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Commit a414ed23 authored by Yutong Zhao's avatar Yutong Zhao
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Included a missing include file for the unit test for State serialization.

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serialization/tests/TestSerializeState.cpp
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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 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/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/Context.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/serialization/XmlSerializer.h"
#include <iostream>
#include <sstream>
using namespace OpenMM;
using namespace std;
void testSerialization() {
// Create a System.
const int numParticles=50;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(6.2, 0, 0), Vec3(0, 6.2, 0), Vec3(0, 0, 6.2 ));
/* -------------------------------------------------------------------------- *
* 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: 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/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/Context.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/serialization/XmlSerializer.h"
#include <iostream>
#include <sstream>
#include <stdlib.h>
using namespace OpenMM;
using namespace std;
void testSerialization() {
// Create a System.
const int numParticles=50;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(6.2, 0, 0), Vec3(0, 6.2, 0), Vec3(0, 0, 6.2 ));
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
nonbonded->setCutoffDistance(0.8);
......@@ -62,87 +63,87 @@ void testSerialization() {
nonbonded->addParticle(1.0, 1.0,0.0);
for (int i = 0; i < numParticles/2; i++)
nonbonded->addParticle(-1.0, 1.0,0.0);
system.addForce(nonbonded);
system.addForce(new AndersenThermostat(393.3, 19.3));
system.addForce(new MonteCarloBarostat(25, 393.3, 25));
Integrator *intg = new LangevinIntegrator(300,79,0.002);
Context *ctxt = new Context(system, *intg);
// Set positions, velocities, forces
vector<Vec3> positions;
for(int i=0;i<numParticles;i++) {
positions.push_back(Vec3( ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2));
}
vector<Vec3> velocities;
for(int i=0;i<numParticles;i++) {
velocities.push_back(Vec3( ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2));
}
ctxt->setPositions(positions);
ctxt->setVelocities(velocities);
// Serialize and then deserialize it.
State s1 = ctxt->getState(State::Positions | State::Velocities | State::Forces | State::Energy | State::Parameters);
stringstream buffer;
XmlSerializer::serialize<State>(&s1, "State", buffer);
State* copy = XmlSerializer::deserialize<State>(buffer);
State& s2 = *copy;
// Compare the two states to see if they are identical.
vector<Vec3> pos1 = s1.getPositions();
vector<Vec3> pos2 = s2.getPositions();
ASSERT_EQUAL(pos1.size(), pos2.size());
ASSERT_EQUAL(pos1.size(), positions.size());
for(int i=0; i<pos1.size(); i++) {
ASSERT_EQUAL_VEC(pos1[i],pos2[i],0);
}
vector<Vec3> vel1 = s1.getVelocities();
vector<Vec3> vel2 = s2.getVelocities();
ASSERT_EQUAL(vel1.size(), vel2.size());
for(int i=0; i<pos1.size(); i++) {
ASSERT_EQUAL_VEC(vel1[i],vel2[i],0);
}
vector<Vec3> forces1 = s1.getForces();
vector<Vec3> forces2 = s2.getForces();
ASSERT_EQUAL(forces1.size(), forces2.size());
for(int i=0; i<pos1.size(); i++) {
ASSERT_EQUAL_VEC(forces1[i],forces2[i],0);
}
Vec3 a1,a2,a3,b1,b2,b3;
s1.getPeriodicBoxVectors(a1,a2,a3);
s2.getPeriodicBoxVectors(b1,b2,b3);
ASSERT_EQUAL_VEC(a1,b1,0);
ASSERT_EQUAL_VEC(a2,b2,0);
ASSERT_EQUAL_VEC(a3,b3,0);
ASSERT_EQUAL(s1.getPotentialEnergy(), s2.getPotentialEnergy());
ASSERT_EQUAL(s1.getKineticEnergy(), s2.getKineticEnergy());
ASSERT_EQUAL(s1.getTime(), s2.getTime());
map<string, double> p1 = s1.getParameters();
map<string, double> p2 = s2.getParameters();
ASSERT_EQUAL(p1.size(), p2.size());
map<string, double>::const_iterator it1=p1.begin();
map<string, double>::const_iterator it2=p2.begin();
//maps are ordered, so iterators should be in the same order.
for(it1=p1.begin(); it1!=p1.end(); it1++, it2++) {
assert((it1->first).compare(it2->first) == 0);
ASSERT_EQUAL(it1->second, it2->second);
}
}
int main() {
try {
testSerialization();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
system.addForce(nonbonded);
system.addForce(new AndersenThermostat(393.3, 19.3));
system.addForce(new MonteCarloBarostat(25, 393.3, 25));
Integrator *intg = new LangevinIntegrator(300,79,0.002);
Context *ctxt = new Context(system, *intg);
// Set positions, velocities, forces
vector<Vec3> positions;
for(int i=0;i<numParticles;i++) {
positions.push_back(Vec3( ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2));
}
vector<Vec3> velocities;
for(int i=0;i<numParticles;i++) {
velocities.push_back(Vec3( ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2));
}
ctxt->setPositions(positions);
ctxt->setVelocities(velocities);
// Serialize and then deserialize it.
State s1 = ctxt->getState(State::Positions | State::Velocities | State::Forces | State::Energy | State::Parameters);
stringstream buffer;
XmlSerializer::serialize<State>(&s1, "State", buffer);
State* copy = XmlSerializer::deserialize<State>(buffer);
State& s2 = *copy;
// Compare the two states to see if they are identical.
vector<Vec3> pos1 = s1.getPositions();
vector<Vec3> pos2 = s2.getPositions();
ASSERT_EQUAL(pos1.size(), pos2.size());
ASSERT_EQUAL(pos1.size(), positions.size());
for(int i=0; i<pos1.size(); i++) {
ASSERT_EQUAL_VEC(pos1[i],pos2[i],0);
}
vector<Vec3> vel1 = s1.getVelocities();
vector<Vec3> vel2 = s2.getVelocities();
ASSERT_EQUAL(vel1.size(), vel2.size());
for(int i=0; i<pos1.size(); i++) {
ASSERT_EQUAL_VEC(vel1[i],vel2[i],0);
}
vector<Vec3> forces1 = s1.getForces();
vector<Vec3> forces2 = s2.getForces();
ASSERT_EQUAL(forces1.size(), forces2.size());
for(int i=0; i<pos1.size(); i++) {
ASSERT_EQUAL_VEC(forces1[i],forces2[i],0);
}
Vec3 a1,a2,a3,b1,b2,b3;
s1.getPeriodicBoxVectors(a1,a2,a3);
s2.getPeriodicBoxVectors(b1,b2,b3);
ASSERT_EQUAL_VEC(a1,b1,0);
ASSERT_EQUAL_VEC(a2,b2,0);
ASSERT_EQUAL_VEC(a3,b3,0);
ASSERT_EQUAL(s1.getPotentialEnergy(), s2.getPotentialEnergy());
ASSERT_EQUAL(s1.getKineticEnergy(), s2.getKineticEnergy());
ASSERT_EQUAL(s1.getTime(), s2.getTime());
map<string, double> p1 = s1.getParameters();
map<string, double> p2 = s2.getParameters();
ASSERT_EQUAL(p1.size(), p2.size());
map<string, double>::const_iterator it1=p1.begin();
map<string, double>::const_iterator it2=p2.begin();
//maps are ordered, so iterators should be in the same order.
for(it1=p1.begin(); it1!=p1.end(); it1++, it2++) {
assert((it1->first).compare(it2->first) == 0);
ASSERT_EQUAL(it1->second, it2->second);
}
}
int main() {
try {
testSerialization();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
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