Merge branch 'master' of github.com:pandegroup/openmm into genpt

plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp

@@ -128,21 +128,15 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int
             center *= 1.0/molecules[i].size();
 
             // Find the displacement to move it into the first periodic box.
-
-            int xcell = (int) floor(center[0]/periodicBoxSize[0][0]);
-            int ycell = (int) floor(center[1]/periodicBoxSize[1][1]);
-            int zcell = (int) floor(center[2]/periodicBoxSize[2][2]);
-            double dx = xcell*periodicBoxSize[0][0];
-            double dy = ycell*periodicBoxSize[1][1];
-            double dz = zcell*periodicBoxSize[2][2];
+            Vec3 diff;
+            diff += periodicBoxSize[2]*floor(center[2]/periodicBoxSize[2][2]);
+            diff += periodicBoxSize[1]*floor((center[1]-diff[1])/periodicBoxSize[1][1]);
+            diff += periodicBoxSize[0]*floor((center[0]-diff[0])/periodicBoxSize[0][0]);
 
             // Translate all the particles in the molecule.
-
             for (int j = 0; j < (int) molecules[i].size(); j++) {
                 Vec3& pos = positions[molecules[i][j]];
-                pos[0] -= dx;
-                pos[1] -= dy;
-                pos[2] -= dz;
+                pos -= diff;
             }
         }
 
@@ -170,7 +164,7 @@ double RPMDIntegrator::computeKineticEnergy() {
 
 void RPMDIntegrator::step(int steps) {
     if (context == NULL)
-        throw OpenMMException("This Integrator is not bound to a context!");    
+        throw OpenMMException("This Integrator is not bound to a context!");
     if (!hasSetPosition) {
         // Initialize the positions from the context.
 

plugins/rpmd/platforms/reference/CMakeLists.txt

@@ -75,6 +75,6 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 
-IF(BUILD_TESTING)
+IF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
     SUBDIRS (tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)

serialization/CMakeLists.txt

@@ -6,6 +6,8 @@ INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/in
 INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/openmm/serialization/SerializationProxy.h)
 INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/openmm/serialization/XmlSerializer.h)
 
-IF(BUILD_TESTING)
+SET(OPENMM_BUILD_SERIALIZATION_TESTS TRUE CACHE BOOL "Whether to build serialization test cases")
+MARK_AS_ADVANCED(OPENMM_BUILD_SERIALIZATION_TESTS)
+IF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)
     ADD_SUBDIRECTORY(tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)

serialization/include/openmm/serialization/CompoundIntegratorProxy.h

+#ifndef OPENMM_COMPOUND_INTEGRATOR_PROXY_H_
+#define OPENMM_COMPOUND_INTEGRATOR_PROXY_H_
+
+#include "openmm/serialization/XmlSerializer.h"
+
+namespace OpenMM {
+
+class CompoundIntegratorProxy : public SerializationProxy {
+public:
+    CompoundIntegratorProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+}
+
+#endif /*OPENMM_COMPOUND_INTEGRATOR_PROXY_H_*/
\ No newline at end of file

serialization/include/openmm/serialization/SerializationNode.h

@@ -105,7 +105,7 @@ public:
     /**
      * Determine whether this node has a property with a particular node.
      *
-     * @param the name of the property to check for
+     * @param name  the name of the property to check for
      */
     bool hasProperty(const std::string& name) const;
     /**

openmmapi/include/openmm/internal/GBVIForceImpl.h → serialization/src/CompoundIntegratorProxy.cpp

-#ifndef OPENMM_GBVIFORCEFIELDIMPL_H_
-#define OPENMM_GBVIFORCEFIELDIMPL_H_
-
 /* -------------------------------------------------------------------------- *
  *                                   OpenMM                                   *
  * -------------------------------------------------------------------------- *
@@ -9,7 +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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -32,46 +29,29 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "ForceImpl.h"
-#include "openmm/GBVIForce.h"
-#include "openmm/Kernel.h"
-#include <string>
-
-namespace OpenMM {
-
-/**
- * This is the internal implementation of GBVIForce.
- */
-
-class GBVIForceImpl : public ForceImpl {
-public:
-    GBVIForceImpl(const GBVIForce& owner);
-    void initialize(ContextImpl& context);
-    const GBVIForce& getOwner() const {
-        return owner;
-    }
-    
-    // calculate scaled radii (Eq. 5 of Labute paper [JCC 29 1693-1698 2008])
-
-    void findScaledRadii( int numberOfParticles, const std::vector<std::vector<int> >& bondIndices,
-                          const std::vector<double> & bondLengths, std::vector<double> & scaledRadii) const;
-
-    // if bond info not set, then use bond forces/constraints
-    int getBondsFromForces(ContextImpl& context);
-
+#include "openmm/serialization/CompoundIntegratorProxy.h"
+#include <OpenMM.h>
+
+using namespace std;
+using namespace OpenMM;
+
+CompoundIntegratorProxy::CompoundIntegratorProxy() : SerializationProxy("CompoundIntegrator") {
+}
+
+void CompoundIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const CompoundIntegrator& integrator = *reinterpret_cast<const CompoundIntegrator*>(object);
+    node.setIntProperty("currentIntegrator", integrator.getCurrentIntegrator());
+    for (int i = 0; i < integrator.getNumIntegrators(); i++)
+        node.createChildNode("Integrator", &integrator.getIntegrator(i));
+}
+
+void* CompoundIntegratorProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    CompoundIntegrator *integrator = new CompoundIntegrator();
+    for (int i = 0; i < node.getChildren().size(); i++)
+        integrator->addIntegrator(node.getChildren()[i].decodeObject<Integrator>());
+    integrator->setCurrentIntegrator(node.getIntProperty("currentIntegrator"));
+    return integrator;
+}
\ No newline at end of file
-    void updateContextState(ContextImpl& context) {
-        // This force field doesn't update the state directly.
-    }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
-    std::map<std::string, double> getDefaultParameters() {
-        return std::map<std::string, double>(); // This force field doesn't define any parameters.
-    }
-    std::vector<std::string> getKernelNames();
-private:
-    const GBVIForce& owner;
-    Kernel kernel;
-};
-
-} // namespace OpenMM
-
-#endif /*OPENMM_GBVIFORCEFIELDIMPL_H_*/

serialization/src/GBVIForceProxy.cpp

-/* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from   *
- * Simbios, the NIH National Center for Physics-Based Simulation of           *
- * Biological Structures at Stanford, funded under the NIH Roadmap for        *
- * Medical Research, grant U54 GM072970. See https://simtk.org.               *
- *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
- * Authors: Peter Eastman                                                     *
- * Contributors:                                                              *
- *                                                                            *
- * Permission is hereby granted, free of charge, to any person obtaining a    *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation  *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
- * and/or sell copies of the Software, and to permit persons to whom the      *
- * Software is furnished to do so, subject to the following conditions:       *
- *                                                                            *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software.                        *
- *                                                                            *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
- * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
- * -------------------------------------------------------------------------- */
-
-#include "openmm/serialization/GBVIForceProxy.h"
-#include "openmm/serialization/SerializationNode.h"
-#include "openmm/Force.h"
-#include "openmm/GBVIForce.h"
-#include <sstream>
-
-using namespace OpenMM;
-using namespace std;
-
-GBVIForceProxy::GBVIForceProxy() : SerializationProxy("GBVIForce") {
-}
-
-void GBVIForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
-    const GBVIForce& force = *reinterpret_cast<const GBVIForce*>(object);
-    node.setIntProperty("forceGroup", force.getForceGroup());
-    node.setIntProperty("method", (int) force.getNonbondedMethod());
-    node.setIntProperty("scalingMethod", (int) force.getBornRadiusScalingMethod());
-    node.setDoubleProperty("quinticLowerLimitFactor", force.getQuinticLowerLimitFactor());
-    node.setDoubleProperty("quinticUpperBornRadiusLimit", force.getQuinticUpperBornRadiusLimit());
-    node.setDoubleProperty("cutoff", force.getCutoffDistance());
-    node.setDoubleProperty("soluteDielectric", force.getSoluteDielectric());
-    node.setDoubleProperty("solventDielectric", force.getSolventDielectric());
-    SerializationNode& particles = node.createChildNode("Particles");
-    for (int i = 0; i < force.getNumParticles(); i++) {
-        double charge, radius, gamma;
-        force.getParticleParameters(i, charge, radius, gamma);
-        particles.createChildNode("Particle").setDoubleProperty("q", charge).setDoubleProperty("r", radius).setDoubleProperty("gamma", gamma);
-    }
-    SerializationNode& bonds = node.createChildNode("Bonds");
-    for (int i = 0; i < force.getNumBonds(); i++) {
-        int particle1, particle2;
-        double distance;
-        force.getBondParameters(i, particle1, particle2, distance);
-        bonds.createChildNode("Bond").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setDoubleProperty("d", distance);
-    }
-}
-
-void* GBVIForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
-        throw OpenMMException("Unsupported version number");
-    GBVIForce* force = new GBVIForce();
-    try {
-        force->setForceGroup(node.getIntProperty("forceGroup", 0));
-        force->setNonbondedMethod((GBVIForce::NonbondedMethod) node.getIntProperty("method"));
-        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
-        force->setSoluteDielectric(node.getDoubleProperty("soluteDielectric"));
-        force->setSolventDielectric(node.getDoubleProperty("solventDielectric"));
-
-        if( node.getIntProperty("version") >= 2 ){
-            force->setBornRadiusScalingMethod( (GBVIForce::BornRadiusScalingMethod) node.getIntProperty( "scalingMethod"));
-            force->setQuinticLowerLimitFactor(node.getDoubleProperty("quinticLowerLimitFactor"));
-            force->setQuinticUpperBornRadiusLimit(node.getDoubleProperty("quinticUpperBornRadiusLimit"));
-        }
-
-        const SerializationNode& particles = node.getChildNode("Particles");
-        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
-            const SerializationNode& particle = particles.getChildren()[i];
-            force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("r"), particle.getDoubleProperty("gamma"));
-        }
-        const SerializationNode& bonds = node.getChildNode("Bonds");
-        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
-            const SerializationNode& bond = bonds.getChildren()[i];
-            force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getDoubleProperty("d"));
-        }
-    }
-    catch (...) {
-        delete force;
-        throw;
-    }
-    return force;
-}

serialization/src/SerializationProxyRegistration.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -33,6 +33,7 @@
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
+#include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomAngleForce.h"
 #include "openmm/CustomBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"
@@ -44,7 +45,6 @@
 #include "openmm/CustomNonbondedForce.h"
 #include "openmm/CustomTorsionForce.h"
 #include "openmm/GBSAOBCForce.h"
-#include "openmm/GBVIForce.h"
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/LangevinIntegrator.h"
@@ -65,6 +65,7 @@
 #include "openmm/serialization/AndersenThermostatProxy.h"
 #include "openmm/serialization/CMAPTorsionForceProxy.h"
 #include "openmm/serialization/CMMotionRemoverProxy.h"
+#include "openmm/serialization/CompoundIntegratorProxy.h"
 #include "openmm/serialization/CustomAngleForceProxy.h"
 #include "openmm/serialization/CustomBondForceProxy.h"
 #include "openmm/serialization/CustomCompoundBondForceProxy.h"
@@ -76,7 +77,6 @@
 #include "openmm/serialization/CustomNonbondedForceProxy.h"
 #include "openmm/serialization/CustomTorsionForceProxy.h"
 #include "openmm/serialization/GBSAOBCForceProxy.h"
-#include "openmm/serialization/GBVIForceProxy.h"
 #include "openmm/serialization/HarmonicAngleForceProxy.h"
 #include "openmm/serialization/HarmonicBondForceProxy.h"
 #include "openmm/serialization/LangevinIntegratorProxy.h"
@@ -112,6 +112,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(BrownianIntegrator), new BrownianIntegratorProxy());
     SerializationProxy::registerProxy(typeid(CMAPTorsionForce), new CMAPTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(CMMotionRemover), new CMMotionRemoverProxy());
+    SerializationProxy::registerProxy(typeid(CompoundIntegrator), new CompoundIntegratorProxy());
     SerializationProxy::registerProxy(typeid(Continuous1DFunction), new Continuous1DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Continuous2DFunction), new Continuous2DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Continuous3DFunction), new Continuous3DFunctionProxy());
@@ -129,7 +130,6 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(Discrete2DFunction), new Discrete2DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Discrete3DFunction), new Discrete3DFunctionProxy());
     SerializationProxy::registerProxy(typeid(GBSAOBCForce), new GBSAOBCForceProxy());
-    SerializationProxy::registerProxy(typeid(GBVIForce), new GBVIForceProxy());
     SerializationProxy::registerProxy(typeid(HarmonicAngleForce), new HarmonicAngleForceProxy());
     SerializationProxy::registerProxy(typeid(HarmonicBondForce), new HarmonicBondForceProxy());
     SerializationProxy::registerProxy(typeid(LangevinIntegrator), new LangevinIntegratorProxy());

serialization/tests/TestSerializeIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Yutong Zhao                                        *
  * Contributors:                                                              *
  *                                                                            *
@@ -32,6 +32,7 @@
 #include "openmm/internal/AssertionUtilities.h"
 
 #include "openmm/BrownianIntegrator.h"
+#include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomIntegrator.h"
 #include "openmm/LangevinIntegrator.h"
 #include "openmm/VariableLangevinIntegrator.h"
@@ -185,6 +186,29 @@ void testSerializeCustomIntegrator() {
     delete intg2;
 }
 
+void testSerializeCompoundIntegrator() {
+    CompoundIntegrator integ;
+    integ.addIntegrator(new LangevinIntegrator(372.4, 1.234, 0.0018));
+    integ.addIntegrator(new VerletIntegrator(0.002));
+    integ.setCurrentIntegrator(1);
+    stringstream ss;
+    XmlSerializer::serialize<Integrator>(&integ, "CompoundIntegrator", ss);
+    CompoundIntegrator *integ2 = dynamic_cast<CompoundIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
+    ASSERT_EQUAL(integ.getCurrentIntegrator(), integ2->getCurrentIntegrator());
+    LangevinIntegrator& langevin1 = dynamic_cast<LangevinIntegrator&>(integ.getIntegrator(0));
+    LangevinIntegrator& langevin2 = dynamic_cast<LangevinIntegrator&>(integ2->getIntegrator(0));
+    ASSERT_EQUAL(langevin1.getConstraintTolerance(), langevin2.getConstraintTolerance());
+    ASSERT_EQUAL(langevin1.getStepSize(), langevin2.getStepSize());
+    ASSERT_EQUAL(langevin1.getTemperature(), langevin2.getTemperature());
+    ASSERT_EQUAL(langevin1.getFriction(), langevin2.getFriction());
+    ASSERT_EQUAL(langevin1.getRandomNumberSeed(), langevin2.getRandomNumberSeed());
+    VerletIntegrator& verlet1 = dynamic_cast<VerletIntegrator&>(integ.getIntegrator(1));
+    VerletIntegrator& verlet2 = dynamic_cast<VerletIntegrator&>(integ2->getIntegrator(1));
+    ASSERT_EQUAL(verlet1.getConstraintTolerance(), verlet2.getConstraintTolerance());
+    ASSERT_EQUAL(verlet1.getStepSize(), verlet2.getStepSize());
+    delete integ2;
+}
+
 int main() {
     try {
         testSerializeBrownianIntegrator();
@@ -193,6 +217,7 @@ int main() {
         testSerializeVariableLangevinIntegrator();
         testSerializeVariableVerletIntegrator();
         testSerializeLangevinIntegrator(); 
+        testSerializeCompoundIntegrator();
     }
     catch(const exception& e) {
 		return 1;

platforms/reference/tests/TestReferenceGBVIForce.cpp → tests/TestCompoundIntegrator.h

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,214 +29,194 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the reference implementation of GBVIForce.
- */
-
 #include "openmm/internal/AssertionUtilities.h"
+#include "openmm/BrownianIntegrator.h"
+#include "openmm/CompoundIntegrator.h"
 #include "openmm/Context.h"
-#include "ReferencePlatform.h"
 #include "openmm/HarmonicBondForce.h"
-#include "openmm/GBVIForce.h"
-#include "openmm/GBSAOBCForce.h"
-#include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
-#include "openmm/NonbondedForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
 #include "SimTKOpenMMRealType.h"
-#include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>
 
 using namespace OpenMM;
 using namespace std;
 
-ReferencePlatform platform;
-
 const double TOL = 1e-5;
 
-void testSingleParticle() {
+void testChangingIntegrator() {
     System system;
     system.addParticle(2.0);
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-
-    GBVIForce* forceField = new GBVIForce();
-
-    double charge         = -1.0;
-    double radius         =  0.15;
-    double gamma          =  1.0;
-    forceField->addParticle(charge, radius, gamma);
-    system.addForce(forceField);
-    ASSERT(!forceField->usesPeriodicBoundaryConditions());
-    ASSERT(!system.usesPeriodicBoundaryConditions());
-
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, 0, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-
-    double bornRadius     = radius; 
-    double eps0           = EPSILON0;
-    double tau            = (1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric());
-
-    double bornEnergy     = (-charge*charge/(8*PI_M*eps0))*tau/bornRadius;
-    double nonpolarEnergy = -gamma*tau*std::pow(radius/bornRadius, 3.0);
-
-    double expectedE      = (bornEnergy+nonpolarEnergy); 
-    double obtainedE      = state.getPotentialEnergy(); 
-    double diff           = fabs((obtainedE - expectedE)/expectedE);
-
-    ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
-}
-
-void testEnergyEthane(int applyBornRadiiScaling) {
-    const int numParticles = 8;
-    System system;
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-
-    // harmonic bond
-
-    double C_HBondDistance   = 0.1097;
-    double C_CBondDistance   = 0.1504;
+    system.addParticle(2.0);
     HarmonicBondForce* bonds = new HarmonicBondForce();
-    bonds->addBond(0, 1, C_HBondDistance, 0.0);
-    bonds->addBond(2, 1, C_HBondDistance, 0.0);
-    bonds->addBond(3, 1, C_HBondDistance, 0.0);
-
-    bonds->addBond(1, 4, C_CBondDistance, 0.0);
-
-    bonds->addBond(5, 4, C_HBondDistance, 0.0);
-    bonds->addBond(6, 4, C_HBondDistance, 0.0);
-    bonds->addBond(7, 4, C_HBondDistance, 0.0);
-
+    bonds->addBond(0, 1, 1.5, 1);
     system.addForce(bonds);
-
-    double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
-
-    int AM1_BCC = 1;
-    H_charge    = -0.053;
-    C_charge    = -3.0*H_charge;
-    if (AM1_BCC) {
-       C_radius =  0.180;
-       C_gamma  = -0.2863;
-       H_radius =  0.125;
-       H_gamma  =  0.2437;
-    }
-    else {
-       C_radius =  0.215;
-       C_gamma  = -1.1087;
-       H_radius =  0.150;
-       H_gamma  =  0.1237;
+    CompoundIntegrator integrator;
+    integrator.addIntegrator(new VerletIntegrator(0.01));
+    integrator.addIntegrator(new LangevinIntegrator(300.0, 10.0, 0.011));
+    integrator.addIntegrator(new BrownianIntegrator(300.0, 10.0, 0.012));
+    Context context(system, integrator, platform);
+    ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    for (int iteration = 0; iteration < 2; ++iteration) {
+        context.setPositions(positions);
+
+        // First integrate with the Verlet integrator and compare it to the analytical solution.
+
+        const double freq = 1.0;
+        State state = context.getState(State::Energy);
+        const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
+        for (int i = 0; i < 100; ++i) {
+            state = context.getState(State::Positions | State::Velocities | State::Energy);
+            double time = state.getTime();
+            double expectedDist = 1.5+0.5*std::cos(freq*time);
+            ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+            ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+            double expectedSpeed = -0.5*freq*std::sin(freq*time);
+            ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
+            ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
+            double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+            ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
+            integrator.step(1);
+        }
+        ASSERT_EQUAL_TOL(100*0.01, context.getState(0).getTime(), 1e-5);
+
+        // Switch to the Langevin integrator and make sure that it heats up.
+
+        integrator.setCurrentIntegrator(1);
+        integrator.step(100);
+        double ke = 0.0;
+        for (int i = 0; i < 1000; ++i) {
+            integrator.step(10);
+            state = context.getState(State::Energy);
+            ke += state.getKineticEnergy();
+        }
+        double expectedKE = 0.5*2*3*BOLTZ*300.0;
+        ASSERT_USUALLY_EQUAL_TOL(expectedKE, ke/1000, 0.1);
+        ASSERT_EQUAL_TOL(100*0.01+10100*0.011, context.getState(0).getTime(), 1e-5);
+        
+        // Now reinitialize the context and repeat all of these tests to make sure that works correctly.
+        
+        context.reinitialize();
+        integrator.setCurrentIntegrator(0);
     }
+}
 
-    NonbondedForce* nonbonded = new NonbondedForce();
-    nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
-
-    GBVIForce* forceField = new GBVIForce();
-    if (applyBornRadiiScaling) {
-        forceField->setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
+void testChangingParameters() {
+    System system;
+    system.addParticle(1.0);
+    CompoundIntegrator integrator;
+    integrator.addIntegrator(new VerletIntegrator(0.01));
+    integrator.addIntegrator(new LangevinIntegrator(300.0, 10.0, 0.02));
+    integrator.addIntegrator(new BrownianIntegrator(300.0, 10.0, 0.03));
+    
+    // Try getting and setting the step size for different component integrators.
+    
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        ASSERT_EQUAL_TOL(0.01*(i+1), integrator.getStepSize(), 1e-7);
     }
-    else {
-        forceField->setBornRadiusScalingMethod(GBVIForce::NoScaling);
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        integrator.setStepSize(0.02*(i+1));
+        ASSERT_EQUAL_TOL(0.02*(i+1), integrator.getStepSize(), 1e-7);
     }
-    for (int i = 0; i < numParticles; i++) {
-       system.addParticle(1.0);
-       forceField->addParticle(H_charge, H_radius, H_gamma);
-       nonbonded->addParticle( H_charge, H_radius, 0.0);
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        ASSERT_EQUAL_TOL(0.02*(i+1), integrator.getStepSize(), 1e-7);
     }
- 
-    forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
-    forceField->setParticleParameters(4, C_charge, C_radius, C_gamma);
- 
-    nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
-    nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
- 
-    forceField->addBond(0, 1, C_HBondDistance);
-    forceField->addBond(2, 1, C_HBondDistance);
-    forceField->addBond(3, 1, C_HBondDistance);
-    forceField->addBond(1, 4, C_CBondDistance);
-    forceField->addBond(5, 4, C_HBondDistance);
-    forceField->addBond(6, 4, C_HBondDistance);
-    forceField->addBond(7, 4, C_HBondDistance);
-    
-    std::vector<pair<int, int> > bondExceptions;
-    std::vector<double> bondDistances;
-    
-    bondExceptions.push_back(pair<int, int>(0, 1)); 
-    bondDistances.push_back(C_HBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(2, 1)); 
-    bondDistances.push_back(C_HBondDistance);
     
-    bondExceptions.push_back(pair<int, int>(3, 1)); 
-    bondDistances.push_back(C_HBondDistance);
+    // Try getting and setting the constraint tolerance for different component integrators.
     
-    bondExceptions.push_back(pair<int, int>(1, 4)); 
-    bondDistances.push_back(C_CBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(5, 4)); 
-    bondDistances.push_back(C_HBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(6, 4)); 
-    bondDistances.push_back(C_HBondDistance);
- 
-    bondExceptions.push_back(pair<int, int>(7, 4));
-    bondDistances.push_back(C_HBondDistance);
- 
-    nonbonded->createExceptionsFromBonds(bondExceptions, 0.0, 0.0);
- 
-    system.addForce(forceField);
-    system.addForce(nonbonded);
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        ASSERT_EQUAL_TOL(1e-5, integrator.getConstraintTolerance(), 1e-7);
+    }
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        integrator.setConstraintTolerance(1e-4*(i+1));
+        ASSERT_EQUAL_TOL(1e-4*(i+1), integrator.getConstraintTolerance(), 1e-7);
+    }
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        ASSERT_EQUAL_TOL(1e-4*(i+1), integrator.getConstraintTolerance(), 1e-7);
+    }
+}
 
+void testDifferentStepSizes() {
+    System system;
+    system.addParticle(2.0);
+    system.addParticle(2.0);
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    bonds->addBond(0, 1, 1.5, 1);
+    system.addForce(bonds);
+    CompoundIntegrator integrator;
+    integrator.addIntegrator(new VerletIntegrator(0.005));
+    integrator.addIntegrator(new VerletIntegrator(0.01));
     Context context(system, integrator, platform);
-    
-    vector<Vec3> positions(numParticles);
-    positions[0] = Vec3(0.5480,    1.7661,    0.0000);
-    positions[1] = Vec3(0.7286,    0.8978,    0.6468);
-    positions[2] = Vec3(0.4974,    0.0000,    0.0588);
-    positions[3] = Vec3(0.0000,    0.9459,    1.4666);
-    positions[4] = Vec3(2.1421,    0.8746,    1.1615);
-    positions[5] = Vec3(2.3239,    0.0050,    1.8065);
-    positions[6] = Vec3(2.8705,    0.8295,    0.3416);
-    positions[7] = Vec3(2.3722,    1.7711,    1.7518);
+    ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
     context.setPositions(positions);
 
-    State state = context.getState(State::Forces | State::Energy);
-    
-    // Take a small step in the direction of the energy gradient.
-    
-    double norm        = 0.0;
-    double forceSum[3] = { 0.0, 0.0, 0.0 };
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 f  = state.getForces()[i];
-        norm        += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
-        forceSum[0] += f[0];
-        forceSum[1] += f[1];
-        forceSum[2] += f[2];
+    // Integrate with the first Verlet integrator and compare it to the analytical solution.
+
+    const double freq = 1.0;
+    double expectedTime = 0;
+    for (int i = 0; i < 100; ++i) {
+        State state = context.getState(State::Positions);
+        double time = state.getTime();
+        ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
+        double expectedDist = 1.5+0.5*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        integrator.step(1);
+        expectedTime += 0.005;
     }
-    norm               = std::sqrt(norm);
-
-    const double delta = 1e-4;
-    double step = delta/norm;
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 p = positions[i];
-        Vec3 f = state.getForces()[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);
-
-    // See whether the potential energy changed by the expected amount.
+    // Now switch to the second Verlet integrator which has a different step size.
+
+    integrator.setCurrentIntegrator(1);
+    for (int i = 0; i < 100; ++i) {
+        State state = context.getState(State::Positions);
+        double time = state.getTime();
+        ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
+        double expectedDist = 1.5+0.5*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        integrator.step(1);
+        expectedTime += 0.01;
+    }
     
-    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
+    // Finally, switch back to the first one again.
+
+    integrator.setCurrentIntegrator(0);
+    for (int i = 0; i < 100; ++i) {
+        State state = context.getState(State::Positions);
+        double time = state.getTime();
+        ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
+        double expectedDist = 1.5+0.5*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        integrator.step(1);
+        expectedTime += 0.005;
+    }
 }
 
-int main() {
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
     try {
-        testSingleParticle();
-        testEnergyEthane(0);
-        testEnergyEthane(1);
+        initializeTests(argc, argv);
+        testChangingIntegrator();
+        testChangingParameters();
+        testDifferentStepSizes();
+        runPlatformTests();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

tests/TestCustomExternalForce.h

@@ -167,6 +167,38 @@ void testPeriodic() {
     }
 }
 
+void testZeroPeriodicDistance() {
+    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);
+    ASSERT(force->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(1);
+    positions[0] = Vec3(x0, y0, z0);
+    context.setPositions(positions);
+
+    State state = context.getState(State::Positions | State::Forces | State::Energy);
+    vector<Vec3> forces = state.getForces();
+    for (int i = 0; i < 3; i++)
+        ASSERT_EQUAL(forces[0][i], forces[0][i]);
+}
+
 void testIllegalVariable() {
     System system;
     system.addParticle(1.0);
@@ -192,6 +224,7 @@ int main(int argc, char* argv[]) {
         testForce();
         testManyParameters();
         testPeriodic();
+        testZeroPeriodicDistance();
         testIllegalVariable();
         runPlatformTests();
     }

serialization/tests/TestSerializeGBVIForce.cpp → tests/TestEnforcePeriodicBox.cpp

@@ -6,8 +6,8 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
- * Authors: Peter Eastman                                                     *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
+ * Authors: Robert McGibbon                                                   *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -30,74 +30,70 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/internal/AssertionUtilities.h"
-#include "openmm/GBVIForce.h"
-#include "openmm/serialization/XmlSerializer.h"
+#include "openmm/Context.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/Platform.h"
+#include "openmm/VerletIntegrator.h"
+#include "sfmt/SFMT.h"
 #include <iostream>
-#include <sstream>
 
 using namespace OpenMM;
 using namespace std;
 
-void testSerialization() {
-    // Create a Force.
-
-    GBVIForce force;
-    force.setForceGroup(3);
-    force.setNonbondedMethod(GBVIForce::CutoffPeriodic);
-    force.setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
-    force.setQuinticLowerLimitFactor(0.123);
-    force.setQuinticUpperBornRadiusLimit(5.123);
-    force.setCutoffDistance(2.0);
-    force.setSoluteDielectric(5.1);
-    force.setSolventDielectric(50.0);
-    force.addParticle(1, 0.1, 0.01);
-    force.addParticle(0.5, 0.2, 0.02);
-    force.addParticle(-0.5, 0.3, 0.03);
-    force.addBond(0, 1, 2.0);
-    force.addBond(3, 5, 1.2);
-
-    // Serialize and then deserialize it.
-
-    stringstream buffer;
-    XmlSerializer::serialize<GBVIForce>(&force, "Force", buffer);
-    GBVIForce* copy = XmlSerializer::deserialize<GBVIForce>(buffer);
-
-    // Compare the two forces to see if they are identical.
-
-    GBVIForce& force2 = *copy;
-    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
-    ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
-    ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
-    ASSERT_EQUAL(force.getSoluteDielectric(), force2.getSoluteDielectric());
-    ASSERT_EQUAL(force.getSolventDielectric(), force2.getSolventDielectric());
-    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
-    ASSERT_EQUAL(force.getQuinticUpperBornRadiusLimit(), force2.getQuinticUpperBornRadiusLimit());
-    ASSERT_EQUAL(force.getQuinticLowerLimitFactor(), force2.getQuinticLowerLimitFactor());
-    ASSERT_EQUAL(force.getBornRadiusScalingMethod(), force2.getBornRadiusScalingMethod());
-    for (int i = 0; i < force.getNumParticles(); i++) {
-        double charge1, radius1, scale1;
-        double charge2, radius2, scale2;
-        force.getParticleParameters(i, charge1, radius1, scale1);
-        force2.getParticleParameters(i, charge2, radius2, scale2);
-        ASSERT_EQUAL(charge1, charge2);
-        ASSERT_EQUAL(radius1, radius2);
-        ASSERT_EQUAL(scale1, scale2);
+void testTruncatedOctahedron() {
+    const int numMolecules = 50;
+    const int numParticles = numMolecules*2;
+    const float cutoff = 2.0;
+    Vec3 a(6.7929, 0, 0);
+    Vec3 b(-2.264163559406279, 6.404455775962287, 0);
+    Vec3 c(-2.264163559406279, -3.2019384603140684, 5.54658849047036);
+        
+    System system;
+    system.setDefaultPeriodicBoxVectors(a, b, c);
+    NonbondedForce* force = new NonbondedForce();
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<Vec3> positions(numParticles);
+    
+    force->setCutoffDistance(cutoff);
+    force->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    
+    for (int i = 0; i < numMolecules; i++) {
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        force->addParticle(-1, 0.2, 0.2);
+        force->addParticle(1, 0.2, 0.2);
+        positions[2*i] = a*(5*genrand_real2(sfmt)-2) + b*(5*genrand_real2(sfmt)-2) + c*(5*genrand_real2(sfmt)-2);
+        positions[2*i+1] = positions[2*i] + Vec3(1.0, 0.0, 0.0);
+        system.addConstraint(2*i, 2*i+1, 1.0);
     }
-    ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
-    for (int i = 0; i < force.getNumBonds(); i++) {
-        int a1, a2, b1, b2;
-        double da, db;
-        force.getBondParameters(i, a1, a2, da);
-        force2.getBondParameters(i, b1, b2, db);
-        ASSERT_EQUAL(a1, b1);
-        ASSERT_EQUAL(a2, b2);
-        ASSERT_EQUAL(da, db);
+    system.addForce(force);
+    
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+    context.setPositions(positions);
+    State initialState = context.getState(State::Positions | State::Energy, true);
+    for (int i = 0; i < numMolecules; i++) {
+        Vec3 center = (initialState.getPositions()[2*i]+initialState.getPositions()[2*i+1])*0.5;
+        ASSERT(center[0] >= 0.0);
+        ASSERT(center[1] >= 0.0);
+        ASSERT(center[2] >= 0.0);
+        ASSERT(center[0] <= a[0]);
+        ASSERT(center[1] <= b[1]);
+        ASSERT(center[2] <= c[2]);
     }
+    double initialEnergy = initialState.getPotentialEnergy();
+
+    context.setState(initialState);
+    State finalState = context.getState(State::Positions | State::Energy, true);
+    double finalEnergy = finalState.getPotentialEnergy();
+
+    ASSERT_EQUAL_TOL(initialEnergy, finalEnergy, 1e-4);
 }
 
-int main() {
+int main(int argc, char* argv[]) {
     try {
-        testSerialization();
+        testTruncatedOctahedron();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

tests/TestGBSAOBCForce.h

@@ -255,7 +255,7 @@ void testForce(int numParticles, NonbondedForce::NonbondedMethod method, GBSAOBC
         State state2 = context.getState(State::Energy);
         context.setPositions(positions3);
         State state3 = context.getState(State::Energy);
-        ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/delta, 1e-2)
+        ASSERT_EQUAL_TOL(state2.getPotentialEnergy(), state3.getPotentialEnergy()+norm*delta, 1e-5)
     }
 }
 

tests/TestLangevinIntegrator.h

@@ -251,8 +251,8 @@ void testRandomSeed() {
 
     for (int i = 0; i < numParticles; i++) {
         for (int j = 0; j < 3; j++) {
-            ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
-            ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
+            ASSERT_EQUAL_TOL(state1.getPositions()[i][j], state2.getPositions()[i][j], 1e-6);
+            ASSERT_EQUAL_TOL(state3.getPositions()[i][j], state4.getPositions()[i][j], 1e-6);
             ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
         }
     }

tests/TestLocalEnergyMinimizer.h

@@ -78,7 +78,7 @@ void testLargeSystem() {
     const int numParticles = numMolecules*2;
     const double cutoff = 2.0;
     const double boxSize = 4.0;
-    const double tolerance = 10;
+    const double tolerance = 15;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     NonbondedForce* nonbonded = new NonbondedForce();

tests/TestVectorize.cpp

@@ -149,6 +149,8 @@ void testMathFunctions() {
     ASSERT_VEC4_EQUAL(max(f1, f2), 1.1, 1.9, 1.3, -3.8);
     ASSERT_VEC4_EQUAL(sqrt(fvec4(1.5, 3.1, 4.0, 15.0)), sqrt(1.5), sqrt(3.1), sqrt(4.0), sqrt(15.0));
     ASSERT_VEC4_EQUAL(rsqrt(fvec4(1.5, 3.1, 4.0, 15.0)), 1.0/sqrt(1.5), 1.0/sqrt(3.1), 1.0/sqrt(4.0), 1.0/sqrt(15.0));
+    ASSERT_VEC4_EQUAL(exp(fvec4(-2.1, -0.5, 1.5, 3.1)), expf(-2.1), expf(-0.5), expf(1.5), expf(3.1));
+    ASSERT_VEC4_EQUAL(log(fvec4(1.5, 3.1, 4.0, 15.0)), logf(1.5), logf(3.1), logf(4.0), logf(15.0));
     ASSERT_EQUAL_TOL(f1[0]*f2[0]+f1[1]*f2[1]+f1[2]*f2[2], dot3(f1, f2), 1e-6);
     ASSERT_EQUAL_TOL(f1[0]*f2[0]+f1[1]*f2[1]+f1[2]*f2[2]+f1[3]*f2[3], dot4(f1, f2), 1e-6);
     ASSERT(any(f1 > 0.5));

wrappers/python/CMakeLists.txt

@@ -69,6 +69,7 @@ foreach(SUBDIR ${SUBDIRS})
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.str"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*psf"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/charmm22.*"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/par*.inp"
     )
     foreach(file ${STAGING_INPUT_FILES1})
         set(STAGING_INPUT_FILES ${STAGING_INPUT_FILES} "${file}")

wrappers/python/filterPythonFiles.py

+
 from __future__ import print_function
+import re
 import sys
+import textwrap
+from inspect import cleandoc
+from numpydoc.docscrape import NumpyDocString
+
 
-# Doxygen does a bad job of generating documentation based on docstrings.  This script is run as a filter
-# on each file, and converts the docstrings into Doxygen style comments so we get better documentation.
+# Doxygen does a bad job of generating documentation based on docstrings.
+# This script is run as a filter
+# on each file, and converts the docstrings into Doxygen style comments
+# so we get better documentation.
 
 input = open(sys.argv[1])
+
 while True:
     line = input.readline()
     if len(line) == 0:
@@ -15,46 +24,57 @@ while True:
         split = stripped.split()
         if split[0] == 'class' and split[1][0].islower():
             # Classes that start with a lowercase letter were defined by SWIG.  We want to hide them.
-            print("%s## @private" % prefix)
+            print("%s## @private" % prefix, end='')
         if split[1][0] == '_' and split[1][1] != '_':
             # Names starting with a single _ are assumed to be private.
-            print("%s## @private" % prefix)
-        
+            print("%s## @private" % prefix, end='')
+
         # We're at the start of a class or function definition.  Find all lines that contain the declaration.
-        
+
         declaration = line
         while len(line) > 0 and line.find(':') == -1:
             line = input.readline()
             declaration += line
-        
+
         # Now look for a docstring.
-        
-        docstrings = []
+        docstringlines = []
         line = input.readline()
-        stripped = line.lstrip()
-        if stripped.startswith('"""'):
-            line = stripped[3:]
-            readingParameters = False
-            while line.find('"""') == -1:
-                docstrings.append(line)
+        l = line.strip()
+        if l.startswith('"""') or l.startswith("'''"):
+            if l.count('"""') == 2 or l.count("'''") == 2:
+                docstringlines.append(l[3:-3])
+            else:
+                docstringlines.append(l[3:])
                 line = input.readline()
-                if line.strip() == 'Parameters:':
-                    readingParameters = True
+                l = line.strip()
+                while l.find('"""') == -1 and l.find("'''") == -1:
+                    docstringlines.append(line.rstrip())
                     line = input.readline()
-                stripped = line.lstrip()
-                if readingParameters and stripped.startswith('- '):
-                    line = "@param %s" % stripped[2:]
-                elif stripped.startswith('Returns:'):
-                    line = "@return %s" % stripped[8:]
-            line = line[:line.find('"""')]
-            docstrings.append(line)            
-        
+                    l = line.strip()
+                if line.rstrip().endswith('"""') or line.rstrip().endswith("'''"):
+                    # last line
+                    docstringlines.append(line.rstrip()[:-3])
+
+        docstring = NumpyDocString(cleandoc('\n'.join(docstringlines)))
+        # print(docstringlines)
+
         # Print out the docstring in Doxygen syntax, followed by the declaration.
-        
-        for s in docstrings:
-            print("%s##%s" % (prefix, s.strip()))
-        print(declaration)
-        if len(docstrings) == 0:
-            print(line)
+        for line in docstring['Summary']:
+            print('{prefix}## {line}'.format(prefix=prefix, line=line))
+        if len(docstring['Extended Summary']) > 0:
+            print('{prefix}##'.format(prefix=prefix))
+            for line in docstring['Extended Summary']:
+                print('{prefix}## {line}'.format(prefix=prefix, line=line.strip()))
+        print('{prefix}##'.format(prefix=prefix))
+        for name, type, descr in docstring['Parameters']:
+            print('{prefix}## @param {name} ({type}) {descr}'.format(prefix=prefix, type=type, name=name, descr=' '.join(descr)))
+        for name, type, descr in docstring['Returns']:
+            if type == '':
+                type = name
+            print('{prefix}## @return ({type}) {descr}'.format(prefix=prefix, type=type, name=name, descr=' '.join(descr)))
+
+        print(declaration, end='')
+        if len(docstringlines) == 0:
+            print(line, end='')
     else:
-        print(line)
+        print(line, end='')
\ No newline at end of file

wrappers/python/setup.py

@@ -193,6 +193,13 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
         if platform.system() == 'Darwin':
             extra_compile_args += ['-stdlib=libc++', '-mmacosx-version-min=10.7']
             extra_link_args += ['-stdlib=libc++', '-mmacosx-version-min=10.7', '-Wl', '-rpath', openmm_lib_path]
+            # Hard-code CC and CXX to clang, since gcc/g++ will *not* work with
+            # Anaconda, despite the fact that distutils will try to use them.
+            # System Python, homebrew, and MacPorts on Macs will always use
+            # clang, so this hack should always work and fix issues with users
+            # that have GCC installed from MacPorts or homebrew *and* Anaconda
+            os.environ['CC'] = 'clang'
+            os.environ['CXX'] = 'clang++'
 
     library_dirs=[openmm_lib_path]
     include_dirs=openmm_include_path.split(';')

wrappers/python/simtk/openmm/amd.py

@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
 Authors: Peter Eastman, Steffen Lindert
 Contributors:
 
-Permission is hereby granted, free of charge, to any person obtaining a 
+Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
 to deal in the Software without restriction, including without limitation
 the rights to use, copy, modify, merge, publish, distribute, sublicense,
@@ -37,22 +37,26 @@ from simtk.unit import kilojoules_per_mole, is_quantity
 
 class AMDIntegrator(CustomIntegrator):
     """AMDIntegrator implements the aMD integration algorithm.
-    
+
     The system is integrated based on a modified potential.  Whenever the energy V(r) is less than a
     cutoff value E, the following effective potential is used:
-    
+
     V*(r) = V(r) + (E-V(r))^2 / (alpha+E-V(r))
-    
+
     For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
     """
-    
+
     def __init__(self, dt, alpha, E):
         """Create an AMDIntegrator.
-        
-        Parameters:
-         - dt (time) The integration time step to use
-         - alpha (energy) The alpha parameter to use
-         - E (energy) The energy cutoff to use
+
+        Parameters
+        ----------
+        dt : time
+            The integration time step to use
+        alpha : energy
+            The alpha parameter to use
+        E : energy
+            The energy cutoff to use
         """
         CustomIntegrator.__init__(self, dt)
         self.addGlobalVariable("alpha", alpha)
@@ -64,23 +68,23 @@ class AMDIntegrator(CustomIntegrator):
         self.addComputePerDof("x", "x+dt*v")
         self.addConstrainPositions()
         self.addComputePerDof("v", "(x-oldx)/dt")
-    
+
     def getAlpha(self):
         """Get the value of alpha for the integrator."""
         return self.getGlobalVariable(0)*kilojoules_per_mole
-    
+
     def setAlpha(self, alpha):
         """Set the value of alpha for the integrator."""
         self.setGlobalVariable(0, alpha)
-    
+
     def getE(self):
         """Get the energy threshold E for the integrator."""
         return self.getGlobalVariable(1)*kilojoules_per_mole
-    
+
     def setE(self, E):
         """Set the energy threshold E for the integrator."""
         self.setGlobalVariable(1, E)
-    
+
     def getEffectiveEnergy(self, energy):
         """Given the actual potential energy of the system, return the value of the effective potential."""
         alpha = self.getAlpha()
@@ -94,21 +98,26 @@ class AMDIntegrator(CustomIntegrator):
 
 class AMDForceGroupIntegrator(CustomIntegrator):
     """AMDForceGroupIntegrator implements a single boost aMD integration algorithm.
-    
+
     This is similar to AMDIntegrator, but is applied based on the energy of a single force group
     (typically representing torsions).
-    
+
     For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
     """
-    
+
     def __init__(self, dt, group, alphaGroup, EGroup):
         """Create a AMDForceGroupIntegrator.
-        
-        Parameters:
-         - dt (time) The integration time step to use
-         - group (int) The force group to apply the boost to
-         - alphaGroup (energy) The alpha parameter to use for the boosted force group
-         - EGroup (energy) The energy cutoff to use for the boosted force group
+
+        Parameters
+        ----------
+        dt : time
+            The integration time step to use
+        group : int
+            The force group to apply the boost to
+        alphaGroup : energy
+            The alpha parameter to use for the boosted force group
+        EGroup : energy
+            The energy cutoff to use for the boosted force group
         """
         CustomIntegrator.__init__(self, dt)
         self.addGlobalVariable("alphaGroup", alphaGroup)
@@ -124,29 +133,35 @@ class AMDForceGroupIntegrator(CustomIntegrator):
         self.addComputePerDof("x", "x+dt*v")
         self.addConstrainPositions()
         self.addComputePerDof("v", "(x-oldx)/dt")
-    
+
     def getAlphaGroup(self):
         """Get the value of alpha for the boosted force group."""
         return self.getGlobalVariable(0)*kilojoules_per_mole
-    
+
     def setAlphaGroup(self, alpha):
         """Set the value of alpha for the boosted force group."""
         self.setGlobalVariable(0, alpha)
-    
+
     def getEGroup(self):
         """Get the energy threshold E for the boosted force group."""
         return self.getGlobalVariable(1)*kilojoules_per_mole
-    
+
     def setEGroup(self, E):
         """Set the energy threshold E for the boosted force group."""
         self.setGlobalVariable(1, E)
-    
+
     def getEffectiveEnergy(self, groupEnergy):
         """Given the actual group energy of the system, return the value of the effective potential.
-        
-        Parameters:
-          - groupEnergy (energy): the actual potential energy of the boosted force group
-        Returns: the value of the effective potential
+
+        Parameters
+        ----------
+        groupEnergy : energy
+            the actual potential energy of the boosted force group
+
+        Returns
+        -------
+        energy
+            the value of the effective potential
         """
         alphaGroup = self.getAlphaGroup()
         EGroup = self.getEGroup()
@@ -161,24 +176,31 @@ class AMDForceGroupIntegrator(CustomIntegrator):
 
 class DualAMDIntegrator(CustomIntegrator):
     """DualAMDIntegrator implements a dual boost aMD integration algorithm.
-    
+
     This is similar to AMDIntegrator, but two different boosts are applied to the potential:
     one based on the total energy, and one based on the energy of a single force group
     (typically representing torsions).
 
     For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
     """
-    
+
     def __init__(self, dt, group, alphaTotal, ETotal, alphaGroup, EGroup):
         """Create a DualAMDIntegrator.
 
-        Parameters:
-         - dt (time) The integration time step to use
-         - group (int) The force group to apply the second boost to
-         - alphaTotal (energy) The alpha parameter to use for the total energy
-         - ETotal (energy) The energy cutoff to use for the total energy
-         - alphaGroup (energy) The alpha parameter to use for the boosted force group
-         - EGroup (energy) The energy cutoff to use for the boosted force group
+        Parameters
+        ----------
+        dt : time
+            The integration time step to use
+        group : int
+            The force group to apply the second boost to
+        alphaTotal : energy
+            The alpha parameter to use for the total energy
+        ETotal : energy
+            The energy cutoff to use for the total energy
+        alphaGroup : energy
+            The alpha parameter to use for the boosted force group
+        EGroup : energy
+            The energy cutoff to use for the boosted force group
         """
         CustomIntegrator.__init__(self, dt)
         self.addGlobalVariable("alphaTotal", alphaTotal)
@@ -201,46 +223,53 @@ class DualAMDIntegrator(CustomIntegrator):
         self.addComputePerDof("x", "x+dt*v")
         self.addConstrainPositions()
         self.addComputePerDof("v", "(x-oldx)/dt")
-    
+
     def getAlphaTotal(self):
         """Get the value of alpha for the total energy."""
         return self.getGlobalVariable(0)*kilojoules_per_mole
-    
+
     def setAlphaTotal(self, alpha):
         """Set the value of alpha for the total energy."""
         self.setGlobalVariable(0, alpha)
-    
+
     def getETotal(self):
         """Get the energy threshold E for the total energy."""
         return self.getGlobalVariable(1)*kilojoules_per_mole
-    
+
     def setETotal(self, E):
         """Set the energy threshold E for the total energy."""
         self.setGlobalVariable(1, E)
-    
+
     def getAlphaGroup(self):
         """Get the value of alpha for the boosted force group."""
         return self.getGlobalVariable(2)*kilojoules_per_mole
-    
+
     def setAlphaGroup(self, alpha):
         """Set the value of alpha for the boosted force group."""
         self.setGlobalVariable(2, alpha)
-    
+
     def getEGroup(self):
         """Get the energy threshold E for the boosted force group."""
         return self.getGlobalVariable(3)*kilojoules_per_mole
-    
+
     def setEGroup(self, E):
         """Set the energy threshold E for the boosted force group."""
         self.setGlobalVariable(3, E)
-    
+
     def getEffectiveEnergy(self, totalEnergy, groupEnergy):
         """Given the actual potential energy of the system, return the value of the effective potential.
-        
-        Parameters:
-         - totalEnergy (energy): the actual potential energy of the whole system
-         - groupEnergy (energy): the actual potential energy of the boosted force group
-        Returns: the value of the effective potential
+
+        Parameters
+        ----------
+        totalEnergy : energy
+            the actual potential energy of the whole system
+        groupEnergy : energy
+            the actual potential energy of the boosted force group
+
+        Returns
+        -------
+        energy
+            the value of the effective potential
         """
         alphaTotal = self.getAlphaTotal()
         ETotal = self.getETotal()