TestReferenceGBSAOBCForceField.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.               *
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 * Portions copyright (c) 2008 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
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/**
 * This tests the reference implementation of GBSAOBCForceField.
 */

#include "../../../tests/AssertionUtilities.h"
#include "OpenMMContext.h"
#include "ReferencePlatform.h"
#include "GBSAOBCForceField.h"
#include "System.h"
#include "LangevinIntegrator.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 testSingleAtom() {
    ReferencePlatform platform;
    System system(1, 0);
    system.setAtomMass(0, 2.0);
    LangevinIntegrator integrator(0, 0.1, 0.01);
    GBSAOBCForceField* forceField = new GBSAOBCForceField(1);
    forceField->setAtomParameters(0, 0.5, 1.5, 1);
    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 = 1.5-0.09; // dielectric offset
    double eps0 = EPSILON0*A2NM*CAL2JOULE;
    double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
    double extendedRadius = bornRadius+1.4; // probe radius
    double nonpolarEnergy = PI_M*0.0216*extendedRadius*extendedRadius*std::pow(1.5/bornRadius, 6.0); // Where did this formula come from?  Just copied it from CpuImplicitSolvent.cpp
    ASSERT_EQUAL_TOL(bornEnergy+nonpolarEnergy, state.getPotentialEnergy(), 0.01);
}

void testForce() {
    ReferencePlatform platform;
    const int numAtoms = 10;
    System system(numAtoms, 0);
    LangevinIntegrator integrator(0, 0.1, 0.01);
    GBSAOBCForceField* forceField = new GBSAOBCForceField(numAtoms);
    for (int i = 0; i < numAtoms; ++i)
        forceField->setAtomParameters(i, i%2 == 0 ? -1 : 1, 1.5, 1);
    system.addForce(forceField);
    OpenMMContext context(system, integrator, platform);
    
    // Set random positions for all the atoms.
    
    vector<Vec3> positions(numAtoms);
    init_gen_rand(0);
    for (int i = 0; i < numAtoms; ++i)
        positions[i] = Vec3(5.0*genrand_real2(), 5.0*genrand_real2(), 5.0*genrand_real2());
    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;
    for (int i = 0; i < numAtoms; ++i) {
        Vec3 f = state.getForces()[i];
        norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
    }
    norm = std::sqrt(norm);
    const double delta = 1e-3;
    double step = delta/norm;
    for (int i = 0; i < numAtoms; ++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);
    
    // See whether the potential energy changed by the expected amount.
    
    State state2 = context.getState(State::Energy);
    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
}

int main() {
    try {
        testSingleAtom();
        testForce();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}