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
386 lines
16 KiB
C++
386 lines
16 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) 2008-2018 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/Context.h"
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#include "openmm/CustomHbondForce.h"
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#include "openmm/HarmonicAngleForce.h"
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#include "openmm/HarmonicBondForce.h"
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#include "openmm/NonbondedForce.h"
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#include "openmm/PeriodicTorsionForce.h"
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#include "openmm/System.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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#include <vector>
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using namespace OpenMM;
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using namespace std;
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const double TOL = 1e-5;
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void testHbond() {
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// Create a system using a CustomHbondForce.
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System customSystem;
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customSystem.addParticle(1.0);
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customSystem.addParticle(1.0);
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customSystem.addParticle(1.0);
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customSystem.addParticle(1.0);
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customSystem.addParticle(1.0);
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CustomHbondForce* custom = new CustomHbondForce("0.5*kr*(distance(d1,a1)-r0)^2 + 0.5*ktheta*(angle(a1,d1,d2)-theta0)^2 + 0.5*kpsi*(angle(d1,a1,a2)-psi0)^2 + kchi*(1+cos(n*dihedral(a3,a2,a1,d1)-chi0))");
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custom->addPerDonorParameter("r0");
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custom->addPerDonorParameter("theta0");
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custom->addPerDonorParameter("psi0");
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custom->addPerAcceptorParameter("chi0");
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custom->addPerAcceptorParameter("n");
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custom->addGlobalParameter("kr", 0.4);
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custom->addGlobalParameter("ktheta", 0.5);
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custom->addGlobalParameter("kpsi", 0.6);
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custom->addGlobalParameter("kchi", 0.7);
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vector<double> parameters(3);
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parameters[0] = 1.5;
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parameters[1] = 1.7;
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parameters[2] = 1.9;
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custom->addDonor(1, 0, -1, parameters);
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parameters.resize(2);
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parameters[0] = 2.1;
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parameters[1] = 2;
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custom->addAcceptor(2, 3, 4, parameters);
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custom->setCutoffDistance(10.0);
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customSystem.addForce(custom);
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ASSERT(!custom->usesPeriodicBoundaryConditions());
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ASSERT(!customSystem.usesPeriodicBoundaryConditions());
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// Create an identical system using HarmonicBondForce, HarmonicAngleForce, and PeriodicTorsionForce.
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System standardSystem;
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standardSystem.addParticle(1.0);
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standardSystem.addParticle(1.0);
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standardSystem.addParticle(1.0);
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standardSystem.addParticle(1.0);
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standardSystem.addParticle(1.0);
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HarmonicBondForce* bond = new HarmonicBondForce();
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bond->addBond(1, 2, 1.5, 0.4);
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standardSystem.addForce(bond);
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HarmonicAngleForce* angle = new HarmonicAngleForce();
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angle->addAngle(0, 1, 2, 1.7, 0.5);
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angle->addAngle(1, 2, 3, 1.9, 0.6);
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standardSystem.addForce(angle);
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PeriodicTorsionForce* torsion = new PeriodicTorsionForce();
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torsion->addTorsion(1, 2, 3, 4, 2, 2.1, 0.7);
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standardSystem.addForce(torsion);
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// Set the atoms in various positions, and verify that both systems give identical forces and energy.
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OpenMM_SFMT::SFMT sfmt;
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init_gen_rand(0, sfmt);
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vector<Vec3> positions(5);
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VerletIntegrator integrator1(0.01);
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VerletIntegrator integrator2(0.01);
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Context c1(customSystem, integrator1, platform);
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Context c2(standardSystem, integrator2, platform);
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for (int i = 0; i < 10; i++) {
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for (int j = 0; j < (int) positions.size(); j++)
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positions[j] = Vec3(2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt));
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c1.setPositions(positions);
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c2.setPositions(positions);
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State s1 = c1.getState(State::Forces | State::Energy);
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State s2 = c2.getState(State::Forces | State::Energy);
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for (int i = 0; i < customSystem.getNumParticles(); i++)
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ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
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ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
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}
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// Try changing the parameters and make sure it's still correct.
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parameters.resize(3);
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parameters[0] = 1.4;
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parameters[1] = 1.7;
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parameters[2] = 1.9;
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custom->setDonorParameters(0, 1, 0, -1, parameters);
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parameters.resize(2);
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parameters[0] = 2.2;
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parameters[1] = 2;
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custom->setAcceptorParameters(0, 2, 3, 4, parameters);
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bond->setBondParameters(0, 1, 2, 1.4, 0.4);
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torsion->setTorsionParameters(0, 1, 2, 3, 4, 2, 2.2, 0.7);
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custom->updateParametersInContext(c1);
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bond->updateParametersInContext(c2);
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torsion->updateParametersInContext(c2);
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State s1 = c1.getState(State::Forces | State::Energy);
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State s2 = c2.getState(State::Forces | State::Energy);
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for (int i = 0; i < customSystem.getNumParticles(); i++)
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ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
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ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
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}
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void testExclusions() {
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System system;
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system.addParticle(1.0);
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system.addParticle(1.0);
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system.addParticle(1.0);
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VerletIntegrator integrator(0.01);
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CustomHbondForce* custom = new CustomHbondForce("(distance(d1,a1)-1)^2");
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custom->addDonor(0, 1, -1, vector<double>());
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custom->addDonor(1, 0, -1, vector<double>());
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custom->addAcceptor(2, 0, -1, vector<double>());
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custom->addExclusion(1, 0);
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system.addForce(custom);
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Context context(system, integrator, platform);
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vector<Vec3> positions(3);
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positions[0] = Vec3(0, 0, 0);
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positions[1] = Vec3(0, 2, 0);
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positions[2] = Vec3(2, 0, 0);
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context.setPositions(positions);
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State state = context.getState(State::Forces | State::Energy);
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const vector<Vec3>& forces = state.getForces();
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ASSERT_EQUAL_VEC(Vec3(2, 0, 0), forces[0], TOL);
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ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
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ASSERT_EQUAL_VEC(Vec3(-2, 0, 0), forces[2], TOL);
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ASSERT_EQUAL_TOL(1.0, state.getPotentialEnergy(), TOL);
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}
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void testCutoff() {
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System system;
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system.addParticle(1.0);
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system.addParticle(1.0);
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system.addParticle(1.0);
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VerletIntegrator integrator(0.01);
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CustomHbondForce* custom = new CustomHbondForce("(distance(d1,a1)-1)^2");
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custom->addDonor(0, 1, -1, vector<double>());
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custom->addDonor(1, 0, -1, vector<double>());
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custom->addAcceptor(2, 0, -1, vector<double>());
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custom->setNonbondedMethod(CustomHbondForce::CutoffNonPeriodic);
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custom->setCutoffDistance(2.5);
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system.addForce(custom);
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Context context(system, integrator, platform);
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vector<Vec3> positions(3);
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positions[0] = Vec3(0, 0, 0);
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positions[1] = Vec3(0, 3, 0);
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positions[2] = Vec3(2, 0, 0);
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context.setPositions(positions);
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State state = context.getState(State::Forces | State::Energy);
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const vector<Vec3>& forces = state.getForces();
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ASSERT_EQUAL_VEC(Vec3(2, 0, 0), forces[0], TOL);
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ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
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ASSERT_EQUAL_VEC(Vec3(-2, 0, 0), forces[2], TOL);
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ASSERT_EQUAL_TOL(1.0, state.getPotentialEnergy(), TOL);
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}
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void testCustomFunctions() {
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System system;
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system.addParticle(1.0);
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system.addParticle(1.0);
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system.addParticle(1.0);
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VerletIntegrator integrator(0.01);
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CustomHbondForce* custom = new CustomHbondForce("foo(distance(d1,a1))");
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custom->addDonor(1, 0, -1, vector<double>());
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custom->addDonor(2, 0, -1, vector<double>());
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custom->addAcceptor(0, 1, -1, vector<double>());
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vector<double> function(2);
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function[0] = 0;
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function[1] = 1;
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custom->addTabulatedFunction("foo", new Continuous1DFunction(function, 0, 10));
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system.addForce(custom);
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Context context(system, integrator, platform);
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vector<Vec3> positions(3);
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positions[0] = Vec3(0, 0, 0);
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positions[1] = Vec3(0, 2, 0);
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positions[2] = Vec3(2, 0, 0);
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context.setPositions(positions);
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State state = context.getState(State::Forces | State::Energy);
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const vector<Vec3>& forces = state.getForces();
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ASSERT_EQUAL_VEC(Vec3(0.1, 0.1, 0), forces[0], TOL);
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ASSERT_EQUAL_VEC(Vec3(0, -0.1, 0), forces[1], TOL);
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ASSERT_EQUAL_VEC(Vec3(-0.1, 0, 0), forces[2], TOL);
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ASSERT_EQUAL_TOL(0.1*2+0.1*2, state.getPotentialEnergy(), TOL);
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// Try updating the tabulated function.
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for (int i = 0; i < function.size(); i++)
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function[i] *= 0.5;
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dynamic_cast<Continuous1DFunction&>(custom->getTabulatedFunction(0)).setFunctionParameters(function, 0, 10);
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custom->updateParametersInContext(context);
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state = context.getState(State::Energy);
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ASSERT_EQUAL_TOL(0.5*(0.1*2+0.1*2), state.getPotentialEnergy(), TOL);
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}
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void test2DFunction() {
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System system;
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system.addParticle(1.0);
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system.addParticle(1.0);
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system.addParticle(1.0);
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VerletIntegrator integrator(0.01);
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CustomHbondForce* custom = new CustomHbondForce("tab(dtype, atype)");
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custom->addPerDonorParameter("dtype");
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custom->addPerAcceptorParameter("atype");
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custom->addDonor(1, 0, -1, {0.0});
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custom->addDonor(2, 0, -1, {2.0});
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custom->addAcceptor(0, 1, -1, {1.0});
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vector<double> function = {0.0, 1.0, 2.0, 5.0, 6.0, 7.0};
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custom->addTabulatedFunction("tab", new Discrete2DFunction(3, 2, function));
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system.addForce(custom);
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Context context(system, integrator, platform);
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vector<Vec3> positions(3);
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positions[0] = Vec3(0, 0, 0);
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positions[1] = Vec3(0, 2, 0);
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positions[2] = Vec3(2, 0, 0);
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context.setPositions(positions);
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State state = context.getState(State::Forces | State::Energy);
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const vector<Vec3>& forces = state.getForces();
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ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], TOL);
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ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
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ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[2], TOL);
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ASSERT_EQUAL_TOL(12.0, state.getPotentialEnergy(), TOL);
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}
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void testIllegalVariable() {
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System system;
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system.addParticle(1.0);
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system.addParticle(1.0);
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CustomHbondForce* force = new CustomHbondForce("1+none");
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force->addDonor(0, -1, -1);
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force->addAcceptor(1, -1, -1);
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system.addForce(force);
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VerletIntegrator integrator(0.001);
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bool threwException = false;
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try {
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Context(system, integrator, platform);
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}
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catch (const exception& e) {
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threwException = true;
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}
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ASSERT(threwException);
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}
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void testParameters() {
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System system;
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system.addParticle(1.0);
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system.addParticle(1.0);
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system.addParticle(1.0);
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VerletIntegrator integrator(0.01);
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CustomHbondForce* custom = new CustomHbondForce("(2*d+a)*distance(d1,a1)");
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custom->addPerDonorParameter("d");
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custom->addPerAcceptorParameter("a");
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custom->addDonor(1, 0, -1, vector<double>({1.5}));
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custom->addDonor(2, 0, -1, vector<double>({1.8}));
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custom->addAcceptor(0, 1, -1, vector<double>({2.1}));
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system.addForce(custom);
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Context context(system, integrator, platform);
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vector<Vec3> positions(3);
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positions[0] = Vec3(0, 0, 0);
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positions[1] = Vec3(0, 2, 0);
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positions[2] = Vec3(2, 0, 0);
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context.setPositions(positions);
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State state = context.getState(State::Forces | State::Energy);
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const vector<Vec3>& forces = state.getForces();
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ASSERT_EQUAL_VEC(Vec3((2*1.8+2.1), (2*1.5+2.1), 0), forces[0], TOL);
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ASSERT_EQUAL_VEC(Vec3(0, -(2*1.5+2.1), 0), forces[1], TOL);
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ASSERT_EQUAL_VEC(Vec3(-(2*1.8+2.1), 0, 0), forces[2], TOL);
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ASSERT_EQUAL_TOL(2*(2*1.8+2.1)+2*(2*1.5+2.1), state.getPotentialEnergy(), TOL);
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}
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void testLargeSystem(CustomHbondForce::NonbondedMethod method) {
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int numParticles = 5000;
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double boxSize = 3.0;
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double cutoff = 1.0;
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System system;
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system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
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CustomHbondForce* custom = new CustomHbondForce("(distance(d1,a1)-1)^2");
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custom->setNonbondedMethod(method);
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custom->setCutoffDistance(cutoff);
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NonbondedForce* nb = new NonbondedForce(); // So that atom reordering will be done
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nb->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
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vector<Vec3> positions(numParticles);
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OpenMM_SFMT::SFMT sfmt;
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init_gen_rand(0, sfmt);
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for (int i = 0; i < numParticles; i++) {
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system.addParticle(1.0);
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if (i%2 == 0)
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custom->addDonor(i, -1, -1);
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else
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custom->addAcceptor(i, -1, -1);
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positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
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nb->addParticle(0.0, 1.0, 0.0);
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}
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system.addForce(custom);
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system.addForce(nb);
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VerletIntegrator integrator(0.01);
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Context context(system, integrator, platform);
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context.setPositions(positions);
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State state = context.getState(State::Energy | State::Forces);
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double expectedEnergy = 0;
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for (int i = 0; i < numParticles; i += 2) {
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Vec3 expectedForce;
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for (int j = 1; j < numParticles; j += 2) {
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Vec3 d = positions[i]-positions[j];
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if (method == CustomHbondForce::CutoffPeriodic) {
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d[0] -= round(d[0]/boxSize)*boxSize;
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d[1] -= round(d[1]/boxSize)*boxSize;
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d[2] -= round(d[2]/boxSize)*boxSize;
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}
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double r = sqrt(d.dot(d));
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if (method == CustomHbondForce::NoCutoff || r < cutoff) {
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expectedEnergy += (r-1)*(r-1);
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expectedForce -= 2*(r-1)*d/r;
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}
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}
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ASSERT_EQUAL_VEC(expectedForce, state.getForces()[i], 1e-5);
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}
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ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
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}
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void runPlatformTests();
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int main(int argc, char* argv[]) {
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try {
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initializeTests(argc, argv);
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testHbond();
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testExclusions();
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testCutoff();
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testCustomFunctions();
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test2DFunction();
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testIllegalVariable();
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testParameters();
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testLargeSystem(CustomHbondForce::NoCutoff);
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testLargeSystem(CustomHbondForce::CutoffNonPeriodic);
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testLargeSystem(CustomHbondForce::CutoffPeriodic);
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runPlatformTests();
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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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