mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
b64a82a89a
* Ensure that neighbor list is valid before solving for charges * Add test with neighbor list that needs to be resized * Try another approach to skip interactions for neighbor list generation only * Increase CG error tolerance for test
1344 lines
50 KiB
C++
1344 lines
50 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) 2008-2025 Stanford University and the Authors. *
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* Authors: Peter Eastman, Evan Pretti *
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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 "ReferencePlatform.h"
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#include "openmm/HarmonicBondForce.h"
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#include "openmm/NonbondedForce.h"
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#include "openmm/CustomNonbondedForce.h"
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#include "openmm/ConstantPotentialForce.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 <iomanip>
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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-4;
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void testCoulomb(bool periodicExceptions) {
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// Ensures that the Coulomb energy and force computation for
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// ConstantPotentialForce without electrodes matches NonbondedForce.
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System refSystem;
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System testSystem;
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NonbondedForce* refForce = new NonbondedForce();
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ConstantPotentialForce* testForce = new ConstantPotentialForce();
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Vec3 a(10, 0, 0);
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Vec3 b(1, 9, 0);
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Vec3 c(2, 3, 8);
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refSystem.setDefaultPeriodicBoxVectors(a, b, c);
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testSystem.setDefaultPeriodicBoxVectors(a, b, c);
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vector<Vec3> positions;
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vector<pair<int, int>> bonds;
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for (int i = 0; i < 10; i++) {
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refSystem.addParticle(1);
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testSystem.addParticle(1);
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double testCharge = (i / 2 + 1) * (i % 2 ? -1 : 1);
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refForce->addParticle(testCharge, 1, 0);
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testForce->addParticle(testCharge);
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double f = 0.1 * i;
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positions.push_back(f * a + f * f * b + f * f * f * c);
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bonds.push_back(pair<int, int>(i, (i + 1) % 10));
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}
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refForce->createExceptionsFromBonds(bonds, 0.5, 0.0);
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testForce->createExceptionsFromBonds(bonds, 0.5);
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refForce->setExceptionsUsePeriodicBoundaryConditions(periodicExceptions);
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testForce->setExceptionsUsePeriodicBoundaryConditions(periodicExceptions);
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refForce->setNonbondedMethod(NonbondedForce::PME);
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refForce->setCutoffDistance(3.0);
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testForce->setCutoffDistance(3.0);
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refSystem.addForce(refForce);
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testSystem.addForce(testForce);
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ASSERT(testForce->usesPeriodicBoundaryConditions());
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ASSERT(testSystem.usesPeriodicBoundaryConditions());
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VerletIntegrator refIntegrator(0.001);
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VerletIntegrator testIntegrator(0.001);
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Context refContext(refSystem, refIntegrator, platform);
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Context testContext(testSystem, testIntegrator, platform);
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refContext.setPositions(positions);
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testContext.setPositions(positions);
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State refState = refContext.getState(State::Energy | State::Forces);
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State testState = testContext.getState(State::Energy | State::Forces);
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const vector<Vec3>& refForces = refState.getForces();
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const vector<Vec3>& testForces = testState.getForces();
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ASSERT_EQUAL_TOL(refState.getPotentialEnergy(), testState.getPotentialEnergy(), TOL);
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for (int i = 0; i < refForces.size(); i++) {
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ASSERT_EQUAL_VEC(refForces[i], testForces[i], TOL);
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}
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}
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void testCoulombOverlap() {
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// Ensures that two particles with an exception can overlap without
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// generating NaN energies and forces.
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System refSystem;
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System testSystem;
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NonbondedForce* refForce = new NonbondedForce();
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ConstantPotentialForce* testForce = new ConstantPotentialForce();
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refSystem.setDefaultPeriodicBoxVectors(Vec3(10, 0, 0), Vec3(0, 10, 0), Vec3(0, 0, 10));
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testSystem.setDefaultPeriodicBoxVectors(Vec3(10, 0, 0), Vec3(0, 10, 0), Vec3(0, 0, 10));
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for (int i = 0; i < 3; i++) {
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refSystem.addParticle(1);
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testSystem.addParticle(1);
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}
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refForce->addParticle(1, 1, 0);
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testForce->addParticle(1);
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refForce->addParticle(1, 1, 0);
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testForce->addParticle(1);
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refForce->addParticle(-2, 1, 0);
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testForce->addParticle(-2);
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refForce->addException(0, 1, 0, 1, 0);
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testForce->addException(0, 1, 0);
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refForce->setNonbondedMethod(NonbondedForce::PME);
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refSystem.addForce(refForce);
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testSystem.addForce(testForce);
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vector<Vec3> positions{
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Vec3(0, 0, 0),
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Vec3(0, 0, 0),
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Vec3(1, 2, 3)
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};
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VerletIntegrator refIntegrator(0.001);
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VerletIntegrator testIntegrator(0.001);
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Context refContext(refSystem, refIntegrator, platform);
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Context testContext(testSystem, testIntegrator, platform);
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refContext.setPositions(positions);
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testContext.setPositions(positions);
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State refState = refContext.getState(State::Energy | State::Forces);
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State testState = testContext.getState(State::Energy | State::Forces);
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const vector<Vec3>& refForces = refState.getForces();
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const vector<Vec3>& testForces = testState.getForces();
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ASSERT_EQUAL_TOL(refState.getPotentialEnergy(), testState.getPotentialEnergy(), TOL);
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for (int i = 0; i < refForces.size(); i++) {
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ASSERT_EQUAL_VEC(refForces[i], testForces[i], TOL);
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}
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}
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void testCoulombNonNeutral() {
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// Ensures that the energy of a non-neutral system at different cutoffs (and
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// thus different values of alpha) matches NonbondedForce. Since the latter
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// includes a neutralizing plasma correction, this ensures that the same
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// correction is working in ConstantPotentialForce.
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System refSystem;
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System testSystem;
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NonbondedForce* refForce = new NonbondedForce();
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ConstantPotentialForce* testForce = new ConstantPotentialForce();
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Vec3 a, b, c;
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a = Vec3(10, 0, 0);
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b = Vec3(1, 9, 0);
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c = Vec3(2, 3, 8);
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refSystem.setDefaultPeriodicBoxVectors(a, b, c);
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testSystem.setDefaultPeriodicBoxVectors(a, b, c);
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vector<Vec3> positions;
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for (int i = 0; i < 10; i++) {
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refSystem.addParticle(1);
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testSystem.addParticle(1);
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double f = 0.1 * i;
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refForce->addParticle((i % 2 ? -1 : 1) + f * f, 1, 0);
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testForce->addParticle((i % 2 ? -1 : 1) + f * f);
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positions.push_back(f * a + f * f * b + f * f * f * c);
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}
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refForce->setNonbondedMethod(NonbondedForce::PME);
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refForce->setCutoffDistance(1.5);
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testForce->setCutoffDistance(1.5);
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refSystem.addForce(refForce);
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testSystem.addForce(testForce);
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VerletIntegrator refIntegrator(0.001);
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VerletIntegrator testIntegrator(0.001);
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Context refContext(refSystem, refIntegrator, platform);
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Context testContext(testSystem, testIntegrator, platform);
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refContext.setPositions(positions);
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testContext.setPositions(positions);
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{
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State refState = refContext.getState(State::Energy | State::Forces);
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State testState = testContext.getState(State::Energy | State::Forces);
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const vector<Vec3>& refForces = refState.getForces();
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const vector<Vec3>& testForces = testState.getForces();
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ASSERT_EQUAL_TOL(refState.getPotentialEnergy(), testState.getPotentialEnergy(), TOL);
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for (int i = 0; i < refForces.size(); i++) {
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ASSERT_EQUAL_VEC(refForces[i], testForces[i], TOL);
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}
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}
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refForce->setCutoffDistance(2.5);
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testForce->setCutoffDistance(2.5);
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refContext.reinitialize(true);
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testContext.reinitialize(true);
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{
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State refState = refContext.getState(State::Energy | State::Forces);
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State testState = testContext.getState(State::Energy | State::Forces);
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const vector<Vec3>& refForces = refState.getForces();
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const vector<Vec3>& testForces = testState.getForces();
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ASSERT_EQUAL_TOL(refState.getPotentialEnergy(), testState.getPotentialEnergy(), TOL);
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for (int i = 0; i < refForces.size(); i++) {
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ASSERT_EQUAL_VEC(refForces[i], testForces[i], TOL);
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}
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}
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}
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void testCoulombGaussian() {
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// Ensures that Gaussian charge interactions are computed correctly by
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// comparing a ConstantPotentialForce-containing system with Gaussian
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// charges to a NonbondedForce-containing system with point charges.
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System testSystem;
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ConstantPotentialForce* testForce = new ConstantPotentialForce();
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testSystem.setDefaultPeriodicBoxVectors(Vec3(10, 0, 0), Vec3(0, 10, 0), Vec3(0, 0, 10));
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testSystem.addParticle(0);
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testSystem.addParticle(0);
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testSystem.addParticle(0);
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testForce->addParticle(2);
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testForce->addParticle(0);
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testForce->addParticle(0);
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set<int> electrode1{1};
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testForce->addElectrode(electrode1, 0, 0.2, 0);
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set<int> electrode2{2};
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testForce->addElectrode(electrode2, 0, 0.3, 0);
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testSystem.addForce(testForce);
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vector<Vec3> positions{Vec3(0, 0, 0), Vec3(0.9, 0, 0), Vec3(0.6, 0.4, 0)};
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VerletIntegrator testIntegrator(0.001);
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Context testContext(testSystem, testIntegrator, platform);
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testContext.setPositions(positions);
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vector<double> charges;
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testForce->getCharges(testContext, charges);
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System refSystem;
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NonbondedForce* refForce = new NonbondedForce();
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refSystem.setDefaultPeriodicBoxVectors(Vec3(10, 0, 0), Vec3(0, 10, 0), Vec3(0, 0, 10));
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refSystem.addParticle(0);
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refSystem.addParticle(0);
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refSystem.addParticle(0);
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refForce->addParticle(charges[0], 1, 0);
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refForce->addParticle(charges[1], 1, 0);
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refForce->addParticle(charges[2], 1, 0);
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refForce->setNonbondedMethod(NonbondedForce::PME);
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refSystem.addForce(refForce);
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VerletIntegrator refIntegrator(0.001);
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Context refContext(refSystem, refIntegrator, platform);
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refContext.setPositions(positions);
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State testState = testContext.getState(State::Energy);
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State refState = refContext.getState(State::Energy);
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Vec3 x01 = positions[1] - positions[0];
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Vec3 x02 = positions[2] - positions[0];
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Vec3 x12 = positions[2] - positions[1];
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double r01 = sqrt(x01.dot(x01));
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double r02 = sqrt(x02.dot(x02));
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double r12 = sqrt(x12.dot(x12));
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double du_pair = -ONE_4PI_EPS0 * (
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charges[0] * charges[1] * erfc(r01 / 0.2) / r01 +
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charges[0] * charges[2] * erfc(r02 / 0.3) / r02 +
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charges[1] * charges[2] * erfc(r12 / sqrt(0.13)) / r12
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);
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double du_self = ONE_4PI_EPS0 * (charges[1] * charges[1] / 0.2 + charges[2] * charges[2] / 0.3) / sqrt(2 * M_PI);
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ASSERT_EQUAL_TOL(refState.getPotentialEnergy() + du_pair + du_self, testState.getPotentialEnergy(), TOL);
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}
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void testFiniteFieldNonPeriodic() {
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// Ensures that the electric field energy is based on an absolute offset
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// from the origin and not affected by periodic wrapping.
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System testSystem;
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Vec3 a, b, c;
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a = Vec3(10, 0, 0);
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b = Vec3(1, 9, 0);
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c = Vec3(2, 3, 8);
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testSystem.setDefaultPeriodicBoxVectors(a, b, c);
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testSystem.addParticle(0);
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Vec3 field(123, -456, 789);
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double charge = -2;
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ConstantPotentialForce* testForce = new ConstantPotentialForce();
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testForce->setEwaldErrorTolerance(1e-4);
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testForce->addParticle(charge);
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testSystem.addForce(testForce);
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VerletIntegrator baseIntegrator(0.001);
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Context baseContext(testSystem, baseIntegrator, platform);
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baseContext.setPositions(vector<Vec3>{Vec3(0, 0, 0)});
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double pmeBaseEnergy = baseContext.getState(State::Energy).getPotentialEnergy();
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testForce->setExternalField(field);
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Vec3 position(30, 20, -10);
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double referenceEnergy = pmeBaseEnergy - charge * field.dot(position);
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Vec3 referenceForce = charge * field;
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VerletIntegrator testIntegrator(0.001);
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Context testContext(testSystem, testIntegrator, platform);
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testContext.setPositions(vector<Vec3>{position});
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testIntegrator.step(1);
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State testState = testContext.getState(State::Energy | State::Forces);
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ASSERT_EQUAL_TOL(referenceEnergy, testState.getPotentialEnergy(), TOL);
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ASSERT_EQUAL_VEC(referenceForce, testState.getForces()[0], TOL);
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}
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void testElectrodesDisjoint() {
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// Ensures that a particle cannot belong to more than one electrode.
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System system;
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ConstantPotentialForce* force = new ConstantPotentialForce();
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for (int i = 0; i < 3; i++) {
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system.addParticle(1);
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force->addParticle(0);
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}
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set<int> electrode1{0, 1};
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set<int> electrode2{1, 2};
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force->addElectrode(electrode1, 0, 0.2, 0);
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force->addElectrode(electrode2, 0, 0.2, 0);
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system.addForce(force);
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VerletIntegrator integrator(0.001);
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bool thrown = false;
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try {
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Context context(system, integrator, platform);
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}
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catch (const OpenMMException& exception) {
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thrown = true;
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}
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ASSERT(thrown);
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}
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void testNoElectrodeExceptions() {
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// Ensures that a particle cannot belong to both an electrode and an
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// exception.
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System system;
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ConstantPotentialForce* force = new ConstantPotentialForce();
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for (int i = 0; i < 3; i++) {
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system.addParticle(1);
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force->addParticle(0);
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}
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set<int> electrode{0, 1};
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force->addElectrode(electrode, 0, 0.2, 0);
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force->addException(1, 2, 0);
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system.addForce(force);
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VerletIntegrator integrator(0.001);
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bool thrown = false;
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try {
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Context context(system, integrator, platform);
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}
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catch (const OpenMMException& exception) {
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thrown = true;
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}
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ASSERT(thrown);
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}
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void testElectrodeMatrixNoMass() {
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// Ensures that we can use the matrix method when electrode particles have
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// no mass, but that we cannot when an electrode particle has mass.
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System system1;
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ConstantPotentialForce* force1 = new ConstantPotentialForce();
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system1.addParticle(0);
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system1.addParticle(0);
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system1.addParticle(1);
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force1->addParticle(0);
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force1->addParticle(0);
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force1->addParticle(0);
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set<int> electrode1{0, 1};
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force1->addElectrode(electrode1, 0, 0.2, 0);
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force1->setConstantPotentialMethod(ConstantPotentialForce::Matrix);
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system1.addForce(force1);
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VerletIntegrator integrator1(0.001);
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Context context1(system1, integrator1, platform);
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System system2;
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ConstantPotentialForce* force2 = new ConstantPotentialForce();
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system2.addParticle(0);
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system2.addParticle(1);
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system2.addParticle(1);
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force2->addParticle(0);
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force2->addParticle(0);
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force2->addParticle(0);
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set<int> electrode2{0, 1};
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force2->addElectrode(electrode2, 0, 0.2, 0);
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force2->setConstantPotentialMethod(ConstantPotentialForce::Matrix);
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system2.addForce(force2);
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VerletIntegrator integrator2(0.001);
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bool thrown = false;
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try {
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Context context2(system2, integrator2, platform);
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}
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catch (const OpenMMException& exception) {
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thrown = true;
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}
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ASSERT(thrown);
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}
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void testSmallSystems(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner) {
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// Ensures that solver convergence is achieved on various small systems with
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// zero or one degrees of freedom.
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// Using one electrode particle with a total charge constraint, the solution
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// is uniquely determined.
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System system1;
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ConstantPotentialForce* force1 = new ConstantPotentialForce();
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system1.addParticle(0);
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system1.addParticle(1);
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force1->addParticle(0);
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force1->addParticle(2);
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set<int> electrode1{0};
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force1->addElectrode(electrode1, 0, 0.2, 0);
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force1->setConstantPotentialMethod(method);
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force1->setUsePreconditioner(usePreconditioner);
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force1->setUseChargeConstraint(true);
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force1->setChargeConstraintTarget(5);
|
|
system1.addForce(force1);
|
|
VerletIntegrator integrator1(0.001);
|
|
Context context1(system1, integrator1, platform);
|
|
vector<Vec3> positions1{Vec3(0, 0, 0), Vec3(0.5, 0, 0)};
|
|
context1.setPositions(positions1);
|
|
vector<double> charges1;
|
|
force1->getCharges(context1, charges1);
|
|
ASSERT_EQUAL(charges1.size(), 2);
|
|
ASSERT_EQUAL_TOL(3, charges1[0], TOL);
|
|
ASSERT_EQUAL(2, charges1[1]);
|
|
|
|
// Using two electrode particles with a total charge constraint, there is
|
|
// one degree of freedom. Make a symmetric system so that we know the
|
|
// solution.
|
|
|
|
System system2;
|
|
ConstantPotentialForce* force2 = new ConstantPotentialForce();
|
|
system2.addParticle(0);
|
|
system2.addParticle(0);
|
|
system2.addParticle(1);
|
|
force2->addParticle(0);
|
|
force2->addParticle(0);
|
|
force2->addParticle(2);
|
|
set<int> electrode2{0, 1};
|
|
force2->addElectrode(electrode2, 0, 0.2, 0);
|
|
force2->setConstantPotentialMethod(method);
|
|
force2->setUsePreconditioner(usePreconditioner);
|
|
force2->setUseChargeConstraint(true);
|
|
force2->setChargeConstraintTarget(5);
|
|
system2.addForce(force2);
|
|
VerletIntegrator integrator2(0.001);
|
|
Context context2(system2, integrator2, platform);
|
|
vector<Vec3> positions2{Vec3(-0.25, 0, 0), Vec3(0.25, 0, 0), Vec3(0, 0, 0)};
|
|
context2.setPositions(positions2);
|
|
vector<double> charges2;
|
|
force2->getCharges(context2, charges2);
|
|
ASSERT_EQUAL(charges2.size(), 3);
|
|
ASSERT_EQUAL_TOL(1.5, charges2[0], TOL);
|
|
ASSERT_EQUAL_TOL(1.5, charges2[1], TOL);
|
|
ASSERT_EQUAL(2, charges2[2]);
|
|
|
|
// Using no electrode particles without a total charge constraint, we should
|
|
// simply recover the fixed charges.
|
|
|
|
System system3;
|
|
ConstantPotentialForce* force3 = new ConstantPotentialForce();
|
|
system3.addParticle(1);
|
|
system3.addParticle(1);
|
|
force3->addParticle(2);
|
|
force3->addParticle(3);
|
|
force3->setConstantPotentialMethod(method);
|
|
force3->setUsePreconditioner(usePreconditioner);
|
|
force3->setUseChargeConstraint(false);
|
|
system3.addForce(force3);
|
|
VerletIntegrator integrator3(0.001);
|
|
Context context3(system3, integrator3, platform);
|
|
vector<Vec3> positions3{Vec3(0, 0, 0), Vec3(0.5, 0, 0)};
|
|
context3.setPositions(positions3);
|
|
vector<double> charges3;
|
|
force3->getCharges(context3, charges3);
|
|
ASSERT_EQUAL(charges3.size(), 2);
|
|
ASSERT_EQUAL(2, charges3[0]);
|
|
ASSERT_EQUAL(3, charges3[1]);
|
|
|
|
// Using one electrode particle without a total charge constraint, there is
|
|
// one degree of freedom. Make a symmetric system so that we know the
|
|
// solution.
|
|
|
|
System system4;
|
|
ConstantPotentialForce* force4 = new ConstantPotentialForce();
|
|
system4.addParticle(0);
|
|
system4.addParticle(1);
|
|
system4.addParticle(1);
|
|
force4->addParticle(0);
|
|
force4->addParticle(1);
|
|
force4->addParticle(-1);
|
|
set<int> electrode4{0};
|
|
force4->addElectrode(electrode4, 0, 0.2, 0);
|
|
force4->setConstantPotentialMethod(method);
|
|
force4->setUsePreconditioner(usePreconditioner);
|
|
force4->setUseChargeConstraint(false);
|
|
system4.addForce(force4);
|
|
VerletIntegrator integrator4(0.001);
|
|
Context context4(system4, integrator4, platform);
|
|
vector<Vec3> positions4{Vec3(0, 0, 0), Vec3(-0.75, 0, 0), Vec3(0.75, 0, 0)};
|
|
context4.setPositions(positions4);
|
|
vector<double> charges4;
|
|
force4->getCharges(context4, charges4);
|
|
ASSERT_EQUAL(charges4.size(), 3);
|
|
ASSERT_EQUAL_TOL(0, charges4[0], TOL);
|
|
ASSERT_EQUAL(1, charges4[1]);
|
|
ASSERT_EQUAL(-1, charges4[2]);
|
|
}
|
|
|
|
void testNoConstraintWithoutElectrode(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner) {
|
|
// If there are no electrodes (no charge degrees of freedom in the system),
|
|
// the user should not be allowed to specify a total charge constraint.
|
|
|
|
System system;
|
|
ConstantPotentialForce* force = new ConstantPotentialForce();
|
|
system.addParticle(1);
|
|
system.addParticle(1);
|
|
force->addParticle(1);
|
|
force->addParticle(1);
|
|
force->setConstantPotentialMethod(method);
|
|
force->setUsePreconditioner(usePreconditioner);
|
|
force->setUseChargeConstraint(true);
|
|
system.addForce(force);
|
|
VerletIntegrator integrator(0.001);
|
|
|
|
bool thrown = false;
|
|
try {
|
|
Context context(system, integrator, platform);
|
|
}
|
|
catch (const OpenMMException& exception) {
|
|
thrown = true;
|
|
}
|
|
ASSERT(thrown);
|
|
}
|
|
|
|
void testConstrainCharge(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner) {
|
|
// Ensures that the total charge constraint works correctly, including when
|
|
// the system charge target is set to a non-neutral value and the
|
|
// non-electrode particles carry a net charge.
|
|
|
|
System system;
|
|
ConstantPotentialForce* force = new ConstantPotentialForce();
|
|
|
|
system.setDefaultPeriodicBoxVectors(Vec3(10, 0, 0), Vec3(0, 10, 0), Vec3(0, 0, 10));
|
|
|
|
vector<Vec3> positions;
|
|
set<int> electrode;
|
|
double electrolyteCharge = 0;
|
|
for (int i = 0; i < 10; i++) {
|
|
system.addParticle(0);
|
|
force->addParticle(0);
|
|
positions.push_back(Vec3(i, 0, 0));
|
|
electrode.insert(i);
|
|
}
|
|
for (int i = 0; i < 10; i++) {
|
|
system.addParticle(1);
|
|
double charge = (i % 2 ? -1 : 1) + 0.01 * i * i;
|
|
force->addParticle(charge);
|
|
positions.push_back(Vec3(i, 5, 5));
|
|
electrolyteCharge += charge;
|
|
}
|
|
double chargeTarget = -2;
|
|
|
|
force->addElectrode(electrode, 0, 0.2, 0);
|
|
force->setConstantPotentialMethod(method);
|
|
force->setUsePreconditioner(usePreconditioner);
|
|
force->setUseChargeConstraint(true);
|
|
force->setChargeConstraintTarget(chargeTarget);
|
|
|
|
system.addForce(force);
|
|
|
|
VerletIntegrator integrator(0.001);
|
|
Context context(system, integrator, platform);
|
|
context.setPositions(positions);
|
|
vector<double> charges;
|
|
force->getCharges(context, charges);
|
|
|
|
ASSERT_EQUAL(20, charges.size());
|
|
double electrodeCharge = 0;
|
|
for (int i = 0; i < 10; i++) {
|
|
electrodeCharge += charges[i];
|
|
}
|
|
ASSERT_EQUAL_TOL(chargeTarget - electrolyteCharge, electrodeCharge, TOL);
|
|
}
|
|
|
|
void makeTestUpdateSystem(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner, System& system, ConstantPotentialForce*& force, vector<Vec3>& positions) {
|
|
// Makes a reference system for tests below checking that the properties of
|
|
// a system can be changed after context creation.
|
|
|
|
system = System();
|
|
system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
|
|
force = new ConstantPotentialForce();
|
|
system.addParticle(1);
|
|
system.addParticle(1);
|
|
system.addParticle(1);
|
|
system.addParticle(0);
|
|
system.addParticle(0);
|
|
force->addParticle(1);
|
|
force->addParticle(2);
|
|
force->addParticle(-3);
|
|
force->addParticle(0);
|
|
force->addParticle(0);
|
|
force->addException(0, 1, 1.5);
|
|
force->addException(1, 2, 0);
|
|
force->addElectrode({3}, 1, 0.02, 0.3);
|
|
force->addElectrode({4}, 2, 0.04, 0.5);
|
|
force->setConstantPotentialMethod(method);
|
|
force->setUsePreconditioner(usePreconditioner);
|
|
force->setUseChargeConstraint(true);
|
|
force->setChargeConstraintTarget(5);
|
|
force->setExternalField(Vec3(1, 2, 3));
|
|
force->setCutoffDistance(1.1);
|
|
system.addForce(force);
|
|
|
|
positions.clear();
|
|
positions.push_back(Vec3(0, 0, 0));
|
|
positions.push_back(Vec3(0, 0, 1));
|
|
positions.push_back(Vec3(0, 1, 1));
|
|
positions.push_back(Vec3(1, 1, 1));
|
|
positions.push_back(Vec3(2, 2, 2));
|
|
}
|
|
|
|
void testUpdate(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner) {
|
|
// Ensures that parameters can be updated and that the results match those
|
|
// computed by a completely different system.
|
|
|
|
System system1, system2;
|
|
ConstantPotentialForce* force1, * force2;
|
|
vector<Vec3> positions1, positions2;
|
|
VerletIntegrator integrator1(0.001), integrator2(0.001);
|
|
vector<double> charges1, charges2;
|
|
makeTestUpdateSystem(method, usePreconditioner, system1, force1, positions1);
|
|
makeTestUpdateSystem(method, usePreconditioner, system2, force2, positions2);
|
|
|
|
// Make sure to get charges before updating so that the constant potential
|
|
// method initializes: we are testing that it reinitializes with the update.
|
|
Context context1(system1, integrator1, platform);
|
|
context1.setPositions(positions1);
|
|
force1->getCharges(context1, charges1);
|
|
force1->setParticleParameters(1, 3);
|
|
force1->setParticleParameters(2, -5);
|
|
force1->setExceptionParameters(0, 0, 1, 1.75);
|
|
force1->setElectrodeParameters(0, {3}, 3, 0.06, 0.7);
|
|
force1->setChargeConstraintTarget(-7);
|
|
force1->setExternalField(Vec3(-6, -4, -2));
|
|
force1->updateParametersInContext(context1);
|
|
force1->getCharges(context1, charges1);
|
|
|
|
// Reinitialize the reference system completely to force an update.
|
|
force2->setParticleParameters(1, 3);
|
|
force2->setParticleParameters(2, -5);
|
|
force2->setExceptionParameters(0, 0, 1, 1.75);
|
|
force2->setElectrodeParameters(0, {3}, 3, 0.06, 0.7);
|
|
force2->setChargeConstraintTarget(-7);
|
|
force2->setExternalField(Vec3(-6, -4, -2));
|
|
Context context2(system2, integrator2, platform);
|
|
context2.setPositions(positions2);
|
|
force2->getCharges(context2, charges2);
|
|
|
|
{
|
|
// Test charges.
|
|
for (int i = 0; i < charges2.size(); i++) {
|
|
ASSERT_EQUAL_TOL(charges2[i], charges1[i], TOL);
|
|
}
|
|
|
|
// Get states and test energies and forces.
|
|
State state1 = context1.getState(State::Energy | State::Forces);
|
|
State state2 = context2.getState(State::Energy | State::Forces);
|
|
const vector<Vec3>& forces1 = state1.getForces();
|
|
const vector<Vec3>& forces2 = state2.getForces();
|
|
ASSERT_EQUAL_TOL(state2.getPotentialEnergy(), state1.getPotentialEnergy(), TOL);
|
|
for (int i = 0; i < forces2.size(); i++) {
|
|
ASSERT_EQUAL_VEC(forces2[i], forces1[i], TOL);
|
|
}
|
|
}
|
|
|
|
// Now test updating the box. Get PME parameters to apply to the second
|
|
// context so that energies and forces can be compared.
|
|
double alpha;
|
|
int nx, ny, nz;
|
|
force1->getPMEParametersInContext(context1, alpha, nx, ny, nz);
|
|
|
|
context1.setPeriodicBoxVectors(Vec3(3.25, 0, 0), Vec3(0, 3.5, 0), Vec3(0, 0, 3.75));
|
|
force1->getCharges(context1, charges1);
|
|
|
|
force2->setPMEParameters(alpha, nx, ny, nz);
|
|
system2.setDefaultPeriodicBoxVectors(Vec3(3.25, 0, 0), Vec3(0, 3.5, 0), Vec3(0, 0, 3.75));
|
|
context2.reinitialize(false);
|
|
context2.setPositions(positions2);
|
|
force2->getCharges(context2, charges2);
|
|
|
|
{
|
|
// Test charges.
|
|
for (int i = 0; i < charges2.size(); i++) {
|
|
ASSERT_EQUAL_TOL(charges2[i], charges1[i], TOL);
|
|
}
|
|
|
|
// Get states and test energies and forces.
|
|
State state1 = context1.getState(State::Energy | State::Forces);
|
|
State state2 = context2.getState(State::Energy | State::Forces);
|
|
const vector<Vec3>& forces1 = state1.getForces();
|
|
const vector<Vec3>& forces2 = state2.getForces();
|
|
ASSERT_EQUAL_TOL(state2.getPotentialEnergy(), state1.getPotentialEnergy(), TOL);
|
|
for (int i = 0; i < forces2.size(); i++) {
|
|
ASSERT_EQUAL_VEC(forces2[i], forces1[i], TOL);
|
|
}
|
|
}
|
|
|
|
// Now test updating positions. This checks that, e.g., a precomputed
|
|
// matrix is invalidated and recomputed when electrode particle positions
|
|
// are adjusted.
|
|
positions1[0] += Vec3(0.1, 0.2, 0.3);
|
|
positions1[4] += Vec3(0.4, 0.5, 0.6);
|
|
context1.setPositions(positions1);
|
|
force1->getCharges(context1, charges1);
|
|
|
|
context2.reinitialize(false);
|
|
context2.setPositions(positions1);
|
|
force2->getCharges(context2, charges2);
|
|
|
|
{
|
|
// Test charges.
|
|
for (int i = 0; i < charges2.size(); i++) {
|
|
ASSERT_EQUAL_TOL(charges2[i], charges1[i], TOL);
|
|
}
|
|
|
|
// Get states and test energies and forces.
|
|
State state1 = context1.getState(State::Energy | State::Forces);
|
|
State state2 = context2.getState(State::Energy | State::Forces);
|
|
const vector<Vec3>& forces1 = state1.getForces();
|
|
const vector<Vec3>& forces2 = state2.getForces();
|
|
ASSERT_EQUAL_TOL(state2.getPotentialEnergy(), state1.getPotentialEnergy(), TOL);
|
|
for (int i = 0; i < forces2.size(); i++) {
|
|
ASSERT_EQUAL_VEC(forces2[i], forces1[i], TOL);
|
|
}
|
|
}
|
|
}
|
|
|
|
void testParallelPlateCapacitorDoubleCell() {
|
|
// Uses the zero field double-cell geometry to test an ideal parallel plate
|
|
// capacitor with vacuum between the plates.
|
|
|
|
double capacitance = EPSILON0 * 2.0 * 3.0 / 7.0;
|
|
|
|
double potential = 100.0;
|
|
|
|
System system;
|
|
ConstantPotentialForce* force = new ConstantPotentialForce();
|
|
|
|
system.setDefaultPeriodicBoxVectors(Vec3(2, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 16));
|
|
|
|
vector<Vec3> positions;
|
|
set<int> electrode1, electrode2;
|
|
for (int iz = 0; iz < 4; iz++) {
|
|
for (int iy = 0; iy < 12; iy++) {
|
|
for (int ix = 0; ix < 8; ix++) {
|
|
electrode1.insert(force->getNumParticles());
|
|
system.addParticle(0);
|
|
force->addParticle(0);
|
|
positions.push_back(Vec3(0.25 * ix, 0.25 * iy, 0.25 * iz));
|
|
|
|
electrode2.insert(force->getNumParticles());
|
|
system.addParticle(0);
|
|
force->addParticle(0);
|
|
positions.push_back(Vec3(0.25 * ix, 0.25 * iy, 0.25 * iz + 8.0));
|
|
}
|
|
}
|
|
}
|
|
force->addElectrode(electrode1, 0, 0.2, 0);
|
|
force->addElectrode(electrode2, potential, 0.2, 0);
|
|
force->setUseChargeConstraint(true);
|
|
|
|
system.addForce(force);
|
|
|
|
VerletIntegrator integrator(0.001);
|
|
Context context(system, integrator, platform);
|
|
context.setPositions(positions);
|
|
vector<double> charges;
|
|
double q1, q2;
|
|
|
|
force->getCharges(context, charges);
|
|
|
|
q1 = 0;
|
|
for (int ii : electrode1) {
|
|
q1 += charges[ii];
|
|
}
|
|
|
|
q2 = 0;
|
|
for (int ii : electrode2) {
|
|
q2 += charges[ii];
|
|
}
|
|
|
|
// Charge on each electrode is doubled since we are using a double-cell.
|
|
// Use a looser tolerance since the analytical formula is for uniform
|
|
// plates with defined edges, not cubic arrays of Gaussian charges.
|
|
ASSERT_EQUAL_TOL(-2.0 * potential * capacitance, q1, 1e-3);
|
|
ASSERT_EQUAL_TOL(2.0 * potential * capacitance, q2, 1e-3);
|
|
|
|
// Update potential to a new value and recompute.
|
|
potential = -200.0;
|
|
force->setElectrodeParameters(1, electrode2, potential, 0.2, 0);
|
|
force->updateParametersInContext(context);
|
|
force->getCharges(context, charges);
|
|
|
|
q1 = 0;
|
|
for (int ii : electrode1) {
|
|
q1 += charges[ii];
|
|
}
|
|
|
|
q2 = 0;
|
|
for (int ii : electrode2) {
|
|
q2 += charges[ii];
|
|
}
|
|
|
|
ASSERT_EQUAL_TOL(-2.0 * potential * capacitance, q1, 1e-3);
|
|
ASSERT_EQUAL_TOL(2.0 * potential * capacitance, q2, 1e-3);
|
|
}
|
|
|
|
void testParallelPlateCapacitorFiniteField() {
|
|
// Uses the finite field geometry (still applying a potential to one
|
|
// electrode) to test an ideal parallel plate capacitor.
|
|
|
|
double capacitance = EPSILON0 * 2.0 * 3.0 / 11.0;
|
|
|
|
double potential = 100.0;
|
|
|
|
System system;
|
|
ConstantPotentialForce* force = new ConstantPotentialForce();
|
|
|
|
system.setDefaultPeriodicBoxVectors(Vec3(2, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 16));
|
|
|
|
vector<Vec3> positions;
|
|
set<int> electrode1, electrode2;
|
|
for (int iz = 0; iz < 4; iz++) {
|
|
for (int iy = 0; iy < 12; iy++) {
|
|
for (int ix = 0; ix < 8; ix++) {
|
|
electrode1.insert(force->getNumParticles());
|
|
system.addParticle(0);
|
|
force->addParticle(0);
|
|
positions.push_back(Vec3(0.25 * ix, 0.25 * iy, 0.25 * iz));
|
|
|
|
electrode2.insert(force->getNumParticles());
|
|
system.addParticle(0);
|
|
force->addParticle(0);
|
|
positions.push_back(Vec3(0.25 * ix, 0.25 * iy, 0.25 * iz + 12.0));
|
|
}
|
|
}
|
|
}
|
|
force->addElectrode(electrode1, 0, 0.2, 0);
|
|
force->addElectrode(electrode2, potential, 0.2, 0);
|
|
force->setUseChargeConstraint(true);
|
|
force->setExternalField(Vec3(0, 0, -potential / 16));
|
|
|
|
system.addForce(force);
|
|
|
|
VerletIntegrator integrator(0.001);
|
|
Context context(system, integrator, platform);
|
|
context.setPositions(positions);
|
|
vector<double> charges;
|
|
force->getCharges(context, charges);
|
|
|
|
double q1 = 0;
|
|
for (int ii : electrode1) {
|
|
q1 += charges[ii];
|
|
}
|
|
|
|
double q2 = 0;
|
|
for (int ii : electrode2) {
|
|
q2 += charges[ii];
|
|
}
|
|
|
|
// Use a looser tolerance since the analytical formula is for uniform
|
|
// plates with defined edges, not cubic arrays of Gaussian charges.
|
|
ASSERT_EQUAL_TOL(-potential * capacitance, q1, 1e-3);
|
|
ASSERT_EQUAL_TOL(potential * capacitance, q2, 1e-3);
|
|
|
|
// Update potential to a new value and recompute.
|
|
potential = -200.0;
|
|
force->setElectrodeParameters(1, electrode2, potential, 0.2, 0);
|
|
force->setExternalField(Vec3(0, 0, -potential / 16));
|
|
force->updateParametersInContext(context);
|
|
force->getCharges(context, charges);
|
|
|
|
q1 = 0;
|
|
for (int ii : electrode1) {
|
|
q1 += charges[ii];
|
|
}
|
|
|
|
q2 = 0;
|
|
for (int ii : electrode2) {
|
|
q2 += charges[ii];
|
|
}
|
|
|
|
ASSERT_EQUAL_TOL(-potential * capacitance, q1, 1e-3);
|
|
ASSERT_EQUAL_TOL(potential * capacitance, q2, 1e-3);
|
|
}
|
|
|
|
void makeTestReferenceSystem(bool freezeAll, System& system, ConstantPotentialForce*& constantPotentialForce, vector<Vec3>& positions) {
|
|
// Generates a test system with SPC/E water in contact with a model
|
|
// electrode.
|
|
|
|
system = System();
|
|
system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 2, 0), Vec3(0, 0, 2));
|
|
|
|
HarmonicBondForce* bondForce = new HarmonicBondForce();
|
|
NonbondedForce* nonbondedForce = new NonbondedForce();
|
|
constantPotentialForce = new ConstantPotentialForce();
|
|
|
|
for (int i = 0; i < 300; i++) {
|
|
system.addParticle((i >= 100 && i < 200) || freezeAll ? 0 : 195.08);
|
|
nonbondedForce->addParticle(0, 0.25, 1);
|
|
constantPotentialForce->addParticle(0);
|
|
}
|
|
|
|
// static const int bondCount = ...;
|
|
// static const int bondIndices[...][2] = {...};
|
|
#include "conp_bond_indices.dat"
|
|
|
|
for (int i = 0; i < bondCount; i++) {
|
|
bondForce->addBond(bondIndices[i][0], bondIndices[i][1], 0.28284271247461906, 10000);
|
|
}
|
|
|
|
for (int i = 0; i < 222; i++) {
|
|
int i1 = system.addParticle(15.99943);
|
|
int i2 = system.addParticle(1.007947);
|
|
int i3 = system.addParticle(1.007947);
|
|
system.addConstraint(i1, i2, 0.1);
|
|
system.addConstraint(i1, i3, 0.1);
|
|
system.addConstraint(i2, i3, 0.1632980861841278);
|
|
nonbondedForce->addParticle(0, 0.3165719505039882, 0.6497752);
|
|
nonbondedForce->addParticle(0, 1, 0);
|
|
nonbondedForce->addParticle(0, 1, 0);
|
|
nonbondedForce->addException(i1, i2, 0, 1, 0);
|
|
nonbondedForce->addException(i1, i3, 0, 1, 0);
|
|
nonbondedForce->addException(i2, i3, 0, 1, 0);
|
|
constantPotentialForce->addParticle(-0.8476);
|
|
constantPotentialForce->addParticle(0.4238);
|
|
constantPotentialForce->addParticle(0.4238);
|
|
constantPotentialForce->addException(i1, i2, 0);
|
|
constantPotentialForce->addException(i1, i3, 0);
|
|
constantPotentialForce->addException(i2, i3, 0);
|
|
}
|
|
|
|
bondForce->setUsesPeriodicBoundaryConditions(true);
|
|
system.addForce(bondForce);
|
|
|
|
nonbondedForce->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
|
|
system.addForce(nonbondedForce);
|
|
|
|
positions.clear();
|
|
positions.resize(system.getNumParticles());
|
|
|
|
// positions[...] = Vec3(..., ..., ...);
|
|
#include "conp_positions.dat"
|
|
|
|
set<int> electrodeLeft;
|
|
set<int> electrodeRight;
|
|
for (int i = 0; i < 300; i++) {
|
|
if (positions[i][0] < 1.5) {
|
|
electrodeLeft.insert(i);
|
|
} else {
|
|
electrodeRight.insert(i);
|
|
}
|
|
}
|
|
|
|
// Initialize the electrodes (parameters will be set later).
|
|
constantPotentialForce->addElectrode(electrodeLeft, 0, 0, 0);
|
|
constantPotentialForce->addElectrode(electrodeRight, 0, 0, 0);
|
|
system.addForce(constantPotentialForce);
|
|
}
|
|
|
|
void testReferenceCharges(bool testThomasFermi, ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner) {
|
|
// Make sure that charges solved for match values computed by an external
|
|
// reference implementation.
|
|
|
|
System testSystem;
|
|
ConstantPotentialForce* testForce;
|
|
vector<Vec3> positions;
|
|
|
|
makeTestReferenceSystem(method == ConstantPotentialForce::Matrix, testSystem, testForce, positions);
|
|
|
|
testForce->setEwaldErrorTolerance(5e-5);
|
|
testForce->setConstantPotentialMethod(method);
|
|
testForce->setUsePreconditioner(usePreconditioner);
|
|
testForce->setUseChargeConstraint(true);
|
|
testForce->setChargeConstraintTarget(0);
|
|
testForce->setCutoffDistance(1);
|
|
|
|
if (!testThomasFermi) {
|
|
// The reference implementation (MetalWalls) doesn't support
|
|
// simultaneous specification of these options.
|
|
testForce->setExternalField(Vec3(100, 50, 25));
|
|
}
|
|
|
|
set<int> electrodeParticles;
|
|
double potential, gaussianWidth, thomasFermiScale;
|
|
testForce->getElectrodeParameters(0, electrodeParticles, potential, gaussianWidth, thomasFermiScale);
|
|
testForce->setElectrodeParameters(0, electrodeParticles, 100, 0.05, testThomasFermi ? 0.50625 : 0.0);
|
|
testForce->getElectrodeParameters(1, electrodeParticles, potential, gaussianWidth, thomasFermiScale);
|
|
testForce->setElectrodeParameters(1, electrodeParticles, 200, 0.1, testThomasFermi ? 0.225 : 0.0);
|
|
|
|
VerletIntegrator integrator(0.001);
|
|
Context testContext(testSystem, integrator, platform);
|
|
|
|
testContext.setPositions(positions);
|
|
|
|
// Charges of electrode atoms should match reference values.
|
|
vector<double> refCharges(300);
|
|
if (testThomasFermi) {
|
|
// refCharges[...] = ...;
|
|
#include "conp_ref_charges_tf.dat"
|
|
} else {
|
|
// refCharges[...] = ...;
|
|
#include "conp_ref_charges.dat"
|
|
}
|
|
vector<double> testCharges;
|
|
testForce->getCharges(testContext, testCharges);
|
|
for (int i = 0; i < 300; i++) {
|
|
ASSERT_EQUAL_TOL(refCharges[i], testCharges[i], TOL);
|
|
}
|
|
}
|
|
|
|
void testChargeUpdate(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner) {
|
|
// Make sure that charges get updated correctly before and after dynamics.
|
|
|
|
System testSystem;
|
|
ConstantPotentialForce* testForce;
|
|
vector<Vec3> positions;
|
|
|
|
makeTestReferenceSystem(method == ConstantPotentialForce::Matrix, testSystem, testForce, positions);
|
|
|
|
testForce->setConstantPotentialMethod(method);
|
|
testForce->setUsePreconditioner(usePreconditioner);
|
|
testForce->setUseChargeConstraint(true);
|
|
testForce->setChargeConstraintTarget(1);
|
|
testForce->setExternalField(Vec3(10, 0, 0));
|
|
|
|
set<int> electrodeParticles;
|
|
double potential, gaussianWidth, thomasFermiScale;
|
|
testForce->getElectrodeParameters(0, electrodeParticles, potential, gaussianWidth, thomasFermiScale);
|
|
testForce->setElectrodeParameters(0, electrodeParticles, 1, 0.05, 1);
|
|
testForce->getElectrodeParameters(1, electrodeParticles, potential, gaussianWidth, thomasFermiScale);
|
|
testForce->setElectrodeParameters(1, electrodeParticles, 2, 0.06, 1.2);
|
|
|
|
VerletIntegrator integrator(0.001);
|
|
Context testContext(testSystem, integrator, platform);
|
|
|
|
testContext.setPositions(positions);
|
|
testContext.setVelocitiesToTemperature(300);
|
|
|
|
// Charges of non-electrode atoms should exactly match charges set.
|
|
vector<double> charges0;
|
|
testForce->getCharges(testContext, charges0);
|
|
for (int i = 300; i < charges0.size(); i++) {
|
|
double refCharge;
|
|
testForce->getParticleParameters(i, refCharge);
|
|
ASSERT_EQUAL(refCharge, charges0[i]);
|
|
}
|
|
|
|
integrator.step(1);
|
|
|
|
// Charges of electrode atoms should be changed, and charges of
|
|
// non-electrode atoms should exactly match charges set.
|
|
vector<double> charges1;
|
|
testForce->getCharges(testContext, charges1);
|
|
for (int i = 0; i < 300; i++) {
|
|
ASSERT(charges1[i] != charges0[i]);
|
|
}
|
|
for (int i = 300; i < charges1.size(); i++) {
|
|
double refCharge;
|
|
testForce->getParticleParameters(i, refCharge);
|
|
ASSERT_EQUAL(refCharge, charges1[i]);
|
|
}
|
|
}
|
|
|
|
void testEnergyConservation(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner, int stepCount) {
|
|
// Do a short dynamics run and ensure that energy is conserved.
|
|
|
|
System system;
|
|
system.setDefaultPeriodicBoxVectors(Vec3(2, 0, 0), Vec3(0, 2, 0), Vec3(0, 0, 3));
|
|
|
|
// WCA potential to keep particles from getting too close to each other.
|
|
CustomNonbondedForce* nonbondedForce = new CustomNonbondedForce("1/r^12-2/r^6+1");
|
|
nonbondedForce->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
|
|
nonbondedForce->setCutoffDistance(1);
|
|
|
|
ConstantPotentialForce* constantPotentialForce = new ConstantPotentialForce();
|
|
constantPotentialForce->setCutoffDistance(1);
|
|
constantPotentialForce->setUseChargeConstraint(true);
|
|
constantPotentialForce->setChargeConstraintTarget(1);
|
|
constantPotentialForce->setExternalField(Vec3(1, 2, 4));
|
|
constantPotentialForce->setConstantPotentialMethod(method);
|
|
constantPotentialForce->setUsePreconditioner(usePreconditioner);
|
|
constantPotentialForce->setEwaldErrorTolerance(1e-4);
|
|
|
|
for (int i = 0; i < 8; i++) {
|
|
system.addParticle(method == ConstantPotentialForce::Matrix ? 0 : 1);
|
|
constantPotentialForce->addParticle(0);
|
|
}
|
|
for (int i = 0; i < 4; i++) {
|
|
system.addParticle(1);
|
|
}
|
|
for (int i = 0; i < 12; i++) {
|
|
nonbondedForce->addParticle();
|
|
}
|
|
constantPotentialForce->addParticle(1);
|
|
constantPotentialForce->addParticle(-1);
|
|
constantPotentialForce->addParticle(-1);
|
|
constantPotentialForce->addParticle(1);
|
|
constantPotentialForce->addElectrode({0, 1, 2, 3}, -8, 0.05, 1);
|
|
constantPotentialForce->addElectrode({4, 5, 6, 7}, 8, 0.1, 1.5);
|
|
|
|
system.addForce(nonbondedForce);
|
|
system.addForce(constantPotentialForce);
|
|
|
|
vector<Vec3> positions{
|
|
Vec3(0.0, 0.0, 0.0),
|
|
Vec3(0.0, 1.0, 0.0),
|
|
Vec3(1.0, 0.0, 0.0),
|
|
Vec3(1.0, 1.0, 0.0),
|
|
Vec3(0.0, 0.0, 2.0),
|
|
Vec3(0.0, 1.0, 2.0),
|
|
Vec3(1.0, 0.0, 2.0),
|
|
Vec3(1.0, 1.0, 2.0),
|
|
Vec3(0.5, 0.5, 1.0),
|
|
Vec3(0.5, 1.5, 1.0),
|
|
Vec3(1.5, 0.5, 1.0),
|
|
Vec3(1.5, 1.5, 1.0)
|
|
};
|
|
|
|
VerletIntegrator integrator(0.002);
|
|
Context context(system, integrator, platform);
|
|
context.setPositions(positions);
|
|
context.setVelocitiesToTemperature(1 / BOLTZ);
|
|
|
|
State state1 = context.getState(State::Energy);
|
|
double energy1 = state1.getPotentialEnergy() + state1.getKineticEnergy();
|
|
|
|
integrator.step(stepCount);
|
|
|
|
State state2 = context.getState(State::Energy);
|
|
double energy2 = state2.getPotentialEnergy() + state2.getKineticEnergy();
|
|
|
|
ASSERT_USUALLY_EQUAL_TOL(energy1, energy2, 5e-4);
|
|
}
|
|
|
|
void compareToReferencePlatform(System& system, ConstantPotentialForce* force, const vector<Vec3>& positions) {
|
|
// Compares results from the current platform to results computed by the
|
|
// reference platform.
|
|
|
|
VerletIntegrator refIntegrator(0.001);
|
|
VerletIntegrator testIntegrator(0.001);
|
|
ReferencePlatform refPlatform;
|
|
Context refContext(system, refIntegrator, refPlatform);
|
|
Context testContext(system, testIntegrator, platform);
|
|
refContext.setPositions(positions);
|
|
testContext.setPositions(positions);
|
|
|
|
State refState = refContext.getState(State::Energy | State::Forces);
|
|
State testState = testContext.getState(State::Energy | State::Forces);
|
|
const vector<Vec3>& refForces = refState.getForces();
|
|
const vector<Vec3>& testForces = testState.getForces();
|
|
vector<double> refCharges, testCharges;
|
|
force->getCharges(refContext, refCharges);
|
|
force->getCharges(testContext, testCharges);
|
|
|
|
ASSERT_EQUAL_TOL(refState.getPotentialEnergy(), testState.getPotentialEnergy(), TOL);
|
|
for (int i = 0; i < system.getNumParticles(); i++) {
|
|
ASSERT_EQUAL_VEC(refForces[i], testForces[i], 3e-3);
|
|
}
|
|
for (int i = 0; i < system.getNumParticles(); i++) {
|
|
ASSERT_EQUAL_TOL(refCharges[i], testCharges[i], TOL);
|
|
}
|
|
}
|
|
|
|
void testCompareToReferencePlatform(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner) {
|
|
// Compares results between the current and reference platforms for a few
|
|
// test systems. This is only called in the runPlatformTests() for
|
|
// platforms other than the reference platform.
|
|
|
|
System system;
|
|
ConstantPotentialForce* force;
|
|
vector<Vec3> positions;
|
|
|
|
makeTestUpdateSystem(method, usePreconditioner, system, force, positions);
|
|
force->setEwaldErrorTolerance(5e-5);
|
|
compareToReferencePlatform(system, force, positions);
|
|
|
|
makeTestReferenceSystem(method == ConstantPotentialForce::Matrix, system, force, positions);
|
|
force->setConstantPotentialMethod(method);
|
|
force->setUsePreconditioner(usePreconditioner);
|
|
force->setUseChargeConstraint(true);
|
|
force->setChargeConstraintTarget(1);
|
|
force->setExternalField(Vec3(10, 0, 0));
|
|
force->setEwaldErrorTolerance(5e-5);
|
|
set<int> electrodeParticles;
|
|
double potential, gaussianWidth, thomasFermiScale;
|
|
force->getElectrodeParameters(0, electrodeParticles, potential, gaussianWidth, thomasFermiScale);
|
|
force->setElectrodeParameters(0, electrodeParticles, 1, 0.05, 1);
|
|
force->getElectrodeParameters(1, electrodeParticles, potential, gaussianWidth, thomasFermiScale);
|
|
force->setElectrodeParameters(1, electrodeParticles, 2, 0.06, 1.2);
|
|
compareToReferencePlatform(system, force, positions);
|
|
}
|
|
|
|
void testLargeNeighborList(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner) {
|
|
// Runs a test where the initial neighbor list should overflow on GPU platforms.
|
|
|
|
const int n = 9;
|
|
const double l = 3.0;
|
|
const double scale = l / n;
|
|
|
|
System system;
|
|
system.setDefaultPeriodicBoxVectors(Vec3(l, 0, 0), Vec3(0, l, 0), Vec3(0, 0, l));
|
|
|
|
ConstantPotentialForce* force = new ConstantPotentialForce();
|
|
force->setConstantPotentialMethod(method);
|
|
force->setUsePreconditioner(usePreconditioner);
|
|
force->setUseChargeConstraint(true);
|
|
force->setCutoffDistance(1.4);
|
|
force->setCGErrorTolerance(5e-4);
|
|
system.addForce(force);
|
|
|
|
vector<Vec3> positions;
|
|
set<int> electrodeParticles;
|
|
for (int ix = 0; ix < n; ix++) {
|
|
for (int iy = 0; iy < n; iy++) {
|
|
for (int iz = 0; iz < n; iz++) {
|
|
positions.push_back(scale * Vec3(ix, iy, iz));
|
|
positions.push_back(scale * Vec3(ix + 0.5, iy + 0.5, iz + 0.5));
|
|
electrodeParticles.insert(system.addParticle(0.0));
|
|
system.addParticle(0.0);
|
|
force->addParticle(0.0);
|
|
force->addParticle(1.0);
|
|
}
|
|
}
|
|
}
|
|
force->addElectrode(electrodeParticles, 0.0, 0.01, 0.0);
|
|
|
|
VerletIntegrator integrator(0.001);
|
|
Context context(system, integrator, platform);
|
|
context.setPositions(positions);
|
|
|
|
// Get charges: if the neighbor list is incomplete, they will not be uniformly equal to -1.
|
|
vector<double> charges;
|
|
force->getCharges(context, charges);
|
|
for (int i : electrodeParticles) {
|
|
ASSERT_EQUAL_TOL(-1.0, charges[i], 2e-3);
|
|
}
|
|
|
|
// Run again, this time doing an energy/force calculation before getting charges.
|
|
context.reinitialize();
|
|
context.setPositions(positions);
|
|
context.getState(State::Energy | State::Forces);
|
|
force->getCharges(context, charges);
|
|
for (int i : electrodeParticles) {
|
|
ASSERT_EQUAL_TOL(-1.0, charges[i], 2e-3);
|
|
}
|
|
}
|
|
|
|
void platformInitialize();
|
|
void runPlatformTests(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner);
|
|
|
|
void runMethodDependentTests(ConstantPotentialForce::ConstantPotentialMethod method, bool usePreconditioner) {
|
|
testSmallSystems(method, usePreconditioner);
|
|
testNoConstraintWithoutElectrode(method, usePreconditioner);
|
|
testConstrainCharge(method, usePreconditioner);
|
|
testUpdate(method, usePreconditioner);
|
|
testReferenceCharges(false, method, usePreconditioner); // External field
|
|
testReferenceCharges(true, method, usePreconditioner); // Thomas-Fermi
|
|
testChargeUpdate(method, usePreconditioner);
|
|
runPlatformTests(method, usePreconditioner);
|
|
}
|
|
|
|
int main(int argc, char* argv[]) {
|
|
try {
|
|
initializeTests(argc, argv);
|
|
platformInitialize();
|
|
|
|
testCoulomb(false); // Non-periodic exceptions
|
|
testCoulomb(true); // Periodic exceptions
|
|
testCoulombOverlap();
|
|
testCoulombNonNeutral();
|
|
testCoulombGaussian();
|
|
testFiniteFieldNonPeriodic();
|
|
|
|
testElectrodesDisjoint();
|
|
testNoElectrodeExceptions();
|
|
testElectrodeMatrixNoMass();
|
|
|
|
testParallelPlateCapacitorDoubleCell();
|
|
testParallelPlateCapacitorFiniteField();
|
|
|
|
runMethodDependentTests(ConstantPotentialForce::Matrix, false); // Matrix inversion (usePreconditioner ignored)
|
|
runMethodDependentTests(ConstantPotentialForce::CG, false); // Conjugate gradient (not preconditioned)
|
|
runMethodDependentTests(ConstantPotentialForce::CG, true); // Conjugate gradient (preconditioned)
|
|
}
|
|
catch(const exception& e) {
|
|
cout << "exception: " << e.what() << endl;
|
|
return 1;
|
|
}
|
|
cout << "Done" << endl;
|
|
return 0;
|
|
}
|