.
-
-        ASSERT_EQUAL_VEC(delta*2, state.getForces()[0], 1e-5);
-        ASSERT_EQUAL_TOL(delta.dot(delta), state.getPotentialEnergy(), 1e-5);
-        integrator.step(1);
-    }
+void runPlatformTests() {
+    testParallelComputation();
 }
-
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
-        testForce();
-        testManyParameters();
-        testParallelComputation();
-        testPeriodic();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
-}
-
-
-

platforms/opencl/tests/TestOpenCLCustomGBForce.cpp

-
 /* -------------------------------------------------------------------------- *
  *                                   OpenMM                                   *
  * -------------------------------------------------------------------------- *
@@ -7,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -30,453 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the OpenCL implementation of CustomGBForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "sfmt/SFMT.h"
-#include "openmm/Context.h"
-#include "OpenCLPlatform.h"
-#include "openmm/CustomGBForce.h"
-#include "openmm/GBSAOBCForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-static OpenCLPlatform platform;
-
-const double TOL = 1e-5;
-
-void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMethod customMethod) {
-    const int numMolecules = 70;
-    const int numParticles = numMolecules*2;
-    const double boxSize = 10.0;
-    const double cutoff = 2.0;
-
-    // Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
-
-    System standardSystem;
-    System customSystem;
-    for (int i = 0; i < numParticles; i++) {
-        standardSystem.addParticle(1.0);
-        customSystem.addParticle(1.0);
-    }
-    standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
-    customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
-    GBSAOBCForce* obc = new GBSAOBCForce();
-    CustomGBForce* custom = new CustomGBForce();
-    obc->setCutoffDistance(cutoff);
-    custom->setCutoffDistance(cutoff);
-    custom->addPerParticleParameter("q");
-    custom->addPerParticleParameter("radius");
-    custom->addPerParticleParameter("scale");
-    custom->addGlobalParameter("solventDielectric", obc->getSolventDielectric());
-    custom->addGlobalParameter("soluteDielectric", obc->getSoluteDielectric());
-    custom->addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
-                                  "U=r+sr2;"
-                                  "C=2*(1/or1-1/L)*step(sr2-r-or1);"
-                                  "L=max(or1, D);"
-                                  "D=abs(r-sr2);"
-                                  "sr2 = scale2*or2;"
-                                  "or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
-    custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
-                                  "psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
-    custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
-    string invCutoffString = "";
-    if (obcMethod != GBSAOBCForce::NoCutoff) {
-        stringstream s;
-        s<<(1.0/cutoff);
-        invCutoffString = s.str();
-    }
-    custom->addEnergyTerm("138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*("+invCutoffString+"-1/f);"
-                          "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
-    vector<Vec3> positions(numParticles);
-    vector<Vec3> velocities(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    vector<double> params(3);
-    for (int i = 0; i < numMolecules; i++) {
-        if (i < numMolecules/2) {
-            obc->addParticle(1.0, 0.2, 0.5);
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.5;
-            custom->addParticle(params);
-            obc->addParticle(-1.0, 0.1, 0.5);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        else {
-            obc->addParticle(1.0, 0.2, 0.8);
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.8;
-            custom->addParticle(params);
-            obc->addParticle(-1.0, 0.1, 0.8);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
-        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
-        velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-    }
-    obc->setNonbondedMethod(obcMethod);
-    custom->setNonbondedMethod(customMethod);
-    standardSystem.addForce(obc);
-    customSystem.addForce(custom);
-    VerletIntegrator integrator1(0.01);
-    VerletIntegrator integrator2(0.01);
-    Context context1(standardSystem, integrator1, platform);
-    context1.setPositions(positions);
-    context1.setVelocities(velocities);
-    State state1 = context1.getState(State::Forces | State::Energy);
-    Context context2(customSystem, integrator2, platform);
-    context2.setPositions(positions);
-    context2.setVelocities(velocities);
-    State state2 = context2.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
-    for (int i = 0; i < numParticles; i++) {
-        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
-    }
-    
-    // Try changing the particle parameters and make sure it's still correct.
-    
-    for (int i = 0; i < numMolecules/2; i++) {
-        obc->setParticleParameters(2*i, 1.1, 0.3, 0.6);
-        params[0] = 1.1;
-        params[1] = 0.3;
-        params[2] = 0.6;
-        custom->setParticleParameters(2*i, params);
-        obc->setParticleParameters(2*i+1, -1.1, 0.2, 0.4);
-        params[0] = -1.1;
-        params[1] = 0.2;
-        params[2] = 0.4;
-        custom->setParticleParameters(2*i+1, params);
-    }
-    obc->updateParametersInContext(context1);
-    custom->updateParametersInContext(context2);
-    state1 = context1.getState(State::Forces | State::Energy);
-    state2 = context2.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
-    for (int i = 0; i < numParticles; i++) {
-        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
-    }
-}
-
-void testMembrane() {
-    const int numMolecules = 70;
-    const int numParticles = numMolecules*2;
-    const double boxSize = 10.0;
-
-    // Create a system with an implicit membrane.
-
-    System system;
-    for (int i = 0; i < numParticles; i++) {
-        system.addParticle(1.0);
-    }
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
-    CustomGBForce* custom = new CustomGBForce();
-    custom->setCutoffDistance(2.0);
-    custom->addPerParticleParameter("q");
-    custom->addPerParticleParameter("radius");
-    custom->addPerParticleParameter("scale");
-    custom->addGlobalParameter("thickness", 3);
-    custom->addGlobalParameter("solventDielectric", 78.3);
-    custom->addGlobalParameter("soluteDielectric", 1);
-    custom->addComputedValue("Imol", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
-                             "U=r+sr2;"
-                             "C=2*(1/or1-1/L)*step(sr2-r-or1);"
-                             "L=max(or1, D);"
-                             "D=abs(r-sr2);"
-                             "sr2 = scale2*or2;"
-                             "or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
-    custom->addComputedValue("Imem", "(1/radius+2*log(2)/thickness)/(1+exp(7.2*(abs(z)+radius-0.5*thickness)))", CustomGBForce::SingleParticle);
-    custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
-                             "psi=max(Imol,Imem)*or; or=radius-0.009", CustomGBForce::SingleParticle);
-    custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
-    custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
-                          "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
-    vector<Vec3> positions(numParticles);
-    vector<Vec3> velocities(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    vector<double> params(3);
-    for (int i = 0; i < numMolecules; i++) {
-        if (i < numMolecules/2) {
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.5;
-            custom->addParticle(params);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        else {
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.8;
-            custom->addParticle(params);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
-        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
-        velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-    }
-    system.addForce(custom);
-    VerletIntegrator integrator(0.01);
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    context.setVelocities(velocities);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-
-    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-    double norm = 0.0;
-    for (int i = 0; i < (int) forces.size(); ++i)
-        norm += forces[i].dot(forces[i]);
-    norm = std::sqrt(norm);
-    const double stepSize = 1e-2;
-    double step = 0.5*stepSize/norm;
-    vector<Vec3> positions2(numParticles), positions3(numParticles);
-    for (int i = 0; i < (int) positions.size(); ++i) {
-        Vec3 p = positions[i];
-        Vec3 f = forces[i];
-        positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-        positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
-    }
-    context.setPositions(positions2);
-    State state2 = context.getState(State::Energy);
-    context.setPositions(positions3);
-    State state3 = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
-}
-
-void testTabulatedFunction() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomGBForce* force = new CustomGBForce();
-    force->addComputedValue("a", "0", CustomGBForce::ParticlePair);
-    force->addEnergyTerm("fn(r)+1", CustomGBForce::ParticlePair);
-    force->addParticle(vector<double>());
-    force->addParticle(vector<double>());
-    vector<double> table;
-    for (int i = 0; i < 21; i++)
-        table.push_back(std::sin(0.25*i));
-    force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
-    system.addForce(force);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (int i = 1; i < 30; i++) {
-        double x = (7.0/30.0)*i;
-        positions[1] = Vec3(x, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        double force = (x < 1.0 || x > 6.0 ? 0.0 : -std::cos(x-1.0));
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
-        ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
-        ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
-    }
-    for (int i = 1; i < 20; i++) {
-        double x = 0.25*i+1.0;
-        positions[1] = Vec3(x, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Energy);
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
-    }
-}
-
-void testMultipleChainRules() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomGBForce* force = new CustomGBForce();
-    force->addComputedValue("a", "2*r", CustomGBForce::ParticlePair);
-    force->addComputedValue("b", "a+1", CustomGBForce::SingleParticle);
-    force->addComputedValue("c", "2*b+a", CustomGBForce::SingleParticle);
-    force->addEnergyTerm("0.1*a+1*b+10*c", CustomGBForce::SingleParticle); // 0.1*(2*r) + 2*r+1 + 10*(3*a+2) = 0.2*r + 2*r+1 + 40*r+20+20*r = 62.2*r+21
-    force->addParticle(vector<double>());
-    force->addParticle(vector<double>());
-    system.addForce(force);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (int i = 1; i < 5; i++) {
-        positions[1] = Vec3(i, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(124.4, 0, 0), forces[0], 1e-4);
-        ASSERT_EQUAL_VEC(Vec3(-124.4, 0, 0), forces[1], 1e-4);
-        ASSERT_EQUAL_TOL(2*(62.2*i+21), state.getPotentialEnergy(), 0.02);
-    }
-}
-
-void testPositionDependence() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomGBForce* force = new CustomGBForce();
-    force->addComputedValue("a", "r", CustomGBForce::ParticlePair);
-    force->addComputedValue("b", "a+x*y", CustomGBForce::SingleParticle);
-    force->addEnergyTerm("b*z", CustomGBForce::SingleParticle);
-    force->addEnergyTerm("b1+b2", CustomGBForce::ParticlePair); // = 2*r+x1*y1+x2*y2
-    force->addParticle(vector<double>());
-    force->addParticle(vector<double>());
-    system.addForce(force);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    vector<Vec3> forces(2);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    for (int i = 0; i < 5; i++) {
-        positions[0] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        positions[1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        Vec3 delta = positions[0]-positions[1];
-        double r = sqrt(delta.dot(delta));
-        double energy = 2*r+positions[0][0]*positions[0][1]+positions[1][0]*positions[1][1];
-        for (int j = 0; j < 2; j++)
-            energy += positions[j][2]*(r+positions[j][0]*positions[j][1]);
-        Vec3 force1(-(1+positions[0][2])*delta[0]/r-(1+positions[0][2])*positions[0][1]-(1+positions[1][2])*delta[0]/r,
-                    -(1+positions[0][2])*delta[1]/r-(1+positions[0][2])*positions[0][0]-(1+positions[1][2])*delta[1]/r,
-                    -(1+positions[0][2])*delta[2]/r-(r+positions[0][0]*positions[0][1])-(1+positions[1][2])*delta[2]/r);
-        Vec3 force2((1+positions[0][2])*delta[0]/r+(1+positions[1][2])*delta[0]/r-(1+positions[1][2])*positions[1][1],
-                    (1+positions[0][2])*delta[1]/r+(1+positions[1][2])*delta[1]/r-(1+positions[1][2])*positions[1][0],
-                    (1+positions[0][2])*delta[2]/r+(1+positions[1][2])*delta[2]/r-(r+positions[1][0]*positions[1][1]));
-        ASSERT_EQUAL_VEC(force1, forces[0], 1e-4);
-        ASSERT_EQUAL_VEC(force2, forces[1], 1e-4);
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
-
-        // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-        double norm = 0.0;
-        for (int i = 0; i < (int) forces.size(); ++i)
-            norm += forces[i].dot(forces[i]);
-        norm = std::sqrt(norm);
-        const double stepSize = 1e-3;
-        double step = 0.5*stepSize/norm;
-        vector<Vec3> positions2(2), positions3(2);
-        for (int i = 0; i < (int) positions.size(); ++i) {
-            Vec3 p = positions[i];
-            Vec3 f = forces[i];
-            positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-            positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
-        }
-        context.setPositions(positions2);
-        State state2 = context.getState(State::Energy);
-        context.setPositions(positions3);
-        State state3 = context.getState(State::Energy);
-        ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
-    }
-}
-
-void testExclusions() {
-    for (int i = 0; i < 4; i++) {
-        System system;
-        system.addParticle(1.0);
-        system.addParticle(1.0);
-        VerletIntegrator integrator(0.01);
-        CustomGBForce* force = new CustomGBForce();
-        force->addComputedValue("a", "r", i < 2 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
-        force->addEnergyTerm("a", CustomGBForce::SingleParticle);
-        force->addEnergyTerm("(1+a1+a2)*r", i%2 == 0 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
-        force->addParticle(vector<double>());
-        force->addParticle(vector<double>());
-        force->addExclusion(0, 1);
-        system.addForce(force);
-        Context context(system, integrator, platform);
-        vector<Vec3> positions(2);
-        positions[0] = Vec3(0, 0, 0);
-        positions[1] = Vec3(1, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        double f, energy;
-        switch (i)
-        {
-            case 0: // e = 0
-                f = 0;
-                energy = 0;
-                break;
-            case 1: // e = r
-                f = 1;
-                energy = 1;
-                break;
-            case 2: // e = 2r
-                f = 2;
-                energy = 2;
-                break;
-            case 3: // e = 3r + 2r^2
-                f = 7;
-                energy = 5;
-                break;
-            default:
-                ASSERT(false);
-        }
-        ASSERT_EQUAL_VEC(Vec3(f, 0, 0), forces[0], 1e-4);
-        ASSERT_EQUAL_VEC(Vec3(-f, 0, 0), forces[1], 1e-4);
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
-
-        // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-        double norm = 0.0;
-        for (int i = 0; i < (int) forces.size(); ++i)
-            norm += forces[i].dot(forces[i]);
-        norm = std::sqrt(norm);
-        const double stepSize = 1e-3;
-        double step = stepSize/norm;
-        for (int i = 0; i < (int) positions.size(); ++i) {
-            Vec3 p = positions[i];
-            Vec3 f = forces[i];
-            positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-        }
-        context.setPositions(positions);
-        State state2 = context.getState(State::Energy);
-        ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/stepSize, 1e-3*abs(state.getPotentialEnergy()));
-    }
-}
+#include "OpenCLTests.h"
+#include "TestCustomGBForce.h"
 
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
-        testOBC(GBSAOBCForce::NoCutoff, CustomGBForce::NoCutoff);
-        testOBC(GBSAOBCForce::CutoffNonPeriodic, CustomGBForce::CutoffNonPeriodic);
-        testOBC(GBSAOBCForce::CutoffPeriodic, CustomGBForce::CutoffPeriodic);
-        testMembrane();
-        testTabulatedFunction();
-        testMultipleChainRules();
-        testPositionDependence();
-        testExclusions();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }

platforms/opencl/tests/TestOpenCLPeriodicTorsionForce.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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,69 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the OpenCL implementation of PeriodicTorsionForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "OpenCLPlatform.h"
-#include "openmm/PeriodicTorsionForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "SimTKOpenMMRealType.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-static OpenCLPlatform platform;
-
-const double TOL = 1e-5;
-
-void testPeriodicTorsions() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    PeriodicTorsionForce* forceField = new PeriodicTorsionForce();
-    forceField->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
-    system.addForce(forceField);
-    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*PI_M/3);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0.5*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*PI_M/3)), state.getPotentialEnergy(), TOL);
-    }
-    
-    // Try changing the torsion parameters and make sure it's still correct.
-    
-    forceField->setTorsionParameters(0, 0, 1, 2, 3, 3, PI_M/3.2, 1.3);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        double dtheta = (3*PI_M/2)-(PI_M/3.2);
-        double torque = -3*1.3*std::sin(dtheta);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0.5*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(1.3*(1+std::cos(dtheta)), state.getPotentialEnergy(), TOL);
-    }
-}
+#include "OpenCLTests.h"
+#include "TestPeriodicTorsionForce.h"
 
 void testParallelComputation() {
     System system;
@@ -121,18 +60,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
-        testPeriodicTorsions();
-        testParallelComputation();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }
-

platforms/opencl/tests/TestOpenCLRBTorsionForce.cpp

@@ -29,88 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the OpenCL implementation of RBTorsionForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "OpenCLPlatform.h"
-#include "openmm/RBTorsionForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "SimTKOpenMMRealType.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-static OpenCLPlatform platform;
-
-const double TOL = 1e-5;
-
-void testRBTorsions() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    RBTorsionForce* forceField = new RBTorsionForce();
-    forceField->addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
-    system.addForce(forceField);
-    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, 1, 1);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        double psi = 0.25*PI_M - PI_M;
-        double torque = 0.0;
-        for (int i = 1; i < 6; ++i) {
-            double c = 0.1*(i+1);
-            torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
-        }
-        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, -0.5*torque), 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);
-        double energy = 0.0;
-        for (int i = 0; i < 6; ++i) {
-            double c = 0.1*(i+1);
-            energy += c*std::pow(std::cos(psi), i);
-        }
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
-    }
-    
-    // Try changing the torsion parameters and make sure it's still correct.
-    
-    forceField->setTorsionParameters(0, 0, 1, 2, 3, 0.11, 0.22, 0.33, 0.44, 0.55, 0.66);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    {
-        const vector<Vec3>& forces = state.getForces();
-        double psi = 0.25*PI_M - PI_M;
-        double torque = 0.0;
-        for (int i = 1; i < 6; ++i) {
-            double c = 0.11*(i+1);
-            torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
-        }
-        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, -0.5*torque), 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);
-        double energy = 0.0;
-        for (int i = 0; i < 6; ++i) {
-            double c = 0.11*(i+1);
-            energy += c*std::pow(std::cos(psi), i);
-        }
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
-    }
-}
+#include "OpenCLTests.h"
+#include "TestRBTorsionForce.h"
 
 void testParallelComputation() {
     System system;
@@ -140,18 +60,6 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
-int main(int argc, char* argv[]) {
-    try {
-        if (argc > 1)
-            platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
-        testRBTorsions();
-        testParallelComputation();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
+    testParallelComputation();
 }
-