/* -------------------------------------------------------------------------- *
 *                                   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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 * copy of this software and associated documentation files (the "Software"), *
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/**
 * This tests the createExceptionsFromBonds() method of NonbondedForce, which identifies pairs of atoms
 * whose nonbonded atoms are either excluded or decreased.  The test system is a chain with branches:
 * 
 * 1  3  5  7  9  11  13  15  17  19
 * |  |  |  |  |  |   |   |   |   |
 * 0--2--4--6--8--10--12--14--16--18
 */

#include "AssertionUtilities.h"
#include "openmm/NonbondedForce.h"
#include <iostream>
#include <set>
#include <vector>

using namespace OpenMM;
using namespace std;

static const int NUM_ATOMS = 20;

/**
 * Add a pair of atoms to the list of exclusions.
 */

void addAtomsToExclusions(int atom1, int atom2, vector<set<int> >& exclusions, int& totalExclusions) {
    if (atom2 < NUM_ATOMS) {
        exclusions[atom1].insert(atom2);
        exclusions[atom2].insert(atom1);
        totalExclusions++;
    }
}

int main() {
    try {
        NonbondedForce nonbonded;
        vector<pair<int, int> > bonds;
        for (int i = 0; i < NUM_ATOMS; i++)
            nonbonded.addParticle(1.0, 1.0, 2.0);
        // loop over all main-chain atoms (even numbered atoms)
        for (int i = 0; i < NUM_ATOMS-1; i += 2) 
        {
            // side-chain bonds
            bonds.push_back(pair<int, int>(i, i+1));
            // main-chain bonds
            if (i < NUM_ATOMS-2) // penultimate atom (NUM_ATOMS-2) has no subsequent main-chain atom
                bonds.push_back(pair<int, int>(i, i+2));
        }
        nonbonded.createExceptionsFromBonds(bonds, 0.2, 0.4);

        // Build lists of the expected exclusions and 1-4s.

        vector<set<int> > expectedExclusions(NUM_ATOMS);
        int totalExclusions = 0;
        for (int i = 0; i < NUM_ATOMS; i += 2) {
            addAtomsToExclusions(i, i+1, expectedExclusions, totalExclusions);
            addAtomsToExclusions(i, i+2, expectedExclusions, totalExclusions);
            addAtomsToExclusions(i, i+3, expectedExclusions, totalExclusions);
            addAtomsToExclusions(i, i+4, expectedExclusions, totalExclusions);
            addAtomsToExclusions(i+1, i+2, expectedExclusions, totalExclusions);
        }
        vector<set<int> > expected14(NUM_ATOMS);
        int total14 = 0;
        for (int i = 0; i < NUM_ATOMS; i += 2) {
            addAtomsToExclusions(i, i+5, expected14, total14);
            addAtomsToExclusions(i, i+6, expected14, total14);
            addAtomsToExclusions(i+1, i+3, expected14, total14);
            addAtomsToExclusions(i+1, i+4, expected14, total14);
        }

        // Compare them to the exceptions that were generated.

        ASSERT_EQUAL(totalExclusions+total14, nonbonded.getNumExceptions());
        for (int i = 0; i < nonbonded.getNumExceptions(); i++) {
            int particle1, particle2;
            double chargeProd, sigma, epsilon;
            nonbonded.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
            if (chargeProd == 0) {
                // This is an exclusion.

                ASSERT_EQUAL(0.0, epsilon);
                ASSERT(expectedExclusions[particle1].find(particle2) != expectedExclusions[particle1].end());
            }
            else {
                // This is a 1-4.

                ASSERT_EQUAL_TOL(0.2, chargeProd, 1e-10);
                ASSERT_EQUAL_TOL(1.0, sigma, 1e-10);
                ASSERT_EQUAL_TOL(0.8, epsilon, 1e-10);
                ASSERT(expected14[particle1].find(particle2) != expected14[particle1].end());
            }
        }
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}
