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Commit 6bde69d9 authored by Andy Simmonett's avatar Andy Simmonett
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Merge branch 'master' of github.com:pandegroup/openmm into genpt

parents e6dbc863 ec799972
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platforms/cpu/tests/TestCpuNonbondedForce.cpp
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......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,684 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests all the different force terms in the CUDA implementation of NonbondedForce.
*/
#include "CpuTests.h"
#include "TestNonbondedForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CpuPlatform.h"
#include "ReferencePlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/internal/ContextImpl.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CpuPlatform platform;
const double TOL = 1e-5;
void testCoulomb() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(0.5, 1, 0);
forceField->addParticle(-1.5, 1, 0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double force = ONE_4PI_EPS0*(-0.75)/4.0;
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(-0.75)/2.0, state.getPotentialEnergy(), TOL);
}
void testLJ() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(0, 1.2, 1);
forceField->addParticle(0, 1.4, 2);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double x = 1.3/2.0;
double eps = SQRT_TWO;
double force = 4.0*eps*(12*std::pow(x, 12.0)-6*std::pow(x, 6.0))/2.0;
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(4.0*eps*(std::pow(x, 12.0)-std::pow(x, 6.0)), state.getPotentialEnergy(), TOL);
}
void testExclusionsAnd14() {
System system;
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < 5; ++i) {
system.addParticle(1.0);
nonbonded->addParticle(0, 1.5, 0);
}
vector<pair<int, int> > bonds;
bonds.push_back(pair<int, int>(0, 1));
bonds.push_back(pair<int, int>(1, 2));
bonds.push_back(pair<int, int>(2, 3));
bonds.push_back(pair<int, int>(3, 4));
nonbonded->createExceptionsFromBonds(bonds, 0.0, 0.0);
int first14, second14;
for (int i = 0; i < nonbonded->getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
nonbonded->getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
if ((particle1 == 0 && particle2 == 3) || (particle1 == 3 && particle2 == 0))
first14 = i;
if ((particle1 == 1 && particle2 == 4) || (particle1 == 4 && particle2 == 1))
second14 = i;
}
system.addForce(nonbonded);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
for (int i = 1; i < 5; ++i) {
// Test LJ forces
vector<Vec3> positions(5);
const double r = 1.0;
for (int j = 0; j < 5; ++j) {
nonbonded->setParticleParameters(j, 0, 1.5, 0);
positions[j] = Vec3(0, j, 0);
}
nonbonded->setParticleParameters(0, 0, 1.5, 1);
nonbonded->setParticleParameters(i, 0, 1.5, 1);
nonbonded->setExceptionParameters(first14, 0, 3, 0, 1.5, i == 3 ? 0.5 : 0.0);
nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0.0);
positions[i] = Vec3(r, 0, 0);
context.reinitialize();
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double x = 1.5/r;
double eps = 1.0;
double force = 4.0*eps*(12*std::pow(x, 12.0)-6*std::pow(x, 6.0))/r;
double energy = 4.0*eps*(std::pow(x, 12.0)-std::pow(x, 6.0));
if (i == 3) {
force *= 0.5;
energy *= 0.5;
}
if (i < 3) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
// Test Coulomb forces
nonbonded->setParticleParameters(0, 2, 1.5, 0);
nonbonded->setParticleParameters(i, 2, 1.5, 0);
nonbonded->setExceptionParameters(first14, 0, 3, i == 3 ? 4/1.2 : 0, 1.5, 0);
nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0);
context.reinitialize();
context.setPositions(positions);
state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces2 = state.getForces();
force = ONE_4PI_EPS0*4/(r*r);
energy = ONE_4PI_EPS0*4/r;
if (i == 3) {
force /= 1.2;
energy /= 1.2;
}
if (i < 3) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces2[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces2[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
}
void testCutoff() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(1.0, 1, 0);
forceField->addParticle(1.0, 1, 0);
forceField->addParticle(1.0, 1, 0);
forceField->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
const double cutoff = 2.9;
forceField->setCutoffDistance(cutoff);
const double eps = 50.0;
forceField->setReactionFieldDielectric(eps);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2, 0);
positions[2] = Vec3(0, 3, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
const double force1 = ONE_4PI_EPS0*(1.0)*(0.25-2.0*krf*2.0);
const double force2 = ONE_4PI_EPS0*(1.0)*(1.0-2.0*krf*1.0);
ASSERT_EQUAL_VEC(Vec3(0, -force1, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, force1-force2, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, force2, 0), forces[2], TOL);
const double energy1 = ONE_4PI_EPS0*(1.0)*(0.5+krf*4.0-crf);
const double energy2 = ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf);
ASSERT_EQUAL_TOL(energy1+energy2, state.getPotentialEnergy(), TOL);
}
void testCutoff14() {
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
for (int i = 0; i < 5; ++i) {
system.addParticle(1.0);
nonbonded->addParticle(0, 1.5, 0);
}
const double cutoff = 3.5;
nonbonded->setCutoffDistance(cutoff);
const double eps = 30.0;
nonbonded->setReactionFieldDielectric(eps);
vector<pair<int, int> > bonds;
bonds.push_back(pair<int, int>(0, 1));
bonds.push_back(pair<int, int>(1, 2));
bonds.push_back(pair<int, int>(2, 3));
bonds.push_back(pair<int, int>(3, 4));
nonbonded->createExceptionsFromBonds(bonds, 0.0, 0.0);
int first14, second14;
for (int i = 0; i < nonbonded->getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
nonbonded->getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
if ((particle1 == 0 && particle2 == 3) || (particle1 == 3 && particle2 == 0))
first14 = i;
if ((particle1 == 1 && particle2 == 4) || (particle1 == 4 && particle2 == 1))
second14 = i;
}
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(5);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
positions[2] = Vec3(2, 0, 0);
positions[3] = Vec3(3, 0, 0);
positions[4] = Vec3(4, 0, 0);
for (int i = 1; i < 5; ++i) {
// Test LJ forces
nonbonded->setParticleParameters(0, 0, 1.5, 1);
for (int j = 1; j < 5; ++j)
nonbonded->setParticleParameters(j, 0, 1.5, 0);
nonbonded->setParticleParameters(i, 0, 1.5, 1);
nonbonded->setExceptionParameters(first14, 0, 3, 0, 1.5, i == 3 ? 0.5 : 0.0);
nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0.0);
context.reinitialize();
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double r = positions[i][0];
double x = 1.5/r;
double e = 1.0;
double force = 4.0*e*(12*std::pow(x, 12.0)-6*std::pow(x, 6.0))/r;
double energy = 4.0*e*(std::pow(x, 12.0)-std::pow(x, 6.0));
if (i == 3) {
force *= 0.5;
energy *= 0.5;
}
if (i < 3 || r > cutoff) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
// Test Coulomb forces
const double q = 0.7;
nonbonded->setParticleParameters(0, q, 1.5, 0);
nonbonded->setParticleParameters(i, q, 1.5, 0);
nonbonded->setExceptionParameters(first14, 0, 3, i == 3 ? q*q/1.2 : 0, 1.5, 0);
nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0);
context.reinitialize();
context.setPositions(positions);
state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces2 = state.getForces();
force = ONE_4PI_EPS0*q*q/(r*r);
energy = ONE_4PI_EPS0*q*q/r;
if (i == 3) {
force /= 1.2;
energy /= 1.2;
}
if (i < 3 || r > cutoff) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces2[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces2[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
}
void testPeriodic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addException(0, 1, 0.0, 1.0, 0.0);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
const double cutoff = 2.0;
nonbonded->setCutoffDistance(cutoff);
system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
positions[2] = Vec3(3, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
const double eps = 78.3;
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
const double force = ONE_4PI_EPS0*(1.0)*(1.0-2.0*krf*1.0);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(2*ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf), state.getPotentialEnergy(), TOL);
}
void testTriclinic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
Vec3 a(3.1, 0, 0);
Vec3 b(0.4, 3.5, 0);
Vec3 c(-0.1, -0.5, 4.0);
system.setDefaultPeriodicBoxVectors(a, b, c);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(1.0, 1, 0);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
const double cutoff = 1.5;
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
const double eps = 78.3;
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
for (int iteration = 0; iteration < 50; iteration++) {
// Generate random positions for the two particles.
positions[0] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
positions[1] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
context.setPositions(positions);
// Loop over all possible periodic copies and find the nearest one.
Vec3 delta;
double distance2 = 100.0;
for (int i = -1; i < 2; i++)
for (int j = -1; j < 2; j++)
for (int k = -1; k < 2; k++) {
Vec3 d = positions[1]-positions[0]+a*i+b*j+c*k;
if (d.dot(d) < distance2) {
delta = d;
distance2 = d.dot(d);
}
}
double distance = sqrt(distance2);
// See if the force and energy are correct.
State state = context.getState(State::Forces | State::Energy);
if (distance >= cutoff) {
ASSERT_EQUAL(0.0, state.getPotentialEnergy());
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[0], 0);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[1], 0);
}
else {
const Vec3 force = delta*ONE_4PI_EPS0*(-1.0/(distance*distance*distance)+2.0*krf);
ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(1.0/distance+krf*distance*distance-crf), state.getPotentialEnergy(), 1e-4);
ASSERT_EQUAL_VEC(force, state.getForces()[0], 2e-5);
ASSERT_EQUAL_VEC(-force, state.getForces()[1], 2e-5);
}
}
}
void testLargeSystem() {
const int numMolecules = 600;
const int numParticles = numMolecules*2;
const double cutoff = 2.0;
const double boxSize = 20.0;
const double tol = 2e-3;
ReferencePlatform reference;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
NonbondedForce* nonbonded = new NonbondedForce();
HarmonicBondForce* bonds = new HarmonicBondForce();
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
nonbonded->addParticle(-1.0, 0.2, 0.1);
nonbonded->addParticle(1.0, 0.1, 0.1);
}
else {
nonbonded->addParticle(-1.0, 0.2, 0.2);
nonbonded->addParticle(1.0, 0.1, 0.2);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
bonds->addBond(2*i, 2*i+1, 1.0, 0.1);
nonbonded->addException(2*i, 2*i+1, 0.0, 0.15, 0.0);
}
// Try with cutoffs but not periodic boundary conditions, and make sure the cl and Reference
// platforms agree.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
system.addForce(bonds);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context cpuContext(system, integrator1, platform);
Context referenceContext(system, integrator2, reference);
cpuContext.setPositions(positions);
cpuContext.setVelocities(velocities);
referenceContext.setPositions(positions);
referenceContext.setVelocities(velocities);
State cpuState = cpuContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(cpuState.getPositions()[i], referenceState.getPositions()[i], tol);
ASSERT_EQUAL_VEC(cpuState.getVelocities()[i], referenceState.getVelocities()[i], tol);
ASSERT_EQUAL_VEC(cpuState.getForces()[i], referenceState.getForces()[i], tol);
}
ASSERT_EQUAL_TOL(cpuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
// Now do the same thing with periodic boundary conditions.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
cpuContext.reinitialize();
referenceContext.reinitialize();
cpuContext.setPositions(positions);
cpuContext.setVelocities(velocities);
referenceContext.setPositions(positions);
referenceContext.setVelocities(velocities);
cpuState = cpuContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
referenceState = referenceContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++) {
double dx = cpuState.getPositions()[i][0]-referenceState.getPositions()[i][0];
double dy = cpuState.getPositions()[i][1]-referenceState.getPositions()[i][1];
double dz = cpuState.getPositions()[i][2]-referenceState.getPositions()[i][2];
ASSERT_EQUAL_TOL(fmod(cpuState.getPositions()[i][0]-referenceState.getPositions()[i][0], boxSize), 0, tol);
ASSERT_EQUAL_TOL(fmod(cpuState.getPositions()[i][1]-referenceState.getPositions()[i][1], boxSize), 0, tol);
ASSERT_EQUAL_TOL(fmod(cpuState.getPositions()[i][2]-referenceState.getPositions()[i][2], boxSize), 0, tol);
ASSERT_EQUAL_VEC(cpuState.getVelocities()[i], referenceState.getVelocities()[i], tol);
ASSERT_EQUAL_VEC(cpuState.getForces()[i], referenceState.getForces()[i], tol);
}
ASSERT_EQUAL_TOL(cpuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
}
void testDispersionCorrection() {
// Create a box full of identical particles.
int gridSize = 5;
int numParticles = gridSize*gridSize*gridSize;
double boxSize = gridSize*0.7;
double cutoff = boxSize/3;
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
vector<Vec3> positions(numParticles);
int index = 0;
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
system.addParticle(1.0);
nonbonded->addParticle(0, 1.1, 0.5);
positions[index] = Vec3(i*boxSize/gridSize, j*boxSize/gridSize, k*boxSize/gridSize);
index++;
}
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
nonbonded->setCutoffDistance(cutoff);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(nonbonded);
// See if the correction has the correct value.
Context context(system, integrator, platform);
context.setPositions(positions);
double energy1 = context.getState(State::Energy).getPotentialEnergy();
nonbonded->setUseDispersionCorrection(false);
context.reinitialize();
context.setPositions(positions);
double energy2 = context.getState(State::Energy).getPotentialEnergy();
double term1 = (0.5*pow(1.1, 12)/pow(cutoff, 9))/9;
double term2 = (0.5*pow(1.1, 6)/pow(cutoff, 3))/3;
double expected = 8*M_PI*numParticles*numParticles*(term1-term2)/(boxSize*boxSize*boxSize);
ASSERT_EQUAL_TOL(expected, energy1-energy2, 1e-4);
// Now modify half the particles to be different, and see if it is still correct.
int numType2 = 0;
for (int i = 0; i < numParticles; i += 2) {
nonbonded->setParticleParameters(i, 0, 1, 1);
numType2++;
}
int numType1 = numParticles-numType2;
nonbonded->updateParametersInContext(context);
energy2 = context.getState(State::Energy).getPotentialEnergy();
nonbonded->setUseDispersionCorrection(true);
context.reinitialize();
context.setPositions(positions);
energy1 = context.getState(State::Energy).getPotentialEnergy();
term1 = ((numType1*(numType1+1))/2)*(0.5*pow(1.1, 12)/pow(cutoff, 9))/9;
term2 = ((numType1*(numType1+1))/2)*(0.5*pow(1.1, 6)/pow(cutoff, 3))/3;
term1 += ((numType2*(numType2+1))/2)*(1*pow(1.0, 12)/pow(cutoff, 9))/9;
term2 += ((numType2*(numType2+1))/2)*(1*pow(1.0, 6)/pow(cutoff, 3))/3;
double combinedSigma = 0.5*(1+1.1);
double combinedEpsilon = sqrt(1*0.5);
term1 += (numType1*numType2)*(combinedEpsilon*pow(combinedSigma, 12)/pow(cutoff, 9))/9;
term2 += (numType1*numType2)*(combinedEpsilon*pow(combinedSigma, 6)/pow(cutoff, 3))/3;
term1 /= (numParticles*(numParticles+1))/2;
term2 /= (numParticles*(numParticles+1))/2;
expected = 8*M_PI*numParticles*numParticles*(term1-term2)/(boxSize*boxSize*boxSize);
ASSERT_EQUAL_TOL(expected, energy1-energy2, 1e-4);
}
void testChangingParameters() {
const int numMolecules = 600;
const int numParticles = numMolecules*2;
const double cutoff = 2.0;
const double boxSize = 20.0;
const double tol = 2e-3;
ReferencePlatform reference;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
NonbondedForce* nonbonded = new NonbondedForce();
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
nonbonded->addParticle(-1.0, 0.2, 0.1);
nonbonded->addParticle(1.0, 0.1, 0.1);
}
else {
nonbonded->addParticle(-1.0, 0.2, 0.2);
nonbonded->addParticle(1.0, 0.1, 0.2);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
system.addConstraint(2*i, 2*i+1, 1.0);
nonbonded->addException(2*i, 2*i+1, 0.0, 0.15, 0.0);
}
nonbonded->setNonbondedMethod(NonbondedForce::PME);
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
// See if Reference and CPU give the same forces and energies.
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context cpuContext(system, integrator1, platform);
Context referenceContext(system, integrator2, reference);
cpuContext.setPositions(positions);
referenceContext.setPositions(positions);
State cpuState = cpuContext.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(cpuState.getForces()[i], referenceState.getForces()[i], tol);
ASSERT_EQUAL_TOL(cpuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
// Now modify parameters and see if they still agree.
for (int i = 0; i < numParticles; i += 5) {
double charge, sigma, epsilon;
nonbonded->getParticleParameters(i, charge, sigma, epsilon);
nonbonded->setParticleParameters(i, 1.5*charge, 1.1*sigma, 1.7*epsilon);
}
nonbonded->updateParametersInContext(cpuContext);
nonbonded->updateParametersInContext(referenceContext);
cpuState = cpuContext.getState(State::Forces | State::Energy);
referenceState = referenceContext.getState(State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(cpuState.getForces()[i], referenceState.getForces()[i], tol);
ASSERT_EQUAL_TOL(cpuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
}
void testSwitchingFunction(NonbondedForce::NonbondedMethod method) {
System system;
system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(0, 1.2, 1);
nonbonded->addParticle(0, 1.4, 2);
nonbonded->setNonbondedMethod(method);
nonbonded->setCutoffDistance(2.0);
nonbonded->setUseSwitchingFunction(true);
nonbonded->setSwitchingDistance(1.5);
nonbonded->setUseDispersionCorrection(false);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
double eps = SQRT_TWO;
// Compute the interaction at various distances.
for (double r = 1.0; r < 2.5; r += 0.1) {
positions[1] = Vec3(r, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// See if the energy is correct.
double x = 1.3/r;
double expectedEnergy = 4.0*eps*(std::pow(x, 12.0)-std::pow(x, 6.0));
double switchValue;
if (r <= 1.5)
switchValue = 1;
else if (r >= 2.0)
switchValue = 0;
else {
double t = (r-1.5)/0.5;
switchValue = 1+t*t*t*(-10+t*(15-t*6));
}
ASSERT_EQUAL_TOL(switchValue*expectedEnergy, state.getPotentialEnergy(), TOL);
// See if the force is the gradient of the energy.
double delta = 1e-3;
positions[1] = Vec3(r-delta, 0, 0);
context.setPositions(positions);
double e1 = context.getState(State::Energy).getPotentialEnergy();
positions[1] = Vec3(r+delta, 0, 0);
context.setPositions(positions);
double e2 = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL((e2-e1)/(2*delta), state.getForces()[0][0], 1e-3);
}
}
int main(int argc, char* argv[]) {
try {
if (!CpuPlatform::isProcessorSupported()) {
cout << "CPU is not supported. Exiting." << endl;
return 0;
}
testCoulomb();
testLJ();
testExclusionsAnd14();
testCutoff();
testCutoff14();
testPeriodic();
testTriclinic();
testLargeSystem();
testDispersionCorrection();
testChangingParameters();
testSwitchingFunction(NonbondedForce::CutoffNonPeriodic);
testSwitchingFunction(NonbondedForce::PME);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cpu/tests/TestCpuPeriodicTorsionForce.cpp
View file @ 6bde69d9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,69 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CPU implementation of PeriodicTorsionForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CpuPlatform.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CpuPlatform platform;
const double TOL = 1e-5;
void testPeriodicTorsions() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
PeriodicTorsionForce* forceField = new PeriodicTorsionForce();
forceField->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 2);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
double torque = -2*1.1*std::sin(2*PI_M/3);
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, 0), forces[3], TOL);
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
ASSERT_EQUAL_TOL(1.1*(1+std::cos(2*PI_M/3)), state.getPotentialEnergy(), TOL);
}
// Try changing the torsion parameters and make sure it's still correct.
forceField->setTorsionParameters(0, 0, 1, 2, 3, 3, PI_M/3.2, 1.3);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
double dtheta = (3*PI_M/2)-(PI_M/3.2);
double torque = -3*1.3*std::sin(dtheta);
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, 0), forces[3], TOL);
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
ASSERT_EQUAL_TOL(1.3*(1+std::cos(dtheta)), state.getPotentialEnergy(), TOL);
}
}
#include "CpuTests.h"
#include "TestPeriodicTorsionForce.h"
void testParallelComputation() {
System system;
......@@ -119,15 +58,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
testPeriodicTorsions();
void runPlatformTests() {
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cpu/tests/TestCpuRBTorsionForce.cpp
View file @ 6bde69d9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,88 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of RBTorsionForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CpuPlatform.h"
#include "openmm/RBTorsionForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CpuPlatform platform;
const double TOL = 1e-5;
void testRBTorsions() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
RBTorsionForce* forceField = new RBTorsionForce();
forceField->addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 1, 1);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
double psi = 0.25*PI_M - PI_M;
double torque = 0.0;
for (int i = 1; i < 6; ++i) {
double c = 0.1*(i+1);
torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
}
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, -0.5*torque), forces[3], TOL);
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
double energy = 0.0;
for (int i = 0; i < 6; ++i) {
double c = 0.1*(i+1);
energy += c*std::pow(std::cos(psi), i);
}
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
// Try changing the torsion parameters and make sure it's still correct.
forceField->setTorsionParameters(0, 0, 1, 2, 3, 0.11, 0.22, 0.33, 0.44, 0.55, 0.66);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
double psi = 0.25*PI_M - PI_M;
double torque = 0.0;
for (int i = 1; i < 6; ++i) {
double c = 0.11*(i+1);
torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
}
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, -0.5*torque), forces[3], TOL);
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
double energy = 0.0;
for (int i = 0; i < 6; ++i) {
double c = 0.11*(i+1);
energy += c*std::pow(std::cos(psi), i);
}
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
}
#include "CpuTests.h"
#include "TestRBTorsionForce.h"
void testParallelComputation() {
System system;
......@@ -138,15 +58,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
testRBTorsions();
void runPlatformTests() {
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cpu/tests/TestCpuSettle.cpp
View file @ 6bde69d9
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
......@@ -7,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -30,91 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CPU implementation of the SETTLE algorithm.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CpuPlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
void testConstraints() {
const int numMolecules = 10;
const int numParticles = numMolecules*3;
const int numConstraints = numMolecules*3;
const double temp = 100.0;
CpuPlatform platform;
System system;
LangevinIntegrator integrator(temp, 2.0, 0.001);
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numMolecules; ++i) {
system.addParticle(16.0);
system.addParticle(1.0);
system.addParticle(1.0);
forceField->addParticle(-0.82, 0.317, 0.65);
forceField->addParticle(0.41, 1.0, 0.0);
forceField->addParticle(0.41, 1.0, 0.0);
system.addConstraint(i*3, i*3+1, 0.1);
system.addConstraint(i*3, i*3+2, 0.1);
system.addConstraint(i*3+1, i*3+2, 0.163);
}
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numMolecules; ++i) {
positions[i*3] = Vec3((i%4)*0.4, (i/4)*0.4, 0);
positions[i*3+1] = positions[i*3]+Vec3(0.1, 0, 0);
positions[i*3+2] = positions[i*3]+Vec3(-0.03333, 0.09428, 0);
velocities[i*3] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
velocities[i*3+1] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
velocities[i*3+2] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
for (int i = 0; i < 1000; ++i) {
integrator.step(1);
State state = context.getState(State::Positions | State::Forces);
for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-5);
}
}
}
#include "CpuTests.h"
#include "TestSettle.h"
int main(int argc, char* argv[]) {
try {
if (!CpuPlatform::isProcessorSupported()) {
cout << "CPU is not supported. Exiting." << endl;
return 0;
}
testConstraints();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/include/CudaExpressionUtilities.h
View file @ 6bde69d9
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009-2014 Stanford University and the Authors. *
* Portions copyright (c) 2009-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -89,6 +89,10 @@ public:
* @param function the function for which to get a placeholder
*/
Lepton::CustomFunction* getFunctionPlaceholder(const TabulatedFunction& function);
/**
* Get a Lepton::CustomFunction that can be used to represent the periodicdistance() function when parsing expressions.
*/
Lepton::CustomFunction* getPeriodicDistancePlaceholder();
private:
class FunctionPlaceholder : public Lepton::CustomFunction {
public:
......@@ -114,13 +118,13 @@ private:
const std::vector<const TabulatedFunction*>& functions, const std::vector<std::pair<std::string, std::string> >& functionNames,
const std::string& prefix, const std::vector<std::vector<double> >& functionParams, const std::vector<Lepton::ParsedExpression>& allExpressions, const std::string& tempType);
std::string getTempName(const Lepton::ExpressionTreeNode& node, const std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& temps);
void findRelatedTabulatedFunctions(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
void findRelatedCustomFunctions(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
std::vector<const Lepton::ExpressionTreeNode*>& nodes);
void findRelatedPowers(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
std::map<int, const Lepton::ExpressionTreeNode*>& powers);
std::vector<std::vector<double> > computeFunctionParameters(const std::vector<const TabulatedFunction*>& functions);
CudaContext& context;
FunctionPlaceholder fp1, fp2, fp3;
FunctionPlaceholder fp1, fp2, fp3, periodicDistance;
};
} // namespace OpenMM
......
platforms/cuda/include/CudaNonbondedUtilities.h
View file @ 6bde69d9
......@@ -138,8 +138,12 @@ public:
void prepareInteractions(int forceGroups);
/**
* Compute the nonbonded interactions.
*
* @param forceGroups the flags specifying which force groups to include
* @param includeForces whether to compute forces
* @param includeEnergy whether to compute the potential energy
*/
void computeInteractions(int forceGroups);
void computeInteractions(int forceGroups, bool includeForces, bool includeEnergy);
/**
* Check to see if the neighbor list arrays are large enough, and make them bigger if necessary.
*
......@@ -235,8 +239,10 @@ public:
* @param useExclusions specifies whether exclusions are applied to this interaction
* @param isSymmetric specifies whether the interaction is symmetric
* @param groups the set of force groups this kernel is for
* @param includeForces whether this kernel should compute forces
* @param includeEnergy whether this kernel should compute potential energy
*/
CUfunction createInteractionKernel(const std::string& source, std::vector<ParameterInfo>& params, std::vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups);
CUfunction createInteractionKernel(const std::string& source, std::vector<ParameterInfo>& params, std::vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups, bool includeForces, bool includeEnergy);
/**
* Create the set of kernels that will be needed for a particular combination of force groups.
*
......@@ -282,7 +288,8 @@ class CudaNonbondedUtilities::KernelSet {
public:
bool hasForces;
double cutoffDistance;
CUfunction forceKernel;
std::string source;
CUfunction forceKernel, energyKernel, forceEnergyKernel;
CUfunction findBlockBoundsKernel;
CUfunction sortBoxDataKernel;
CUfunction findInteractingBlocksKernel;
......
platforms/cuda/src/CudaBondedUtilities.cpp
View file @ 6bde69d9
......@@ -99,7 +99,7 @@ void CudaBondedUtilities::initialize(const System& system) {
s<<CudaKernelSources::vectorOps;
for (int i = 0; i < (int) prefixCode.size(); i++)
s<<prefixCode[i];
s<<"extern \"C\" __global__ void computeBondedForces(unsigned long long* __restrict__ forceBuffer, real* __restrict__ energyBuffer, const real4* __restrict__ posq, int groups";
s<<"extern \"C\" __global__ void computeBondedForces(unsigned long long* __restrict__ forceBuffer, real* __restrict__ energyBuffer, const real4* __restrict__ posq, int groups, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ";
for (int force = 0; force < numForces; force++) {
for (int i = 0; i < (int) atomIndices[force].size(); i++) {
int indexWidth = atomIndices[force][i]->getElementSize()/4;
......@@ -161,6 +161,11 @@ void CudaBondedUtilities::computeInteractions(int groups) {
kernelArgs.push_back(&context.getEnergyBuffer().getDevicePointer());
kernelArgs.push_back(&context.getPosq().getDevicePointer());
kernelArgs.push_back(NULL);
kernelArgs.push_back(context.getPeriodicBoxSizePointer());
kernelArgs.push_back(context.getInvPeriodicBoxSizePointer());
kernelArgs.push_back(context.getPeriodicBoxVecXPointer());
kernelArgs.push_back(context.getPeriodicBoxVecYPointer());
kernelArgs.push_back(context.getPeriodicBoxVecZPointer());
for (int i = 0; i < (int) atomIndices.size(); i++)
for (int j = 0; j < (int) atomIndices[i].size(); j++)
kernelArgs.push_back(&atomIndices[i][j]->getDevicePointer());
......
platforms/cuda/src/CudaExpressionUtilities.cpp
View file @ 6bde69d9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009-2014 Stanford University and the Authors. *
* Portions copyright (c) 2009-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -33,7 +33,7 @@ using namespace OpenMM;
using namespace Lepton;
using namespace std;
CudaExpressionUtilities::CudaExpressionUtilities(CudaContext& context) : context(context), fp1(1), fp2(2), fp3(3) {
CudaExpressionUtilities::CudaExpressionUtilities(CudaContext& context) : context(context), fp1(1), fp2(2), fp3(3), periodicDistance(6) {
}
string CudaExpressionUtilities::createExpressions(const map<string, ParsedExpression>& expressions, const map<string, string>& variables,
......@@ -79,11 +79,6 @@ void CudaExpressionUtilities::processExpression(stringstream& out, const Express
throw OpenMMException("Unknown variable in expression: "+node.getOperation().getName());
case Operation::CUSTOM:
{
int i;
for (i = 0; i < (int) functionNames.size() && functionNames[i].first != node.getOperation().getName(); i++)
;
if (i == functionNames.size())
throw OpenMMException("Unknown function in expression: "+node.getOperation().getName());
out << "0.0f;\n";
temps.push_back(make_pair(node, name));
hasRecordedNode = true;
......@@ -93,7 +88,7 @@ void CudaExpressionUtilities::processExpression(stringstream& out, const Express
vector<const ExpressionTreeNode*> nodes;
for (int j = 0; j < (int) allExpressions.size(); j++)
findRelatedTabulatedFunctions(node, allExpressions[j].getRootNode(), nodes);
findRelatedCustomFunctions(node, allExpressions[j].getRootNode(), nodes);
vector<string> nodeNames;
nodeNames.push_back(name);
for (int j = 1; j < (int) nodes.size(); j++) {
......@@ -103,6 +98,52 @@ void CudaExpressionUtilities::processExpression(stringstream& out, const Express
temps.push_back(make_pair(*nodes[j], name2));
}
out << "{\n";
if (node.getOperation().getName() == "periodicdistance") {
// This is the periodicdistance() function.
out << tempType << "3 periodicDistance_delta = make_real3(";
for (int i = 0; i < 3; i++) {
if (i > 0)
out << ", ";
out << getTempName(node.getChildren()[i], temps) << "-" << getTempName(node.getChildren()[i+3], temps);
}
out << ");\n";
out << "APPLY_PERIODIC_TO_DELTA(periodicDistance_delta)\n";
out << tempType << " periodicDistance_rinv = RSQRT(periodicDistance_delta.x*periodicDistance_delta.x + periodicDistance_delta.y*periodicDistance_delta.y + periodicDistance_delta.z*periodicDistance_delta.z);\n";
for (int j = 0; j < nodes.size(); j++) {
const vector<int>& derivOrder = dynamic_cast<const Operation::Custom*>(&nodes[j]->getOperation())->getDerivOrder();
int argIndex = -1;
for (int k = 0; k < 6; k++) {
if (derivOrder[k] > 0) {
if (derivOrder[k] > 1 || argIndex != -1)
throw OpenMMException("Unsupported derivative of periodicdistance"); // Should be impossible for this to happen.
argIndex = k;
}
}
if (argIndex == -1)
out << nodeNames[j] << " = RECIP(periodicDistance_rinv);\n";
else if (argIndex == 0)
out << nodeNames[j] << " = periodicDistance_delta.x*periodicDistance_rinv;\n";
else if (argIndex == 1)
out << nodeNames[j] << " = periodicDistance_delta.y*periodicDistance_rinv;\n";
else if (argIndex == 2)
out << nodeNames[j] << " = periodicDistance_delta.z*periodicDistance_rinv;\n";
else if (argIndex == 3)
out << nodeNames[j] << " = -periodicDistance_delta.x*periodicDistance_rinv;\n";
else if (argIndex == 4)
out << nodeNames[j] << " = -periodicDistance_delta.y*periodicDistance_rinv;\n";
else if (argIndex == 5)
out << nodeNames[j] << " = -periodicDistance_delta.z*periodicDistance_rinv;\n";
}
}
else {
// This is a tabulated function.
int i;
for (i = 0; i < (int) functionNames.size() && functionNames[i].first != node.getOperation().getName(); i++)
;
if (i == functionNames.size())
throw OpenMMException("Unknown function in expression: "+node.getOperation().getName());
vector<string> paramsFloat, paramsInt;
for (int j = 0; j < (int) functionParams[i].size(); j++) {
paramsFloat.push_back(context.doubleToString(functionParams[i][j]));
......@@ -275,6 +316,7 @@ void CudaExpressionUtilities::processExpression(stringstream& out, const Express
}
}
}
}
out << "}";
break;
}
......@@ -483,7 +525,7 @@ string CudaExpressionUtilities::getTempName(const ExpressionTreeNode& node, cons
throw OpenMMException(out.str());
}
void CudaExpressionUtilities::findRelatedTabulatedFunctions(const ExpressionTreeNode& node, const ExpressionTreeNode& searchNode,
void CudaExpressionUtilities::findRelatedCustomFunctions(const ExpressionTreeNode& node, const ExpressionTreeNode& searchNode,
vector<const Lepton::ExpressionTreeNode*>& nodes) {
if (searchNode.getOperation().getId() == Operation::CUSTOM && node.getOperation().getName() == searchNode.getOperation().getName()) {
// Make sure the arguments are identical.
......@@ -504,7 +546,7 @@ void CudaExpressionUtilities::findRelatedTabulatedFunctions(const ExpressionTree
}
else
for (int i = 0; i < (int) searchNode.getChildren().size(); i++)
findRelatedTabulatedFunctions(node, searchNode.getChildren()[i], nodes);
findRelatedCustomFunctions(node, searchNode.getChildren()[i], nodes);
}
void CudaExpressionUtilities::findRelatedPowers(const ExpressionTreeNode& node, const ExpressionTreeNode& searchNode, map<int, const ExpressionTreeNode*>& powers) {
......@@ -730,3 +772,7 @@ Lepton::CustomFunction* CudaExpressionUtilities::getFunctionPlaceholder(const Ta
return &fp3;
throw OpenMMException("getFunctionPlaceholder: Unknown function type");
}
Lepton::CustomFunction* CudaExpressionUtilities::getPeriodicDistancePlaceholder() {
return &periodicDistance;
}
platforms/cuda/src/CudaKernels.cpp
View file @ 6bde69d9
......@@ -105,7 +105,7 @@ void CudaCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool
double CudaCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups, bool& valid) {
cu.getBondedUtilities().computeInteractions(groups);
cu.getNonbondedUtilities().computeInteractions(groups);
cu.getNonbondedUtilities().computeInteractions(groups, includeForces, includeEnergy);
double sum = 0.0;
for (vector<CudaContext::ForcePostComputation*>::iterator iter = cu.getPostComputations().begin(); iter != cu.getPostComputations().end(); ++iter)
sum += (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
......@@ -3652,7 +3652,9 @@ void CudaCalcCustomExternalForceKernel::initialize(const System& system, const C
globalParamNames[i] = force.getGlobalParameterName(i);
globalParamValues[i] = (float) force.getGlobalParameterDefaultValue(i);
}
Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
map<string, Lepton::CustomFunction*> customFunctions;
customFunctions["periodicdistance"] = cu.getExpressionUtilities().getPeriodicDistancePlaceholder();
Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction(), customFunctions).optimize();
Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x").optimize();
Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y").optimize();
Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z").optimize();
......
platforms/cuda/src/CudaNonbondedUtilities.cpp
View file @ 6bde69d9
......@@ -388,12 +388,15 @@ void CudaNonbondedUtilities::prepareInteractions(int forceGroups) {
lastCutoff = kernels.cutoffDistance;
}
void CudaNonbondedUtilities::computeInteractions(int forceGroups) {
void CudaNonbondedUtilities::computeInteractions(int forceGroups, bool includeForces, bool includeEnergy) {
if ((forceGroups&groupFlags) == 0)
return;
KernelSet& kernels = groupKernels[forceGroups];
if (kernels.hasForces) {
context.executeKernel(kernels.forceKernel, &forceArgs[0], numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
CUfunction& kernel = (includeForces ? (includeEnergy ? kernels.forceEnergyKernel : kernels.forceKernel) : kernels.energyKernel);
if (kernel == NULL)
kernel = createInteractionKernel(kernels.source, parameters, arguments, true, true, forceGroups, includeForces, includeEnergy);
context.executeKernel(kernel, &forceArgs[0], numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
}
}
......@@ -454,8 +457,8 @@ void CudaNonbondedUtilities::createKernelsForGroups(int groups) {
}
kernels.hasForces = (source.size() > 0);
kernels.cutoffDistance = cutoff;
if (kernels.hasForces)
kernels.forceKernel = createInteractionKernel(source, parameters, arguments, true, true, groups);
kernels.source = source;
kernels.forceKernel = kernels.energyKernel = kernels.forceEnergyKernel = NULL;
if (useCutoff) {
double padding = (usePadding ? 0.1*cutoff : 0.0);
double paddedCutoff = cutoff+padding;
......@@ -478,7 +481,7 @@ void CudaNonbondedUtilities::createKernelsForGroups(int groups) {
groupKernels[groups] = kernels;
}
CUfunction CudaNonbondedUtilities::createInteractionKernel(const string& source, vector<ParameterInfo>& params, vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups) {
CUfunction CudaNonbondedUtilities::createInteractionKernel(const string& source, vector<ParameterInfo>& params, vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups, bool includeForces, bool includeEnergy) {
map<string, string> replacements;
replacements["COMPUTE_INTERACTION"] = source;
const string suffixes[] = {"x", "y", "z", "w"};
......@@ -654,6 +657,10 @@ CUfunction CudaNonbondedUtilities::createInteractionKernel(const string& source,
defines["USE_SYMMETRIC"] = "1";
if (useShuffle)
defines["ENABLE_SHUFFLE"] = "1";
if (includeForces)
defines["INCLUDE_FORCES"] = "1";
if (includeEnergy)
defines["INCLUDE_ENERGY"] = "1";
defines["THREAD_BLOCK_SIZE"] = context.intToString(forceThreadBlockSize);
double maxCutoff = 0.0;
for (int i = 0; i < 32; i++) {
......
platforms/cuda/src/kernels/nonbonded.cu
View file @ 6bde69d9
......@@ -112,7 +112,7 @@ extern "C" __global__ void computeNonbonded(
const unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/TILE_SIZE; // global warpIndex
const unsigned int tgx = threadIdx.x & (TILE_SIZE-1); // index within the warp
const unsigned int tbx = threadIdx.x - tgx; // block warpIndex
real energy = 0.0f;
mixed energy = 0;
// used shared memory if the device cannot shuffle
#ifndef ENABLE_SHUFFLE
__shared__ AtomData localData[THREAD_BLOCK_SIZE];
......@@ -175,6 +175,7 @@ extern "C" __global__ void computeNonbonded(
real tempEnergy = 0.0f;
COMPUTE_INTERACTION
energy += 0.5f*tempEnergy;
#ifdef INCLUDE_FORCES
#ifdef USE_SYMMETRIC
force.x -= delta.x*dEdR;
force.y -= delta.y*dEdR;
......@@ -184,6 +185,7 @@ extern "C" __global__ void computeNonbonded(
force.y -= dEdR1.y;
force.z -= dEdR1.z;
#endif
#endif
#ifdef USE_EXCLUSIONS
excl >>= 1;
#endif
......@@ -241,6 +243,7 @@ extern "C" __global__ void computeNonbonded(
real tempEnergy = 0.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
#ifdef USE_SYMMETRIC
delta *= dEdR;
force.x -= delta.x;
......@@ -270,11 +273,12 @@ extern "C" __global__ void computeNonbonded(
localData[tbx+tj].fz += dEdR2.z;
#endif
#endif // end USE_SYMMETRIC
#ifdef USE_EXCLUSIONS
excl >>= 1;
#endif
#ifdef ENABLE_SHUFFLE
SHUFFLE_WARP_DATA
#endif
#endif
#ifdef USE_EXCLUSIONS
excl >>= 1;
#endif
// cycles the indices
// 0 1 2 3 4 5 6 7 -> 1 2 3 4 5 6 7 0
......@@ -282,6 +286,7 @@ extern "C" __global__ void computeNonbonded(
}
const unsigned int offset = y*TILE_SIZE + tgx;
// write results for off diagonal tiles
#ifdef INCLUDE_FORCES
#ifdef ENABLE_SHUFFLE
atomicAdd(&forceBuffers[offset], static_cast<unsigned long long>((long long) (shflForce.x*0x100000000)));
atomicAdd(&forceBuffers[offset+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (shflForce.y*0x100000000)));
......@@ -290,13 +295,16 @@ extern "C" __global__ void computeNonbonded(
atomicAdd(&forceBuffers[offset], static_cast<unsigned long long>((long long) (localData[threadIdx.x].fx*0x100000000)));
atomicAdd(&forceBuffers[offset+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (localData[threadIdx.x].fy*0x100000000)));
atomicAdd(&forceBuffers[offset+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (localData[threadIdx.x].fz*0x100000000)));
#endif
#endif
}
// Write results for on and off diagonal tiles
#ifdef INCLUDE_FORCES
const unsigned int offset = x*TILE_SIZE + tgx;
atomicAdd(&forceBuffers[offset], static_cast<unsigned long long>((long long) (force.x*0x100000000)));
atomicAdd(&forceBuffers[offset+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (force.y*0x100000000)));
atomicAdd(&forceBuffers[offset+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (force.z*0x100000000)));
#endif
}
// Second loop: tiles without exclusions, either from the neighbor list (with cutoff) or just enumerating all
......@@ -441,6 +449,7 @@ extern "C" __global__ void computeNonbonded(
real tempEnergy = 0.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
#ifdef USE_SYMMETRIC
delta *= dEdR;
force.x -= delta.x;
......@@ -472,6 +481,7 @@ extern "C" __global__ void computeNonbonded(
#endif // end USE_SYMMETRIC
#ifdef ENABLE_SHUFFLE
SHUFFLE_WARP_DATA
#endif
#endif
tj = (tj + 1) & (TILE_SIZE - 1);
}
......@@ -509,6 +519,7 @@ extern "C" __global__ void computeNonbonded(
real tempEnergy = 0.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
#ifdef USE_SYMMETRIC
delta *= dEdR;
force.x -= delta.x;
......@@ -540,12 +551,14 @@ extern "C" __global__ void computeNonbonded(
#endif // end USE_SYMMETRIC
#ifdef ENABLE_SHUFFLE
SHUFFLE_WARP_DATA
#endif
#endif
tj = (tj + 1) & (TILE_SIZE - 1);
}
}
// Write results.
#ifdef INCLUDE_FORCES
atomicAdd(&forceBuffers[atom1], static_cast<unsigned long long>((long long) (force.x*0x100000000)));
atomicAdd(&forceBuffers[atom1+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (force.y*0x100000000)));
atomicAdd(&forceBuffers[atom1+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (force.z*0x100000000)));
......@@ -565,8 +578,11 @@ extern "C" __global__ void computeNonbonded(
atomicAdd(&forceBuffers[atom2+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (localData[threadIdx.x].fz*0x100000000)));
#endif
}
#endif
}
pos++;
}
energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;
#ifdef INCLUDE_ENERGY
energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += (real) energy;
#endif
}
\ No newline at end of file
platforms/cuda/tests/CudaTests.h 0 → 100644
View file @ 6bde69d9
/* -------------------------------------------------------------------------- *
* 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) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "CudaPlatform.h"
#include <string>
OpenMM::CudaPlatform platform;
void initializeTests(int argc, char* argv[]) {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
}
platforms/cuda/tests/TestCudaAndersenThermostat.cpp
View file @ 6bde69d9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,191 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of AndersenThermostat.
*/
#include "CudaTests.h"
#include "TestAndersenThermostat.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
void testTemperature() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
const int numSteps = 5000;
System system;
VerletIntegrator integrator(0.003);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermstat);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
context.setPositions(positions);
context.setVelocitiesToTemperature(temp);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double ke = 0.0;
for (int i = 0; i < numSteps; ++i) {
State state = context.getState(State::Energy);
ke += state.getKineticEnergy();
integrator.step(10);
}
ke /= numSteps;
double expected = 0.5*numParticles*3*BOLTZ*temp;
ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.1);
}
void testConstraints() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
const int numSteps = 15000;
System system;
VerletIntegrator integrator(0.004);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
system.addConstraint(0, 1, 1);
system.addConstraint(1, 2, 1);
system.addConstraint(2, 3, 1);
system.addConstraint(3, 0, 1);
system.addConstraint(4, 5, 1);
system.addConstraint(5, 6, 1);
system.addConstraint(6, 7, 1);
system.addConstraint(7, 4, 1);
AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermstat);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
positions[2] = Vec3(1, 1, 0);
positions[3] = Vec3(0, 1, 0);
positions[4] = Vec3(1, 0, 1);
positions[5] = Vec3(1, 1, 1);
positions[6] = Vec3(0, 1, 1);
positions[7] = Vec3(0, 0, 1);
context.setPositions(positions);
context.setVelocitiesToTemperature(temp);
// Let it equilibrate.
integrator.step(5000);
// Now run it for a while and see if the temperature is correct.
double ke = 0.0;
for (int i = 0; i < numSteps; ++i) {
State state = context.getState(State::Energy);
ke += state.getKineticEnergy();
integrator.step(1);
}
ke /= numSteps;
double expected = 0.5*(numParticles*3-system.getNumConstraints())*BOLTZ*temp;
ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.1);
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermostat);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(0, 0, 0);
}
// Try twice with the same random seed.
thermostat->setRandomNumberSeed(5);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state1 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state2 = context.getState(State::Positions);
// Try twice with a different random seed.
thermostat->setRandomNumberSeed(10);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state3 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state4 = context.getState(State::Positions);
// Compare the results.
for (int i = 0; i < numParticles; i++) {
for (int j = 0; j < 3; j++) {
ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
}
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testTemperature();
testConstraints();
testRandomSeed();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaBrownianIntegrator.cpp
View file @ 6bde69d9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,252 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/System.h"
#include "CudaTests.h"
#include "TestBrownianIntegrator.h"
/**
* This tests the CUDA implementation of BrownianIntegrator.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/BrownianIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void testSingleBond() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
double dt = 0.01;
BrownianIntegrator integrator(0, 0.1, dt);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// This is simply an overdamped harmonic oscillator, so compare it to the analytical solution.
double rate = 2*1.0/(0.1*2.0);
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities);
double time = state.getTime();
double expectedDist = 1.5+0.5*std::exp(-rate*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
if (i > 0) {
double expectedSpeed = -0.5*rate*std::exp(-rate*(time-0.5*dt));
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.11);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.11);
}
integrator.step(1);
}
}
void testTemperature() {
const int numParticles = 8;
const int numBonds = numParticles-1;
const double temp = 10.0;
System system;
BrownianIntegrator integrator(temp, 2.0, 0.01);
HarmonicBondForce* forceField = new HarmonicBondForce();
for (int i = 0; i < numParticles; ++i)
system.addParticle(2.0);
for (int i = 0; i < numBonds; ++i)
forceField->addBond(i, i+1, 1.0, 5.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3(i, 0, 0);
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double pe = 0.0;
const int steps = 50000;
for (int i = 0; i < steps; ++i) {
State state = context.getState(State::Energy);
pe += state.getPotentialEnergy();
integrator.step(1);
}
pe /= steps;
double expected = 0.5*numBonds*BOLTZ*temp;
ASSERT_USUALLY_EQUAL_TOL(expected, pe, 0.1*expected);
}
void testConstraints() {
const int numParticles = 8;
const int numConstraints = 5;
const double temp = 20.0;
System system;
BrownianIntegrator integrator(temp, 2.0, 0.001);
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
system.addConstraint(0, 1, 1.0);
system.addConstraint(1, 2, 1.0);
system.addConstraint(2, 3, 1.0);
system.addConstraint(4, 5, 1.0);
system.addConstraint(6, 7, 1.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i, 0, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions);
for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-4);
}
integrator.step(1);
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
BrownianIntegrator integrator(300.0, 2.0, 0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
System system;
BrownianIntegrator integrator(temp, 2.0, 0.001);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(0, 0, 0);
}
// Try twice with the same random seed.
integrator.setRandomNumberSeed(5);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state1 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state2 = context.getState(State::Positions);
// Try twice with a different random seed.
integrator.setRandomNumberSeed(10);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state3 = context.getState(State::Positions);
context.reinitialize();
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
State state4 = context.getState(State::Positions);
// Compare the results.
for (int i = 0; i < numParticles; i++) {
for (int j = 0; j < 3; j++) {
ASSERT(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
}
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testSingleBond();
testTemperature();
testConstraints();
testConstrainedMasslessParticles();
testRandomSeed();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaCMAPTorsionForce.cpp
View file @ 6bde69d9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,149 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CMAPTorsionForce.
*/
#include "CudaTests.h"
#include "TestCMAPTorsionForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CMAPTorsionForce.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void testCMAPTorsions() {
const int mapSize = 36;
// Create two systems: one with a pair of periodic torsions, and one with a CMAP torsion
// that approximates the same force.
System system1;
for (int i = 0; i < 5; i++)
system1.addParticle(1.0);
PeriodicTorsionForce* periodic = new PeriodicTorsionForce();
periodic->addTorsion(0, 1, 2, 3, 2, M_PI/4, 1.5);
periodic->addTorsion(1, 2, 3, 4, 3, M_PI/3, 2.0);
system1.addForce(periodic);
System system2;
for (int i = 0; i < 5; i++)
system2.addParticle(1.0);
CMAPTorsionForce* cmap = new CMAPTorsionForce();
vector<double> mapEnergy(mapSize*mapSize);
for (int i = 0; i < mapSize; i++) {
double angle1 = i*2*M_PI/mapSize;
double energy1 = 1.5*(1+cos(2*angle1-M_PI/4));
for (int j = 0; j < mapSize; j++) {
double angle2 = j*2*M_PI/mapSize;
double energy2 = 2.0*(1+cos(3*angle2-M_PI/3));
mapEnergy[i+j*mapSize] = energy1+energy2;
}
}
cmap->addMap(mapSize, mapEnergy);
cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4);
system2.addForce(cmap);
// Set the atoms in various positions, and verify that both systems give equal forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(5);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(system1, integrator1, platform);
Context c2(system2, integrator2, platform);
for (int i = 0; i < 50; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < system1.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 0.05);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-3);
}
}
void testChangingParameters() {
// Create a system with two maps and one torsion.
const int mapSize = 8;
System system;
for (int i = 0; i < 5; i++)
system.addParticle(1.0);
CMAPTorsionForce* cmap = new CMAPTorsionForce();
vector<double> mapEnergy1(mapSize*mapSize);
vector<double> mapEnergy2(mapSize*mapSize);
for (int i = 0; i < mapSize; i++) {
double angle1 = i*2*M_PI/mapSize;
double energy1 = cos(angle1);
for (int j = 0; j < mapSize; j++) {
double angle2 = j*2*M_PI/mapSize;
double energy2 = 10*sin(angle2);
mapEnergy1[i+j*mapSize] = energy1+energy2;
mapEnergy2[i+j*mapSize] = energy1-energy2;
}
}
cmap->addMap(mapSize, mapEnergy1);
cmap->addMap(mapSize, mapEnergy2);
cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4);
system.addForce(cmap);
// Set particle positions so angle1=0 and angle2=PI/4.
vector<Vec3> positions(5);
positions[0] = Vec3(0, 0, 1);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 1);
positions[4] = Vec3(0.5, -0.5, 1);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
// Check that the energy is correct.
double energy = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(1+10*sin(M_PI/4), energy, 1e-5);
// Modify the parameters.
cmap->setTorsionParameters(0, 1, 0, 1, 2, 3, 1, 2, 3, 4);
for (int i = 0; i < mapSize*mapSize; i++)
mapEnergy2[i] *= 2.0;
cmap->setMapParameters(1, mapSize, mapEnergy2);
cmap->updateParametersInContext(context);
// See if the results are correct.
energy = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(2-20*sin(M_PI/4), energy, 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testCMAPTorsions();
testChangingParameters();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaCMMotionRemover.cpp
View file @ 6bde69d9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,94 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of AndersenThermostat.
*/
#include "CudaTests.h"
#include "TestCMMotionRemover.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
Vec3 calcCM(const vector<Vec3>& values, System& system) {
Vec3 cm;
for (int j = 0; j < system.getNumParticles(); ++j) {
cm[0] += values[j][0]*system.getParticleMass(j);
cm[1] += values[j][1]*system.getParticleMass(j);
cm[2] += values[j][2]*system.getParticleMass(j);
}
return cm;
}
void testMotionRemoval(Integrator& integrator) {
const int numParticles = 8;
System system;
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(2, 3, 2.0, 0.5);
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i+1);
nonbonded->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(nonbonded);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Now run it for a while and see if the center of mass remains fixed.
Vec3 cmPos = calcCM(context.getState(State::Positions).getPositions(), system);
for (int i = 0; i < 1000; ++i) {
integrator.step(1);
State state = context.getState(State::Positions | State::Velocities);
Vec3 pos = calcCM(state.getPositions(), system);
ASSERT_EQUAL_VEC(cmPos, pos, 1e-2);
Vec3 vel = calcCM(state.getVelocities(), system);
if (i > 0) {
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), vel, 1e-2);
}
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
LangevinIntegrator langevin(0.0, 1e-5, 0.01);
testMotionRemoval(langevin);
VerletIntegrator verlet(0.01);
testMotionRemoval(verlet);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
platforms/cuda/tests/TestCudaCheckpoints.cpp
View file @ 6bde69d9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2012-2013 Stanford University and the Authors. *
* Portions copyright (c) 2012-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,45 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests creating and loading checkpoints with the CUDA platform.
*/
#include "CudaPlatform.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/Context.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <sstream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void compareStates(State& s1, State& s2) {
ASSERT_EQUAL_TOL(s1.getTime(), s2.getTime(), TOL);
int numParticles = s1.getPositions().size();
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(s1.getPositions()[i], s2.getPositions()[i], TOL);
ASSERT_EQUAL_VEC(s1.getVelocities()[i], s2.getVelocities()[i], TOL);
Vec3 a1, b1, c1, a2, b2, c2;
s1.getPeriodicBoxVectors(a1, b1, c1);
s2.getPeriodicBoxVectors(a2, b2, c2);
ASSERT_EQUAL_VEC(a1, a2, TOL);
ASSERT_EQUAL_VEC(b1, b2, TOL);
ASSERT_EQUAL_VEC(c1, c2, TOL);
for (map<string, double>::const_iterator iter = s1.getParameters().begin(); iter != s1.getParameters().end(); ++iter)
ASSERT_EQUAL(iter->second, (*s2.getParameters().find(iter->first)).second);
}
}
#include "CudaTests.h"
#include "TestCheckpoints.h"
void testCheckpoint() {
const int numParticles = 100;
......@@ -159,71 +122,6 @@ void testCheckpoint() {
compareStates(s6, s8);
}
void testSetState() {
const int numParticles = 10;
const double boxSize = 3.0;
const double temperature = 200.0;
System system;
system.addForce(new AndersenThermostat(0.0, 100.0));
NonbondedForce* nonbonded = new NonbondedForce();
system.addForce(nonbonded);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
}
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
context.setParameter(AndersenThermostat::Temperature(), temperature);
// Run for a little while.
integrator.step(100);
// Record the current state.
State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
// Continue the simulation for a few more steps and record a partial state.
integrator.step(10);
State s2 = context.getState(State::Positions);
// Restore the original state and see if everything gets restored correctly.
context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
context.setParameter(AndersenThermostat::Temperature(), temperature+10);
context.setState(s1);
State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
compareStates(s1, s3);
// Set the partial state and see if the correct things were set.
context.setState(s2);
State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(s2.getPositions()[i], s4.getPositions()[i], TOL);
ASSERT_EQUAL_VEC(s1.getVelocities()[i], s4.getVelocities()[i], TOL);
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
void runPlatformTests() {
testCheckpoint();
testSetState();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cuda/tests/TestCudaCustomAngleForce.cpp
View file @ 6bde69d9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,107 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomAngleForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomAngleForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void testAngles() {
// Create a system using a CustomAngleForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomAngleForce* custom = new CustomAngleForce("scale*k*(theta-theta0)^2");
custom->addPerAngleParameter("theta0");
custom->addPerAngleParameter("k");
custom->addGlobalParameter("scale", 0.5);
vector<double> parameters(2);
parameters[0] = 1.5;
parameters[1] = 0.8;
custom->addAngle(0, 1, 2, parameters);
parameters[0] = 2.0;
parameters[1] = 0.5;
custom->addAngle(1, 2, 3, parameters);
customSystem.addForce(custom);
// Create an identical system using a HarmonicAngleForce.
System harmonicSystem;
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
harmonicSystem.addParticle(1.0);
HarmonicAngleForce* harmonic = new HarmonicAngleForce();
harmonic->addAngle(0, 1, 2, 1.5, 0.8);
harmonic->addAngle(1, 2, 3, 2.0, 0.5);
harmonicSystem.addForce(harmonic);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(4);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(harmonicSystem, integrator2, platform);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
// Try changing the angle parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[1] = 0.9;
custom->setAngleParameters(0, 0, 1, 2, parameters);
parameters[0] = 2.1;
parameters[1] = 0.6;
custom->setAngleParameters(1, 1, 2, 3, parameters);
custom->updateParametersInContext(c1);
harmonic->setAngleParameters(0, 0, 1, 2, 1.6, 0.9);
harmonic->setAngleParameters(1, 1, 2, 3, 2.1, 0.6);
harmonic->updateParametersInContext(c2);
{
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
#include "CudaTests.h"
#include "TestCustomAngleForce.h"
void testParallelComputation() {
System system;
......@@ -160,17 +61,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testAngles();
void runPlatformTests() {
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cuda/tests/TestCudaCustomBondForce.cpp
View file @ 6bde69d9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,111 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CustomBondForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomBondForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
CudaPlatform platform;
void testBonds() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomBondForce* forceField = new CustomBondForce("scale*k*(r-r0)^2");
forceField->addPerBondParameter("r0");
forceField->addPerBondParameter("k");
forceField->addGlobalParameter("scale", 0.5);
vector<double> parameters(2);
parameters[0] = 1.5;
parameters[1] = 0.8;
forceField->addBond(0, 1, parameters);
parameters[0] = 1.2;
parameters[1] = 0.7;
forceField->addBond(1, 2, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[1] = 0.9;
forceField->setBondParameters(0, 0, 1, parameters);
parameters[0] = 1.3;
parameters[1] = 0.8;
forceField->setBondParameters(1, 1, 2, parameters);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.9*0.4, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.8*0.3, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.9*0.4*0.4 + 0.5*0.8*0.3*0.3, state.getPotentialEnergy(), TOL);
}
}
void testManyParameters() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomBondForce* forceField = new CustomBondForce("(a+b+c+d+e+f+g+h+i)*r");
forceField->addPerBondParameter("a");
forceField->addPerBondParameter("b");
forceField->addPerBondParameter("c");
forceField->addPerBondParameter("d");
forceField->addPerBondParameter("e");
forceField->addPerBondParameter("f");
forceField->addPerBondParameter("g");
forceField->addPerBondParameter("h");
forceField->addPerBondParameter("i");
vector<double> parameters(forceField->getNumPerBondParameters());
for (int i = 0; i < parameters.size(); i++)
parameters[i] = i;
forceField->addBond(0, 1, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2.5, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double f = 1+2+3+4+5+6+7+8;
ASSERT_EQUAL_VEC(Vec3(0, f, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -f, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(f*2.5, state.getPotentialEnergy(), TOL);
}
#include "CudaTests.h"
#include "TestCustomBondForce.h"
void testParallelComputation() {
System system;
......@@ -164,18 +61,6 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testBonds();
testManyParameters();
void runPlatformTests() {
testParallelComputation();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cuda/tests/TestCudaCustomCentroidBondForce.cpp
View file @ 6bde69d9
......@@ -29,247 +29,8 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the reference implementation of CustomCompoundBondForce.
*/
#include "CudaTests.h"
#include "TestCustomCentroidBondForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/CustomCentroidBondForce.h"
#include "openmm/CustomCompoundBondForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CudaPlatform platform;
const double TOL = 1e-5;
void testHarmonicBond() {
System system;
system.addParticle(1.0);
system.addParticle(2.0);
system.addParticle(3.0);
system.addParticle(4.0);
system.addParticle(5.0);
CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "k*distance(g1,g2)^2");
force->addPerBondParameter("k");
vector<int> particles1;
particles1.push_back(0);
particles1.push_back(1);
vector<int> particles2;
particles2.push_back(2);
particles2.push_back(3);
particles2.push_back(4);
force->addGroup(particles1);
force->addGroup(particles2);
vector<int> groups;
groups.push_back(0);
groups.push_back(1);
vector<double> parameters;
parameters.push_back(1.0);
force->addBond(groups, parameters);
system.addForce(force);
ASSERT(!system.usesPeriodicBoundaryConditions());
// The center of mass of group 0 is (1.5, 0, 0).
vector<Vec3> positions(5);
positions[0] = Vec3(2.5, 0, 0);
positions[1] = Vec3(1, 0, 0);
// The center of mass of group 1 is (-1, 0, 0).
positions[2] = Vec3(-6, 0, 0);
positions[3] = Vec3(-1, 0, 0);
positions[4] = Vec3(2, 0, 0);
// Check the forces and energy.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(2.5*2.5, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(Vec3(-2*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-2*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_VEC(Vec3(2*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(2*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
ASSERT_EQUAL_VEC(Vec3(2*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
// Update the per-bond parameter and see if the results change.
parameters[0] = 2.0;
force->setBondParameters(0, groups, parameters);
force->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(2*2.5*2.5, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(Vec3(-4*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-4*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
ASSERT_EQUAL_VEC(Vec3(4*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
// All the particles should be treated as a single molecule.
vector<std::vector<int> > molecules = context.getMolecules();
ASSERT_EQUAL(1, molecules.size());
ASSERT_EQUAL(5, molecules[0].size());
}
void testComplexFunction() {
int numParticles = 5;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(2.0);
vector<double> table(20);
for (int i = 0; i < 20; i++)
table[i] = sin(0.11*i);
// When every group contains only one particle, a CustomCentroidBondForce is identical to a
// CustomCompoundBondForce. Use that to test a complicated energy function with lots of terms.
CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+fn(distance(p1,p2))*angle(p3,p2,p4)+scale*dihedral(p2,p1,p4,p3)");
CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+fn(distance(g1,g2))*angle(g3,g2,g4)+scale*dihedral(g2,g1,g4,g3)");
compound->addGlobalParameter("scale", 0.5);
centroid->addGlobalParameter("scale", 0.5);
compound->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
centroid->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
// Add two bonds to the CustomCompoundBondForce.
vector<int> particles(4);
vector<double> parameters;
particles[0] = 0;
particles[1] = 1;
particles[2] = 2;
particles[3] = 3;
compound->addBond(particles, parameters);
particles[0] = 2;
particles[1] = 4;
particles[2] = 3;
particles[3] = 1;
compound->addBond(particles, parameters);
// Add identical bonds to the CustomCentroidBondForce. As a stronger test, make sure that
// group number is different from particle number.
vector<int> groupMembers(1);
groupMembers[0] = 3;
centroid->addGroup(groupMembers);
groupMembers[0] = 0;
centroid->addGroup(groupMembers);
groupMembers[0] = 1;
centroid->addGroup(groupMembers);
groupMembers[0] = 2;
centroid->addGroup(groupMembers);
groupMembers[0] = 4;
centroid->addGroup(groupMembers);
vector<int> groups(4);
groups[0] = 1;
groups[1] = 2;
groups[2] = 3;
groups[3] = 0;
centroid->addBond(groups, parameters);
groups[0] = 3;
groups[1] = 4;
groups[2] = 0;
groups[3] = 2;
centroid->addBond(groups, parameters);
// Add both forces as different force groups, and create a context.
centroid->setForceGroup(1);
system.addForce(compound);
system.addForce(centroid);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
// Evaluate the force and energy for various positions and see if they match.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < numParticles; j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy, false, 1<<0);
State state2 = context.getState(State::Forces | State::Energy, false, 1<<1);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), TOL);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], TOL);
}
}
void testCustomWeights() {
System system;
system.addParticle(1.0);
system.addParticle(2.0);
system.addParticle(3.0);
system.addParticle(4.0);
CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "distance(g1,g2)^2");
vector<int> particles(2);
vector<double> weights(2);
particles[0] = 0;
particles[1] = 1;
weights[0] = 0.5;
weights[1] = 1.5;
force->addGroup(particles, weights);
particles[0] = 2;
particles[1] = 3;
weights[0] = 2.0;
weights[1] = 1.0;
force->addGroup(particles, weights);
vector<int> groups;
groups.push_back(0);
groups.push_back(1);
vector<double> parameters;
force->addBond(groups, parameters);
system.addForce(force);
// The center of mass of group 0 is (0, 1, 0).
vector<Vec3> positions(4);
positions[0] = Vec3(0, 4, 0);
positions[1] = Vec3(0, 0, 0);
// The center of mass of group 1 is (0, 10, 0).
positions[2] = Vec3(0, 9, 0);
positions[3] = Vec3(0, 12, 0);
// Check the forces and energy.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(9.0*9.0, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(Vec3(0, 2*9*(0.5/2.0), 0), state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 2*9*(1.5/2.0), 0), state.getForces()[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -2*9*(2.0/3.0), 0), state.getForces()[2], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -2*9*(1.0/3.0), 0), state.getForces()[3], TOL);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testHarmonicBond();
testComplexFunction();
testCustomWeights();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
void runPlatformTests() {
}
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