mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
05472c9a81
* Replace SimTK-containing file headers * Update file headers for new Tinker reader files added
286 lines
11 KiB
C++
286 lines
11 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) 2008-2024 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/CustomExternalForce.h"
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#include "openmm/System.h"
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#include "openmm/VerletIntegrator.h"
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#include "SimTKOpenMMRealType.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 testForce() {
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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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CustomExternalForce* forceField = new CustomExternalForce("scale*(x+yscale*(y-y0)^2)");
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forceField->addPerParticleParameter("y0");
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forceField->addPerParticleParameter("yscale");
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forceField->addGlobalParameter("scale", 0.5);
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vector<double> parameters(2);
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parameters[0] = 0.5;
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parameters[1] = 2.0;
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forceField->addParticle(0, parameters);
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parameters[0] = 1.5;
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parameters[1] = 3.0;
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forceField->addParticle(2, parameters);
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system.addForce(forceField);
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ASSERT(!forceField->usesPeriodicBoundaryConditions());
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ASSERT(!system.usesPeriodicBoundaryConditions());
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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, 2, 0);
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positions[1] = Vec3(0, 0, 1);
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positions[2] = Vec3(1, 0, 1);
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context.setPositions(positions);
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State state = context.getState(State::Forces | State::Energy);
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{
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const vector<Vec3>& forces = state.getForces();
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ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 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(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
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ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.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[0] = 1.4;
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parameters[1] = 3.5;
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forceField->setParticleParameters(1, 2, parameters);
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forceField->updateParametersInContext(context);
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state = context.getState(State::Forces | State::Energy);
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{
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const vector<Vec3>& forces = state.getForces();
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ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 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(-0.5, 0.5*3.5*2.0*1.4, 0), forces[2], TOL);
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ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.5*1.4*1.4), state.getPotentialEnergy(), TOL);
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}
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}
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void testManyParameters() {
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System system;
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system.addParticle(1.0);
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VerletIntegrator integrator(0.01);
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CustomExternalForce* forceField = new CustomExternalForce("xscale*(x-x0)^2+yscale*(y-y0)^2+zscale*(z-z0)^2");
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forceField->addPerParticleParameter("x0");
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forceField->addPerParticleParameter("y0");
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forceField->addPerParticleParameter("z0");
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forceField->addPerParticleParameter("xscale");
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forceField->addPerParticleParameter("yscale");
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forceField->addPerParticleParameter("zscale");
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vector<double> parameters(6);
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parameters[0] = 1.0;
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parameters[1] = 2.0;
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parameters[2] = 3.0;
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parameters[3] = 0.1;
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parameters[4] = 0.2;
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parameters[5] = 0.3;
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forceField->addParticle(0, parameters);
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system.addForce(forceField);
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Context context(system, integrator, platform);
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vector<Vec3> positions(1);
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positions[0] = Vec3(0, -1, 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*0.1*1.0, 2*0.2*3.0, 2*0.3*3.0), forces[0], TOL);
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ASSERT_EQUAL_TOL(0.1*1*1 + 0.2*3*3 + 0.3*3*3, state.getPotentialEnergy(), TOL);
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}
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void testPeriodic() {
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Vec3 vx(5, 0, 0);
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Vec3 vy(0, 6, 0);
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Vec3 vz(1, 2, 7);
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double x0 = 51, y0 = -17, z0 = 11.2;
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System system;
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system.setDefaultPeriodicBoxVectors(vx, vy, vz);
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system.addParticle(1.0);
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CustomExternalForce* force = new CustomExternalForce("periodicdistance(x, y, z, x0, y0, z0)^2");
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force->addPerParticleParameter("x0");
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force->addPerParticleParameter("y0");
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force->addPerParticleParameter("z0");
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vector<double> params(3);
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params[0] = x0;
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params[1] = y0;
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params[2] = z0;
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force->addParticle(0, params);
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system.addForce(force);
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ASSERT(force->usesPeriodicBoundaryConditions());
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ASSERT(system.usesPeriodicBoundaryConditions());
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VerletIntegrator integrator(0.01);
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Context context(system, integrator, platform);
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vector<Vec3> positions(1);
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positions[0] = Vec3(0, 2, 0);
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context.setPositions(positions);
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for (int i = 0; i < 100; i++) {
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State state = context.getState(State::Positions | State::Forces | State::Energy);
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// Apply periodic boundary conditions to the difference between the two positions.
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Vec3 delta = Vec3(x0, y0, z0)-state.getPositions()[0];
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delta -= vz*floor(delta[2]/vz[2]+0.5);
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delta -= vy*floor(delta[1]/vy[1]+0.5);
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delta -= vx*floor(delta[0]/vx[0]+0.5);
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// Verify that the force and energy are correct.
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ASSERT_EQUAL_VEC(delta*2, state.getForces()[0], TOL);
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ASSERT_EQUAL_TOL(delta.dot(delta), state.getPotentialEnergy(), TOL);
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integrator.step(1);
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}
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}
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void testZeroPeriodicDistance() {
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Vec3 vx(5, 0, 0);
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Vec3 vy(0, 6, 0);
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Vec3 vz(1, 2, 7);
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double x0 = 51, y0 = -17, z0 = 11.2;
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System system;
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system.setDefaultPeriodicBoxVectors(vx, vy, vz);
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system.addParticle(1.0);
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CustomExternalForce* force = new CustomExternalForce("periodicdistance(x, y, z, x0, y0, z0)^2");
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force->addPerParticleParameter("x0");
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force->addPerParticleParameter("y0");
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force->addPerParticleParameter("z0");
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vector<double> params(3);
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params[0] = x0;
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params[1] = y0;
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params[2] = z0;
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force->addParticle(0, params);
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system.addForce(force);
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ASSERT(force->usesPeriodicBoundaryConditions());
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ASSERT(system.usesPeriodicBoundaryConditions());
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VerletIntegrator integrator(0.01);
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Context context(system, integrator, platform);
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vector<Vec3> positions(1);
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positions[0] = Vec3(x0, y0, z0);
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context.setPositions(positions);
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State state = context.getState(State::Positions | State::Forces | State::Energy);
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vector<Vec3> forces = state.getForces();
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for (int i = 0; i < 3; i++)
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ASSERT_EQUAL(forces[0][i], forces[0][i]);
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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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CustomExternalForce* force = new CustomExternalForce("x+none");
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force->addParticle(0);
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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 testAtan2() {
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System system;
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system.addParticle(1.0);
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CustomExternalForce* force = new CustomExternalForce("atan2(x, y)");
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force->addParticle(0);
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system.addForce(force);
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VerletIntegrator integrator(0.01);
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Context context(system, integrator, platform);
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vector<Vec3> positions(1);
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positions[0] = Vec3(1.5, -2.1, 1.2);
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context.setPositions(positions);
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State state = context.getState(State::Energy);
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ASSERT_EQUAL_TOL(atan2(positions[0][0], positions[0][1]), state.getPotentialEnergy(), 1e-5);
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}
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void testParallelComputation() {
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System system;
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const int numParticles = 200;
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for (int i = 0; i < numParticles; i++)
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system.addParticle(1.0);
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CustomExternalForce* force = new CustomExternalForce("x^2+y^2+z^2");
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vector<double> params;
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for (int i = 0; i < numParticles; i++)
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force->addParticle(i, params);
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system.addForce(force);
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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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for (int i = 0; i < numParticles; i++)
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positions[i] = Vec3(5*genrand_real2(sfmt), 5*genrand_real2(sfmt), 5*genrand_real2(sfmt));
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VerletIntegrator integrator1(0.01);
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Context context1(system, integrator1, platform);
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context1.setPositions(positions);
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State state1 = context1.getState(State::Forces | State::Energy);
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VerletIntegrator integrator2(0.01);
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string deviceIndex = platform.getPropertyValue(context1, "DeviceIndex");
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map<string, string> props;
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props["DeviceIndex"] = deviceIndex+","+deviceIndex;
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Context context2(system, integrator2, platform, props);
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context2.setPositions(positions);
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State state2 = context2.getState(State::Forces | State::Energy);
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ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
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for (int i = 0; i < numParticles; i++)
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ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 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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testForce();
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testManyParameters();
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testPeriodic();
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testZeroPeriodicDistance();
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testIllegalVariable();
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testAtan2();
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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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