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https://github.com/openmm/openmm
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05472c9a81
* Replace SimTK-containing file headers * Update file headers for new Tinker reader files added
232 lines
9.3 KiB
C++
232 lines
9.3 KiB
C++
/* -------------------------------------------------------------------------- *
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* OpenMM *
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* -------------------------------------------------------------------------- *
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* This is part of the OpenMM molecular simulation toolkit. *
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* See https://openmm.org/development. *
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* *
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* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
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* Authors: Peter Eastman *
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* Contributors: *
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* *
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* Permission is hereby granted, free of charge, to any person obtaining a *
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* copy of this software and associated documentation files (the "Software"), *
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* to deal in the Software without restriction, including without limitation *
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* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
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* and/or sell copies of the Software, and to permit persons to whom the *
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* Software is furnished to do so, subject to the following conditions: *
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* *
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* The above copyright notice and this permission notice shall be included in *
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* all copies or substantial portions of the Software. *
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* *
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
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* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
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* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
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* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
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* USE OR OTHER DEALINGS IN THE SOFTWARE. *
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* -------------------------------------------------------------------------- */
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#include "openmm/internal/AssertionUtilities.h"
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#include "openmm/CustomNonbondedForce.h"
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#include "openmm/NonbondedForce.h"
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#include "openmm/OpenMMException.h"
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#include <iostream>
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#include <set>
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#include <vector>
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using namespace OpenMM;
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using namespace std;
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static const int NUM_ATOMS = 20;
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/**
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* Add a pair of atoms to the list of exclusions.
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*/
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void addAtomsToExclusions(int atom1, int atom2, vector<set<int> >& exclusions, int& totalExclusions) {
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if (atom2 < NUM_ATOMS) {
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exclusions[atom1].insert(atom2);
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exclusions[atom2].insert(atom1);
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totalExclusions++;
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}
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}
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/**
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* This tests the createExceptionsFromBonds() method of NonbondedForce, which identifies pairs of atoms
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* whose nonbonded atoms are either excluded or decreased. The test system is a chain with branches:
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*
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* 1 3 5 7 9 11 13 15 17 19
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* | | | | | | | | | |
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* 0--2--4--6--8--10--12--14--16--18
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*/
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void testFindExceptions() {
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NonbondedForce nonbonded;
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vector<pair<int, int> > bonds;
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for (int i = 0; i < NUM_ATOMS; i++)
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nonbonded.addParticle(1.0, 1.0, 2.0);
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// loop over all main-chain atoms (even numbered atoms)
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for (int i = 0; i < NUM_ATOMS-1; i += 2)
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{
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// side-chain bonds
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bonds.push_back(pair<int, int>(i, i+1));
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// main-chain bonds
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if (i < NUM_ATOMS-2) // penultimate atom (NUM_ATOMS-2) has no subsequent main-chain atom
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bonds.push_back(pair<int, int>(i, i+2));
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}
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nonbonded.createExceptionsFromBonds(bonds, 0.2, 0.4);
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// Build lists of the expected exclusions and 1-4s.
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vector<set<int> > expectedExclusions(NUM_ATOMS);
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int totalExclusions = 0;
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for (int i = 0; i < NUM_ATOMS; i += 2) {
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addAtomsToExclusions(i, i+1, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i, i+2, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i, i+3, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i, i+4, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i+1, i+2, expectedExclusions, totalExclusions);
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}
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vector<set<int> > expected14(NUM_ATOMS);
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int total14 = 0;
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for (int i = 0; i < NUM_ATOMS; i += 2) {
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addAtomsToExclusions(i, i+5, expected14, total14);
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addAtomsToExclusions(i, i+6, expected14, total14);
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addAtomsToExclusions(i+1, i+3, expected14, total14);
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addAtomsToExclusions(i+1, i+4, expected14, total14);
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}
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// Compare them to the exceptions that were generated.
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ASSERT_EQUAL(totalExclusions+total14, nonbonded.getNumExceptions());
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for (int i = 0; i < nonbonded.getNumExceptions(); i++) {
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int particle1, particle2;
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double chargeProd, sigma, epsilon;
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nonbonded.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
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if (chargeProd == 0) {
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// This is an exclusion.
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ASSERT_EQUAL(0.0, epsilon);
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ASSERT(expectedExclusions[particle1].find(particle2) != expectedExclusions[particle1].end());
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}
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else {
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// This is a 1-4.
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ASSERT_EQUAL_TOL(0.2, chargeProd, 1e-10);
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ASSERT_EQUAL_TOL(1.0, sigma, 1e-10);
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ASSERT_EQUAL_TOL(0.8, epsilon, 1e-10);
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ASSERT(expected14[particle1].find(particle2) != expected14[particle1].end());
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}
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}
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}
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/**
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* Test replacing existing exclusions.
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*/
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void testReplaceExceptions() {
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NonbondedForce nonbonded;
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for (int i = 0; i < 10; i++)
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nonbonded.addParticle(1.0, 1.0, 0.0);
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nonbonded.addException(0, 1, 1.0, 0.0, 0.0);
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nonbonded.addException(0, 2, 2.0, 0.0, 0.0);
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nonbonded.addException(0, 3, 3.0, 0.0, 0.0);
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try {
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nonbonded.addException(0, 3, 4.0, 0.0, 0.0);
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throw std::exception();
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}
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catch (const OpenMMException ex) {
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// This should have thrown an exception.
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}
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int p1, p2;
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double charge, sigma, epsilon;
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nonbonded.getExceptionParameters(2, p1, p2, charge, sigma, epsilon);
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ASSERT(p1 == 0);
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ASSERT(p2 == 3);
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ASSERT(charge == 3.0);
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ASSERT(nonbonded.addException(0, 3, 4.0, 0.0, 0.0, true) == 2);
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nonbonded.getExceptionParameters(2, p1, p2, charge, sigma, epsilon);
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ASSERT(p1 == 0);
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ASSERT(p2 == 3);
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ASSERT(charge == 4.0);
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ASSERT(nonbonded.addException(1, 3, 4.0, 0.0, 0.0) == 3);
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try {
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nonbonded.addException(3, 0, 5.0, 0.0, 0.0);
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throw std::exception();
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}
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catch (const OpenMMException ex) {
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// This should have thrown an exception.
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}
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ASSERT(nonbonded.addException(3, 0, 5.0, 0.0, 0.0, true) == 2);
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nonbonded.getExceptionParameters(2, p1, p2, charge, sigma, epsilon);
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ASSERT(p1 == 3);
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ASSERT(p2 == 0);
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ASSERT(charge == 5.0);
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}
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/**
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* This is the same as testFindExceptions(), except it tests adding exclusions to a CustomNonbondedForce.
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*/
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void testFindCustomExclusions() {
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CustomNonbondedForce nonbonded("r");
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vector<pair<int, int> > bonds;
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vector<double> params;
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for (int i = 0; i < NUM_ATOMS; i++)
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nonbonded.addParticle(params);
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// loop over all main-chain atoms (even numbered atoms)
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for (int i = 0; i < NUM_ATOMS-1; i += 2)
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{
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// side-chain bonds
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bonds.push_back(pair<int, int>(i, i+1));
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// main-chain bonds
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if (i < NUM_ATOMS-2) // penultimate atom (NUM_ATOMS-2) has no subsequent main-chain atom
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bonds.push_back(pair<int, int>(i, i+2));
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}
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nonbonded.createExclusionsFromBonds(bonds, 3);
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// Build lists of the expected exclusions.
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vector<set<int> > expectedExclusions(NUM_ATOMS);
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int totalExclusions = 0;
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for (int i = 0; i < NUM_ATOMS; i += 2) {
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addAtomsToExclusions(i, i+1, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i, i+2, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i, i+3, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i, i+4, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i+1, i+2, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i, i+5, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i, i+6, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i+1, i+3, expectedExclusions, totalExclusions);
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addAtomsToExclusions(i+1, i+4, expectedExclusions, totalExclusions);
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}
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for (int i = 0; i < nonbonded.getNumExclusions(); i++) {
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int particle1, particle2;
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nonbonded.getExclusionParticles(i, particle1, particle2);
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}
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// Compare them to the exceptions that were generated.
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ASSERT_EQUAL(totalExclusions, nonbonded.getNumExclusions());
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for (int i = 0; i < nonbonded.getNumExclusions(); i++) {
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int particle1, particle2;
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nonbonded.getExclusionParticles(i, particle1, particle2);
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ASSERT(expectedExclusions[particle1].find(particle2) != expectedExclusions[particle1].end());
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}
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}
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int main() {
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try {
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testFindExceptions();
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testReplaceExceptions();
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testFindCustomExclusions();
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}
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catch(const exception& e) {
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cout << "exception: " << e.what() << endl;
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return 1;
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}
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cout << "Done" << endl;
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return 0;
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}
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