mirror of
https://github.com/openmm/openmm
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05472c9a81
* Replace SimTK-containing file headers * Update file headers for new Tinker reader files added
166 lines
7.6 KiB
C++
166 lines
7.6 KiB
C++
/* -------------------------------------------------------------------------- *
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* OpenMM *
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* -------------------------------------------------------------------------- *
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* This is part of the OpenMM molecular simulation toolkit. *
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* See https://openmm.org/development. *
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* *
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* Portions copyright (c) 2010-2023 Stanford University and the Authors. *
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* Authors: Peter Eastman *
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* Contributors: *
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* *
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* Permission is hereby granted, free of charge, to any person obtaining a *
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* copy of this software and associated documentation files (the "Software"), *
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* to deal in the Software without restriction, including without limitation *
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* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
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* and/or sell copies of the Software, and to permit persons to whom the *
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* Software is furnished to do so, subject to the following conditions: *
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* *
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* The above copyright notice and this permission notice shall be included in *
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* all copies or substantial portions of the Software. *
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* *
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
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* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
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* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
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* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
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* USE OR OTHER DEALINGS IN THE SOFTWARE. *
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* -------------------------------------------------------------------------- */
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#include "openmm/internal/AssertionUtilities.h"
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#include "openmm/HarmonicBondForce.h"
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#include "openmm/System.h"
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#include "openmm/VirtualSite.h"
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#include "openmm/serialization/XmlSerializer.h"
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#include <iostream>
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#include <sstream>
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using namespace OpenMM;
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using namespace std;
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void compareSystems(System& system, System& system2) {
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ASSERT_EQUAL(system.getNumParticles(), system2.getNumParticles());
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for (int i = 0; i < system.getNumParticles(); i++)
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ASSERT_EQUAL(system.getParticleMass(i), system2.getParticleMass(i));
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ASSERT_EQUAL(system.getNumConstraints(), system2.getNumConstraints());
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for (int i = 0; i < system.getNumConstraints(); i++) {
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int p1, p2, p3, p4;
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double d1, d2;
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system.getConstraintParameters(i, p1, p2, d1);
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system2.getConstraintParameters(i, p3, p4, d2);
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ASSERT_EQUAL(p1, p3);
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ASSERT_EQUAL(p2, p4);
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ASSERT_EQUAL(d1, d2);
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}
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Vec3 a, b, c;
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Vec3 a2, b2, c2;
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system.getDefaultPeriodicBoxVectors(a, b, c);
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system2.getDefaultPeriodicBoxVectors(a2, b2, c2);
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ASSERT_EQUAL_VEC(a, a2, 0);
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ASSERT_EQUAL_VEC(b, b2, 0);
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ASSERT_EQUAL_VEC(c, c2, 0);
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for (int i = 0; i < system.getNumParticles(); i++)
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ASSERT_EQUAL(system.isVirtualSite(i), system2.isVirtualSite(i));
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const TwoParticleAverageSite& site5 = dynamic_cast<const TwoParticleAverageSite&>(system2.getVirtualSite(5));
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ASSERT_EQUAL(0, site5.getParticle(0));
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ASSERT_EQUAL(1, site5.getParticle(1));
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ASSERT_EQUAL(0.3, site5.getWeight(0));
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ASSERT_EQUAL(0.7, site5.getWeight(1));
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const ThreeParticleAverageSite& site6 = dynamic_cast<const ThreeParticleAverageSite&>(system2.getVirtualSite(6));
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ASSERT_EQUAL(2, site6.getParticle(0));
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ASSERT_EQUAL(4, site6.getParticle(1));
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ASSERT_EQUAL(3, site6.getParticle(2));
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ASSERT_EQUAL(0.5, site6.getWeight(0));
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ASSERT_EQUAL(0.2, site6.getWeight(1));
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ASSERT_EQUAL(0.3, site6.getWeight(2));
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const OutOfPlaneSite& site7 = dynamic_cast<const OutOfPlaneSite&>(system2.getVirtualSite(7));
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ASSERT_EQUAL(0, site7.getParticle(0));
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ASSERT_EQUAL(3, site7.getParticle(1));
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ASSERT_EQUAL(1, site7.getParticle(2));
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ASSERT_EQUAL(0.1, site7.getWeight12());
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ASSERT_EQUAL(0.2, site7.getWeight13());
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ASSERT_EQUAL(0.5, site7.getWeightCross());
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const LocalCoordinatesSite& site8 = dynamic_cast<const LocalCoordinatesSite&>(system2.getVirtualSite(8));
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ASSERT_EQUAL(4, site8.getNumParticles());
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ASSERT_EQUAL(4, site8.getParticle(0));
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ASSERT_EQUAL(3, site8.getParticle(1));
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ASSERT_EQUAL(2, site8.getParticle(2));
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ASSERT_EQUAL(1, site8.getParticle(3));
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ASSERT_EQUAL(Vec3(-0.5, 1.0, 1.5), site8.getLocalPosition());
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vector<double> wo, wx, wy;
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site8.getOriginWeights(wo);
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site8.getXWeights(wx);
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site8.getYWeights(wy);
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vector<double> woExpected = {0.1, 0.2, 0.3, 0.4};
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vector<double> wxExpected = {-1.0, 0.4, 0.4, 0.2};
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vector<double> wyExpected = {0.3, 0.7, 0.0, -1.0};
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ASSERT_EQUAL_CONTAINERS(woExpected, wo);
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ASSERT_EQUAL_CONTAINERS(wxExpected, wx);
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ASSERT_EQUAL_CONTAINERS(wyExpected, wy);
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const SymmetrySite& site9 = dynamic_cast<const SymmetrySite&>(system2.getVirtualSite(9));
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ASSERT_EQUAL(3, site9.getParticle(0));
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Vec3 Rx, Ry, Rz;
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site9.getRotationMatrix(Rx, Ry, Rz);
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double ct = cos(1.1);
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double st = sin(1.1);
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ASSERT_EQUAL_VEC(Vec3(ct, 0, -st), Rx, 0);
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ASSERT_EQUAL_VEC(Vec3(0, 1, 0), Ry, 0);
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ASSERT_EQUAL_VEC(Vec3(st, 0, ct), Rz, 0);
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ASSERT_EQUAL_VEC(Vec3(1, 2, 3), site9.getOffsetVector(), 0);
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ASSERT(site9.getUseBoxVectors());
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ASSERT_EQUAL(system.getNumForces(), system2.getNumForces());
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for (int i = 0; i < system.getNumForces(); i++)
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ASSERT(typeid(system.getForce(i)) == typeid(system2.getForce(i)))
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}
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void testSerialization() {
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// Create a System.
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System system;
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for (int i = 0; i < 5; i++)
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system.addParticle(0.1*i+1);
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for (int i = 0; i < 5; i++)
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system.addParticle(0.0);
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system.addConstraint(0, 1, 3.0);
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system.addConstraint(1, 2, 2.5);
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system.addConstraint(4, 1, 1.001);
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system.setDefaultPeriodicBoxVectors(Vec3(5, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 1.5));
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system.setVirtualSite(5, new TwoParticleAverageSite(0, 1, 0.3, 0.7));
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system.setVirtualSite(6, new ThreeParticleAverageSite(2, 4, 3, 0.5, 0.2, 0.3));
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system.setVirtualSite(7, new OutOfPlaneSite(0, 3, 1, 0.1, 0.2, 0.5));
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system.setVirtualSite(8, new LocalCoordinatesSite({4, 3, 2, 1}, {0.1, 0.2, 0.3, 0.4}, {-1.0, 0.4, 0.4, 0.2}, {0.3, 0.7, 0.0, -1.0}, Vec3(-0.5, 1.0, 1.5)));
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double ct = cos(1.1);
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double st = sin(1.1);
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Vec3 Rx(ct, 0, -st), Ry(0, 1, 0), Rz(st, 0, ct), v(1, 2, 3);
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system.setVirtualSite(9, new SymmetrySite(3, Rx, Ry, Rz, v, true));
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system.addForce(new HarmonicBondForce());
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// Serialize and then deserialize it, then make sure the systems are identical.
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stringstream buffer;
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XmlSerializer::serialize<System>(&system, "System", buffer);
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System* copy = XmlSerializer::deserialize<System>(buffer);
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compareSystems(system, *copy);
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delete copy;
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// Now do the same thing but by calling clone().
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copy = XmlSerializer::clone(system);
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compareSystems(system, *copy);
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delete copy;
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}
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int main() {
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try {
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testSerialization();
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}
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catch(const exception& e) {
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cout << "exception: " << e.what() << endl;
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return 1;
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}
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cout << "Done" << endl;
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return 0;
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}
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