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https://github.com/openmm/openmm
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05472c9a81
* Replace SimTK-containing file headers * Update file headers for new Tinker reader files added
103 lines
4.6 KiB
C++
103 lines
4.6 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) 2010-2015 Stanford University and the Authors. *
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* Authors: Robert McGibbon *
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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/Context.h"
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#include "openmm/NonbondedForce.h"
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#include "openmm/Platform.h"
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#include "openmm/VerletIntegrator.h"
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#include "sfmt/SFMT.h"
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#include <iostream>
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using namespace OpenMM;
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using namespace std;
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void testTruncatedOctahedron() {
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const int numMolecules = 50;
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const int numParticles = numMolecules*2;
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const float cutoff = 2.0;
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Vec3 a(6.7929, 0, 0);
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Vec3 b(-2.264163559406279, 6.404455775962287, 0);
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Vec3 c(-2.264163559406279, -3.2019384603140684, 5.54658849047036);
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System system;
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system.setDefaultPeriodicBoxVectors(a, b, c);
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NonbondedForce* force = new NonbondedForce();
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OpenMM_SFMT::SFMT sfmt;
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init_gen_rand(0, sfmt);
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vector<Vec3> positions(numParticles);
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force->setCutoffDistance(cutoff);
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force->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
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for (int i = 0; i < numMolecules; i++) {
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system.addParticle(1.0);
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system.addParticle(1.0);
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force->addParticle(-1, 0.2, 0.2);
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force->addParticle(1, 0.2, 0.2);
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positions[2*i] = a*(5*genrand_real2(sfmt)-2) + b*(5*genrand_real2(sfmt)-2) + c*(5*genrand_real2(sfmt)-2);
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positions[2*i+1] = positions[2*i] + Vec3(1.0, 0.0, 0.0);
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system.addConstraint(2*i, 2*i+1, 1.0);
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}
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system.addForce(force);
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VerletIntegrator integrator(0.01);
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Context context(system, integrator, Platform::getPlatform("Reference"));
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context.setPositions(positions);
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State initialState = context.getState(State::Positions | State::Energy, true);
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for (int i = 0; i < numMolecules; i++) {
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Vec3 center = (initialState.getPositions()[2*i]+initialState.getPositions()[2*i+1])*0.5;
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ASSERT(center[0] >= 0.0);
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ASSERT(center[1] >= 0.0);
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ASSERT(center[2] >= 0.0);
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ASSERT(center[0] <= a[0]);
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ASSERT(center[1] <= b[1]);
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ASSERT(center[2] <= c[2]);
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}
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double initialEnergy = initialState.getPotentialEnergy();
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context.setState(initialState);
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State finalState = context.getState(State::Positions | State::Energy, true);
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double finalEnergy = finalState.getPotentialEnergy();
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ASSERT_EQUAL_TOL(initialEnergy, finalEnergy, 1e-4);
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}
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int main(int argc, char* argv[]) {
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try {
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testTruncatedOctahedron();
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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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