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Commit 5a06df78 authored by tic20's avatar tic20
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Merge https://github.com/openmm/openmm

parents 8dd60914 a9223eea
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plugins/drude/platforms/reference/tests/TestReferenceDrudeNoseHoover.cpp 0 → 100644
View file @ 5a06df78
/* -------------------------------------------------------------------------- *
* 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) 2013 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 "ReferenceTests.h"
#include "openmm/Platform.h"
using namespace OpenMM;
using namespace std;
//extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories();
Platform& initializePlatform(int argc, char* argv[]) {
/* registerDrudeReferenceKernelFactories();
*/
return Platform::getPlatformByName("Reference");
}
#include "TestDrudeNoseHoover.h"
void runPlatformTests() { }
plugins/drude/serialization/include/openmm/serialization/DrudeNoseHooverIntegratorProxy.h 0 → 100644
View file @ 5a06df78
#ifndef OPENMM_DRUDE_NOSE_HOOVER_INTEGRATOR_PROXY_H_
#define OPENMM_DRUDE_NOSE_HOOVER_INTEGRATOR_PROXY_H_
#include "openmm/serialization/SerializationProxy.h"
#include "openmm/internal/windowsExportDrude.h"
namespace OpenMM {
class OPENMM_EXPORT_DRUDE DrudeNoseHooverIntegratorProxy : public SerializationProxy {
public:
DrudeNoseHooverIntegratorProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
}
#endif /*OPENMM_DRUDE_NOSE_HOOVER_INTEGRATOR_PROXY_H_*/
plugins/drude/serialization/src/DrudeNoseHooverIntegratorProxy.cpp 0 → 100644
View file @ 5a06df78
/* -------------------------------------------------------------------------- *
* 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 Stanford University and the Authors. *
* Authors: Andrew C. Simmonett, Andreas Krämer *
* 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/DrudeNoseHooverIntegratorProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/DrudeNoseHooverIntegrator.h"
#include <vector>
#include <assert.h>
#include <OpenMM.h>
using namespace std;
using namespace OpenMM;
DrudeNoseHooverIntegratorProxy::DrudeNoseHooverIntegratorProxy() : SerializationProxy("DrudeNoseHooverIntegrator") {
}
void DrudeNoseHooverIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const DrudeNoseHooverIntegrator& integrator = *reinterpret_cast<const DrudeNoseHooverIntegrator*>(object);
node.setDoubleProperty("stepSize", integrator.getStepSize());
node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
node.setDoubleProperty("maximumPairDistance", integrator.getMaximumPairDistance());
assert(not integrator.hasSubsystemThermostats());
node.setDoubleProperty("temperature", integrator.getTemperature());
node.setDoubleProperty("relativeTemperature", integrator.getRelativeTemperature());
node.setDoubleProperty("collisionFrequency", integrator.getCollisionFrequency());
node.setDoubleProperty("relativeCollisionFrequency", integrator.getRelativeCollisionFrequency());
node.setIntProperty("chainLength", integrator.getThermostat().getChainLength());
node.setIntProperty("numMTS", integrator.getThermostat().getNumMultiTimeSteps());
node.setIntProperty("numYS", integrator.getThermostat().getNumYoshidaSuzukiTimeSteps());
}
void* DrudeNoseHooverIntegratorProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
DrudeNoseHooverIntegrator* integrator;
integrator = new DrudeNoseHooverIntegrator(
node.getDoubleProperty("temperature"),
node.getDoubleProperty("collisionFrequency"),
node.getDoubleProperty("relativeTemperature"),
node.getDoubleProperty("relativeCollisionFrequency"),
node.getDoubleProperty("stepSize"),
node.getIntProperty("chainLength"),
node.getIntProperty("numMTS"),
node.getIntProperty("numYS")
);
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setMaximumPairDistance(node.getDoubleProperty("maximumPairDistance"));
return integrator;
}
plugins/drude/serialization/src/DrudeSerializationProxyRegistration.cpp
View file @ 5a06df78
......@@ -42,11 +42,13 @@
#include "openmm/DrudeForce.h"
#include "openmm/DrudeLangevinIntegrator.h"
#include "openmm/DrudeNoseHooverIntegrator.h"
#include "openmm/serialization/SerializationProxy.h"
#include "openmm/serialization/DrudeForceProxy.h"
#include "openmm/serialization/DrudeLangevinIntegratorProxy.h"
#include "openmm/serialization/DrudeNoseHooverIntegratorProxy.h"
#if defined(WIN32)
#include <windows.h>
......@@ -65,4 +67,5 @@ using namespace OpenMM;
extern "C" OPENMM_EXPORT_DRUDE void registerDrudeSerializationProxies() {
SerializationProxy::registerProxy(typeid(DrudeForce), new DrudeForceProxy());
SerializationProxy::registerProxy(typeid(DrudeLangevinIntegrator), new DrudeLangevinIntegratorProxy());
SerializationProxy::registerProxy(typeid(DrudeNoseHooverIntegrator), new DrudeNoseHooverIntegratorProxy());
}
plugins/drude/serialization/tests/TestSerializeDrudeNoseHooverIntegrator.cpp 0 → 100644
View file @ 5a06df78
/* -------------------------------------------------------------------------- *
* 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: Andrew C. Simmonett and Andreas Kraemer
* 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/DrudeNoseHooverIntegrator.h"
#include "ReferencePlatform.h"
#include "openmm/serialization/XmlSerializer.h"
#include "openmm/System.h"
#include "openmm/DrudeForce.h"
#include "openmm/Context.h"
#include <iostream>
#include <sstream>
using namespace OpenMM;
using namespace std;
extern "C" void registerDrudeSerializationProxies();
//extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories();
//extern "C" OPENMM_EXPORT void registerKernelFactories();
void assertIntegratorsEqual(const DrudeNoseHooverIntegrator& integrator1, const DrudeNoseHooverIntegrator& integrator2){
ASSERT_EQUAL(integrator1.getStepSize(), integrator2.getStepSize());
ASSERT_EQUAL(integrator1.getConstraintTolerance(), integrator2.getConstraintTolerance());
ASSERT_EQUAL(integrator1.getMaximumPairDistance(), integrator2.getMaximumPairDistance());
ASSERT_EQUAL(integrator1.getNumThermostats(), integrator2.getNumThermostats());
for (int i = 0; i < integrator1.getNumThermostats(); i++) {
const auto &thermostat1 = integrator1.getThermostat(i);
const auto &thermostat2 = integrator2.getThermostat(i);
ASSERT_EQUAL(thermostat1.getTemperature(), thermostat2.getTemperature());
ASSERT_EQUAL(thermostat1.getCollisionFrequency(), thermostat2.getCollisionFrequency());
ASSERT_EQUAL(thermostat1.getRelativeTemperature(), thermostat2.getRelativeTemperature());
ASSERT_EQUAL(thermostat1.getRelativeCollisionFrequency(), thermostat2.getRelativeCollisionFrequency());
ASSERT_EQUAL(thermostat1.getChainLength(), thermostat2.getChainLength());
ASSERT_EQUAL(thermostat1.getNumMultiTimeSteps(), thermostat2.getNumMultiTimeSteps());
ASSERT_EQUAL(thermostat1.getNumYoshidaSuzukiTimeSteps(), thermostat2.getNumYoshidaSuzukiTimeSteps());
ASSERT_EQUAL(thermostat1.getChainID(), thermostat2.getChainID());
const auto &thermostat1Atoms = thermostat1.getThermostatedAtoms();
const auto &thermostat2Atoms = thermostat2.getThermostatedAtoms();
ASSERT_EQUAL(thermostat1Atoms.size(), thermostat2Atoms.size());
for (int j = 0; j < thermostat1Atoms.size(); ++j) {
ASSERT_EQUAL(thermostat1Atoms[j], thermostat2Atoms[j]);
}
const auto &thermostat1Pairs = thermostat1.getThermostatedPairs();
const auto &thermostat2Pairs = thermostat2.getThermostatedPairs();
ASSERT_EQUAL(thermostat1Pairs.size(), thermostat2Pairs.size());
for (int j = 0; j < thermostat1Pairs.size(); ++j) {
ASSERT_EQUAL(thermostat1Pairs[j].first, thermostat2Pairs[j].first);
ASSERT_EQUAL(thermostat1Pairs[j].second, thermostat2Pairs[j].second);
}
}
}
void testSerialization() {
// Check with default constructor
System system;
system.addForce(new DrudeForce());
for (int i=0; i<10; i++) system.addParticle(1.0);
DrudeNoseHooverIntegrator integrator(331, 0.21, 1.1, 0.1, 0.004, 5, 5, 5);
// Serialize and then deserialize it.
stringstream buffer2;
XmlSerializer::serialize<DrudeNoseHooverIntegrator>(&integrator, "Integrator", buffer2);
DrudeNoseHooverIntegrator* copy = XmlSerializer::deserialize<DrudeNoseHooverIntegrator>(buffer2);
ASSERT_EQUAL(copy->getThermostat(0).getThermostatedAtoms().size(), 0);
assertIntegratorsEqual(integrator, *copy);
}
int main() {
try {
testSerialization();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
plugins/drude/tests/TestDrudeNoseHoover.h 0 → 100644
View file @ 5a06df78
/* -------------------------------------------------------------------------- *
* 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) 2019 Stanford University and the Authors. *
* Authors: Andreas Krämer and Andrew C. Simmonett *
* 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/NoseHooverChain.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/DrudeNoseHooverIntegrator.h"
#include "openmm/Context.h"
#include "openmm/State.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/VirtualSite.h"
#include "openmm/NonbondedForce.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/System.h"
#include "openmm/DrudeForce.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <sstream>
#include <iomanip>
#include <vector>
#include <algorithm>
#include <numeric>
using namespace OpenMM;
using namespace std;
extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories();
extern "C" OPENMM_EXPORT void registerKernelFactories();
Platform& initializePlatform(int argc, char* argv[]);
void build_waterbox(System &system, int gridSize, double polarizability, vector<Vec3> & positions) {
// Create a box of SWM4-NDP water molecules. This involves constraints, virtual sites,
// and Drude particles.
const int numMolecules = gridSize*gridSize*gridSize;
const double spacing = 0.8;
const double boxSize = spacing*(gridSize+1);
NonbondedForce* nonbonded = new NonbondedForce();
DrudeForce* drude = new DrudeForce();
CMMotionRemover* cmm = new CMMotionRemover(1);
system.addForce(cmm);
system.addForce(nonbonded);
system.addForce(drude);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
nonbonded->setCutoffDistance(1.2);
nonbonded->setSwitchingDistance(0.8);
for (int i = 0; i < numMolecules; i++) {
int startIndex = system.getNumParticles();
system.addParticle(15.6); // O
system.addParticle(0.4); // D
system.addParticle(1.0); // H1
system.addParticle(1.0); // H2
system.addParticle(0.0); // M
nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
nonbonded->addParticle(-1.71636, 1, 0);
nonbonded->addParticle(0.55733, 1, 0);
nonbonded->addParticle(0.55733, 1, 0);
nonbonded->addParticle(-1.11466, 1, 0);
for (int j = 0; j < 5; j++)
for (int k = 0; k < j; k++)
nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
system.addConstraint(startIndex, startIndex+2, 0.09572);
system.addConstraint(startIndex, startIndex+3, 0.09572);
system.addConstraint(startIndex+2, startIndex+3, 0.15139);
system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, polarizability, 1, 1);
}
for (int i = 0; i < gridSize; i++) {
for (int j = 0; j < gridSize; j++) {
for (int k = 0; k < gridSize; k++) {
Vec3 pos(i*spacing, j*spacing, k*spacing);
positions.push_back(pos);
positions.push_back(pos);
positions.push_back(pos+Vec3(0.09572, 0, 0));
positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
positions.push_back(pos);
}
}
}
}
void testWaterBox(Platform& platform) {
// Create a box of SWM4-NDP water molecules. This involves constraints, virtual sites,
// and Drude particles.
System system;
const int gridSize = 3;
vector<Vec3> positions;
double polarizability = ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184);
build_waterbox(system, gridSize, polarizability, positions);
const int numMolecules = gridSize*gridSize*gridSize;
int numStandardDof = 3*3*numMolecules - system.getNumConstraints();
int numDrudeDof = 3*numMolecules;
int numDof = numStandardDof+numDrudeDof;
const double temperature = 300.0;
const double temperatureDrude = 10.0;
// Simulate it and check the temperature.
int chainLength = 4;
int numMTS = 4;
int numYS = 5;
double frequency = 800.0;
double frequencyDrude = 2000.0;
int randomSeed = 100;
DrudeNoseHooverIntegrator integ(temperature, frequency,
temperatureDrude, frequencyDrude, 0.0005,
chainLength, numMTS, numYS);
Context context(system, integ, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(temperature, randomSeed);
std::vector<Vec3> velocities = context.getState(State::Velocities).getVelocities();
for (int i = 0; i < numMolecules; i++){
Vec3 noize;
for (int j = 0; j < 3; j++){
noize[j] = float(((i+18311)*(j+18253) * 313419097822414) % 18313) / float(18313);
noize[j] *= sqrt(3 * BOLTZ * temperatureDrude / 0.4);
}
velocities[5*i+1] = velocities[5*i] + noize;
}
context.setVelocities(velocities);
context.applyConstraints(1e-6);
// Equilibrate.
integ.step(500);
// Compute the internal and center of mass temperatures.
double totalKE = 0;
const int numSteps = 4000;
double meanTemp = 0.0;
double meanDrudeTemp = 0.0;
double meanConserved = 0.0;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
State state = context.getState(State::Energy);
double KE = state.getKineticEnergy();
double PE = state.getPotentialEnergy();
double fullKE = integ.computeTotalKineticEnergy();
double drudeKE = integ.computeDrudeKineticEnergy();
double temp = KE/(0.5*numStandardDof*BOLTZ);
double drudeTemp = drudeKE/(0.5*numDrudeDof*BOLTZ);
meanTemp = (i*meanTemp + temp)/(i+1);
meanDrudeTemp = (i*meanDrudeTemp + drudeTemp)/(i+1);
double heatBathEnergy = integ.computeHeatBathEnergy();
double conserved = PE + fullKE + heatBathEnergy;
meanConserved = (i*meanConserved + conserved)/(i+1);
totalKE += KE;
ASSERT(fabs(meanConserved - conserved) < 0.6);
}
totalKE /= numSteps;
ASSERT_USUALLY_EQUAL_TOL(temperature, meanTemp, 0.004);
ASSERT_USUALLY_EQUAL_TOL(temperatureDrude, meanDrudeTemp, 0.004);
}
double testWaterBoxWithHardWallConstraint(Platform& platform, double hardWallConstraint){
// Create a box of SWM4-NDP water molecules. This involves constraints, virtual sites,
// and Drude particles.
System system;
const int gridSize = 3;
vector<Vec3> positions;
double polarizability = 1e-2;
build_waterbox(system, gridSize, polarizability, positions);
const int numMolecules = gridSize*gridSize*gridSize;
int numStandardDof = 3*3*numMolecules - system.getNumConstraints();
int numDrudeDof = 3*numMolecules;
int numDof = numStandardDof+numDrudeDof;
const double temperature = 300.0;
const double temperatureDrude = 10.0;
// Simulate it and check the temperature.
int chainLength = 4;
int numMTS = 3;
int numYS = 3;
double frequency = 25.0;
double frequencyDrude = 25.0;
int randomSeed = 100;
DrudeNoseHooverIntegrator integ(temperature, frequency,
temperatureDrude, frequencyDrude, 0.0005,
chainLength, numMTS, numYS);
integ.setMaxDrudeDistance(hardWallConstraint);
Context context(system, integ, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(temperature, randomSeed);
std::vector<Vec3> velocities = context.getState(State::Velocities).getVelocities();
for (int i = 0; i < numMolecules; i++){
Vec3 noize;
for (int j = 0; j < 3; j++){
noize[j] = float(((i+18311)*(j+18253) * 313419097822414) % 18313) / float(18313);
noize[j] *= sqrt(3 * BOLTZ * temperatureDrude / 0.4);
}
velocities[5*i+1] = velocities[5*i] + noize;
}
context.setVelocities(velocities);
context.applyConstraints(1e-6);
// Equilibrate.
integ.step(10);
// Compute the internal and center of mass temperatures.
double totalKE = 0;
const int numSteps = 10;
double meanTemp = 0.0;
double meanDrudeTemp = 0.0;
double meanConserved = 0.0;
double maxR = 0.0;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
State state = context.getState(State::Energy | State::Positions);
double KE = state.getKineticEnergy();
double PE = state.getPotentialEnergy();
double fullKE = integ.computeTotalKineticEnergy();
double drudeKE = integ.computeDrudeKineticEnergy();
double temp = KE/(0.5*numStandardDof*BOLTZ);
double drudeTemp = drudeKE/(0.5*numDrudeDof*BOLTZ);
meanTemp = (i*meanTemp + temp)/(i+1);
meanDrudeTemp = (i*meanDrudeTemp + drudeTemp)/(i+1);
double heatBathEnergy = integ.computeHeatBathEnergy();
double conserved = PE + fullKE + heatBathEnergy;
meanConserved = (i*meanConserved + conserved)/(i+1);
const auto & positions = state.getPositions();
for(int mol = 0; mol < gridSize*gridSize*gridSize; ++mol) {
auto dR = positions[5*mol+1] - positions[5*mol];
maxR = std::max(maxR, std::sqrt(dR.dot(dR)));
}
totalKE += KE;
}
totalKE /= numSteps;
return maxR;
}
int main(int argc, char* argv[]) {
try {
registerKernelFactories();
Platform& platform = initializePlatform(argc, argv);
testWaterBox(platform);
double maxDrudeDistance = 0.005;
double observedDrudeDistance = testWaterBoxWithHardWallConstraint(platform, 0.0);
ASSERT(observedDrudeDistance > maxDrudeDistance);
observedDrudeDistance = testWaterBoxWithHardWallConstraint(platform, maxDrudeDistance);
ASSERT(observedDrudeDistance < maxDrudeDistance);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
plugins/rpmd/platforms/cuda/CMakeLists.txt
View file @ 5a06df78
......@@ -63,27 +63,28 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/include)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_BINARY_DIR}/platforms/cuda/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/common/include)
# Set variables needed for encoding kernel sources into a C++ class
SET(CUDA_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
SET(CUDA_SOURCE_CLASS CudaRpmdKernelSources)
SET(CUDA_KERNELS_CPP ${CMAKE_CURRENT_BINARY_DIR}/src/${CUDA_SOURCE_CLASS}.cpp)
SET(CUDA_KERNELS_H ${CMAKE_CURRENT_BINARY_DIR}/src/${CUDA_SOURCE_CLASS}.h)
SET(SOURCE_FILES ${SOURCE_FILES} ${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H})
SET(KERNEL_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
SET(KERNEL_SOURCE_CLASS CudaRpmdKernelSources)
SET(KERNELS_CPP ${CMAKE_CURRENT_BINARY_DIR}/src/${KERNEL_SOURCE_CLASS}.cpp)
SET(KERNELS_H ${CMAKE_CURRENT_BINARY_DIR}/src/${KERNEL_SOURCE_CLASS}.h)
SET(SOURCE_FILES ${SOURCE_FILES} ${KERNELS_CPP} ${KERNELS_H})
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}/src)
# Create the library
INCLUDE_DIRECTORIES(${CUDA_TOOLKIT_INCLUDE})
FILE(GLOB CUDA_KERNELS ${CUDA_SOURCE_DIR}/kernels/*.cu)
ADD_CUSTOM_COMMAND(OUTPUT ${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H}
FILE(GLOB CUDA_KERNELS ${KERNEL_SOURCE_DIR}/kernels/*.cu)
ADD_CUSTOM_COMMAND(OUTPUT ${KERNELS_CPP} ${KERNELS_H}
COMMAND ${CMAKE_COMMAND}
ARGS -D CUDA_SOURCE_DIR=${CUDA_SOURCE_DIR} -D CUDA_KERNELS_CPP=${CUDA_KERNELS_CPP} -D CUDA_KERNELS_H=${CUDA_KERNELS_H} -D CUDA_SOURCE_CLASS=${CUDA_SOURCE_CLASS} -P ${CMAKE_SOURCE_DIR}/platforms/cuda/EncodeCUDAFiles.cmake
ARGS -D KERNEL_SOURCE_DIR=${KERNEL_SOURCE_DIR} -D KERNELS_CPP=${KERNELS_CPP} -D KERNELS_H=${KERNELS_H} -D KERNEL_SOURCE_CLASS=${KERNEL_SOURCE_CLASS} -D KERNEL_FILE_EXTENSION=cu -P ${CMAKE_SOURCE_DIR}/cmake_modules/EncodeKernelFiles.cmake
DEPENDS ${CUDA_KERNELS}
)
SET_SOURCE_FILES_PROPERTIES(${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H} PROPERTIES GENERATED TRUE)
SET_SOURCE_FILES_PROPERTIES(${KERNELS_CPP} ${KERNELS_H} PROPERTIES GENERATED TRUE)
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
......
plugins/rpmd/platforms/cuda/src/CudaRpmdKernelSources.h.in
View file @ 5a06df78
......@@ -39,7 +39,7 @@ namespace OpenMM {
class CudaRpmdKernelSources {
public:
@CUDA_FILE_DECLARATIONS@
@KERNEL_FILE_DECLARATIONS@
};
} // namespace OpenMM
......
plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp
View file @ 5a06df78
......@@ -307,7 +307,7 @@ void CudaIntegrateRPMDStepKernel::setPositions(int copy, const vector<Vec3>& pos
double4 periodicBoxSize = cu.getPeriodicBoxSize();
vector<Vec3> offsetPos(numParticles);
for (int i = 0; i < numParticles; ++i) {
int4 offset = cu.getPosCellOffsets()[i];
mm_int4 offset = cu.getPosCellOffsets()[i];
offsetPos[order[i]] = pos[order[i]] + Vec3(offset.x*periodicBoxSize.x, offset.y*periodicBoxSize.y, offset.z*periodicBoxSize.z);
}
......
plugins/rpmd/platforms/opencl/CMakeLists.txt
View file @ 5a06df78
......@@ -62,27 +62,28 @@ ENDFOREACH(subdir)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/opencl/include)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/opencl/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/common/include)
# Set variables needed for encoding kernel sources into a C++ class
SET(CL_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
SET(CL_SOURCE_CLASS OpenCLRpmdKernelSources)
SET(CL_KERNELS_CPP ${CMAKE_CURRENT_BINARY_DIR}/src/${CL_SOURCE_CLASS}.cpp)
SET(CL_KERNELS_H ${CMAKE_CURRENT_BINARY_DIR}/src/${CL_SOURCE_CLASS}.h)
SET(SOURCE_FILES ${SOURCE_FILES} ${CL_KERNELS_CPP} ${CL_KERNELS_H})
SET(KERNEL_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
SET(KERNEL_SOURCE_CLASS OpenCLRpmdKernelSources)
SET(KERNELS_CPP ${CMAKE_CURRENT_BINARY_DIR}/src/${KERNEL_SOURCE_CLASS}.cpp)
SET(KERNELS_H ${CMAKE_CURRENT_BINARY_DIR}/src/${KERNEL_SOURCE_CLASS}.h)
SET(SOURCE_FILES ${SOURCE_FILES} ${KERNELS_CPP} ${KERNELS_H})
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}/src)
# Create the library
INCLUDE_DIRECTORIES(${OPENCL_INCLUDE_DIR})
FILE(GLOB OPENCL_KERNELS ${CL_SOURCE_DIR}/kernels/*.cl)
ADD_CUSTOM_COMMAND(OUTPUT ${CL_KERNELS_CPP} ${CL_KERNELS_H}
FILE(GLOB OPENCL_KERNELS ${KERNEL_SOURCE_DIR}/kernels/*.cl)
ADD_CUSTOM_COMMAND(OUTPUT ${KERNELS_CPP} ${KERNELS_H}
COMMAND ${CMAKE_COMMAND}
ARGS -D CL_SOURCE_DIR=${CL_SOURCE_DIR} -D CL_KERNELS_CPP=${CL_KERNELS_CPP} -D CL_KERNELS_H=${CL_KERNELS_H} -D CL_SOURCE_CLASS=${CL_SOURCE_CLASS} -P ${CMAKE_SOURCE_DIR}/platforms/opencl/EncodeCLFiles.cmake
ARGS -D KERNEL_SOURCE_DIR=${KERNEL_SOURCE_DIR} -D KERNELS_CPP=${KERNELS_CPP} -D KERNELS_H=${KERNELS_H} -D KERNEL_SOURCE_CLASS=${KERNEL_SOURCE_CLASS} -D KERNEL_FILE_EXTENSION=cl -P ${CMAKE_SOURCE_DIR}/cmake_modules/EncodeKernelFiles.cmake
DEPENDS ${OPENCL_KERNELS}
)
SET_SOURCE_FILES_PROPERTIES(${CL_KERNELS_CPP} ${CL_KERNELS_H} PROPERTIES GENERATED TRUE)
SET_SOURCE_FILES_PROPERTIES(${KERNELS_CPP} ${KERNELS_H} PROPERTIES GENERATED TRUE)
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
......
plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernelSources.h.in
View file @ 5a06df78
......@@ -39,7 +39,7 @@ namespace OpenMM {
class OpenCLRpmdKernelSources {
public:
@CL_FILE_DECLARATIONS@
@KERNEL_FILE_DECLARATIONS@
};
} // namespace OpenMM
......
serialization/include/openmm/serialization/LangevinMiddleIntegratorProxy.h 0 → 100644
View file @ 5a06df78
#ifndef OPENMM_LANGEVIN_MIDDLE_INTEGRATOR_PROXY_H_
#define OPENMM_LANGEVIN_MIDDLE_INTEGRATOR_PROXY_H_
#include "openmm/serialization/XmlSerializer.h"
namespace OpenMM {
class LangevinMiddleIntegratorProxy : public SerializationProxy {
public:
LangevinMiddleIntegratorProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
}
#endif /*OPENMM_LANGEVIN_MIDDLE_INTEGRATOR_PROXY_H_*/
\ No newline at end of file
serialization/include/openmm/serialization/BAOABLangevinIntegratorProxy.h → serialization/include/openmm/serialization/NoseHooverIntegratorProxy.h
View file @ 5a06df78
#ifndef OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_
#define OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_
#include "openmm/serialization/XmlSerializer.h"
namespace OpenMM {
class BAOABLangevinIntegratorProxy : public SerializationProxy {
public:
BAOABLangevinIntegratorProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
}
#endif /*OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_*/
\ No newline at end of file
#ifndef OPENMM_NOSE_HOOVER_INTEGRATOR_PROXY_H_
#define OPENMM_NOSE_HOOVER_INTEGRATOR_PROXY_H_
#include "openmm/serialization/XmlSerializer.h"
namespace OpenMM {
class NoseHooverIntegratorProxy : public SerializationProxy {
public:
NoseHooverIntegratorProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
}
#endif /*OPENMM_NOSE_HOOVER_INTEGRATOR_PROXY_H_*/
serialization/src/BAOABLangevinIntegratorProxy.cpp → serialization/src/LangevinMiddleIntegratorProxy.cpp
View file @ 5a06df78
......@@ -29,19 +29,19 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/BAOABLangevinIntegratorProxy.h"
#include "openmm/serialization/LangevinMiddleIntegratorProxy.h"
#include <OpenMM.h>
using namespace std;
using namespace OpenMM;
BAOABLangevinIntegratorProxy::BAOABLangevinIntegratorProxy() : SerializationProxy("BAOABLangevinIntegrator") {
LangevinMiddleIntegratorProxy::LangevinMiddleIntegratorProxy() : SerializationProxy("LangevinMiddleIntegrator") {
}
void BAOABLangevinIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
void LangevinMiddleIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const BAOABLangevinIntegrator& integrator = *reinterpret_cast<const BAOABLangevinIntegrator*>(object);
const LangevinMiddleIntegrator& integrator = *reinterpret_cast<const LangevinMiddleIntegrator*>(object);
node.setDoubleProperty("stepSize", integrator.getStepSize());
node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
node.setDoubleProperty("temperature", integrator.getTemperature());
......@@ -49,10 +49,10 @@ void BAOABLangevinIntegratorProxy::serialize(const void* object, SerializationNo
node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
}
void* BAOABLangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
void* LangevinMiddleIntegratorProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
BAOABLangevinIntegrator *integrator = new BAOABLangevinIntegrator(node.getDoubleProperty("temperature"),
LangevinMiddleIntegrator *integrator = new LangevinMiddleIntegrator(node.getDoubleProperty("temperature"),
node.getDoubleProperty("friction"), node.getDoubleProperty("stepSize"));
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
......
serialization/src/NonbondedForceProxy.cpp
View file @ 5a06df78
......@@ -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) 2010-2018 Stanford University and the Authors. *
* Portions copyright (c) 2010-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,7 +42,7 @@ NonbondedForceProxy::NonbondedForceProxy() : SerializationProxy("NonbondedForce"
}
void NonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 3);
node.setIntProperty("version", 4);
const NonbondedForce& force = *reinterpret_cast<const NonbondedForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setIntProperty("method", (int) force.getNonbondedMethod());
......@@ -52,6 +52,7 @@ void NonbondedForceProxy::serialize(const void* object, SerializationNode& node)
node.setDoubleProperty("ewaldTolerance", force.getEwaldErrorTolerance());
node.setDoubleProperty("rfDielectric", force.getReactionFieldDielectric());
node.setIntProperty("dispersionCorrection", force.getUseDispersionCorrection());
node.setIntProperty("exceptionsUsePeriodic", force.getExceptionsUsePeriodicBoundaryConditions());
double alpha;
int nx, ny, nz;
force.getPMEParameters(alpha, nx, ny, nz);
......@@ -101,7 +102,7 @@ void NonbondedForceProxy::serialize(const void* object, SerializationNode& node)
void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
int version = node.getIntProperty("version");
if (version < 1 || version > 3)
if (version < 1 || version > 4)
throw OpenMMException("Unsupported version number");
NonbondedForce* force = new NonbondedForce();
try {
......@@ -137,6 +138,8 @@ void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
for (auto& offset : exceptionOffsets.getChildren())
force->addExceptionParameterOffset(offset.getStringProperty("parameter"), offset.getIntProperty("exception"), offset.getDoubleProperty("q"), offset.getDoubleProperty("sig"), offset.getDoubleProperty("eps"));
}
if (version >= 4)
force->setExceptionsUsePeriodicBoundaryConditions(node.getIntProperty("exceptionsUsePeriodic"));
const SerializationNode& particles = node.getChildNode("Particles");
for (auto& particle : particles.getChildren())
force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("sig"), particle.getDoubleProperty("eps"));
......
serialization/src/NoseHooverIntegratorProxy.cpp 0 → 100644
View file @ 5a06df78
/* -------------------------------------------------------------------------- *
* 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 Stanford University and the Authors. *
* Authors: Andrew C. Simmonett, Andreas Krämer *
* 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/NoseHooverIntegratorProxy.h"
#include <vector>
#include <OpenMM.h>
using namespace std;
using namespace OpenMM;
NoseHooverIntegratorProxy::NoseHooverIntegratorProxy() : SerializationProxy("NoseHooverIntegrator") {
}
void NoseHooverIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const NoseHooverIntegrator& integrator = *reinterpret_cast<const NoseHooverIntegrator*>(object);
node.setDoubleProperty("stepSize", integrator.getStepSize());
node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
node.setDoubleProperty("maximumPairDistance", integrator.getMaximumPairDistance());
node.setBoolProperty("hasSubsystemThermostats", integrator.hasSubsystemThermostats());
if (integrator.hasSubsystemThermostats()) {
// Serialize all thermostats separately
for (int i = 0; i < integrator.getNumThermostats(); i++){
const auto& chain = integrator.getThermostat(i);
auto& chainNode = node.createChildNode("Thermostat");
chainNode.setDoubleProperty("temperature", chain.getTemperature());
chainNode.setDoubleProperty("collisionFrequency", chain.getCollisionFrequency());
chainNode.setDoubleProperty("relativeTemperature", chain.getRelativeTemperature());
chainNode.setDoubleProperty("relativeCollisionFrequency", chain.getRelativeCollisionFrequency());
chainNode.setIntProperty("chainLength", chain.getChainLength());
chainNode.setIntProperty("numMTS", chain.getNumMultiTimeSteps());
chainNode.setIntProperty("numYS", chain.getNumYoshidaSuzukiTimeSteps());
auto& particlesNode = chainNode.createChildNode("ThermostatedAtoms");
for (int particle: chain.getThermostatedAtoms()){
particlesNode.createChildNode("Particle").setIntProperty("index", particle);
}
auto& pairsNode = chainNode.createChildNode("ThermostatedPairs");
for (auto& pair: chain.getThermostatedPairs()){
auto& pairNode = pairsNode.createChildNode("Pair");
pairNode.setIntProperty("index1", pair.first);
pairNode.setIntProperty("index2", pair.second);
}
}
} else { // Serialize standard thermostat
node.setDoubleProperty("temperature", integrator.getTemperature());
node.setDoubleProperty("collisionFrequency", integrator.getCollisionFrequency());
node.setIntProperty("chainLength", integrator.getThermostat().getChainLength());
node.setIntProperty("numMTS", integrator.getThermostat().getNumMultiTimeSteps());
node.setIntProperty("numYS", integrator.getThermostat().getNumYoshidaSuzukiTimeSteps());
}
}
void* NoseHooverIntegratorProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
NoseHooverIntegrator* integrator;
if (node.getBoolProperty("hasSubsystemThermostats")){
// deserialize all chains
integrator = new NoseHooverIntegrator(node.getDoubleProperty("stepSize"));
for (auto& chainNode : node.getChildren()) {
// particles
const auto& particlesNode = chainNode.getChildNode("ThermostatedAtoms");
vector<int> particles;
for (auto& particleNode: particlesNode.getChildren()){
particles.push_back(particleNode.getIntProperty("index"));
}
// pairs
const auto& pairsNode = chainNode.getChildNode("ThermostatedPairs");
vector<pair<int, int>> pairs;
for (auto& pairNode: pairsNode.getChildren()){
pairs.emplace_back(pairNode.getIntProperty("index1"), pairNode.getIntProperty("index2"));
}
integrator->addSubsystemThermostat(
particles, pairs,
chainNode.getDoubleProperty("temperature"),
chainNode.getDoubleProperty("collisionFrequency"),
chainNode.getDoubleProperty("relativeTemperature"),
chainNode.getDoubleProperty("relativeCollisionFrequency"),
chainNode.getIntProperty("chainLength"),
chainNode.getIntProperty("numMTS"),
chainNode.getIntProperty("numYS")
);
}
} else {
integrator = new NoseHooverIntegrator(
node.getDoubleProperty("temperature"),
node.getDoubleProperty("collisionFrequency"),
node.getDoubleProperty("stepSize"),
node.getIntProperty("chainLength"),
node.getIntProperty("numMTS"),
node.getIntProperty("numYS")
);
}
integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
integrator->setMaximumPairDistance(node.getDoubleProperty("maximumPairDistance"));
return integrator;
}
serialization/src/SerializationProxyRegistration.cpp
View file @ 5a06df78
......@@ -30,7 +30,6 @@
* -------------------------------------------------------------------------- */
#include "openmm/AndersenThermostat.h"
#include "openmm/BAOABLangevinIntegrator.h"
#include "openmm/BrownianIntegrator.h"
#include "openmm/CMAPTorsionForce.h"
#include "openmm/CMMotionRemover.h"
......@@ -52,10 +51,12 @@
#include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/LangevinMiddleIntegrator.h"
#include "openmm/MonteCarloAnisotropicBarostat.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/MonteCarloMembraneBarostat.h"
#include "openmm/NonbondedForce.h"
#include "openmm/NoseHooverIntegrator.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/RBTorsionForce.h"
#include "openmm/RMSDForce.h"
......@@ -66,7 +67,6 @@
#include "openmm/VerletIntegrator.h"
#include "openmm/serialization/SerializationProxy.h"
#include "openmm/serialization/BAOABLangevinIntegratorProxy.h"
#include "openmm/serialization/BrownianIntegratorProxy.h"
#include "openmm/serialization/AndersenThermostatProxy.h"
#include "openmm/serialization/CMAPTorsionForceProxy.h"
......@@ -89,10 +89,12 @@
#include "openmm/serialization/HarmonicAngleForceProxy.h"
#include "openmm/serialization/HarmonicBondForceProxy.h"
#include "openmm/serialization/LangevinIntegratorProxy.h"
#include "openmm/serialization/LangevinMiddleIntegratorProxy.h"
#include "openmm/serialization/MonteCarloAnisotropicBarostatProxy.h"
#include "openmm/serialization/MonteCarloBarostatProxy.h"
#include "openmm/serialization/MonteCarloMembraneBarostatProxy.h"
#include "openmm/serialization/NonbondedForceProxy.h"
#include "openmm/serialization/NoseHooverIntegratorProxy.h"
#include "openmm/serialization/PeriodicTorsionForceProxy.h"
#include "openmm/serialization/RBTorsionForceProxy.h"
#include "openmm/serialization/RMSDForceProxy.h"
......@@ -119,7 +121,6 @@ using namespace OpenMM;
extern "C" void registerSerializationProxies() {
SerializationProxy::registerProxy(typeid(AndersenThermostat), new AndersenThermostatProxy());
SerializationProxy::registerProxy(typeid(BAOABLangevinIntegrator), new BAOABLangevinIntegratorProxy());
SerializationProxy::registerProxy(typeid(BrownianIntegrator), new BrownianIntegratorProxy());
SerializationProxy::registerProxy(typeid(CMAPTorsionForce), new CMAPTorsionForceProxy());
SerializationProxy::registerProxy(typeid(CMMotionRemover), new CMMotionRemoverProxy());
......@@ -147,10 +148,12 @@ extern "C" void registerSerializationProxies() {
SerializationProxy::registerProxy(typeid(HarmonicAngleForce), new HarmonicAngleForceProxy());
SerializationProxy::registerProxy(typeid(HarmonicBondForce), new HarmonicBondForceProxy());
SerializationProxy::registerProxy(typeid(LangevinIntegrator), new LangevinIntegratorProxy());
SerializationProxy::registerProxy(typeid(LangevinMiddleIntegrator), new LangevinMiddleIntegratorProxy());
SerializationProxy::registerProxy(typeid(MonteCarloAnisotropicBarostat), new MonteCarloAnisotropicBarostatProxy());
SerializationProxy::registerProxy(typeid(MonteCarloBarostat), new MonteCarloBarostatProxy());
SerializationProxy::registerProxy(typeid(MonteCarloMembraneBarostat), new MonteCarloMembraneBarostatProxy());
SerializationProxy::registerProxy(typeid(NonbondedForce), new NonbondedForceProxy());
SerializationProxy::registerProxy(typeid(NoseHooverIntegrator), new NoseHooverIntegratorProxy());
SerializationProxy::registerProxy(typeid(PeriodicTorsionForce), new PeriodicTorsionForceProxy());
SerializationProxy::registerProxy(typeid(RBTorsionForce), new RBTorsionForceProxy());
SerializationProxy::registerProxy(typeid(RMSDForce), new RMSDForceProxy());
......@@ -159,4 +162,4 @@ extern "C" void registerSerializationProxies() {
SerializationProxy::registerProxy(typeid(VariableLangevinIntegrator), new VariableLangevinIntegratorProxy());
SerializationProxy::registerProxy(typeid(VariableVerletIntegrator), new VariableVerletIntegratorProxy());
SerializationProxy::registerProxy(typeid(VerletIntegrator), new VerletIntegratorProxy());
}
\ No newline at end of file
}
serialization/tests/TestSerializeIntegrator.cpp
View file @ 5a06df78
......@@ -31,11 +31,11 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/BAOABLangevinIntegrator.h"
#include "openmm/BrownianIntegrator.h"
#include "openmm/CompoundIntegrator.h"
#include "openmm/CustomIntegrator.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/LangevinMiddleIntegrator.h"
#include "openmm/VariableLangevinIntegrator.h"
#include "openmm/VariableVerletIntegrator.h"
#include "openmm/VerletIntegrator.h"
......@@ -75,11 +75,11 @@ void testSerializeLangevinIntegrator() {
delete intg2;
}
void testSerializeBAOABLangevinIntegrator() {
BAOABLangevinIntegrator *intg = new BAOABLangevinIntegrator(372.4, 1.234, 0.0018);
void testSerializeLangevinMiddleIntegrator() {
LangevinMiddleIntegrator *intg = new LangevinMiddleIntegrator(372.4, 1.234, 0.0018);
stringstream ss;
XmlSerializer::serialize<Integrator>(intg, "BAOABLangevinIntegrator", ss);
BAOABLangevinIntegrator *intg2 = dynamic_cast<BAOABLangevinIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
XmlSerializer::serialize<Integrator>(intg, "LangevinMiddleIntegrator", ss);
LangevinMiddleIntegrator *intg2 = dynamic_cast<LangevinMiddleIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
ASSERT_EQUAL(intg->getConstraintTolerance(), intg2->getConstraintTolerance());
ASSERT_EQUAL(intg->getStepSize(), intg2->getStepSize());
ASSERT_EQUAL(intg->getTemperature(), intg2->getTemperature());
......@@ -259,7 +259,7 @@ int main() {
testSerializeVariableLangevinIntegrator();
testSerializeVariableVerletIntegrator();
testSerializeLangevinIntegrator();
testSerializeBAOABLangevinIntegrator();
testSerializeLangevinMiddleIntegrator();
testSerializeCompoundIntegrator();
}
catch(const exception& e) {
......
serialization/tests/TestSerializeNonbondedForce.cpp
View file @ 5a06df78
......@@ -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) 2010-2018 Stanford University and the Authors. *
* Portions copyright (c) 2010-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -50,6 +50,7 @@ void testSerialization() {
force.setEwaldErrorTolerance(1e-3);
force.setReactionFieldDielectric(50.0);
force.setUseDispersionCorrection(false);
force.setExceptionsUsePeriodicBoundaryConditions(true);
double alpha = 0.5;
int nx = 3, ny = 5, nz = 7;
force.setPMEParameters(alpha, nx, ny, nz);
......@@ -83,6 +84,7 @@ void testSerialization() {
ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
ASSERT_EQUAL(force.getExceptionsUsePeriodicBoundaryConditions(), force2.getExceptionsUsePeriodicBoundaryConditions());
ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
ASSERT_EQUAL(force.getNumGlobalParameters(), force2.getNumGlobalParameters());
......
serialization/tests/TestSerializeNoseHooverIntegrator.cpp 0 → 100644
View file @ 5a06df78
/* -------------------------------------------------------------------------- *
* 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: Andrew C. Simmonett and Andreas Kraemer
* 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/NoseHooverIntegrator.h"
#include "openmm/serialization/XmlSerializer.h"
#include "openmm/System.h"
#include "openmm/Context.h"
#include <iostream>
#include <sstream>
using namespace OpenMM;
using namespace std;
void assertIntegratorsEqual(const NoseHooverIntegrator& integrator1, const NoseHooverIntegrator& integrator2){
ASSERT_EQUAL(integrator1.getStepSize(), integrator2.getStepSize());
ASSERT_EQUAL(integrator1.getConstraintTolerance(), integrator2.getConstraintTolerance());
ASSERT_EQUAL(integrator1.getMaximumPairDistance(), integrator2.getMaximumPairDistance());
ASSERT_EQUAL(integrator1.getNumThermostats(), integrator2.getNumThermostats());
for (int i = 0; i < integrator1.getNumThermostats(); i++) {
const auto &thermostat1 = integrator1.getThermostat(i);
const auto &thermostat2 = integrator2.getThermostat(i);
ASSERT_EQUAL(thermostat1.getTemperature(), thermostat2.getTemperature());
ASSERT_EQUAL(thermostat1.getCollisionFrequency(), thermostat2.getCollisionFrequency());
ASSERT_EQUAL(thermostat1.getRelativeTemperature(), thermostat2.getRelativeTemperature());
ASSERT_EQUAL(thermostat1.getRelativeCollisionFrequency(), thermostat2.getRelativeCollisionFrequency());
ASSERT_EQUAL(thermostat1.getChainLength(), thermostat2.getChainLength());
ASSERT_EQUAL(thermostat1.getNumMultiTimeSteps(), thermostat2.getNumMultiTimeSteps());
ASSERT_EQUAL(thermostat1.getNumYoshidaSuzukiTimeSteps(), thermostat2.getNumYoshidaSuzukiTimeSteps());
ASSERT_EQUAL(thermostat1.getChainID(), thermostat2.getChainID());
const auto &thermostat1Atoms = thermostat1.getThermostatedAtoms();
const auto &thermostat2Atoms = thermostat2.getThermostatedAtoms();
ASSERT_EQUAL(thermostat1Atoms.size(), thermostat2Atoms.size());
for (int j = 0; j < thermostat1Atoms.size(); ++j) {
ASSERT_EQUAL(thermostat1Atoms[j], thermostat2Atoms[j]);
}
const auto &thermostat1Pairs = thermostat1.getThermostatedPairs();
const auto &thermostat2Pairs = thermostat2.getThermostatedPairs();
ASSERT_EQUAL(thermostat1Pairs.size(), thermostat2Pairs.size());
for (int j = 0; j < thermostat1Pairs.size(); ++j) {
ASSERT_EQUAL(thermostat1Pairs[j].first, thermostat2Pairs[j].first);
ASSERT_EQUAL(thermostat1Pairs[j].second, thermostat2Pairs[j].second);
}
}
}
void testSerialization() {
// Check with custom subsystem thermostats
NoseHooverIntegrator integrator_sub (0.0006);
integrator_sub.setConstraintTolerance(0.0404);
integrator_sub.setMaximumPairDistance(0.0051);
integrator_sub.addSubsystemThermostat(
{0,1,2,3,4,7}, {{0,7}}, 301.1, 1.1, 1.2, 1.3, 9, 2, 5
);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<NoseHooverIntegrator>(&integrator_sub, "Integrator", buffer);
NoseHooverIntegrator* copy = XmlSerializer::deserialize<NoseHooverIntegrator>(buffer);
assertIntegratorsEqual(integrator_sub, *copy);
// Check with default constructor
System system;
for (int i=0; i<10; i++) system.addParticle(1.0);
NoseHooverIntegrator integrator(331, 1.1, 0.004, 5, 5, 5);
Context context(system, integrator);
// Serialize and then deserialize it.
stringstream buffer2;
XmlSerializer::serialize<NoseHooverIntegrator>(&integrator, "Integrator", buffer2);
copy = XmlSerializer::deserialize<NoseHooverIntegrator>(buffer2);
// for thermostats that apply to the whole system, the particles are not serialized ...
ASSERT_EQUAL(copy->getThermostat(0).getThermostatedAtoms().size(), 0);
// ... but assigned when creating a context.
Context context2(system, *copy);
assertIntegratorsEqual(integrator, *copy);
}
int main() {
try {
testSerialization();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
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