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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) 2010-2021 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/NonbondedForce.h"
#include "openmm/serialization/XmlSerializer.h"
#include <iostream>
#include <sstream>
using namespace OpenMM;
using namespace std;
void testSerialization() {
// Create a Force.
NonbondedForce force;
force.setForceGroup(3);
force.setName("custom name");
force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
force.setSwitchingDistance(1.5);
force.setUseSwitchingFunction(true);
force.setCutoffDistance(2.0);
force.setEwaldErrorTolerance(1e-3);
force.setReactionFieldDielectric(50.0);
force.setUseDispersionCorrection(false);
force.setExceptionsUsePeriodicBoundaryConditions(true);
force.setIncludeDirectSpace(false);
double alpha = 0.5;
int nx = 3, ny = 5, nz = 7;
force.setPMEParameters(alpha, nx, ny, nz);
double dalpha = 0.8;
int dnx = 4, dny = 6, dnz = 7;
force.setLJPMEParameters(dalpha, dnx, dny, dnz);
force.addParticle(1, 0.1, 0.01);
force.addParticle(0.5, 0.2, 0.02);
force.addParticle(-0.5, 0.3, 0.03);
force.addException(0, 1, 2, 0.5, 0.1);
force.addException(1, 2, 0.2, 0.4, 0.2);
force.addGlobalParameter("scale1", 1.0);
force.addGlobalParameter("scale2", 2.0);
force.addParticleParameterOffset("scale1", 2, 1.5, 2.0, 2.5);
force.addExceptionParameterOffset("scale2", 1, -0.1, -0.2, -0.3);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<NonbondedForce>(&force, "Force", buffer);
NonbondedForce* copy = XmlSerializer::deserialize<NonbondedForce>(buffer);
// Compare the two forces to see if they are identical.
NonbondedForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getName(), force2.getName());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
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());
ASSERT_EQUAL(force.getNumParticleParameterOffsets(), force2.getNumParticleParameterOffsets());
ASSERT_EQUAL(force.getNumExceptionParameterOffsets(), force2.getNumExceptionParameterOffsets());
ASSERT_EQUAL(force.getIncludeDirectSpace(), force2.getIncludeDirectSpace());
double alpha2;
int nx2, ny2, nz2;
force2.getPMEParameters(alpha2, nx2, ny2, nz2);
ASSERT_EQUAL(alpha, alpha2);
ASSERT_EQUAL(nx, nx2);
ASSERT_EQUAL(ny, ny2);
ASSERT_EQUAL(nz, nz2);
double dalpha2;
int dnx2, dny2, dnz2;
force2.getLJPMEParameters(dalpha2, dnx2, dny2, dnz2);
ASSERT_EQUAL(dalpha, dalpha2);
ASSERT_EQUAL(dnx, dnx2);
ASSERT_EQUAL(dny, dny2);
ASSERT_EQUAL(dnz, dnz2);
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
}
for (int i = 0; i < force.getNumParticleParameterOffsets(); i++) {
int index1, index2;
string param1, param2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getParticleParameterOffset(i, param1, index1, charge1, sigma1, epsilon1);
force2.getParticleParameterOffset(i, param2, index2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(index1, index1);
ASSERT_EQUAL(param1, param2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
int index1, index2;
string param1, param2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getExceptionParameterOffset(i, param1, index1, charge1, sigma1, epsilon1);
force2.getExceptionParameterOffset(i, param2, index2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(index1, index1);
ASSERT_EQUAL(param1, param2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
for (int i = 0; i < force.getNumParticles(); i++) {
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getParticleParameters(i, charge1, sigma1, epsilon1);
force2.getParticleParameters(i, charge2, sigma2, epsilon2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
for (int i = 0; i < force.getNumExceptions(); i++) {
int a1, a2, b1, b2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getExceptionParameters(i, a1, b1, charge1, sigma1, epsilon1);
force2.getExceptionParameters(i, a2, b2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(a1, a2);
ASSERT_EQUAL(b1, b2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
}
int main() {
try {
testSerialization();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
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