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/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
* -------------------------------------------------------------------------- *
* 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) 2010-2016 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/Platform.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/AmoebaVdwForce.h"
#include "openmm/serialization/XmlSerializer.h"
#include <iostream>
#include <sstream>
using namespace OpenMM;
using namespace std;
extern "C" void registerAmoebaSerializationProxies();
void testSerialization() {
// Create a Force.
AmoebaVdwForce force1;
force1.setForceGroup(3);
force1.setName("custom name");
force1.setSigmaCombiningRule("GEOMETRIC");
force1.setEpsilonCombiningRule("GEOMETRIC");
force1.setCutoff(0.9);
force1.setNonbondedMethod(AmoebaVdwForce::CutoffPeriodic);
force1.setAlchemicalMethod(AmoebaVdwForce::None);
force1.setPotentialFunction(AmoebaVdwForce::Buffered147);
force1.addParticle(0, 1.0, 2.0, 0.9, false);
force1.addParticle(1, 1.1, 2.1, 0.9, true);
force1.addParticle(2, 1.3, 4.1, 0.9, false);
for (int i = 0; i < 3; i++) {
std::vector< int > exclusions;
exclusions.push_back(i);
exclusions.push_back(i + 1);
exclusions.push_back(i + 10);
force1.setParticleExclusions(i, exclusions);
}
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<AmoebaVdwForce>(&force1, "Force", buffer);
AmoebaVdwForce* copy = XmlSerializer::deserialize<AmoebaVdwForce>(buffer);
// Compare the two forces to see if they are identical.
AmoebaVdwForce& force2 = *copy;
ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force1.getName(), force2.getName());
ASSERT_EQUAL(force1.getSigmaCombiningRule(), force2.getSigmaCombiningRule());
ASSERT_EQUAL(force1.getEpsilonCombiningRule(), force2.getEpsilonCombiningRule());
ASSERT_EQUAL(force1.getCutoff(), force2.getCutoff());
ASSERT_EQUAL(force1.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force1.getAlchemicalMethod(), force2.getAlchemicalMethod());
ASSERT_EQUAL(force1.getPotentialFunction(), force2.getPotentialFunction());
ASSERT_EQUAL(force1.getNumParticles(), force2.getNumParticles());
for (int i = 0; i < force1.getNumParticles(); i++) {
int ivIndex1, type1;
int ivIndex2, type2;
double sigma1, epsilon1, reductionFactor1;
double sigma2, epsilon2, reductionFactor2;
bool isAlchemical1;
bool isAlchemical2;
force1.getParticleParameters(i, ivIndex1, sigma1, epsilon1, reductionFactor1, isAlchemical1, type1);
force2.getParticleParameters(i, ivIndex2, sigma2, epsilon2, reductionFactor2, isAlchemical2, type2);
ASSERT_EQUAL(ivIndex1, ivIndex2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
ASSERT_EQUAL(reductionFactor1, reductionFactor2);
ASSERT_EQUAL(isAlchemical1, isAlchemical2);
ASSERT_EQUAL(type1, type2);
}
for (int i = 0; i < force1.getNumParticles(); i++) {
std::vector< int > exclusions1;
std::vector< int > exclusions2;
force1.getParticleExclusions(i, exclusions1);
force2.getParticleExclusions(i, exclusions2);
ASSERT_EQUAL(exclusions1.size(), exclusions2.size());
for (int j = 0; j < exclusions1.size(); j++) {
int hit = 0;
for (int kk = 0; kk < exclusions2.size(); kk++) {
if (exclusions2[j] == exclusions1[kk])hit++;
}
ASSERT_EQUAL(hit, 1);
}
}
}
void testSerializeTypes() {
// Create a Force that specifies parameters by type.
AmoebaVdwForce force1;
force1.setPotentialFunction(AmoebaVdwForce::LennardJones);
force1.addParticle(0, 2, 1.0, false);
force1.addParticle(1, 2, 0.9, true);
force1.addParticle(2, 0, 1.0, false);
force1.addParticle(3, 1, 0.9, false);
force1.addParticleType(1.1, 2.0);
force1.addParticleType(1.2, 2.1);
force1.addParticleType(1.3, 2.2);
force1.addTypePair(0, 2, 1.5, 2.5);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<AmoebaVdwForce>(&force1, "Force", buffer);
AmoebaVdwForce* copy = XmlSerializer::deserialize<AmoebaVdwForce>(buffer);
// Compare the two forces to see if they are identical.
AmoebaVdwForce& force2 = *copy;
ASSERT_EQUAL(force1.getPotentialFunction(), force2.getPotentialFunction());
ASSERT_EQUAL(force1.getNumParticles(), force2.getNumParticles());
ASSERT_EQUAL(force1.getNumParticleTypes(), force2.getNumParticleTypes());
ASSERT_EQUAL(force1.getNumTypePairs(), force2.getNumTypePairs());
for (int i = 0; i < force1.getNumParticles(); i++) {
int ivIndex1, type1;
int ivIndex2, type2;
double sigma1, epsilon1, reductionFactor1;
double sigma2, epsilon2, reductionFactor2;
bool isAlchemical1;
bool isAlchemical2;
force1.getParticleParameters(i, ivIndex1, sigma1, epsilon1, reductionFactor1, isAlchemical1, type1);
force2.getParticleParameters(i, ivIndex2, sigma2, epsilon2, reductionFactor2, isAlchemical2, type2);
ASSERT_EQUAL(ivIndex1, ivIndex2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
ASSERT_EQUAL(reductionFactor1, reductionFactor2);
ASSERT_EQUAL(isAlchemical1, isAlchemical2);
ASSERT_EQUAL(type1, type2);
}
for (int i = 0; i < force1.getNumParticleTypes(); i++) {
double sigma1, epsilon1;
double sigma2, epsilon2;
force1.getParticleTypeParameters(i, sigma1, epsilon1);
force2.getParticleTypeParameters(i, sigma2, epsilon2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
for (int i = 0; i < force1.getNumTypePairs(); i++) {
int type11, type21;
int type12, type22;
double sigma1, epsilon1;
double sigma2, epsilon2;
force1.getTypePairParameters(i, type11, type21, sigma1, epsilon1);
force2.getTypePairParameters(i, type12, type22, sigma2, epsilon2);
ASSERT_EQUAL(type11, type12);
ASSERT_EQUAL(type21, type22);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
}
int main() {
try {
registerAmoebaSerializationProxies();
testSerialization();
testSerializeTypes();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
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