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Commit bcc6216d authored by Peter Eastman's avatar Peter Eastman
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Periodic box dimensions can be changed in the middle of a simulation

parent 149c6ec6
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Showing with 121 additions and 63 deletions
platforms/reference/src/ReferenceKernels.cpp
View file @ bcc6216d
......@@ -54,6 +54,7 @@
#include "SimTKReference/ReferenceVariableVerletDynamics.h"
#include "SimTKReference/ReferenceVerletDynamics.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/Context.h"
#include "openmm/System.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/CustomHbondForceImpl.h"
......@@ -661,11 +662,6 @@ void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const N
}
nonbondedMethod = CalcNonbondedForceKernel::NonbondedMethod(force.getNonbondedMethod());
nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
if (nonbondedMethod == NoCutoff)
neighborList = NULL;
else
......@@ -690,7 +686,13 @@ void ReferenceCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
bool periodic = (nonbondedMethod == CutoffPeriodic);
bool ewald = (nonbondedMethod == Ewald);
bool pme = (nonbondedMethod == PME);
RealOpenMM periodicBoxSize[3];
if (nonbondedMethod != NoCutoff) {
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, (periodic || ewald || pme) ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
clj.setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
}
......@@ -714,7 +716,13 @@ double ReferenceCalcNonbondedForceKernel::executeEnergy(ContextImpl& context) {
bool periodic = (nonbondedMethod == CutoffPeriodic);
bool ewald = (nonbondedMethod == Ewald);
bool pme = (nonbondedMethod == PME);
RealOpenMM periodicBoxSize[3];
if (nonbondedMethod != NoCutoff) {
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, (periodic || ewald || pme) ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
clj.setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
}
......@@ -835,11 +843,6 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
}
nonbondedMethod = CalcCustomNonbondedForceKernel::NonbondedMethod(force.getNonbondedMethod());
nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
if (nonbondedMethod == NoCutoff)
neighborList = NULL;
else
......@@ -878,7 +881,13 @@ void ReferenceCalcCustomNonbondedForceKernel::executeForces(ContextImpl& context
RealOpenMM** forceData = extractForces(context);
ReferenceCustomNonbondedIxn ixn(energyExpression, forceExpression, parameterNames);
bool periodic = (nonbondedMethod == CutoffPeriodic);
RealOpenMM periodicBoxSize[3];
if (nonbondedMethod != NoCutoff) {
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
ixn.setUseCutoff(nonbondedCutoff, *neighborList);
}
......@@ -896,7 +905,13 @@ double ReferenceCalcCustomNonbondedForceKernel::executeEnergy(ContextImpl& conte
RealOpenMM energy = 0;
ReferenceCustomNonbondedIxn ixn(energyExpression, forceExpression, parameterNames);
bool periodic = (nonbondedMethod == CutoffPeriodic);
RealOpenMM periodicBoxSize[3];
if (nonbondedMethod != NoCutoff) {
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
ixn.setUseCutoff(nonbondedCutoff, *neighborList);
}
......@@ -936,15 +951,7 @@ void ReferenceCalcGBSAOBCForceKernel::initialize(const System& system, const GBS
obcParameters->setSoluteDielectric( static_cast<RealOpenMM>(force.getSoluteDielectric()) );
if (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff)
obcParameters->setUseCutoff(static_cast<RealOpenMM>(force.getCutoffDistance()));
if (force.getNonbondedMethod() == GBSAOBCForce::CutoffPeriodic) {
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
RealOpenMM periodicBoxSize[3];
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
obcParameters->setPeriodic(periodicBoxSize);
}
isPeriodic = (force.getNonbondedMethod() == GBSAOBCForce::CutoffPeriodic);
obc = new CpuObc(obcParameters);
obc->setIncludeAceApproximation(true);
}
......@@ -952,12 +959,30 @@ void ReferenceCalcGBSAOBCForceKernel::initialize(const System& system, const GBS
void ReferenceCalcGBSAOBCForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
if (isPeriodic) {
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
RealOpenMM periodicBoxSize[3];
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
obc->getObcParameters()->setPeriodic(periodicBoxSize);
}
obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
}
double ReferenceCalcGBSAOBCForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
if (isPeriodic) {
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
RealOpenMM periodicBoxSize[3];
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
obc->getObcParameters()->setPeriodic(periodicBoxSize);
}
obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
disposeRealArray(forceData, context.getSystem().getNumParticles());
return obc->getEnergy();
......@@ -991,15 +1016,7 @@ void ReferenceCalcGBVIForceKernel::initialize(const System& system, const GBVIFo
gBVIParameters->setSoluteDielectric(static_cast<RealOpenMM>(force.getSoluteDielectric()));
if (force.getNonbondedMethod() != GBVIForce::NoCutoff)
gBVIParameters->setUseCutoff(static_cast<RealOpenMM>(force.getCutoffDistance()));
if (force.getNonbondedMethod() == GBVIForce::CutoffPeriodic) {
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
RealOpenMM periodicBoxSize[3];
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
gBVIParameters->setPeriodic(periodicBoxSize);
}
isPeriodic = (force.getNonbondedMethod() == GBVIForce::CutoffPeriodic);
gbvi = new CpuGBVI(gBVIParameters);
}
......@@ -1008,6 +1025,15 @@ void ReferenceCalcGBVIForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
RealOpenMM* bornRadii = new RealOpenMM[context.getSystem().getNumParticles()];
if (isPeriodic) {
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
RealOpenMM periodicBoxSize[3];
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
gbvi->getGBVIParameters()->setPeriodic(periodicBoxSize);
}
gbvi->computeBornRadii(posData, bornRadii, NULL );
gbvi->computeBornForces(bornRadii, posData, &charges[0], forceData);
delete[] bornRadii;
......@@ -1016,6 +1042,15 @@ void ReferenceCalcGBVIForceKernel::executeForces(ContextImpl& context) {
double ReferenceCalcGBVIForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM* bornRadii = new RealOpenMM[context.getSystem().getNumParticles()];
if (isPeriodic) {
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
RealOpenMM periodicBoxSize[3];
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
gbvi->getGBVIParameters()->setPeriodic(periodicBoxSize);
}
gbvi->computeBornRadii(posData, bornRadii, NULL );
RealOpenMM energy = gbvi->computeBornEnergy(bornRadii ,posData, &charges[0]);
delete[] bornRadii;
......@@ -1069,11 +1104,6 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
globalParameterNames.push_back(force.getGlobalParameterName(i));
nonbondedMethod = CalcCustomGBForceKernel::NonbondedMethod(force.getNonbondedMethod());
nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
if (nonbondedMethod == NoCutoff)
neighborList = NULL;
else
......@@ -1153,12 +1183,19 @@ void ReferenceCalcCustomGBForceKernel::executeForces(ContextImpl& context) {
ReferenceCustomGBIxn ixn(valueExpressions, valueDerivExpressions, valueGradientExpressions, valueNames, valueTypes, energyExpressions,
energyDerivExpressions, energyGradientExpressions, energyTypes, particleParameterNames);
bool periodic = (nonbondedMethod == CutoffPeriodic);
RealOpenMM periodicBoxSize[3];
if (periodic) {
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
ixn.setPeriodic(periodicBoxSize);
}
if (nonbondedMethod != NoCutoff) {
computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
ixn.setUseCutoff(nonbondedCutoff, *neighborList);
}
if (periodic)
ixn.setPeriodic(periodicBoxSize);
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
......@@ -1172,12 +1209,19 @@ double ReferenceCalcCustomGBForceKernel::executeEnergy(ContextImpl& context) {
ReferenceCustomGBIxn ixn(valueExpressions, valueDerivExpressions, valueGradientExpressions, valueNames, valueTypes, energyExpressions,
energyDerivExpressions, energyGradientExpressions, energyTypes, particleParameterNames);
bool periodic = (nonbondedMethod == CutoffPeriodic);
RealOpenMM periodicBoxSize[3];
if (periodic) {
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
ixn.setPeriodic(periodicBoxSize);
}
if (nonbondedMethod != NoCutoff) {
computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
ixn.setUseCutoff(nonbondedCutoff, *neighborList);
}
if (periodic)
ixn.setPeriodic(periodicBoxSize);
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
......@@ -1303,11 +1347,6 @@ void ReferenceCalcCustomHbondForceKernel::initialize(const System& system, const
}
NonbondedMethod nonbondedMethod = CalcCustomHbondForceKernel::NonbondedMethod(force.getNonbondedMethod());
nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
// Create custom functions for the tabulated functions.
......@@ -1336,11 +1375,9 @@ void ReferenceCalcCustomHbondForceKernel::initialize(const System& system, const
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
ixn = new ReferenceCustomHbondIxn(donorParticles, acceptorParticles, energyExpression, donorParameterNames, acceptorParameterNames, distances, angles, dihedrals);
bool periodic = (nonbondedMethod == CutoffPeriodic);
isPeriodic = (nonbondedMethod == CutoffPeriodic);
if (nonbondedMethod != NoCutoff)
ixn->setUseCutoff(nonbondedCutoff);
if (periodic)
ixn->setPeriodic(periodicBoxSize);
// Delete the custom functions.
......@@ -1351,6 +1388,15 @@ void ReferenceCalcCustomHbondForceKernel::initialize(const System& system, const
void ReferenceCalcCustomHbondForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
if (isPeriodic) {
RealOpenMM periodicBoxSize[3];
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
ixn->setPeriodic(periodicBoxSize);
}
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
......@@ -1360,6 +1406,15 @@ void ReferenceCalcCustomHbondForceKernel::executeForces(ContextImpl& context) {
double ReferenceCalcCustomHbondForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(numParticles, 3);
if (isPeriodic) {
RealOpenMM periodicBoxSize[3];
Vec3 boxVectors[3];
context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
ixn->setPeriodic(periodicBoxSize);
}
RealOpenMM energy = 0;
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
......
platforms/reference/src/ReferenceKernels.h
View file @ bcc6216d
......@@ -435,7 +435,7 @@ private:
int numParticles, num14;
int **exclusionArray, **bonded14IndexArray;
RealOpenMM **particleParamArray, **bonded14ParamArray;
RealOpenMM nonbondedCutoff, periodicBoxSize[3], rfDielectric, ewaldAlpha;
RealOpenMM nonbondedCutoff, rfDielectric, ewaldAlpha;
int kmax[3], gridSize[3];
std::vector<std::set<int> > exclusions;
NonbondedMethod nonbondedMethod;
......@@ -513,6 +513,7 @@ public:
private:
CpuObc* obc;
std::vector<RealOpenMM> charges;
bool isPeriodic;
};
/**
......@@ -547,6 +548,7 @@ public:
private:
CpuGBVI * gbvi;
std::vector<RealOpenMM> charges;
bool isPeriodic;
};
/**
......@@ -579,8 +581,9 @@ public:
double executeEnergy(ContextImpl& context);
private:
int numParticles;
bool isPeriodic;
RealOpenMM **particleParamArray;
RealOpenMM nonbondedCutoff, periodicBoxSize[3];
RealOpenMM nonbondedCutoff;
std::vector<std::set<int> > exclusions;
std::vector<std::string> particleParameterNames, globalParameterNames, valueNames;
std::vector<Lepton::ExpressionProgram> valueExpressions;
......@@ -661,9 +664,10 @@ public:
double executeEnergy(ContextImpl& context);
private:
int numDonors, numAcceptors, numParticles;
bool isPeriodic;
int **exclusionArray;
RealOpenMM **donorParamArray, **acceptorParamArray;
RealOpenMM nonbondedCutoff, periodicBoxSize[3];
RealOpenMM nonbondedCutoff;
ReferenceCustomHbondIxn* ixn;
std::vector<std::set<int> > exclusions;
std::vector<std::string> globalParameterNames;
......
platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp
View file @ bcc6216d
......@@ -123,7 +123,6 @@ ReferenceCustomGBIxn::~ReferenceCustomGBIxn( ){
void ReferenceCustomGBIxn::setPeriodic( RealOpenMM* boxSize ) {
assert(cutoff);
assert(boxSize[0] >= 2.0*cutoffDistance);
assert(boxSize[1] >= 2.0*cutoffDistance);
assert(boxSize[2] >= 2.0*cutoffDistance);
......
platforms/reference/tests/TestReferenceCustomGBForce.cpp
View file @ bcc6216d
......@@ -66,8 +66,8 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
}
standardSystem.setPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
customSystem.setPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
GBSAOBCForce* obc = new GBSAOBCForce();
CustomGBForce* custom = new CustomGBForce();
obc->setCutoffDistance(2.0);
......@@ -747,8 +747,8 @@ void testGBVI(GBVIForce::NonbondedMethod gbviMethod, CustomGBForce::NonbondedMet
standardSystem.addParticle(1.0);
customGbviSystem.addParticle(1.0);
}
standardSystem.setPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
customGbviSystem.setPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
customGbviSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
gbvi->setCutoffDistance(2.0);
// create customGbviForce GBVI force
......
platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp
View file @ bcc6216d
......@@ -187,7 +187,7 @@ void testPeriodic() {
forceField->addParticle(vector<double>());
forceField->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
forceField->setCutoffDistance(2.0);
system.setPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
......
platforms/reference/tests/TestReferenceEwald.cpp
View file @ bcc6216d
......@@ -74,7 +74,7 @@ void testEwaldExact() {
nonbonded->addParticle(-1.0, 1.0,0.0);
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setEwaldErrorTolerance(EWALD_TOL);
system.addForce(nonbonded);
Context context(system, integrator, platform);
......@@ -126,7 +126,7 @@ void testEwaldPME() {
nonbonded->addParticle(-1.0, 1.0,0.0);
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setEwaldErrorTolerance(EWALD_TOL);
system.addForce(nonbonded);
Context context(system, integrator, platform);
......@@ -228,7 +228,7 @@ void testEwald2Ions() {
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
const double cutoff = 2.0;
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
nonbonded->setEwaldErrorTolerance(EWALD_TOL);
system.addForce(nonbonded);
Context context(system, integrator, platform);
......@@ -264,7 +264,7 @@ void testWaterSystem() {
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
const double cutoff = 0.8;
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setEwaldErrorTolerance(EWALD_TOL);
system.addForce(nonbonded);
Context context(system, integrator, platform);
......@@ -308,7 +308,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
const int numParticles = 51;
const double boxWidth = 5.0;
System system;
system.setPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
vector<Vec3> positions(numParticles);
......
platforms/reference/tests/TestReferenceGBSAOBCForce.cpp
View file @ bcc6216d
......@@ -87,7 +87,7 @@ void testCutoffAndPeriodic() {
const double boxSize = 10.0;
nonbonded->setCutoffDistance(cutoffDistance);
gbsa->setCutoffDistance(cutoffDistance);
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(gbsa);
system.addForce(nonbonded);
vector<Vec3> positions(2);
......
platforms/reference/tests/TestReferenceNonbondedForce.cpp
View file @ bcc6216d
......@@ -333,7 +333,7 @@ void testPeriodic() {
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
const double cutoff = 2.0;
nonbonded->setCutoffDistance(cutoff);
system.setPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
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);
......
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