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:                                                              *
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/**
 * This tests the reference implementation of GBVIForce.
 */

#include "../../../tests/AssertionUtilities.h"
#include "OpenMMContext.h"
#include "ReferencePlatform.h"
#include "HarmonicBondForce.h"
#include "GBVIForce.h"
#include "GBSAOBCForce.h"
#include "System.h"
#include "LangevinIntegrator.h"
#include "NonbondedForce.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/sfmt/SFMT.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

const double TOL = 1e-5;

void testSingleParticle() {
    ReferencePlatform platform;
    System system;
    system.addParticle(2.0);
    LangevinIntegrator integrator(0, 0.1, 0.01);

    GBVIForce* forceField = new GBVIForce();

    double charge         = 0.0;
    double radius         = 0.15;
    double gamma          = 1.0;
    forceField->addParticle(charge, radius, gamma);
    system.addForce(forceField);

    OpenMMContext 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 = -CAL2JOULE*gamma*tau*std::pow( radius/bornRadius, 3.0);

    double expectedE      = (bornEnergy+nonpolarEnergy); 
    double obtainedE      = state.getPotentialEnergy(); 
    double diff           = fabs( obtainedE - expectedE );
    (void) fprintf( stderr, "testSingleParticle expected=%14.6e obtained=%14.6e diff=%14.6e breakdown:[%14.6e %14.6e]\n",
                    expectedE, obtainedE, diff, bornEnergy, nonpolarEnergy );
    ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
}

/*
void testCutoffAndPeriodic() {
    ReferencePlatform platform;
    System system(2, 0);
    LangevinIntegrator integrator(0, 0.1, 0.01);
    GBSAOBCForce* gbsa = new GBSAOBCForce(2);
    NonbondedForce* nonbonded = new NonbondedForce(2, 0);
    gbsa->setParticleParameters(0, -1, 0.15, 1);
    nonbonded->setParticleParameters(0, -1, 1, 0);
    gbsa->setParticleParameters(1, 1, 0.15, 1);
    nonbonded->setParticleParameters(1, 1, 1, 0);
    const double cutoffDistance = 3.0;
    const double boxSize = 10.0;
    nonbonded->setCutoffDistance(cutoffDistance);
    nonbonded->setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    system.addForce(gbsa);
    system.addForce(nonbonded);
    vector<Vec3> positions(2);
    positions[0] = Vec3(0, 0, 0);
    positions[1] = Vec3(2, 0, 0);

    // Calculate the forces for both cutoff and periodic with two different atom positions.

    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    OpenMMContext context(system, integrator, platform);
    context.setPositions(positions);
    State state1 = context.getState(State::Forces);
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    context.reinitialize();
    context.setPositions(positions);
    State state2 = context.getState(State::Forces);
    positions[1][0]+= boxSize;
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    context.reinitialize();
    context.setPositions(positions);
    State state3 = context.getState(State::Forces);
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    context.reinitialize();
    context.setPositions(positions);
    State state4 = context.getState(State::Forces);

    // All forces should be identical, exception state3 which should be zero.

    ASSERT_EQUAL_VEC(state1.getForces()[0], state2.getForces()[0], 0.01);
    ASSERT_EQUAL_VEC(state1.getForces()[1], state2.getForces()[1], 0.01);
    ASSERT_EQUAL_VEC(state1.getForces()[0], state4.getForces()[0], 0.01);
    ASSERT_EQUAL_VEC(state1.getForces()[1], state4.getForces()[1], 0.01);
    ASSERT_EQUAL_VEC(state3.getForces()[0], Vec3(0, 0, 0), 0.01);
    ASSERT_EQUAL_VEC(state3.getForces()[1], Vec3(0, 0, 0), 0.01);
}
*/

void testEnergyEthane() {

    ReferencePlatform platform;
    const int numParticles = 8;
    System system;
    LangevinIntegrator integrator(0, 0.1, 0.01);

    //void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k)
    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;
    }

    int VI = 1;
    if( VI ){
       (void) fprintf( stderr, "Applying GB/VI\n" );
       GBVIForce* forceField = new GBVIForce();
       for( int i = 0; i < numParticles; i++ ){
          system.addParticle(1.0);
          forceField->addParticle( H_charge, H_radius, H_gamma);
       }
       forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
       forceField->setParticleParameters(4, C_charge, C_radius, C_gamma);
       system.addForce(forceField);
    } else {
       (void) fprintf( stderr, "Applying GBSA OBC\n" );
       GBSAOBCForce* forceField = new GBSAOBCForce();
       double H_scale           =  0.85;
       double C_scale           =  0.72;
       for( int i = 0; i < numParticles; i++ ){
          system.addParticle(1.0);
          forceField->addParticle(H_charge, H_radius, H_scale );
       }
       forceField->setParticleParameters(1, C_charge, C_radius, C_scale);
       forceField->setParticleParameters(4, C_charge, C_radius, C_scale);
       system.addForce(forceField);
    }

    OpenMMContext context(system, integrator, platform);
    
/*    
    0.5480    1.7661    0.0000 H   0  0  0  0  0  0           0  0  0
    0.7286    0.8978    0.6468 C   0  0  0  0  0  0           0  0  0
    0.4974    0.0000    0.0588 H   0  0  0  0  0  0           0  0  0
    0.0000    0.9459    1.4666 H   0  0  0  0  0  0           0  0  0
    2.1421    0.8746    1.1615 C   0  0  0  0  0  0           0  0  0
    2.3239    0.0050    1.8065 H   0  0  0  0  0  0           0  0  0
    2.8705    0.8295    0.3416 H   0  0  0  0  0  0           0  0  0
    2.3722    1.7711    1.7518 H   0  0  0  0  0  0           0  0  0
*/

    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);
    (void) fprintf( stderr, "Energy %.4e\n", state.getPotentialEnergy() );
    
    // 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];
        (void) fprintf( stderr, "F %d [%14.6e %14.6e %14.6e]\n", i, f[0], f[1], f[2] );
        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);
    (void) fprintf( stderr, "Fsum [%14.6e %14.6e %14.6e] norm=%14.6e\n", forceSum[0], forceSum[1], forceSum[2], 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);

    (void) fprintf( stderr, "Energies %.8e %.8e\n", state.getPotentialEnergy(), state2.getPotentialEnergy() );

    // See whether the potential energy changed by the expected amount.
    
    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
}

void testEnergyTwoParticle() {

    ReferencePlatform platform;
    const int numParticles = 2;
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    LangevinIntegrator integrator(0, 0.1, 0.01);

    //void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k)
    double C_HBondDistance   = 3.0;
    HarmonicBondForce* bonds = new HarmonicBondForce();
    bonds->addBond(0, 1, C_HBondDistance, 0.0);
    system.addForce(bonds);

    double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
/*
    H_charge    = -1.0;
    C_charge    =  1.0;

    H_gamma     =  1.0;
    C_gamma     =  1.0;

    H_radius    =  1.0;
    C_radius    =  1.0;
*/ 
    H_charge    = -0.5;
    C_charge    =  0.5;

    H_gamma     =  0.5;
    C_gamma     =  0.5;

    H_radius    =  1.5;
    C_radius    =  1.5;
 
    int VI = 1;
    if( VI ){
       (void) fprintf( stderr, "Applying GB/VI\n" );
       GBVIForce* forceField = new GBVIForce();
       forceField->addParticle(H_charge, H_radius, H_gamma);
       forceField->addParticle(C_charge, C_radius, C_gamma);
       system.addForce(forceField);
    } else {
       (void) fprintf( stderr, "Applying GBSA OBC\n" );
       GBSAOBCForce* forceField = new GBSAOBCForce();
       forceField->addParticle(H_charge, H_radius, 1.0);
       forceField->addParticle(C_charge, C_radius, 1.0);
       system.addForce(forceField);
    }

    OpenMMContext context(system, integrator, platform);
    
    vector<Vec3> positions(numParticles);
    positions[0] = Vec3(         0.0000,    0.0000,    0.0000);
    positions[1] = Vec3(C_HBondDistance,    0.0000,    0.0000);
    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];
        (void) fprintf( stderr, "F %d [%14.6e %14.6e %14.6e]\n", i, f[0], f[1], f[2] );
        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);
    (void) fprintf( stderr, "Fsum [%14.6e %14.6e %14.6e] norm=%14.6e\n", forceSum[0], forceSum[1], forceSum[2], 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);

    double diff = fabs( norm - (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta );
    (void) fprintf( stderr, "Energies %14.6e %14.6e diff=%14.6e [%14.6e %14.6e]\n",
                    state.getPotentialEnergy(), state2.getPotentialEnergy(), diff, norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta );

    // 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();
        testCutoffAndPeriodic();
        testForce();
        testEnergyEthane();
        testEnergy1();
*/
//        testSingleParticle();
        testEnergyTwoParticle();
        testEnergyEthane();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}