Merge master

plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h

@@ -82,14 +82,14 @@ public:
      * Get the force field parameters for a stretch-bend term.
      * 
      * @param index              the index of the stretch-bend for which to get parameters
-     * @param particle1     the index of the first particle connected by the stretch-bend
-     * @param particle2     the index of the second particle connected by the stretch-bend
-     * @param particle3     the index of the third particle connected by the stretch-bend
-     * @param lengthAB      the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
-     * @param lengthCB      the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
-     * @param angle         the equilibrium angle in radians
-     * @param k1            the force constant of the product of bond ab and angle a-b-c
-     * @param k2            the force constant of the product of bond bc and angle a-b-c
+     * @param[out] particle1     the index of the first particle connected by the stretch-bend
+     * @param[out] particle2     the index of the second particle connected by the stretch-bend
+     * @param[out] particle3     the index of the third particle connected by the stretch-bend
+     * @param[out] lengthAB      the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
+     * @param[out] lengthCB      the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
+     * @param[out] angle         the equilibrium angle in radians
+     * @param[out] k1            the force constant of the product of bond ab and angle a-b-c
+     * @param[out] k2            the force constant of the product of bond bc and angle a-b-c
      */
     void getStretchBendParameters(int index, int& particle1, int& particle2, int& particle3, double& lengthAB,
                                   double& lengthCB, double& angle, double& k1, double& k2) const;

plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h

@@ -90,13 +90,13 @@ public:
      * Get the force field parameters for a torsion-torsion term.
      *
      * @param index                          the index of the torsion-torsion for which to get parameters
-     * @param particle1                 the index of the first particle connected by the torsion-torsion
-     * @param particle2                 the index of the second particle connected by the torsion-torsion
-     * @param particle3                 the index of the third particle connected by the torsion-torsion
-     * @param particle4                 the index of the fourth particle connected by the torsion-torsion
-     * @param particle5                 the index of the fifth particle connected by the torsion-torsion
-     * @param chiralCheckAtomIndex      the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
-     * @param gridIndex                 the grid index
+     * @param[out] particle1                 the index of the first particle connected by the torsion-torsion
+     * @param[out] particle2                 the index of the second particle connected by the torsion-torsion
+     * @param[out] particle3                 the index of the third particle connected by the torsion-torsion
+     * @param[out] particle4                 the index of the fourth particle connected by the torsion-torsion
+     * @param[out] particle5                 the index of the fifth particle connected by the torsion-torsion
+     * @param[out] chiralCheckAtomIndex      the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
+     * @param[out] gridIndex                 the grid index
      */
     void getTorsionTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& chiralCheckAtomIndex, int& gridIndex) const;
 
@@ -117,7 +117,7 @@ public:
     /**
      * Get the torsion-torsion grid at the specified index
      *
-     * @param gridIndex     the grid index
+     * @param  index        the grid index
      * @return grid         return grid reference
      */
     const std::vector<std::vector<std::vector<double> > >& getTorsionTorsionGrid(int index) const;
@@ -172,7 +172,7 @@ public:
     }
     TorsionTorsionInfo(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) :
                        particle1(particle1), particle2(particle2), particle3(particle3),
-                       particle4(particle4), particle5(particle5), gridIndex(gridIndex), chiralCheckAtomIndex(chiralCheckAtomIndex) {
+                       particle4(particle4), particle5(particle5), chiralCheckAtomIndex(chiralCheckAtomIndex), gridIndex(gridIndex) {
 
     }
 };

plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h

@@ -98,10 +98,10 @@ public:
      * Get the force field parameters for a vdw particle.
      *
      * @param particleIndex        the particle index
-     * @param parentIndex     the index of the parent particle
-     * @param sigma           vdw sigma
-     * @param epsilon         vdw epsilon
-     * @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
+     * @param[out] parentIndex     the index of the parent particle
+     * @param[out] sigma           vdw sigma
+     * @param[out] epsilon         vdw epsilon
+     * @param[out] reductionFactor the fraction of the distance along the line from the parent particle to this particle
      *                             at which the interaction site should be placed
      */
     void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, double& reductionFactor) const;
@@ -179,7 +179,7 @@ public:
      * Get exclusions for specified particle
      *
      * @param particleIndex   particle index
-     * @param exclusions vector of exclusions
+     * @param[out] exclusions vector of exclusions
      */
     void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const;
 
@@ -253,7 +253,7 @@ public:
         epsilon              = 0.0;
     }
     VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor) :
-        parentIndex(parentIndex), sigma(sigma), epsilon(epsilon), reductionFactor(reductionFactor)  {
+        parentIndex(parentIndex), reductionFactor(reductionFactor), sigma(sigma), epsilon(epsilon)  {
     }
 };
 

plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h

@@ -76,8 +76,8 @@ public:
      * Get the force field parameters for a WCA dispersion particle.
      * 
      * @param particleIndex        the particle index
-     * @param radius          radius
-     * @param epsilon         epsilon 
+     * @param[out] radius          radius
+     * @param[out] epsilon         epsilon 
      */
     void getParticleParameters(int particleIndex, double& radius, double& epsilon) const;
 

plugins/drude/openmmapi/include/openmm/DrudeForce.h

@@ -92,18 +92,18 @@ public:
      * Get the parameters for a Drude particle.
      *
      * @param index                the index of the Drude particle for which to get parameters
-     * @param particle        the index within the System of the Drude particle
-     * @param particle1       the index within the System of the particle to which the Drude particle is attached
-     * @param particle2       the index within the System of the second particle used for defining anisotropic polarizability.
+     * @param[out] particle        the index within the System of the Drude particle
+     * @param[out] particle1       the index within the System of the particle to which the Drude particle is attached
+     * @param[out] particle2       the index within the System of the second particle used for defining anisotropic polarizability.
      *                             This may be set to -1, in which case aniso12 will be ignored.
-     * @param particle3       the index within the System of the third particle used for defining anisotropic polarizability.
+     * @param[out] particle3       the index within the System of the third particle used for defining anisotropic polarizability.
      *                             This may be set to -1, in which case aniso34 will be ignored.
-     * @param particle4       the index within the System of the fourth particle used for defining anisotropic polarizability.
+     * @param[out] particle4       the index within the System of the fourth particle used for defining anisotropic polarizability.
      *                             This may be set to -1, in which case aniso34 will be ignored.
-     * @param charge          The charge on the Drude particle
-     * @param polarizability  The isotropic polarizability
-     * @param aniso12         The scale factor for the polarizability along the direction defined by particle1 and particle2
-     * @param aniso34         The scale factor for the polarizability along the direction defined by particle3 and particle4
+     * @param[out] charge          The charge on the Drude particle
+     * @param[out] polarizability  The isotropic polarizability
+     * @param[out] aniso12         The scale factor for the polarizability along the direction defined by particle1 and particle2
+     * @param[out] aniso34         The scale factor for the polarizability along the direction defined by particle3 and particle4
      */
     void getParticleParameters(int index, int& particle, int& particle1, int& particle2, int& particle3, int& particle4, double& charge, double& polarizability, double& aniso12, double& aniso34) const;
     /**
@@ -137,9 +137,9 @@ public:
      * Get the force field parameters for screened pair.
      *
      * @param index           the index of the pair for which to get parameters
-     * @param particle1  the index within this Force of the first particle involved in the interaction
-     * @param particle2  the index within this Force of the second particle involved in the interaction
-     * @param thole      the Thole screening factor
+     * @param[out] particle1  the index within this Force of the first particle involved in the interaction
+     * @param[out] particle2  the index within this Force of the second particle involved in the interaction
+     * @param[out] thole      the Thole screening factor
      */
     void getScreenedPairParameters(int index, int& particle1, int& particle2, double& thole) const;
     /**

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[0]*static_cast<int>(center[0]/periodicBoxSize[0][0]);
+            diff -= periodicBoxSize[1]*static_cast<int>(center[1]/periodicBoxSize[1][1]);
+            diff -= periodicBoxSize[2]*static_cast<int>(center[2]/periodicBoxSize[2][2]);
 
             // 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;
             }
         }
 

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;
     /**

serialization/src/CompoundIntegratorProxy.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) 2015 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/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

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"
@@ -65,6 +66,7 @@
 #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"
@@ -112,6 +114,7 @@ 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());

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;

tests/TestCompoundIntegrator.h

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2015 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/internal/AssertionUtilities.h"
+#include "openmm/BrownianIntegrator.h"
+#include "openmm/CompoundIntegrator.h"
+#include "openmm/Context.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/LangevinIntegrator.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;
+
+void testChangingIntegrator() {
+    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(0.01));
+    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);
+    }
+}
+
+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);
+    }
+    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 < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        ASSERT_EQUAL_TOL(0.02*(i+1), integrator.getStepSize(), 1e-7);
+    }
+    
+    // Try getting and setting the constraint tolerance for different component integrators.
+    
+    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);
+    ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    context.setPositions(positions);
+
+    // 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;
+    }
+    
+    // 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;
+    }
+    
+    // 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;
+    }
+}
+
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
+    try {
+        initializeTests(argc, argv);
+        testChangingIntegrator();
+        testChangingParameters();
+        testDifferentStepSizes();
+        runPlatformTests();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

tests/TestEnforcePeriodicBox.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) 2010-2015 Stanford University and the Authors.      *
+ * Authors: Robert McGibbon                                                   *
+ * 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/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/Platform.h"
+#include "openmm/VerletIntegrator.h"
+#include "sfmt/SFMT.h"
+#include <iostream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testTruncatedOctahedron() {
+    const int numMolecules = 5;
+    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*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
+        positions[2*i+1] = positions[2*i] + Vec3(1.0, 0.0, 0.0);
+        system.addConstraint(2*i, 2*i+1, 1.0);
+    }
+    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);
+    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 argc, char* argv[]) {
+    try {
+        testTruncatedOctahedron();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

wrappers/python/simtk/openmm/amd.py

@@ -49,10 +49,14 @@ class AMDIntegrator(CustomIntegrator):
     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)
@@ -104,11 +108,16 @@ class AMDForceGroupIntegrator(CustomIntegrator):
     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)
@@ -144,9 +153,15 @@ class AMDForceGroupIntegrator(CustomIntegrator):
     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()
@@ -172,13 +187,20 @@ class DualAMDIntegrator(CustomIntegrator):
     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)
@@ -237,10 +259,17 @@ class DualAMDIntegrator(CustomIntegrator):
     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()

wrappers/python/simtk/openmm/app/amberinpcrdfile.py

@@ -60,12 +60,17 @@ class AmberInpcrdFile(object):
     def __init__(self, file, loadVelocities=None, loadBoxVectors=None):
         """Load an inpcrd file.
 
-        An inpcrd file contains atom positions and, optionally, velocities and periodic box dimensions.
-
-        Parameters:
-         - file (string) the name of the file to load
-         - loadVelocities (boolean=None) deprecated. Velocities are loaded automatically if present
-         - loadBoxVectors (boolean=None) deprecated. Box vectors are loaded automatically if present
+        An inpcrd file contains atom positions and, optionally, velocities and
+        periodic box dimensions.
+
+        Parameters
+        ----------
+        file : str
+             The name of the file to load
+        loadVelocities : bool
+             Deprecated. Velocities are loaded automatically if present
+        loadBoxVectors : bool
+            Deprecated. Box vectors are loaded automatically if present
         """
         self.file = file
         if loadVelocities is not None or loadBoxVectors is not None:
@@ -84,8 +89,11 @@ class AmberInpcrdFile(object):
     def getPositions(self, asNumpy=False):
         """Get the atomic positions.
 
-        Parameters:
-         - asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
+        Parameters
+        ----------
+        asNumpy : bool=False
+            if true, the values are returned as a numpy array instead of a list
+            of Vec3s
         """
         if asNumpy:
             if self._numpyPositions is None:
@@ -97,8 +105,10 @@ class AmberInpcrdFile(object):
     def getVelocities(self, asNumpy=False):
         """Get the atomic velocities.
 
-        Parameters:
-         - asNumpy (boolean=False) if true, the vectors are returned as numpy arrays instead of Vec3s
+        Parameters
+        ----------
+        asNumpy : bool=False
+            if true, the vectors are returned as numpy arrays instead of Vec3s
         """
         if self.velocities is None:
             raise AttributeError('velocities not found in %s' % self.file)
@@ -112,8 +122,11 @@ class AmberInpcrdFile(object):
     def getBoxVectors(self, asNumpy=False):
         """Get the periodic box vectors.
 
-        Parameters:
-         - asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
+        Parameters
+        ----------
+        asNumpy : bool=False
+            if true, the values are returned as a numpy array instead of a list
+            of Vec3s
         """
         if self.boxVectors is None:
             raise AttributeError('Box information not found in %s' % self.file)

wrappers/python/simtk/openmm/app/amberprmtopfile.py

@@ -151,29 +151,52 @@ class AmberPrmtopFile(object):
                      implicitSolventKappa=None, temperature=298.15*unit.kelvin,
                      soluteDielectric=1.0, solventDielectric=78.5,
                      removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005):
-        """Construct an OpenMM System representing the topology described by this prmtop file.
+        """Construct an OpenMM System representing the topology described by this
+        prmtop file.
 
-        Parameters:
-         - nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions.  Allowed values are
+        Parameters
+        ----------
+        nonbondedMethod : object=NoCutoff
+            The method to use for nonbonded interactions.  Allowed values are
             NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
-         - nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions
-         - constraints (object=None) Specifies which bonds angles should be implemented with constraints.
+        nonbondedCutoff : distance=1*nanometer
+            The cutoff distance to use for nonbonded interactions
+        constraints : object=None
+            Specifies which bonds angles should be implemented with constraints.
             Allowed values are None, HBonds, AllBonds, or HAngles.
-         - rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
-         - implicitSolvent (object=None) If not None, the implicit solvent model to use.  Allowed values are HCT, OBC1, OBC2, GBn, or GBn2.
-         - implicitSolventSaltConc (float=0.0*unit.moles/unit.liter) The salt concentration for GB 
-                    calculations (modelled as a debye screening parameter). It is converted to the debye length (kappa)
+        rigidWater : boolean=True
+            If true, water molecules will be fully rigid regardless of the value
+            passed for the constraints argument
+        implicitSolvent : object=None
+            If not None, the implicit solvent model to use.  Allowed values are
+            HCT, OBC1, OBC2, GBn, or GBn2.
+        implicitSolventSaltConc : float=0.0*unit.moles/unit.liter
+            The salt concentration for GB calculations (modelled as a debye
+            screening parameter). It is converted to the debye length (kappa)
             using the provided temperature and solventDielectric
-         - temperature (float=300*kelvin) Temperature of the system. Only used to compute the Debye length from
-                    implicitSolventSoltConc
-         - implicitSolventKappa (float units of 1/length) If this value is set, implicitSolventSaltConc will be ignored.
-         - soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model.
-         - solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model.
-         - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
-         - hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms.  Any mass added to a hydrogen is
-           subtracted from the heavy atom to keep their total mass the same.
-         - ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
-        Returns: the newly created System
+        temperature : float=300*kelvin
+            Temperature of the system. Only used to compute the Debye length
+            from implicitSolventSoltConc
+        implicitSolventKappa : float units of 1/length
+            If this value is set, implicitSolventSaltConc will be ignored.
+        soluteDielectric : float=1.0
+            The solute dielectric constant to use in the implicit solvent model.
+        solventDielectric : float=78.5
+            The solvent dielectric constant to use in the implicit solvent
+            model.
+        removeCMMotion : boolean=True
+            If true, a CMMotionRemover will be added to the System
+        hydrogenMass : mass=None
+            The mass to use for hydrogen atoms bound to heavy atoms.  Any mass
+            added to a hydrogen is subtracted from the heavy atom to keep their
+            total mass the same.
+        ewaldErrorTolerance : float=0.0005
+            The error tolerance to use if nonbondedMethod is Ewald or PME.
+
+        Returns
+        -------
+        System
+            the newly created System
         """
         if self._prmtop.chamber:
             raise ValueError("CHAMBER-style topology file detected. CHAMBER "

wrappers/python/simtk/openmm/app/charmmcrdfiles.py

@@ -49,12 +49,17 @@ class CharmmCrdFile(object):
     Reads and parses a CHARMM coordinate file (.crd) into its components,
     namely the coordinates, CHARMM atom types, resid, resname, etc.
 
-    Main attributes:
-        - natom (int) : Number of atoms in the system
-        - resname (list) : Names of all residues
-        - positions (list) : All cartesian coordinates [x1, y1, z1, x2, ...]
-
-    Example:
+    Attributes
+    ----------
+    natom : int
+        Number of atoms in the system
+    resname : list
+        Names of all residues
+    positions : list
+        All cartesian coordinates [x1, y1, z1, x2, ...]
+
+    Examples
+    --------
     >>> chm = CharmmCrdFile('testfiles/1tnm.crd')
     >>> print '%d atoms; %d coords' % (chm.natom, len(chm.positions))
     1414 atoms; 1414 coords
@@ -131,14 +136,21 @@ class CharmmRstFile(object):
     Reads and parses data, velocities and coordinates from a CHARMM restart
     file (.rst) of file name 'fname' into class attributes
 
-    Main attributes:
-        - natom (int) : Number of atoms in the system
-        - resname (list) : Names of all residues
-        - positions (list) : All cartesian coordinates [x1, y1, z1, x2, ...]
-        - positionsold (list) : Old cartesian coordinates
-        - velocities (list) : List of all cartesian velocities
-
-    Example:
+    Attributes
+    ----------
+    natom : int
+        Number of atoms in the system
+    resname : list
+        Names of all residues
+    positions : list
+        All cartesian coordinates [x1, y1, z1, x2, ...]
+    positionsold : list
+        Old cartesian coordinates
+    velocities : list
+        List of all cartesian velocities
+
+    Examples
+    --------
     >>> chm = CharmmRstFile('testfiles/sample-charmm.rst')
     >>> print chm.header[0]
     REST    37     1

wrappers/python/simtk/openmm/app/charmmparameterset.py

@@ -51,18 +51,19 @@ class CharmmParameterSet(object):
     the information found in the MASS section of the CHARMM topology file
     (TOP/RTF) and all of the information in the parameter files (PAR)
 
-    Parameters:
-        - filenames : List of topology, parameter, and stream files to load into
-          the parameter set. The following file type suffixes are recognized.
-          Unrecognized file types raise a TypeError
-            .rtf, .top -- Residue topology file
-            .par, .prm -- Parameter file
-            .str -- Stream file
-            .inp -- If "par" is in the file name, it is a parameter file. If
+    Parameters
+    ----------
+    filenames : List of topology, parameter, and stream files to load into the parameter set.
+        The following file type suffixes are recognized. Unrecognized file types raise a TypeError
+          * .rtf, .top -- Residue topology file
+          * .par, .prm -- Parameter file
+          * .str -- Stream file
+          * .inp -- If "par" is in the file name, it is a parameter file. If
                     "top" is in the file name, it is a topology file. Otherwise,
                     raise TypeError
 
-    Attributes:
+    Attributes
+    ----------
     All type lists are dictionaries whose keys are tuples (with however
     many elements are needed to define that type of parameter). The types
     that can be in any order are SORTED.
@@ -85,7 +86,8 @@ class CharmmParameterSet(object):
     when only the integer or string is available the other dictionaries are
     helpful
 
-    Example:
+    Examples
+    --------
     >>> params = CharmmParameterSet('charmm22.top', 'charmm22.par', 'file.str')
     """
 
@@ -150,18 +152,25 @@ class CharmmParameterSet(object):
         Instantiates a CharmmParameterSet from a Topology file and a Parameter
         file (or just a Parameter file if it has all information)
 
-        Parameters:
-            - tfile (str) : Name of the Topology (RTF/TOP) file
-            - pfile (str) : Name of the Parameter (PAR) file
-            - sfiles (list of str) : List or tuple of stream (STR) file names.
-            - permissive (bool) : Accept non-bonbded parameters for undefined 
-                                  atom types (default False)
-
-        Returns:
+        Parameters
+        -----------
+        tfile : str
+            Name of the Topology (RTF/TOP) file
+        pfile : str
+            Name of the Parameter (PAR) file
+        sfiles : list of str
+            List or tuple of stream (STR) file names.
+        permissive : bool=False
+            Accept non-bonbded parameters for undefined atom types
+
+        Returns
+        -------
+        CharmmParameterSet
             New CharmmParameterSet populated with the parameters found in the
             provided files.
 
-        Notes:
+        Notes
+        -----
         The RTF file is read first (if provided), followed by the PAR file,
         followed by the list of stream files (in the order they are
         provided). Parameters in each stream file will overwrite those that
@@ -183,21 +192,24 @@ class CharmmParameterSet(object):
         return inst
 
     def readParameterFile(self, pfile, permissive=False):
-        """
-        Reads all of the parameters from a parameter file. Versions 36 and
-        later of the CHARMM force field files have an ATOMS section defining
-        all of the atom types.  Older versions need to load this information
-        from the RTF/TOP files.
-
-        Parameters:
-            - pfile (str) : Name of the CHARMM PARameter file to read
-            - permissive (bool) : Accept non-bonbded parameters for undefined 
-                                  atom types (default False)
-
-        Notes: The atom types must all be loaded by the end of this routine.
-        Either supply a PAR file with atom definitions in them or read in a
-        RTF/TOP file first. Failure to do so will result in a raised
-        RuntimeError.
+        """Reads all of the parameters from a parameter file. Versions 36 and later
+        of the CHARMM force field files have an ATOMS section defining all of
+        the atom types.  Older versions need to load this information from the
+        RTF/TOP files.
+
+        Parameters
+        ----------
+        pfile : str
+            Name of the CHARMM PARameter file to read
+        permissive : bool
+            Accept non-bonbded parameters for undefined atom types (default:
+            False).
+
+        Notes
+        -----
+        The atom types must all be loaded by the end of this routine. Either
+        supply a PAR file with atom definitions in them or read in a RTF/TOP
+        file first. Failure to do so will result in a raised RuntimeError.
         """
         conv = CharmmParameterSet._convert
         if isinstance(pfile, str):
@@ -518,14 +530,17 @@ class CharmmParameterSet(object):
         if own_handle: f.close()
 
     def readTopologyFile(self, tfile):
-        """
-        Reads _only_ the atom type definitions from a topology file. This is
+        """Reads _only_ the atom type definitions from a topology file. This is
         unnecessary for versions 36 and later of the CHARMM force field.
 
-        Parameters:
-            - tfile (str) : Name of the CHARMM TOPology file to read
+        Parameters
+        ----------
+        tfile : str
+            : Name of the CHARMM TOPology file to read
 
-        Note: The CHARMM TOPology file is also called a Residue Topology File
+        Notes
+        -----
+        The CHARMM TOPology file is also called a Residue Topology File
         """
         conv = CharmmParameterSet._convert
         if isinstance(tfile, str):
@@ -564,12 +579,13 @@ class CharmmParameterSet(object):
         if own_handle: f.close()
 
     def readStreamFile(self, sfile):
-        """
-        Reads RTF and PAR sections from a stream file and dispatches the
+        """Reads RTF and PAR sections from a stream file and dispatches the
         sections to readTopologyFile or readParameterFile
 
-        Parameters:
-            - sfile (str or CharmmStreamFile) : Stream file to parse
+        Parameters
+        ----------
+        sfile : str or CharmmStreamFile
+            Stream file to parse
         """
         if isinstance(sfile, CharmmStreamFile):
             f = sfile
@@ -594,14 +610,8 @@ class CharmmParameterSet(object):
         bond, angle, dihedral, improper, or cmap type will pair with EVERY key
         in the type mapping dictionaries that points to the equivalent type
 
-        Returns:
-            - Returns the instance that is being condensed.
-
-        Notes:
-            The return value allows you to condense the types at construction
-            time.
-
-        Example:
+        Example
+        -------
         >>> params = CharmmParameterSet('charmm.prm').condense()
         """
         # First scan through all of the bond types
@@ -631,8 +641,10 @@ class CharmmParameterSet(object):
         """
         Loops through the given dict and condenses all types.
 
-        Parameter:
-            - typedict : Type dictionary to condense
+        Parameters
+        ----------
+        typedict
+            Type dictionary to condense
         """
         keylist = list(typedict.keys())
         for i in range(len(keylist) - 1):

wrappers/python/simtk/openmm/app/charmmpsffile.py

@@ -116,11 +116,7 @@ def _strip_optunit(thing, unit):
 _resre = re.compile(r'(\d+)([a-zA-Z]*)')
 
 class CharmmPsfFile(object):
-    """
-    A chemical structure instantiated from CHARMM files.
-
-    Example:
-    >>> cs = CharmmPsfFile("testfiles/test.psf")
+    """A chemical structure instantiated from CHARMM files.
 
     This structure has numerous attributes that are lists of the elements of
     this structure, including atoms, bonds, torsions, etc. The attributes are
@@ -144,7 +140,8 @@ class CharmmPsfFile(object):
     The lengths of each of these lists gives the pointers (e.g., natom, nres,
     etc.)
 
-    Example:
+    Examples
+    --------
     >>> cs = CharmmPsfFile("testfiles/test.psf")
     >>> len(cs.atom_list)
     33
@@ -166,14 +163,16 @@ class CharmmPsfFile(object):
 
     @_catchindexerror
     def __init__(self, psf_name):
-        """
-        Opens and parses a PSF file, then instantiates a CharmmPsfFile
+        """Opens and parses a PSF file, then instantiates a CharmmPsfFile
         instance from the data.
 
-        Parameters:
-            psf_name (str) : Name of the PSF file (it must exist)
+        Parameters
+        ----------
+        psf_name : str
+            Name of the PSF file (it must exist)
 
-        Exceptions Raised:
+        Raises
+        ------
         IOError : If file "psf_name" does not exist
         CharmmPSFError: If any parsing errors are encountered
         """
@@ -388,14 +387,17 @@ class CharmmPsfFile(object):
 
     @staticmethod
     def _convert(string, type, message):
-        """
-        Converts a string to a specific type, making sure to raise
+        """Converts a string to a specific type, making sure to raise
         CharmmPSFError with the given message in the event of a failure.
 
-        Parameters:
-            - string (str) : Input string to process
-            - type (type) : Type of data to convert to
-            - message (str) : Error message to put in exception if failed
+        Parameters
+        ----------
+        string : str
+            Input string to process
+        type : type
+            Type of data to convert to
+        message : str
+            Error message to put in exception if failed
         """
         try:
             return type(string)
@@ -405,23 +407,24 @@ class CharmmPsfFile(object):
 
     @staticmethod
     def _parse_psf_section(psf):
-        """
-        This method parses a section of the PSF file
-
-        Parameters:
-            - psf (CharmmFile) : Open file that is pointing to the first line
-                                 of the section that is to be parsed
-        
-        Returns:
-            (title, pointers, data)
-
-            - title (str) : The label of the PSF section we are parsing
-            - pointers (int/tuple of ints) : If one pointer is set, pointers is
-                    simply the integer that is value of that pointer. Otherwise
-                    it is a tuple with every pointer value defined in the first
-                    line
-            - data (list) : A list of all data in the parsed section converted
-                    to `dtype'
+        """This method parses a section of the PSF file
+
+        Parameters
+        ----------
+         psf : CharmmFile
+             Open file that is pointing to the first line of the section
+             that is to be parsed
+
+        Returns
+        --------
+        str
+            The label of the PSF section we are parsing
+        int/tuple of ints
+            If one pointer is set, pointers is simply the integer that is
+            value of that pointer. Otherwise it is a tuple with every pointer
+            value defined in the first line
+        list
+            A list of all data in the parsed section converted to `dtype'
         """
         conv = CharmmPsfFile._convert
         line = psf.readline()
@@ -462,22 +465,22 @@ class CharmmPsfFile(object):
         return title, pointers, data
 
     def loadParameters(self, parmset):
-        """
-        Loads parameters from a parameter set that was loaded via CHARMM RTF,
+        """Loads parameters from a parameter set that was loaded via CHARMM RTF,
         PAR, and STR files.
 
-        Parameters:
-            - parmset (CharmmParameterSet) : List of all parameters
+        Parameters
+        ----------
+        parmset : CharmmParameterSet
+            List of all parameters
 
-        Notes:
+        Notes
+        -----
         - If any parameters that are necessary cannot be found, a
           MissingParameter exception is raised.
-
         - If any dihedral or improper parameters cannot be found, I will try
           inserting wildcards (at either end for dihedrals and as the two
           central atoms in impropers) and see if that matches.  Wild-cards
           will apply ONLY if specific parameters cannot be found.
-
         - This method will expand the dihedral_parameter_list attribute by
           adding a separate Dihedral object for each term for types that
           have a multi-term expansion
@@ -588,13 +591,22 @@ class CharmmPsfFile(object):
 
     def setBox(self, a, b, c, alpha=90.0*u.degrees, beta=90.0*u.degrees,
                gamma=90.0*u.degrees):
-        """
-        Sets the periodic box boundary conditions.
-
-        Parameters:
-            - a, b, c (floats) : Lengths of the periodic cell
-            - alpha, beta, gamma (floats, optional) : Angles between the
-                periodic cell vectors.
+        """Sets the periodic box boundary conditions.
+
+        Parameters
+        ----------
+        a : length
+            Lengths of the periodic cell
+        b : length
+            Lengths of the periodic cell
+        c : length
+            Lengths of the periodic cell
+        alpha : floats, optional
+            Angles between the periodic cell vectors.
+        beta : floats, optional
+            Angles between the periodic cell vectors.
+        gamma : floats, optional
+            Angles between the periodic cell vectors.
         """
         try:
             # Since we are setting the box, delete the cached box lengths if we
@@ -752,52 +764,60 @@ class CharmmPsfFile(object):
                      ewaldErrorTolerance=0.0005,
                      flexibleConstraints=True,
                      verbose=False):
-        """
-        Construct an OpenMM System representing the topology described by the
+        """Construct an OpenMM System representing the topology described by the
         prmtop file. You MUST have loaded a parameter set into this PSF before
         calling createSystem. If not, AttributeError will be raised. ValueError
         is raised for illegal input.
 
-        Parameters:
-         -  params (CharmmParameterSet) The parameter set to use to parametrize
-               this molecule
-         -  nonbondedMethod (object=NoCutoff) The method to use for nonbonded
-               interactions. Allowed values are NoCutoff, CutoffNonPeriodic,
-               CutoffPeriodic, Ewald, or PME.
-         -  nonbondedCutoff (distance=1*nanometer) The cutoff distance to use
-               for nonbonded interactions.
-         -  switchDistance (distance=0*nanometer) The distance at which the
-               switching function is active for nonbonded interactions. If the
-               switchDistance evaluates to boolean False (if it is 0), no
-               switching function will be used. Illegal values will raise a
-               ValueError
-         -  constraints (object=None) Specifies which bonds or angles should be
-               implemented with constraints. Allowed values are None, HBonds,
-               AllBonds, or HAngles.
-         -  rigidWater (boolean=True) If true, water molecules will be fully
-               rigid regardless of the value passed for the constraints argument
-         -  implicitSolvent (object=None) If not None, the implicit solvent
-               model to use. Allowed values are HCT, OBC1, OBC2, or GBn
-         -  implicitSolventKappa (float=None): Debye screening parameter to
-               model salt concentrations in GB solvent.
-         -  implicitSolventSaltConc (float=0.0*u.moles/u.liter): Salt
-               concentration for GB simulations. Converted to Debye length
+        Parameters
+        ----------
+        params : CharmmParameterSet
+            The parameter set to use to parametrize this molecule
+        nonbondedMethod : object=NoCutoff
+            The method to use for nonbonded interactions. Allowed values are
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+        nonbondedCutoff : distance=1*nanometer
+            The cutoff distance to use for nonbonded interactions.
+        switchDistance : distance=0*nanometer
+            The distance at which the switching function is active for nonbonded
+            interactions. If the switchDistance evaluates to boolean False (if
+            it is 0), no switching function will be used. Illegal values will
+            raise a ValueError
+        constraints : object=None
+            Specifies which bonds or angles should be implemented with
+            constraints. Allowed values are None, HBonds, AllBonds, or HAngles.
+        rigidWater : boolean=True
+            If true, water molecules will be fully rigid regardless of the value
+            passed for the constraints argument
+        implicitSolvent : object=None
+            If not None, the implicit solvent model to use. Allowed values are
+            HCT, OBC1, OBC2, or GBn
+        implicitSolventKappa : float=None
+            Debye screening parameter to model salt concentrations in GB
+            solvent.
+        implicitSolventSaltConc : float=0.0*u.moles/u.liter
+            Salt concentration for GB simulations. Converted to Debye length
             `kappa'
-         -  temperature (float=298.15*u.kelvin): Temperature used in the salt
-               concentration-to-kappa conversion for GB salt concentration term
-         -  soluteDielectric (float=1.0) The solute dielectric constant to use
-               in the implicit solvent model.
-         -  solventDielectric (float=78.5) The solvent dielectric constant to
-               use in the implicit solvent model.
-         -  removeCMMotion (boolean=True) If true, a CMMotionRemover will be
-               added to the System.
-         -  hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to
-               heavy atoms. Any mass added to a hydrogen is subtracted from the
-               heavy atom to keep their total mass the same.
-         -  ewaldErrorTolerance (float=0.0005) The error tolerance to use if the
-               nonbonded method is Ewald or PME.
-         -  flexibleConstraints (bool=True) Are our constraints flexible or not?
-         -  verbose (bool=False) Optionally prints out a running progress report
+        temperature : float=298.15*u.kelvin
+            Temperature used in the salt concentration-to-kappa conversion for
+            GB salt concentration term
+        soluteDielectric : float=1.0
+            The solute dielectric constant to use in the implicit solvent model.
+        solventDielectric : float=78.5
+            The solvent dielectric constant to use in the implicit solvent
+            model.
+        removeCMMotion : boolean=True
+            If true, a CMMotionRemover will be added to the System.
+        hydrogenMass : mass=None
+            The mass to use for hydrogen atoms bound to heavy atoms. Any mass
+            added to a hydrogen is subtracted from the heavy atom to keep their
+            total mass the same.
+        ewaldErrorTolerance : float=0.0005
+            The error tolerance to use if the nonbonded method is Ewald or PME.
+        flexibleConstraints : bool=True
+            Are our constraints flexible or not?
+        verbose : bool=False
+            Optionally prints out a running progress report
         """
         # Load the parameter set
         self.loadParameters(params.condense())

wrappers/python/simtk/openmm/app/checkpointreporter.py

@@ -71,10 +71,12 @@ class CheckpointReporter(object):
     def __init__(self, file, reportInterval):
         """Create a CheckpointReporter.
 
-        Parameters:
-         - file (string or open file object) The file to write to. Any current
-           contents will be overwritten.
-         - reportInterval (int) The interval (in time steps) at which to write checkpoints
+        Parameters
+        ----------
+        file : string or open file object
+            The file to write to. Any current contents will be overwritten.
+        reportInterval : int
+            The interval (in time steps) at which to write checkpoints.
         """
 
         self._reportInterval = reportInterval
@@ -88,12 +90,18 @@ class CheckpointReporter(object):
     def describeNextReport(self, simulation):
         """Get information about the next report this object will generate.
 
-        Parameters:
-         - simulation (Simulation) The Simulation to generate a report for
-
-        Returns: A five element tuple.  The first element is the number of steps until the
-        next report.  The remaining elements specify whether that report will require
-        positions, velocities, forces, and energies respectively.
+        Parameters
+        ----------
+        simulation : Simulation
+            The Simulation to generate a report for
+
+        Returns
+        -------
+        tuple
+            A five element tuple. The first element is the number of steps
+            until the next report. The remaining elements specify whether
+            that report will require positions, velocities, forces, and
+            energies respectively.
         """
         steps = self._reportInterval - simulation.currentStep%self._reportInterval
         return (steps, False, False, False, False)
@@ -101,9 +109,12 @@ class CheckpointReporter(object):
     def report(self, simulation, state):
         """Generate a report.
 
-        Parameters:
-         - simulation (Simulation) The Simulation to generate a report for
-         - state (State) The current state of the simulation
+        Parameters
+        ----------
+        simulation : Simulation
+            The Simulation to generate a report for
+        state : State
+            The current state of the simulation
         """
         self._out.seek(0)
         chk = simulation.context.createCheckpoint()