TestReferenceNeighborList.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 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
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 * Software is furnished to do so, subject to the following conditions:       *
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 * The above copyright notice and this permission notice shall be included in *
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#include "openmm/internal/AssertionUtilities.h"
#include "ReferenceNeighborList.h"
#include "sfmt/SFMT.h"
#include <cassert>
#include <iostream>
#include <vector>

using namespace std;
using namespace OpenMM;

void testNeighborList()
{
    vector<RealVec> particleList(2);
    particleList[0] = RealVec(13.6, 0, 0);
    particleList[1] = RealVec(0, 0, 0);
    vector<set<int> > exclusions(2);
    
    NeighborList neighborList;

    RealVec boxVectors[3];
    computeNeighborListNaive(neighborList, 2, particleList, exclusions, boxVectors, false, 13.7, 0.01);
    assert(neighborList.size() == 1);
    
    computeNeighborListNaive(neighborList, 2, particleList, exclusions, boxVectors, false, 13.5, 0.01);
    assert(neighborList.size() == 0);
    
    computeNeighborListVoxelHash(neighborList, 2, particleList, exclusions, boxVectors, false, 13.7, 0.01);
    assert(neighborList.size() == 1);
    
    computeNeighborListVoxelHash(neighborList, 2, particleList, exclusions, boxVectors, false, 13.5, 0.01);
    assert(neighborList.size() == 0);
}

double periodicDifference(double val1, double val2, double period) {
    double diff = val1-val2;
    double base = floor(diff/period+0.5)*period;
    return diff-base;
}

double distance2(RealVec& pos1, RealVec& pos2, const RealVec& periodicBoxSize) {
    double dx = periodicDifference(pos1[0], pos2[0], periodicBoxSize[0]);
    double dy = periodicDifference(pos1[1], pos2[1], periodicBoxSize[1]);
    double dz = periodicDifference(pos1[2], pos2[2], periodicBoxSize[2]);
    return dx*dx+dy*dy+dz*dz;
}

void verifyNeighborList(NeighborList& list, int numParticles, vector<RealVec>& positions, const RealVec& periodicBoxSize, double cutoff) {
    for (int i = 0; i < (int) list.size(); i++) {
        int particle1 = list[i].first;
        int particle2 = list[i].second;
        ASSERT(distance2(positions[particle1], positions[particle2], periodicBoxSize) <= cutoff*cutoff);
    }
    int count = 0;
    for (int i = 0; i < numParticles; i++)
        for (int j = i+1; j < numParticles; j++)
            if (distance2(positions[i], positions[j], periodicBoxSize) <= cutoff*cutoff)
                count++;
    ASSERT_EQUAL(count, list.size());
}

void testPeriodic() {
    const int numParticles = 100;
    const double cutoff = 3.0;
    const RealVec periodicBoxSize(20.0, 15.0, 22.0);
    RealVec periodicBoxVectors[3];
    periodicBoxVectors[0] = RealVec(20, 0, 0);
    periodicBoxVectors[1] = RealVec(0, 15, 0);
    periodicBoxVectors[2] = RealVec(0, 0, 22);
    vector<RealVec> particleList(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);

    for (int i = 0; i <numParticles; i++) {
        particleList[i][0] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxSize[0]*3);
        particleList[i][1] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxSize[1]*3);
        particleList[i][2] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxSize[2]*3);
    }
    vector<set<int> > exclusions(numParticles);
    NeighborList neighborList;
    computeNeighborListNaive(neighborList, numParticles, particleList, exclusions, periodicBoxVectors, true, cutoff);
    verifyNeighborList(neighborList, numParticles, particleList, periodicBoxSize, cutoff);
    computeNeighborListVoxelHash(neighborList, numParticles, particleList, exclusions, periodicBoxVectors, true, cutoff);
    verifyNeighborList(neighborList, numParticles, particleList, periodicBoxSize, cutoff);
}

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