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Commit 2d2f05ce authored by Andy Simmonett's avatar Andy Simmonett
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Merge branch 'master' of github.com:pandegroup/openmm into genpt

parents 94823d84 4d32047c
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Showing with 602 additions and 264 deletions
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
View file @ 2d2f05ce
......@@ -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;
}
}
......
plugins/rpmd/platforms/reference/CMakeLists.txt
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
......@@ -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 0 → 100644
View file @ 2d2f05ce
#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
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
#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);
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_*/
#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/GBVIForceProxy.cpp deleted 100644 → 0
View file @ 94823d84
/* -------------------------------------------------------------------------- *
* 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
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
......@@ -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());
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);
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
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);
double bornRadius = radius;
double eps0 = EPSILON0;
double tau = (1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric());
// Switch to the Langevin integrator and make sure that it heats up.
double bornEnergy = (-charge*charge/(8*PI_M*eps0))*tau/bornRadius;
double nonpolarEnergy = -gamma*tau*std::pow(radius/bornRadius, 3.0);
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);
double expectedE = (bornEnergy+nonpolarEnergy);
double obtainedE = state.getPotentialEnergy();
double diff = fabs((obtainedE - expectedE)/expectedE);
// Now reinitialize the context and repeat all of these tests to make sure that works correctly.
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
context.reinitialize();
integrator.setCurrentIntegrator(0);
}
}
void testEnergyEthane(int applyBornRadiiScaling) {
const int numParticles = 8;
void testChangingParameters() {
System system;
LangevinIntegrator integrator(0, 0.1, 0.01);
// harmonic bond
double C_HBondDistance = 0.1097;
double C_CBondDistance = 0.1504;
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);
system.addForce(bonds);
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));
double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
// Try getting and setting the step size for different component integrators.
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;
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);
}
else {
C_radius = 0.215;
C_gamma = -1.1087;
H_radius = 0.150;
H_gamma = 0.1237;
for (int i = 0; i < 3; i++) {
integrator.setCurrentIntegrator(i);
ASSERT_EQUAL_TOL(0.02*(i+1), integrator.getStepSize(), 1e-7);
}
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
// Try getting and setting the constraint tolerance for different component integrators.
GBVIForce* forceField = new GBVIForce();
if (applyBornRadiiScaling) {
forceField->setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
for (int i = 0; i < 3; i++) {
integrator.setCurrentIntegrator(i);
ASSERT_EQUAL_TOL(1e-5, integrator.getConstraintTolerance(), 1e-7);
}
else {
forceField->setBornRadiusScalingMethod(GBVIForce::NoScaling);
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 < 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(1e-4*(i+1), integrator.getConstraintTolerance(), 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);
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);
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
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
......@@ -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.
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);
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);
System system;
system.setDefaultPeriodicBoxVectors(a, b, c);
NonbondedForce* force = new NonbondedForce();
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
// Serialize and then deserialize it.
force->setCutoffDistance(cutoff);
force->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
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);
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
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
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:
......@@ -15,10 +24,10 @@ 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.
......@@ -28,33 +37,44 @@ while True:
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 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)))
for s in docstrings:
print("%s##%s" % (prefix, s.strip()))
print(declaration)
if len(docstrings) == 0:
print(line)
print(declaration, end='')
if len(docstringlines) == 0:
print(line, end='')
else:
print(line)
\ No newline at end of file
print(line, end='')
wrappers/python/setup.py
View file @ 2d2f05ce
......@@ -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
View file @ 2d2f05ce
......@@ -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()
......
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