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Commit 21847f4a authored by Peter Eastman's avatar Peter Eastman
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Began implementing switching function for Lennard-Jones

parent c4d89122
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openmmapi/include/openmm/CustomNonbondedForce.h
View file @ 21847f4a
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -179,11 +179,13 @@ public:
*/
void setCutoffDistance(double distance);
/**
* Get whether a switching is applied to the interaction.
* Get whether a switching function is applied to the interaction. If the nonbonded method is set
* to NoCutoff, this option is ignored.
*/
bool getUseSwitchingFunction() const;
/**
* Set whether a switching is applied to the interaction.
* Set whether a switching function is applied to the interaction. If the nonbonded method is set
* to NoCutoff, this option is ignored.
*/
void setUseSwitchingFunction(bool use);
/**
......
openmmapi/include/openmm/NonbondedForce.h
View file @ 21847f4a
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -65,6 +65,12 @@ namespace OpenMM {
* This class provides a convenience method for this case called createExceptionsFromBonds(). You pass to it
* a list of bonds and the scale factors to use for 1-4 interactions. It identifies all pairs of particles which
* are separated by 1, 2, or 3 bonds, then automatically creates exceptions for them.
*
* When using a cutoff, by default Lennard-Jones interactions are sharply truncated at the cutoff distance.
* Optionally you can instead use a switching function to make the interaction smoothly go to zero over a finite
* distance range. To enable this, call setUseSwitchingFunction(). You must also call setSwitchingDistance()
* to specify the distance at which the interaction should begin to decrease. The switching distance must be
* less than the cutoff distance.
*/
class OPENMM_EXPORT NonbondedForce : public Force {
......@@ -138,6 +144,26 @@ public:
* @param distance the cutoff distance, measured in nm
*/
void setCutoffDistance(double distance);
/**
* Get whether a switching function is applied to the Lennard-Jones interaction. If the nonbonded method is set
* to NoCutoff, this option is ignored.
*/
bool getUseSwitchingFunction() const;
/**
* Set whether a switching function is applied to the Lennard-Jones interaction. If the nonbonded method is set
* to NoCutoff, this option is ignored.
*/
void setUseSwitchingFunction(bool use);
/**
* Get the distance at which the switching function begins to reduce the Lennard-Jones interaction. This must be
* less than the cutoff distance.
*/
double getSwitchingDistance() const;
/**
* Set the distance at which the switching function begins to reduce the Lennard-Jones interaction. This must be
* less than the cutoff distance.
*/
void setSwitchingDistance(double distance);
/**
* Get the dielectric constant to use for the solvent in the reaction field approximation.
*/
......@@ -301,8 +327,8 @@ private:
class ParticleInfo;
class ExceptionInfo;
NonbondedMethod nonbondedMethod;
double cutoffDistance, rfDielectric, ewaldErrorTol;
bool useDispersionCorrection;
double cutoffDistance, switchingDistance, rfDielectric, ewaldErrorTol;
bool useSwitchingFunction, useDispersionCorrection;
int recipForceGroup;
void addExclusionsToSet(const std::vector<std::set<int> >& bonded12, std::set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const;
std::vector<ParticleInfo> particles;
......
openmmapi/src/NonbondedForce.cpp
View file @ 21847f4a
......@@ -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) 2008-2010 Stanford University and the Authors. *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -47,7 +47,8 @@ using std::string;
using std::stringstream;
using std::vector;
NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), rfDielectric(78.3), ewaldErrorTol(5e-4), useDispersionCorrection(true), recipForceGroup(-1) {
NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), switchingDistance(-1.0), rfDielectric(78.3),
ewaldErrorTol(5e-4), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1) {
}
NonbondedForce::NonbondedMethod NonbondedForce::getNonbondedMethod() const {
......@@ -66,6 +67,22 @@ void NonbondedForce::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
bool NonbondedForce::getUseSwitchingFunction() const {
return useSwitchingFunction;
}
void NonbondedForce::setUseSwitchingFunction(bool use) {
useSwitchingFunction = use;
}
double NonbondedForce::getSwitchingDistance() const {
return switchingDistance;
}
void NonbondedForce::setSwitchingDistance(double distance) {
switchingDistance = distance;
}
double NonbondedForce::getReactionFieldDielectric() const {
return rfDielectric;
}
......
openmmapi/src/NonbondedForceImpl.cpp
View file @ 21847f4a
......@@ -57,6 +57,10 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
const System& system = context.getSystem();
if (owner.getNumParticles() != system.getNumParticles())
throw OpenMMException("NonbondedForce must have exactly as many particles as the System it belongs to.");
if (owner.getUseSwitchingFunction()) {
if (owner.getSwitchingDistance() < 0 || owner.getSwitchingDistance() >= owner.getCutoffDistance())
throw OpenMMException("NonbondedForce: Switching distance must satisfy 0 <= r_switch < r_cutoff");
}
vector<set<int> > exceptions(owner.getNumParticles());
for (int i = 0; i < owner.getNumExceptions(); i++) {
int particle1, particle2;
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 21847f4a
......@@ -867,10 +867,15 @@ void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const N
}
nonbondedMethod = CalcNonbondedForceKernel::NonbondedMethod(force.getNonbondedMethod());
nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
if (nonbondedMethod == NoCutoff)
if (nonbondedMethod == NoCutoff) {
neighborList = NULL;
else
useSwitchingFunction = false;
}
else {
neighborList = new NeighborList();
useSwitchingFunction = force.getUseSwitchingFunction();
switchingDistance = force.getSwitchingDistance();
}
if (nonbondedMethod == Ewald) {
double alpha;
NonbondedForceImpl::calcEwaldParameters(system, force, alpha, kmax[0], kmax[1], kmax[2]);
......@@ -911,6 +916,8 @@ double ReferenceCalcNonbondedForceKernel::execute(ContextImpl& context, bool inc
clj.setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
if (pme)
clj.setUsePME(ewaldAlpha, gridSize);
if (useSwitchingFunction)
clj.setUseSwitchingFunction(switchingDistance);
clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, includeEnergy ? &energy : NULL, includeDirect, includeReciprocal);
if (includeDirect) {
ReferenceBondForce refBondForce;
......
platforms/reference/src/ReferenceKernels.h
View file @ 21847f4a
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -574,8 +574,9 @@ private:
int numParticles, num14;
int **exclusionArray, **bonded14IndexArray;
RealOpenMM **particleParamArray, **bonded14ParamArray;
RealOpenMM nonbondedCutoff, rfDielectric, ewaldAlpha, dispersionCoefficient;
RealOpenMM nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, dispersionCoefficient;
int kmax[3], gridSize[3];
bool useSwitchingFunction;
std::vector<std::set<int> > exclusions;
NonbondedMethod nonbondedMethod;
NeighborList* neighborList;
......
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
View file @ 21847f4a
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -46,7 +46,7 @@ using OpenMM::RealVec;
--------------------------------------------------------------------------------------- */
ReferenceLJCoulombIxn::ReferenceLJCoulombIxn( ) : cutoff(false), periodic(false), ewald(false), pme(false) {
ReferenceLJCoulombIxn::ReferenceLJCoulombIxn( ) : cutoff(false), useSwitch(false), periodic(false), ewald(false), pme(false) {
// ---------------------------------------------------------------------------------------
......@@ -91,6 +91,19 @@ ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn( ){
crf = (1.0/cutoffDistance)*(3.0*solventDielectric)/(2.0*solventDielectric+1.0);
}
/**---------------------------------------------------------------------------------------
Set the force to use a switching function on the Lennard-Jones interaction.
@param distance the switching distance
--------------------------------------------------------------------------------------- */
void ReferenceLJCoulombIxn::setUseSwitchingFunction( RealOpenMM distance ) {
useSwitch = true;
switchingDistance = distance;
}
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
......@@ -357,6 +370,12 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxSize, deltaR[0] );
RealOpenMM r = deltaR[0][ReferenceForce::RIndex];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM switchValue = 1, switchDeriv = 0;
if (useSwitch && r > switchingDistance) {
RealOpenMM t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
switchValue = 1+t*t*t*(-10+t*(15-t*6));
switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
}
RealOpenMM alphaR = alphaEwald * r;
......@@ -368,7 +387,12 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
sig2 *= sig2;
RealOpenMM sig6 = sig2*sig2*sig2;
RealOpenMM eps = atomParameters[ii][EpsIndex]*atomParameters[jj][EpsIndex];
dEdR += eps*( twelve*sig6 - six )*sig6*inverseR*inverseR;
dEdR += switchValue*eps*( twelve*sig6 - six )*sig6*inverseR*inverseR;
vdwEnergy = eps*(sig6-one)*sig6;
if (useSwitch) {
dEdR -= vdwEnergy*switchDeriv*inverseR;
vdwEnergy *= switchValue;
}
// accumulate forces
......@@ -381,7 +405,6 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
// accumulate energies
realSpaceEwaldEnergy = (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erfc(alphaR));
vdwEnergy = eps*(sig6-one)*sig6;
totalVdwEnergy += vdwEnergy;
totalRealSpaceEwaldEnergy += realSpaceEwaldEnergy;
......@@ -554,18 +577,36 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at
RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM switchValue = 1, switchDeriv = 0;
if (useSwitch) {
RealOpenMM r = deltaR[0][ReferenceForce::RIndex];
if (r > switchingDistance) {
RealOpenMM t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
switchValue = 1+t*t*t*(-10+t*(15-t*6));
switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
}
}
RealOpenMM sig = atomParameters[ii][SigIndex] + atomParameters[jj][SigIndex];
RealOpenMM sig2 = inverseR*sig;
sig2 *= sig2;
RealOpenMM sig6 = sig2*sig2*sig2;
RealOpenMM eps = atomParameters[ii][EpsIndex]*atomParameters[jj][EpsIndex];
RealOpenMM dEdR = eps*( twelve*sig6 - six )*sig6;
if (cutoff)
dEdR += (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR-2.0f*krf*r2));
else
dEdR += (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR);
dEdR *= inverseR*inverseR;
RealOpenMM dEdR = switchValue*eps*( twelve*sig6 - six )*sig6;
if (cutoff)
dEdR += (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR-2.0f*krf*r2));
else
dEdR += (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR);
dEdR *= inverseR*inverseR;
RealOpenMM energy = eps*(sig6-one)*sig6;
if (useSwitch) {
dEdR -= energy*switchDeriv*inverseR;
energy *= switchValue;
}
if (cutoff)
energy += (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR+krf*r2-crf));
else
energy += (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR);
// accumulate forces
......@@ -575,22 +616,13 @@ void ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, vector<RealVec>& at
forces[jj][kk] -= force;
}
RealOpenMM energy = 0.0;
// accumulate energies
if( totalEnergy || energyByAtom ) {
if (cutoff)
energy = (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR+krf*r2-crf));
else
energy = (RealOpenMM) (ONE_4PI_EPS0*atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR);
energy += eps*(sig6-one)*sig6;
if( totalEnergy )
*totalEnergy += energy;
if( energyByAtom ){
energyByAtom[ii] += energy;
energyByAtom[jj] += energy;
}
if( totalEnergy )
*totalEnergy += energy;
if( energyByAtom ){
energyByAtom[ii] += energy;
energyByAtom[jj] += energy;
}
}
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.h
View file @ 21847f4a
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -35,12 +35,13 @@ class ReferenceLJCoulombIxn {
private:
bool cutoff;
bool useSwitch;
bool periodic;
bool ewald;
bool pme;
const OpenMM::NeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance;
RealOpenMM cutoffDistance, switchingDistance;
RealOpenMM krf, crf;
RealOpenMM alphaEwald;
int numRx, numRy, numRz;
......@@ -100,6 +101,16 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */
void setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors, RealOpenMM solventDielectric );
/**---------------------------------------------------------------------------------------
Set the force to use a switching function on the Lennard-Jones interaction.
@param distance the switching distance
--------------------------------------------------------------------------------------- */
void setUseSwitchingFunction( RealOpenMM distance );
/**---------------------------------------------------------------------------------------
......
platforms/reference/tests/TestReferenceNonbondedForce.cpp
View file @ 21847f4a
......@@ -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) 2008-2010 Stanford University and the Authors. *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -419,6 +419,62 @@ void testDispersionCorrection() {
ASSERT_EQUAL_TOL(expected, energy1-energy2, 1e-4);
}
void testSwitchingFunction(NonbondedForce::NonbondedMethod method) {
ReferencePlatform platform;
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() {
try {
testCoulomb();
......@@ -428,6 +484,8 @@ int main() {
testCutoff14();
testPeriodic();
testDispersionCorrection();
testSwitchingFunction(NonbondedForce::CutoffNonPeriodic);
testSwitchingFunction(NonbondedForce::PME);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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