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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 140 additions and 101 deletions
platforms/reference/tests/TestReferenceBrownianIntegrator.cpp
View file @ 64493da6
......@@ -52,13 +52,13 @@ const double TOL = 1e-5;
void testSingleBond() {
ReferencePlatform 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);
......@@ -89,14 +89,14 @@ void testTemperature() {
const int numBonds = numParticles-1;
const double temp = 10.0;
ReferencePlatform 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);
......@@ -126,16 +126,16 @@ void testConstraints() {
const int numParticles = 8;
const double temp = 100.0;
ReferencePlatform platform;
System system(numParticles, numParticles-1);
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);
}
for (int i = 0; i < numParticles-1; ++i)
system.setConstraintParameters(i, i, i+1, 1.0);
system.addConstraint(i, i+1, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......@@ -167,11 +167,11 @@ void testRandomSeed() {
const double temp = 100.0;
const double collisionFreq = 10.0;
ReferencePlatform 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/reference/tests/TestReferenceCMMotionRemover.cpp
View file @ 64493da6
......@@ -64,14 +64,14 @@ void testMotionRemoval() {
const double temp = 100.0;
const double collisionFreq = 10.0;
ReferencePlatform platform;
System system(numParticles, 0);
System system;
VerletIntegrator integrator(0.01);
HarmonicBondForce* bonds = new HarmonicBondForce(1);
bonds->setBondParameters(0, 2, 3, 2.0, 0.5);
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/reference/tests/TestReferenceEwald.cpp
View file @ 64493da6
......@@ -51,7 +51,9 @@ const double TOL = 1e-5;
void testEwald() {
ReferencePlatform 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);
......
platforms/reference/tests/TestReferenceGBSAOBCForce.cpp
View file @ 64493da6
......@@ -52,11 +52,11 @@ const double TOL = 1e-5;
void testSingleParticle() {
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);
......@@ -73,13 +73,15 @@ void testSingleParticle() {
void testCutoffAndPeriodic() {
ReferencePlatform platform;
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;
......@@ -124,11 +126,13 @@ void testCutoffAndPeriodic() {
void testForce() {
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/reference/tests/TestReferenceGBVIForce.cpp
View file @ 64493da6
......@@ -54,16 +54,16 @@ const double TOL = 1e-5;
void testSingleParticle() {
ReferencePlatform platform;
System system(1, 0);
system.setParticleMass(0, 2.0);
System system;
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBVIForce* forceField = new GBVIForce(1);
GBVIForce* forceField = new GBVIForce();
double charge = 0.0;
double radius = 0.15;
double gamma = 1.0;
forceField->setParticleParameters(0, charge, radius, gamma);
forceField->addParticle(charge, radius, gamma);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
......@@ -143,22 +143,22 @@ void testEnergyEthane() {
ReferencePlatform platform;
const int numParticles = 8;
System system(numParticles, 0);
System system;
LangevinIntegrator integrator(0, 0.1, 0.01);
//void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k)
double C_HBondDistance = 0.1097;
double C_CBondDistance = 0.1504;
HarmonicBondForce* bonds = new HarmonicBondForce(7);
bonds->setBondParameters(0, 0, 1, C_HBondDistance, 0.0);
bonds->setBondParameters(1, 2, 1, C_HBondDistance, 0.0);
bonds->setBondParameters(2, 3, 1, C_HBondDistance, 0.0);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, C_HBondDistance, 0.0);
bonds->addBond(2, 1, C_HBondDistance, 0.0);
bonds->addBond(3, 1, C_HBondDistance, 0.0);
bonds->setBondParameters(3, 1, 4, C_CBondDistance, 0.0);
bonds->addBond(1, 4, C_CBondDistance, 0.0);
bonds->setBondParameters(4, 5, 4, C_HBondDistance, 0.0);
bonds->setBondParameters(5, 6, 4, C_HBondDistance, 0.0);
bonds->setBondParameters(6, 7, 4, C_HBondDistance, 0.0);
bonds->addBond(5, 4, C_HBondDistance, 0.0);
bonds->addBond(6, 4, C_HBondDistance, 0.0);
bonds->addBond(7, 4, C_HBondDistance, 0.0);
system.addForce(bonds);
......@@ -182,20 +182,22 @@ void testEnergyEthane() {
int VI = 1;
if( VI ){
(void) fprintf( stderr, "Applying GB/VI\n" );
GBVIForce* forceField = new GBVIForce(numParticles);
GBVIForce* forceField = new GBVIForce();
for( int i = 0; i < numParticles; i++ ){
forceField->setParticleParameters(i, H_charge, H_radius, H_gamma);
system.addParticle(1.0);
forceField->addParticle( H_charge, H_radius, H_gamma);
}
forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
forceField->setParticleParameters(4, C_charge, C_radius, C_gamma);
system.addForce(forceField);
} else {
(void) fprintf( stderr, "Applying GBSA OBC\n" );
GBSAOBCForce* forceField = new GBSAOBCForce(numParticles);
GBSAOBCForce* forceField = new GBSAOBCForce();
double H_scale = 0.85;
double C_scale = 0.72;
for( int i = 0; i < numParticles; i++ ){
forceField->setParticleParameters(i, H_charge, H_radius, H_scale );
system.addParticle(1.0);
forceField->addParticle(H_charge, H_radius, H_scale );
}
forceField->setParticleParameters(1, C_charge, C_radius, C_scale);
forceField->setParticleParameters(4, C_charge, C_radius, C_scale);
......@@ -266,13 +268,15 @@ void testEnergyTwoParticle() {
ReferencePlatform platform;
const int numParticles = 2;
System system(numParticles, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
//void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k)
double C_HBondDistance = 3.0;
HarmonicBondForce* bonds = new HarmonicBondForce(1);
bonds->setBondParameters(0, 0, 1, C_HBondDistance, 0.0);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, C_HBondDistance, 0.0);
system.addForce(bonds);
double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
......@@ -298,15 +302,15 @@ void testEnergyTwoParticle() {
int VI = 1;
if( VI ){
(void) fprintf( stderr, "Applying GB/VI\n" );
GBVIForce* forceField = new GBVIForce(numParticles);
forceField->setParticleParameters(0, H_charge, H_radius, H_gamma);
forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
GBVIForce* forceField = new GBVIForce();
forceField->addParticle(H_charge, H_radius, H_gamma);
forceField->addParticle(C_charge, C_radius, C_gamma);
system.addForce(forceField);
} else {
(void) fprintf( stderr, "Applying GBSA OBC\n" );
GBSAOBCForce* forceField = new GBSAOBCForce(numParticles);
forceField->setParticleParameters(0, H_charge, H_radius, 1.0);
forceField->setParticleParameters(1, C_charge, C_radius, 1.0);
GBSAOBCForce* forceField = new GBSAOBCForce();
forceField->addParticle(H_charge, H_radius, 1.0);
forceField->addParticle(C_charge, C_radius, 1.0);
system.addForce(forceField);
}
......
platforms/reference/tests/TestReferenceHarmonicAngleForce.cpp
View file @ 64493da6
......@@ -50,11 +50,15 @@ const double TOL = 1e-5;
void testAngles() {
ReferencePlatform platform;
System system(4, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(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/reference/tests/TestReferenceHarmonicBondForce.cpp
View file @ 64493da6
......@@ -50,11 +50,14 @@ const double TOL = 1e-5;
void testBonds() {
ReferencePlatform platform;
System system(3, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(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/reference/tests/TestReferenceKineticEnergy.cpp
View file @ 64493da6
......@@ -48,9 +48,9 @@ const double TOL = 1e-5;
void testCalcKE() {
ReferencePlatform platform;
System system(4, 0);
System system;
for (int i = 0; i < 4; ++i)
system.setParticleMass(i, i+1);
system.addParticle(i+1);
VerletIntegrator integrator(0.01);
OpenMMContext context(system, integrator, platform);
vector<Vec3> velocities(4);
......
platforms/reference/tests/TestReferenceLangevinIntegrator.cpp
View file @ 64493da6
......@@ -52,12 +52,12 @@ const double TOL = 1e-5;
void testSingleBond() {
ReferencePlatform 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;
ReferencePlatform 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);
......@@ -133,16 +133,16 @@ void testConstraints() {
const int numParticles = 8;
const double temp = 100.0;
ReferencePlatform platform;
System system(numParticles, numParticles-1);
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);
}
for (int i = 0; i < numParticles-1; ++i)
system.setConstraintParameters(i, i, i+1, 1.0);
system.addConstraint(i, i+1, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......@@ -174,11 +174,11 @@ void testRandomSeed() {
const double temp = 100.0;
const double collisionFreq = 10.0;
ReferencePlatform 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/reference/tests/TestReferenceNonbondedForce.cpp
View file @ 64493da6
......@@ -51,7 +51,9 @@ const double TOL = 1e-5;
void testCoulomb() {
ReferencePlatform platform;
System system(2, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(0.5, 1, 0);
......@@ -72,7 +74,9 @@ void testCoulomb() {
void testLJ() {
ReferencePlatform platform;
System system(2, 0);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(0, 1.2, 1);
......@@ -95,11 +99,13 @@ void testLJ() {
void testExclusionsAnd14() {
ReferencePlatform platform;
System system(5, 0);
System system;
VerletIntegrator integrator(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));
......@@ -181,7 +187,10 @@ void testExclusionsAnd14() {
void testCutoff() {
ReferencePlatform platform;
System system(3, 0);
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);
......@@ -214,11 +223,13 @@ void testCutoff() {
void testCutoff14() {
ReferencePlatform platform;
System system(5, 0);
System system;
VerletIntegrator integrator(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);
}
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
const double cutoff = 3.5;
nonbonded->setCutoffDistance(cutoff);
......@@ -309,7 +320,10 @@ void testCutoff14() {
void testPeriodic() {
ReferencePlatform platform;
System system(3, 0);
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);
......
platforms/reference/tests/TestReferencePeriodicTorsionForce.cpp
View file @ 64493da6
......@@ -50,10 +50,14 @@ const double TOL = 1e-5;
void testPeriodicTorsions() {
ReferencePlatform platform;
System system(4, 0);
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(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/reference/tests/TestReferenceRBTorsionForce.cpp
View file @ 64493da6
......@@ -50,10 +50,14 @@ const double TOL = 1e-5;
void testRBTorsions() {
ReferencePlatform platform;
System system(4, 0);
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(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/reference/tests/TestReferenceVerletIntegrator.cpp
View file @ 64493da6
......@@ -52,12 +52,12 @@ const double TOL = 1e-5;
void testSingleBond() {
ReferencePlatform 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);
......@@ -89,16 +89,16 @@ void testConstraints() {
const int numParticles = 8;
const double temp = 100.0;
ReferencePlatform platform;
System system(numParticles, numParticles-1);
System system;
VerletIntegrator integrator(0.002);
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);
}
for (int i = 0; i < numParticles-1; ++i)
system.setConstraintParameters(i, i, i+1, 1.0);
system.addConstraint(i, i+1, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......
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