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/* -------------------------------------------------------------------------- *
* 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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