Merge pull request #1271 from peastman/gbvi

Deleted GBVIForce

platforms/reference/tests/TestReferenceGBVIForce.cpp

-/* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from   *
- * Simbios, the NIH National Center for Physics-Based Simulation of           *
- * Biological Structures at Stanford, funded under the NIH Roadmap for        *
- * Medical Research, grant U54 GM072970. See https://simtk.org.               *
- *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
- * Authors: Peter Eastman                                                     *
- * Contributors:                                                              *
- *                                                                            *
- * Permission is hereby granted, free of charge, to any person obtaining a    *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation  *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
- * and/or sell copies of the Software, and to permit persons to whom the      *
- * Software is furnished to do so, subject to the following conditions:       *
- *                                                                            *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software.                        *
- *                                                                            *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
- * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
- * -------------------------------------------------------------------------- */
-
-/**
- * This tests the reference implementation of GBVIForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "ReferencePlatform.h"
-#include "openmm/HarmonicBondForce.h"
-#include "openmm/GBVIForce.h"
-#include "openmm/GBSAOBCForce.h"
-#include "openmm/System.h"
-#include "openmm/LangevinIntegrator.h"
-#include "openmm/NonbondedForce.h"
-#include "SimTKOpenMMRealType.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-ReferencePlatform platform;
-
-const double TOL = 1e-5;
-
-void testSingleParticle() {
-    System system;
-    system.addParticle(2.0);
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-
-    GBVIForce* forceField = new GBVIForce();
-
-    double charge         = -1.0;
-    double radius         =  0.15;
-    double gamma          =  1.0;
-    forceField->addParticle(charge, radius, gamma);
-    system.addForce(forceField);
-    ASSERT(!forceField->usesPeriodicBoundaryConditions());
-    ASSERT(!system.usesPeriodicBoundaryConditions());
-
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, 0, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-
-    double bornRadius     = radius; 
-    double eps0           = EPSILON0;
-    double tau            = (1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric());
-
-    double bornEnergy     = (-charge*charge/(8*PI_M*eps0))*tau/bornRadius;
-    double nonpolarEnergy = -gamma*tau*std::pow(radius/bornRadius, 3.0);
-
-    double expectedE      = (bornEnergy+nonpolarEnergy); 
-    double obtainedE      = state.getPotentialEnergy(); 
-    double diff           = fabs((obtainedE - expectedE)/expectedE);
-
-    ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
-}
-
-void testEnergyEthane(int applyBornRadiiScaling) {
-    const int numParticles = 8;
-    System system;
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-
-    // harmonic bond
-
-    double C_HBondDistance   = 0.1097;
-    double C_CBondDistance   = 0.1504;
-    HarmonicBondForce* bonds = new HarmonicBondForce();
-    bonds->addBond(0, 1, C_HBondDistance, 0.0);
-    bonds->addBond(2, 1, C_HBondDistance, 0.0);
-    bonds->addBond(3, 1, C_HBondDistance, 0.0);
-
-    bonds->addBond(1, 4, C_CBondDistance, 0.0);
-
-    bonds->addBond(5, 4, C_HBondDistance, 0.0);
-    bonds->addBond(6, 4, C_HBondDistance, 0.0);
-    bonds->addBond(7, 4, C_HBondDistance, 0.0);
-
-    system.addForce(bonds);
-
-    double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
-
-    int AM1_BCC = 1;
-    H_charge    = -0.053;
-    C_charge    = -3.0*H_charge;
-    if (AM1_BCC) {
-       C_radius =  0.180;
-       C_gamma  = -0.2863;
-       H_radius =  0.125;
-       H_gamma  =  0.2437;
-    }
-    else {
-       C_radius =  0.215;
-       C_gamma  = -1.1087;
-       H_radius =  0.150;
-       H_gamma  =  0.1237;
-    }
-
-    NonbondedForce* nonbonded = new NonbondedForce();
-    nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
-
-    GBVIForce* forceField = new GBVIForce();
-    if (applyBornRadiiScaling) {
-        forceField->setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
-    }
-    else {
-        forceField->setBornRadiusScalingMethod(GBVIForce::NoScaling);
-    }
-    for (int i = 0; i < numParticles; i++) {
-       system.addParticle(1.0);
-       forceField->addParticle(H_charge, H_radius, H_gamma);
-       nonbonded->addParticle( H_charge, H_radius, 0.0);
-    }
- 
-    forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
-    forceField->setParticleParameters(4, C_charge, C_radius, C_gamma);
- 
-    nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
-    nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
- 
-    forceField->addBond(0, 1, C_HBondDistance);
-    forceField->addBond(2, 1, C_HBondDistance);
-    forceField->addBond(3, 1, C_HBondDistance);
-    forceField->addBond(1, 4, C_CBondDistance);
-    forceField->addBond(5, 4, C_HBondDistance);
-    forceField->addBond(6, 4, C_HBondDistance);
-    forceField->addBond(7, 4, C_HBondDistance);
-    
-    std::vector<pair<int, int> > bondExceptions;
-    std::vector<double> bondDistances;
-    
-    bondExceptions.push_back(pair<int, int>(0, 1)); 
-    bondDistances.push_back(C_HBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(2, 1)); 
-    bondDistances.push_back(C_HBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(3, 1)); 
-    bondDistances.push_back(C_HBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(1, 4)); 
-    bondDistances.push_back(C_CBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(5, 4)); 
-    bondDistances.push_back(C_HBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(6, 4)); 
-    bondDistances.push_back(C_HBondDistance);
- 
-    bondExceptions.push_back(pair<int, int>(7, 4));
-    bondDistances.push_back(C_HBondDistance);
- 
-    nonbonded->createExceptionsFromBonds(bondExceptions, 0.0, 0.0);
- 
-    system.addForce(forceField);
-    system.addForce(nonbonded);
-
-    Context context(system, integrator, platform);
-    
-    vector<Vec3> positions(numParticles);
-    positions[0] = Vec3(0.5480,    1.7661,    0.0000);
-    positions[1] = Vec3(0.7286,    0.8978,    0.6468);
-    positions[2] = Vec3(0.4974,    0.0000,    0.0588);
-    positions[3] = Vec3(0.0000,    0.9459,    1.4666);
-    positions[4] = Vec3(2.1421,    0.8746,    1.1615);
-    positions[5] = Vec3(2.3239,    0.0050,    1.8065);
-    positions[6] = Vec3(2.8705,    0.8295,    0.3416);
-    positions[7] = Vec3(2.3722,    1.7711,    1.7518);
-    context.setPositions(positions);
-
-    State state = context.getState(State::Forces | State::Energy);
-    
-    // Take a small step in the direction of the energy gradient.
-    
-    double norm        = 0.0;
-    double forceSum[3] = { 0.0, 0.0, 0.0 };
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 f  = state.getForces()[i];
-        norm        += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
-        forceSum[0] += f[0];
-        forceSum[1] += f[1];
-        forceSum[2] += f[2];
-    }
-    norm               = std::sqrt(norm);
-
-    const double delta = 1e-4;
-    double step = delta/norm;
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 p = positions[i];
-        Vec3 f = state.getForces()[i];
-        positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-    }
-    context.setPositions(positions);
-    
-    State state2 = context.getState(State::Energy);
-
-    // See whether the potential energy changed by the expected amount.
-    
-    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
-}
-
-int main() {
-    try {
-        testSingleParticle();
-        testEnergyEthane(0);
-        testEnergyEthane(1);
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
-}