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Commit 64493da6 authored by Peter Eastman's avatar Peter Eastman
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Modified the API for lots of classes so that the number of... 

Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.
parent 29e3fa57
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Showing with 201 additions and 139 deletions
platforms/brook/tests/TestBrookNonbondedForce.cpp
View file @ 64493da6
......@@ -68,7 +68,9 @@ void testBrookCoulomb( FILE* log ){
}
BrookPlatform platform( 32, "cal", log );
System system( numberOfParticles, 0 );
System system;
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int index, double charge, double radius, double depth
......@@ -136,7 +138,9 @@ void testBrookLJ( FILE* log ){
BrookPlatform platform( 32, "cal", log );
// ReferencePlatform platform;
System system( numberOfParticles, 0 );
System system;
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int index, double charge, double radius, double depth
......@@ -203,14 +207,16 @@ void testBrookExclusionsAnd14( FILE* log ){
BrookPlatform platform( 32, "cpu", log );
//ReferencePlatform platform;
System system( numberOfParticles, 0 );
System system;
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int index, double charge, double radius, double depth
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < numberOfParticles; i++)
for (int i = 0; i < numberOfParticles; 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));
......
platforms/brook/tests/TestBrookPeriodicTorsionForce.cpp
View file @ 64493da6
......@@ -68,15 +68,19 @@ void testBrookPeriodicTorsions( FILE* log ){
}
BrookPlatform platform( 32, "cal", log );
System system( numberOfParticles, 0 );
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
PeriodicTorsionForce* forceField = new PeriodicTorsionForce( 1 );
PeriodicTorsionForce* forceField = new PeriodicTorsionForce();
// int index, int atom1, int atom2, int atom3, double angle, double k
forceField->setTorsionParameters(0, 0, 1, 2, 3, 2, PI_M/3, 1.1);
forceField->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
......
platforms/brook/tests/TestBrookRBTorsionForce.cpp
View file @ 64493da6
......@@ -69,11 +69,15 @@ void testBrookRBTorsions( FILE* log ){
BrookPlatform platform( 32, "cal", log );
//ReferencePlatform platform;
System system( numberOfParticles, 0 );
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator( 0, 0.1, 0.01 );
RBTorsionForce* forceField = new RBTorsionForce( 1 );
forceField->setTorsionParameters(0, 0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
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);
OpenMMContext context(system, integrator, platform);
......
platforms/brook/tests/TestBrookVerletIntegrator.cpp
View file @ 64493da6
......@@ -73,14 +73,14 @@ void testVerletSingleBond( FILE* log ){
BrookPlatform platform( 32, "cal", log );
System system( numberOfParticles, 0 );
system.setParticleMass(0, 2.0);
system.setParticleMass(1, 2.0);
System system;
system.addParticle(2.0);
system.addParticle(2.0);
VerletIntegrator integrator(0.001);
HarmonicBondForce* forceField = new HarmonicBondForce(1);
forceField->setBondParameters(0, 0, 1, 1.5, 1);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
// CMMotionRemover* remover = new CMMotionRemover();
......@@ -180,16 +180,16 @@ void testVerletConstraints( FILE* log ){
//ReferencePlatform platform;
BrookPlatform platform( 32, "cal", log );
System system(numParticles, numConstraints);
System system;
VerletIntegrator integrator(0.001);
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, mass );
system.addParticle(mass);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
for (int i = 0; i < numConstraints; ++i){
system.setConstraintParameters(i, 2*i, 2*i+1, 1.0);
system.addConstraint(2*i, 2*i+1, 1.0);
}
system.addForce(forceField);
......
platforms/brook/tests/TstBrookGBSAOBCForce.cpp
View file @ 64493da6
......@@ -154,13 +154,15 @@ static OpenMMContext* testObcForceSetup( int numParticles, int brookContext, FIL
platform = new ReferencePlatform();
}
System* system = new System( numParticles, 0 );
System* system = new System();
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
LangevinIntegrator* integrator = new LangevinIntegrator(0, 0.1, 0.01);
GBSAOBCForce* forceField = new GBSAOBCForce(numParticles);
GBSAOBCForce* forceField = new GBSAOBCForce();
for (int i = 0; i < numParticles; ++i){
// charge radius scalingFactor
forceField->setParticleParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1);
forceField->addParticle(i%2 == 0 ? -1 : 1, 0.15, 1);
//forceField->setParticleParameters(i, i%2 == 0 ? -1 : 1, 1.5, 1);
}
system->addForce(forceField);
......@@ -280,8 +282,10 @@ static OpenMMContext* testObcForceFileSetup( std::string fileName, int brookCont
*numParticles = numberOfParticles;
lineCount++;
System* system = new System( *numParticles, 0 );
GBSAOBCForce* forceField = new GBSAOBCForce(numberOfParticles);
System* system = new System();
for (int i = 0; i < numberOfParticles; i++)
system.addParticle(1.0);
GBSAOBCForce* forceField = new GBSAOBCForce();
vector<Vec3> positions(numberOfParticles);
int index = 0;
......@@ -309,7 +313,7 @@ static OpenMMContext* testObcForceFileSetup( std::string fileName, int brookCont
positions[index++] = Vec3( coordX, coordY, coordZ );
// charge radius scalingFactor
forceField->setParticleParameters( i, charge, radius, scalingFactor );
forceField->addParticle( charge, radius, scalingFactor );
if( log ){
(void) fprintf( log, "%d [%.6f %.6f %.6f] q=%.6f rad=%.6f scl=%.6f bR=%.6f\n", i,
......@@ -431,11 +435,11 @@ void testObcSingleParticle( FILE* log ){
BrookPlatform platform( 32, "cal", log );
//ReferencePlatform platform;
System system(1, 0);
system.setParticleMass(0, 2.0);
System system;
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* forceField = new GBSAOBCForce(1);
forceField->setParticleParameters(0, 0.5, 0.15, 1);
GBSAOBCForce* forceField = new GBSAOBCForce();
forceField->addParticle(0.5, 0.15, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(1);
......@@ -468,11 +472,13 @@ void testObcEConsistentForce( FILE* log ){
//ReferencePlatform platform;
const int numParticles = 10;
System system(numParticles, 0);
System system;
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* forceField = new GBSAOBCForce(numParticles);
for (int i = 0; i < numParticles; ++i)
forceField->setParticleParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1);
GBSAOBCForce* forceField = new GBSAOBCForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(1.0);
forceField->addParticle(i%2 == 0 ? -1 : 1, 0.15, 1);
}
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
......
platforms/cuda/tests/TestCudaAndersenThermostat.cpp
View file @ 64493da6
......@@ -53,11 +53,11 @@ void testTemperature() {
const double temp = 100.0;
const double collisionFreq = 10.0;
CudaPlatform platform;
System system(numParticles, 0);
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 2.0);
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
......@@ -91,11 +91,11 @@ void testRandomSeed() {
const double temp = 100.0;
const double collisionFreq = 10.0;
CudaPlatform platform;
System system(numParticles, 0);
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 2.0);
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
......
platforms/cuda/tests/TestCudaBrownianIntegrator.cpp
View file @ 64493da6
......@@ -55,13 +55,13 @@ const double TOL = 1e-5;
void testSingleBond() {
CudaPlatform platform;
System system(2, 0);
system.setParticleMass(0, 2.0);
system.setParticleMass(1, 2.0);
System system;
system.addParticle(2.0);
system.addParticle(2.0);
double dt = 0.01;
BrownianIntegrator integrator(0, 0.1, dt);
HarmonicBondForce* forceField = new HarmonicBondForce(1);
forceField->setBondParameters(0, 0, 1, 1.5, 1);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -92,13 +92,13 @@ void testTemperature() {
const int numBonds = numParticles-1;
const double temp = 10.0;
CudaPlatform platform;
System system(numParticles, 0);
System system;
BrownianIntegrator integrator(temp, 2.0, 0.01);
HarmonicBondForce* forceField = new HarmonicBondForce(numBonds);
HarmonicBondForce* forceField = new HarmonicBondForce();
for (int i = 0; i < numParticles; ++i)
system.setParticleMass(i, 2.0);
system.addParticle(2.0);
for (int i = 0; i < numBonds; ++i)
forceField->setBondParameters(i, i, i+1, 1.0, 5.0);
forceField->addBond(i, i+1, 1.0, 5.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......@@ -129,19 +129,19 @@ void testConstraints() {
const int numConstraints = 5;
const double temp = 20.0;
CudaPlatform platform;
System system(numParticles, numConstraints);
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.setParticleMass(i, 10.0);
system.addParticle(10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
system.setConstraintParameters(0, 0, 1, 1.0);
system.setConstraintParameters(1, 1, 2, 1.0);
system.setConstraintParameters(2, 2, 3, 1.0);
system.setConstraintParameters(3, 4, 5, 1.0);
system.setConstraintParameters(4, 6, 7, 1.0);
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);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......@@ -176,11 +176,11 @@ void testRandomSeed() {
const double temp = 100.0;
const double collisionFreq = 10.0;
CudaPlatform platform;
System system(numParticles, 0);
System system;
BrownianIntegrator integrator(temp, 2.0, 0.001);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 2.0);
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
......
platforms/cuda/tests/TestCudaCMMotionRemover.cpp
View file @ 64493da6
......@@ -63,13 +63,13 @@ Vec3 calcCM(const vector<Vec3>& values, System& system) {
void testMotionRemoval(Integrator& integrator) {
const int numParticles = 8;
CudaPlatform platform;
System system(numParticles, 0);
HarmonicBondForce* bonds = new HarmonicBondForce(1);
bonds->setBondParameters(0, 2, 3, 2.0, 0.5);
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.setParticleMass(i, i+1);
system.addParticle(i+1);
nonbonded->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(nonbonded);
......
platforms/cuda/tests/TestCudaEwald.cpp
View file @ 64493da6
......@@ -56,7 +56,9 @@ const double TOL = 1e-5;
void testEwald() {
CudaPlatform platform;
System system(2, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
......@@ -85,10 +87,13 @@ void testEwald() {
void testPeriodic() {
CudaPlatform platform;
System system(3, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
HarmonicBondForce* bonds = new HarmonicBondForce(1);
bonds->setBondParameters(0, 0, 1, 1, 0);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1, 0);
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
......
platforms/cuda/tests/TestCudaGBSAOBCForce.cpp
View file @ 64493da6
......@@ -53,12 +53,12 @@ const double TOL = 1e-5;
void testSingleParticle() {
CudaPlatform platform;
System system(1, 0);
system.setParticleMass(0, 2.0);
System system;
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* gbsa = new GBSAOBCForce(1);
GBSAOBCForce* gbsa = new GBSAOBCForce();
NonbondedForce* nonbonded = new NonbondedForce();
gbsa->setParticleParameters(0, 0.5, 0.15, 1);
gbsa->addParticle( 0.5, 0.15, 1);
nonbonded->addParticle(0.5, 1, 0);
system.addForce(gbsa);
system.addForce(nonbonded);
......@@ -77,13 +77,15 @@ void testSingleParticle() {
void testCutoffAndPeriodic() {
CudaPlatform cuda;
System system(2, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* gbsa = new GBSAOBCForce(2);
GBSAOBCForce* gbsa = new GBSAOBCForce();
NonbondedForce* nonbonded = new NonbondedForce();
gbsa->setParticleParameters(0, -1, 0.15, 1);
gbsa->addParticle(-1, 0.15, 1);
nonbonded->addParticle(-1, 1, 0);
gbsa->setParticleParameters(1, 1, 0.15, 1);
gbsa->addParticle(1, 0.15, 1);
nonbonded->addParticle(1, 1, 0);
const double cutoffDistance = 3.0;
const double boxSize = 10.0;
......@@ -128,13 +130,14 @@ void testCutoffAndPeriodic() {
void testForce(int numParticles, NonbondedForce::NonbondedMethod method) {
CudaPlatform cuda;
ReferencePlatform reference;
System system(numParticles, 0);
System system;
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* gbsa = new GBSAOBCForce(numParticles);
GBSAOBCForce* gbsa = new GBSAOBCForce();
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(1.0);
double charge = i%2 == 0 ? -1 : 1;
gbsa->setParticleParameters(i, charge, 0.15, 1);
gbsa->addParticle(charge, 0.15, 1);
nonbonded->addParticle(charge, 1, 0);
}
nonbonded->setNonbondedMethod(method);
......
platforms/cuda/tests/TestCudaHarmonicAngleForce.cpp
View file @ 64493da6
......@@ -50,11 +50,15 @@ const double TOL = 1e-5;
void testAngles() {
CudaPlatform platform;
System system(4, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
HarmonicAngleForce* forceField = new HarmonicAngleForce(2);
forceField->setAngleParameters(0, 0, 1, 2, PI_M/3, 1.1);
forceField->setAngleParameters(1, 1, 2, 3, PI_M/2, 1.2);
HarmonicAngleForce* forceField = new HarmonicAngleForce();
forceField->addAngle(0, 1, 2, PI_M/3, 1.1);
forceField->addAngle(1, 2, 3, PI_M/2, 1.2);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(4);
......
platforms/cuda/tests/TestCudaHarmonicBondForce.cpp
View file @ 64493da6
......@@ -50,11 +50,14 @@ const double TOL = 1e-5;
void testBonds() {
CudaPlatform platform;
System system(3, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
HarmonicBondForce* forceField = new HarmonicBondForce(2);
forceField->setBondParameters(0, 0, 1, 1.5, 0.8);
forceField->setBondParameters(1, 1, 2, 1.2, 0.7);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 0.8);
forceField->addBond(1, 2, 1.2, 0.7);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(3);
......
platforms/cuda/tests/TestCudaLangevinIntegrator.cpp
View file @ 64493da6
......@@ -52,12 +52,12 @@ const double TOL = 1e-5;
void testSingleBond() {
CudaPlatform platform;
System system(2, 0);
system.setParticleMass(0, 2.0);
system.setParticleMass(1, 2.0);
System system;
system.addParticle(2.0);
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
HarmonicBondForce* forceField = new HarmonicBondForce(1);
forceField->setBondParameters(0, 0, 1, 1.5, 1);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -98,11 +98,11 @@ void testTemperature() {
const int numParticles = 8;
const double temp = 100.0;
CudaPlatform platform;
System system(numParticles, 0);
System system;
LangevinIntegrator integrator(temp, 2.0, 0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 2.0);
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
......@@ -134,19 +134,19 @@ void testConstraints() {
const int numConstraints = 5;
const double temp = 100.0;
CudaPlatform platform;
System system(numParticles, numConstraints);
System system;
LangevinIntegrator integrator(temp, 2.0, 0.01);
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 10.0);
system.addParticle(10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
system.setConstraintParameters(0, 0, 1, 1.0);
system.setConstraintParameters(1, 1, 2, 1.0);
system.setConstraintParameters(2, 2, 3, 1.0);
system.setConstraintParameters(3, 4, 5, 1.0);
system.setConstraintParameters(4, 6, 7, 1.0);
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);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......@@ -181,11 +181,11 @@ void testRandomSeed() {
const double temp = 100.0;
const double collisionFreq = 10.0;
CudaPlatform platform;
System system(numParticles, 0);
System system;
LangevinIntegrator integrator(temp, 2.0, 0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 2.0);
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
......
platforms/cuda/tests/TestCudaNonbondedForce.cpp
View file @ 64493da6
......@@ -56,7 +56,9 @@ const double TOL = 1e-5;
void testCoulomb() {
CudaPlatform platform;
System system(2, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(0.5, 1, 0);
......@@ -77,7 +79,9 @@ void testCoulomb() {
void testLJ() {
CudaPlatform platform;
System system(2, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(0, 1.2, 1);
......@@ -100,11 +104,13 @@ void testLJ() {
void testExclusionsAnd14() {
CudaPlatform platform;
System system(5, 0);
System system;
LangevinIntegrator integrator(0.0, 0.1, 0.01);
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < 5; ++i)
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));
......@@ -185,7 +191,10 @@ void testExclusionsAnd14() {
void testCutoff() {
CudaPlatform platform;
System system(3, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(1.0, 1, 0);
......@@ -218,12 +227,14 @@ void testCutoff() {
void testCutoff14() {
CudaPlatform platform;
System system(5, 0);
System system;
LangevinIntegrator integrator(0.0, 0.1, 0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
for (int i = 0; i < 5; ++i)
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);
vector<pair<int, int> > bonds;
......@@ -313,7 +324,10 @@ void testCutoff14() {
void testPeriodic() {
CudaPlatform platform;
System system(3, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
......@@ -351,10 +365,12 @@ void testLargeSystem() {
const double tol = 1e-3;
CudaPlatform cuda;
ReferencePlatform reference;
System system(numParticles, 0);
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
HarmonicBondForce* bonds = new HarmonicBondForce(numMolecules);
HarmonicBondForce* bonds = new HarmonicBondForce();
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
......@@ -371,7 +387,7 @@ void testLargeSystem() {
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(), genrand_real2(), genrand_real2());
velocities[2*i+1] = Vec3(genrand_real2(), genrand_real2(), genrand_real2());
bonds->setBondParameters(i, 2*i, 2*i+1, 1.0, 0.1);
bonds->addBond(2*i, 2*i+1, 1.0, 0.1);
}
// Try with cutoffs but not periodic boundary conditions, and make sure the Cuda and Reference
......@@ -423,12 +439,13 @@ void testBlockInteractions(bool periodic) {
const double cutoff = 1.0;
const double boxSize = (periodic ? 5.1 : 1.1);
CudaPlatform cuda;
System system(numParticles, 0);
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
vector<Vec3> positions(numParticles);
init_gen_rand(0);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
nonbonded->addParticle(1.0, 0.2, 0.2);
positions[i] = Vec3(boxSize*(3*genrand_real2()-1), boxSize*(3*genrand_real2()-1), boxSize*(3*genrand_real2()-1));
}
......
platforms/cuda/tests/TestCudaPeriodicTorsionForce.cpp
View file @ 64493da6
......@@ -50,10 +50,14 @@ const double TOL = 1e-5;
void testPeriodicTorsions() {
CudaPlatform platform;
System system(4, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
PeriodicTorsionForce* forceField = new PeriodicTorsionForce(1);
forceField->setTorsionParameters(0, 0, 1, 2, 3, 2, PI_M/3, 1.1);
PeriodicTorsionForce* forceField = new PeriodicTorsionForce();
forceField->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(4);
......
platforms/cuda/tests/TestCudaRBTorsionForce.cpp
View file @ 64493da6
......@@ -50,10 +50,14 @@ const double TOL = 1e-5;
void testRBTorsions() {
CudaPlatform platform;
System system(4, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
RBTorsionForce* forceField = new RBTorsionForce(1);
forceField->setTorsionParameters(0, 0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
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);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(4);
......
platforms/cuda/tests/TestCudaSettle.cpp
View file @ 64493da6
......@@ -53,20 +53,20 @@ void testConstraints() {
const int numConstraints = numMolecules*3;
const double temp = 100.0;
CudaPlatform platform;
System system(numParticles, numConstraints);
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.setParticleMass(i*3, 16.0);
system.setParticleMass(i*3+1, 1.0);
system.setParticleMass(i*3+2, 1.0);
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.setConstraintParameters(i*3, i*3, i*3+1, 0.1);
system.setConstraintParameters(i*3+1, i*3, i*3+2, 0.1);
system.setConstraintParameters(i*3+2, i*3+1, i*3+2, 0.163);
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);
OpenMMContext context(system, integrator, platform);
......
platforms/cuda/tests/TestCudaStreams.cpp
View file @ 64493da6
......@@ -49,7 +49,9 @@ template <class T, int WIDTH>
void testStream(Stream::DataType type, T scale) {
const int size = 100;
CudaPlatform platform;
System system(size, 0);
System system;
for (int i = 0; i < size; i++)
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
OpenMMContext context(system, integrator, platform);
OpenMMContextImpl* impl = *reinterpret_cast<OpenMMContextImpl**>(&context);
......
platforms/cuda/tests/TestCudaVerletIntegrator.cpp
View file @ 64493da6
......@@ -52,12 +52,12 @@ const double TOL = 1e-5;
void testSingleBond() {
CudaPlatform platform;
System system(2, 0);
system.setParticleMass(0, 2.0);
system.setParticleMass(1, 2.0);
System system;
system.addParticle(2.0);
system.addParticle(2.0);
VerletIntegrator integrator(0.01);
HarmonicBondForce* forceField = new HarmonicBondForce(1);
forceField->setBondParameters(0, 0, 1, 1.5, 1);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -90,19 +90,19 @@ void testConstraints() {
const int numConstraints = 5;
const double temp = 100.0;
CudaPlatform platform;
System system(numParticles, numConstraints);
System system;
VerletIntegrator integrator(0.001);
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 10.0);
system.addParticle(10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
system.setConstraintParameters(0, 0, 1, 1.0);
system.setConstraintParameters(1, 1, 2, 1.0);
system.setConstraintParameters(2, 2, 3, 1.0);
system.setConstraintParameters(3, 4, 5, 1.0);
system.setConstraintParameters(4, 6, 7, 1.0);
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);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......
platforms/reference/tests/TestReferenceAndersenThermostat.cpp
View file @ 64493da6
......@@ -53,11 +53,11 @@ void testTemperature() {
const double temp = 100.0;
const double collisionFreq = 10.0;
ReferencePlatform platform;
System system(numParticles, 0);
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 2.0);
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
......@@ -91,11 +91,11 @@ void testRandomSeed() {
const double temp = 100.0;
const double collisionFreq = 10.0;
ReferencePlatform platform;
System system(numParticles, 0);
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 2.0);
system.addParticle(2.0);
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
......
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