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Commit 01f9e415 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #1533 from peastman/amoeba 

Made AMOEBA API more consistent
parents e79abd3d 6e79e69e
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Showing with 110 additions and 66 deletions
plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ 01f9e415
......@@ -147,11 +147,34 @@ public:
*/
void setCutoffDistance(double distance);
/**
* Get the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
* @param[out] alpha the separation parameter
* @param[out] nx the number of grid points along the X axis
* @param[out] ny the number of grid points along the Y axis
* @param[out] nz the number of grid points along the Z axis
*/
void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
/**
* Set the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
*/
void setPMEParameters(double alpha, int nx, int ny, int nz);
/**
* Get the Ewald alpha parameter. If this is 0 (the default), a value is chosen automatically
* based on the Ewald error tolerance.
*
* @return the Ewald alpha parameter
* @deprecated This method exists only for backward compatibility. Use getPMEParameters() instead.
*/
double getAEwald() const;
......@@ -160,6 +183,7 @@ public:
* based on the Ewald error tolerance.
*
* @param aewald alpha parameter
* @deprecated This method exists only for backward compatibility. Use setPMEParameters() instead.
*/
void setAEwald(double aewald);
......@@ -175,6 +199,7 @@ public:
* are chosen automatically based on the Ewald error tolerance.
*
* @return the PME grid dimensions
* @deprecated This method exists only for backward compatibility. Use getPMEParameters() instead.
*/
void getPmeGridDimensions(std::vector<int>& gridDimension) const;
......@@ -183,6 +208,7 @@ public:
* are chosen automatically based on the Ewald error tolerance.
*
* @param gridDimension the PME grid dimensions
* @deprecated This method exists only for backward compatibility. Use setPMEParameters() instead.
*/
void setPmeGridDimensions(const std::vector<int>& gridDimension);
......@@ -408,9 +434,8 @@ private:
NonbondedMethod nonbondedMethod;
PolarizationType polarizationType;
double cutoffDistance;
double aewald;
int pmeBSplineOrder;
std::vector<int> pmeGridDimension;
double alpha;
int pmeBSplineOrder, nx, ny, nz;
int mutualInducedMaxIterations;
std::vector<double> extrapolationCoefficients;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h
View file @ 01f9e415
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -183,13 +183,34 @@ public:
*/
void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const;
/**
* Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @return the cutoff distance, measured in nm
*/
double getCutoffDistance() const;
/**
* Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @param distance the cutoff distance, measured in nm
*/
void setCutoffDistance(double distance);
/**
* Set the cutoff distance.
*
* @deprecated This method exists only for backward compatibility. Use setCutoffDistance() instead.
*/
void setCutoff(double cutoff);
/**
* Get the cutoff distance.
*
* @deprecated This method exists only for backward compatibility. Use getCutoffDistance() instead.
*/
double getCutoff() const;
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 01f9e415
......@@ -40,9 +40,7 @@ using std::string;
using std::vector;
AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), polarizationType(Mutual), pmeBSplineOrder(5), cutoffDistance(1.0), ewaldErrorTol(1e-4), mutualInducedMaxIterations(60),
mutualInducedTargetEpsilon(1.0e-02), scalingDistanceCutoff(100.0), electricConstant(138.9354558456), aewald(0.0) {
pmeGridDimension.resize(3);
pmeGridDimension[0] = pmeGridDimension[1] = pmeGridDimension[2];
mutualInducedTargetEpsilon(1.0e-02), scalingDistanceCutoff(100.0), electricConstant(138.9354558456), alpha(0.0), nx(0), ny(0), nz(0) {
extrapolationCoefficients.push_back(-0.154);
extrapolationCoefficients.push_back(0.017);
extrapolationCoefficients.push_back(0.658);
......@@ -81,12 +79,26 @@ void AmoebaMultipoleForce::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
void AmoebaMultipoleForce::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
alpha = this->alpha;
nx = this->nx;
ny = this->ny;
nz = this->nz;
}
void AmoebaMultipoleForce::setPMEParameters(double alpha, int nx, int ny, int nz) {
this->alpha = alpha;
this->nx = nx;
this->ny = ny;
this->nz = nz;
}
double AmoebaMultipoleForce::getAEwald() const {
return aewald;
return alpha;
}
void AmoebaMultipoleForce::setAEwald(double inputAewald) {
aewald = inputAewald;
alpha = inputAewald;
}
int AmoebaMultipoleForce::getPmeBSplineOrder() const {
......@@ -94,26 +106,18 @@ int AmoebaMultipoleForce::getPmeBSplineOrder() const {
}
void AmoebaMultipoleForce::getPmeGridDimensions(std::vector<int>& gridDimension) const {
if (gridDimension.size() < 3) {
if (gridDimension.size() < 3)
gridDimension.resize(3);
}
if (pmeGridDimension.size() > 2) {
gridDimension[0] = pmeGridDimension[0];
gridDimension[1] = pmeGridDimension[1];
gridDimension[2] = pmeGridDimension[2];
} else {
gridDimension[0] = gridDimension[1] = gridDimension[2] = 0;
}
return;
gridDimension[0] = nx;
gridDimension[1] = ny;
gridDimension[2] = nz;
}
void AmoebaMultipoleForce::setPmeGridDimensions(const std::vector<int>& gridDimension) {
pmeGridDimension.resize(3);
pmeGridDimension[0] = gridDimension[0];
pmeGridDimension[1] = gridDimension[1];
pmeGridDimension[2] = gridDimension[2];
return;
}
nx = gridDimension[0];
ny = gridDimension[1];
nz = gridDimension[2];
}
void AmoebaMultipoleForce::getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const {
dynamic_cast<const AmoebaMultipoleForceImpl&>(getImplInContext(context)).getPMEParameters(alpha, nx, ny, nz);
......
plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp
View file @ 01f9e415
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -102,12 +102,20 @@ void AmoebaVdwForce::getParticleExclusions(int particleIndex, std::vector< int >
}
void AmoebaVdwForce::setCutoff(double inputCutoff) {
double AmoebaVdwForce::getCutoffDistance() const {
return cutoff;
}
void AmoebaVdwForce::setCutoffDistance(double inputCutoff) {
cutoff = inputCutoff;
}
void AmoebaVdwForce::setCutoff(double inputCutoff) {
setCutoffDistance(inputCutoff);
}
double AmoebaVdwForce::getCutoff() const {
return cutoff;
return getCutoffDistance();
}
AmoebaVdwForce::NonbondedMethod AmoebaVdwForce::getNonbondedMethod() const {
......
plugins/amoeba/openmmapi/src/AmoebaVdwForceImpl.cpp
View file @ 01f9e415
......@@ -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 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -62,7 +62,7 @@ void AmoebaVdwForceImpl::initialize(ContextImpl& context) {
if (owner.getNonbondedMethod() == AmoebaVdwForce::CutoffPeriodic) {
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
double cutoff = owner.getCutoff();
double cutoff = owner.getCutoffDistance();
if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
throw OpenMMException("AmoebaVdwForce: The cutoff distance cannot be greater than half the periodic box size.");
}
......@@ -103,7 +103,7 @@ double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const
}
// Compute the VdW tapering coefficients. Mostly copied from amoebaCudaGpu.cpp.
double cutoff = force.getCutoff();
double cutoff = force.getCutoffDistance();
double vdwTaper = 0.90; // vdwTaper is a scaling factor, it is not a distance.
double c0 = 0.0;
double c1 = 0.0;
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 01f9e415
......@@ -1146,11 +1146,10 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
coefficients << cu.doubleToString(sum);
}
defines["EXTRAPOLATION_COEFFICIENTS_SUM"] = coefficients.str();
alpha = force.getAEwald();
if (usePME) {
vector<int> pmeGridDimension;
force.getPmeGridDimensions(pmeGridDimension);
if (pmeGridDimension[0] == 0 || alpha == 0.0) {
int nx, ny, nz;
force.getPMEParameters(alpha, nx, ny, nz);
if (nx == 0 || alpha == 0.0) {
NonbondedForce nb;
nb.setEwaldErrorTolerance(force.getEwaldErrorTolerance());
nb.setCutoffDistance(force.getCutoffDistance());
......@@ -1159,9 +1158,9 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
gridSizeY = CudaFFT3D::findLegalDimension(gridSizeY);
gridSizeZ = CudaFFT3D::findLegalDimension(gridSizeZ);
} else {
gridSizeX = CudaFFT3D::findLegalDimension(pmeGridDimension[0]);
gridSizeY = CudaFFT3D::findLegalDimension(pmeGridDimension[1]);
gridSizeZ = CudaFFT3D::findLegalDimension(pmeGridDimension[2]);
gridSizeX = CudaFFT3D::findLegalDimension(nx);
gridSizeY = CudaFFT3D::findLegalDimension(ny);
gridSizeZ = CudaFFT3D::findLegalDimension(nz);
}
defines["EWALD_ALPHA"] = cu.doubleToString(alpha);
defines["SQRT_PI"] = cu.doubleToString(sqrt(M_PI));
......@@ -2601,15 +2600,15 @@ void CudaCalcAmoebaVdwForceKernel::initialize(const System& system, const Amoeba
replacements["EPSILON_COMBINING_RULE"] = "4";
else
throw OpenMMException("Illegal combining rule for sigma: "+sigmaCombiningRule);
double cutoff = force.getCutoff();
double cutoff = force.getCutoffDistance();
double taperCutoff = cutoff*0.9;
replacements["CUTOFF_DISTANCE"] = cu.doubleToString(force.getCutoff());
replacements["CUTOFF_DISTANCE"] = cu.doubleToString(force.getCutoffDistance());
replacements["TAPER_CUTOFF"] = cu.doubleToString(taperCutoff);
replacements["TAPER_C3"] = cu.doubleToString(10/pow(taperCutoff-cutoff, 3.0));
replacements["TAPER_C4"] = cu.doubleToString(15/pow(taperCutoff-cutoff, 4.0));
replacements["TAPER_C5"] = cu.doubleToString(6/pow(taperCutoff-cutoff, 5.0));
bool useCutoff = (force.getNonbondedMethod() != AmoebaVdwForce::NoCutoff);
nonbonded->addInteraction(useCutoff, useCutoff, true, force.getCutoff(), exclusions,
nonbonded->addInteraction(useCutoff, useCutoff, true, force.getCutoffDistance(), exclusions,
cu.replaceStrings(CudaAmoebaKernelSources::amoebaVdwForce2, replacements), 0);
// Create the other kernels.
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 01f9e415
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -594,9 +594,9 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
nonbondedMethod = force.getNonbondedMethod();
if (nonbondedMethod == AmoebaMultipoleForce::PME) {
usePme = true;
alphaEwald = force.getAEwald();
pmeGridDimension.resize(3);
force.getPMEParameters(alphaEwald, pmeGridDimension[0], pmeGridDimension[1], pmeGridDimension[2]);
cutoffDistance = force.getCutoffDistance();
force.getPmeGridDimensions(pmeGridDimension);
if (pmeGridDimension[0] == 0 || alphaEwald == 0.0) {
NonbondedForce nb;
nb.setEwaldErrorTolerance(force.getEwaldErrorTolerance());
......@@ -996,7 +996,7 @@ void ReferenceCalcAmoebaVdwForceKernel::initialize(const System& system, const A
epsilonCombiningRule = force.getEpsilonCombiningRule();
useCutoff = (force.getNonbondedMethod() != AmoebaVdwForce::NoCutoff);
usePBC = (force.getNonbondedMethod() == AmoebaVdwForce::CutoffPeriodic);
cutoff = force.getCutoff();
cutoff = force.getCutoffDistance();
neighborList = useCutoff ? new NeighborList() : NULL;
dispersionCoefficient = force.getUseDispersionCorrection() ? AmoebaVdwForceImpl::calcDispersionCorrection(system, force) : 0.0;
......
plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp
View file @ 01f9e415
......@@ -74,20 +74,18 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
node.setIntProperty("forceGroup", force.getForceGroup());
node.setIntProperty("nonbondedMethod", force.getNonbondedMethod());
node.setIntProperty("polarizationType", force.getPolarizationType());
//node.setIntProperty("pmeBSplineOrder", force.getPmeBSplineOrder());
//node.setIntProperty("mutualInducedIterationMethod", force.getMutualInducedIterationMethod());
node.setIntProperty("mutualInducedMaxIterations", force.getMutualInducedMaxIterations());
node.setDoubleProperty("cutoffDistance", force.getCutoffDistance());
node.setDoubleProperty("aEwald", force.getAEwald());
double alpha;
int nx, ny, nz;
force.getPMEParameters(alpha, nx, ny, nz);
node.setDoubleProperty("aEwald", alpha);
node.setDoubleProperty("mutualInducedTargetEpsilon", force.getMutualInducedTargetEpsilon());
//node.setDoubleProperty("electricConstant", force.getElectricConstant());
node.setDoubleProperty("ewaldErrorTolerance", force.getEwaldErrorTolerance());
std::vector<int> gridDimensions;
force.getPmeGridDimensions(gridDimensions);
SerializationNode& gridDimensionsNode = node.createChildNode("MultipoleParticleGridDimension");
gridDimensionsNode.setIntProperty("d0", gridDimensions[0]).setIntProperty("d1", gridDimensions[1]).setIntProperty("d2", gridDimensions[2]);
gridDimensionsNode.setIntProperty("d0", nx).setIntProperty("d1", ny).setIntProperty("d2", nz);
SerializationNode& coefficients = node.createChildNode("ExtrapolationCoefficients");
vector<double> coeff = force.getExtrapolationCoefficients();
......@@ -144,22 +142,14 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
force->setNonbondedMethod(static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty("nonbondedMethod")));
if (version >= 2)
force->setPolarizationType(static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty("polarizationType")));
//force->setPmeBSplineOrder(node.getIntProperty("pmeBSplineOrder"));
//force->setMutualInducedIterationMethod(static_cast<AmoebaMultipoleForce::MutualInducedIterationMethod>(node.getIntProperty("mutualInducedIterationMethod")));
force->setMutualInducedMaxIterations(node.getIntProperty("mutualInducedMaxIterations"));
force->setCutoffDistance(node.getDoubleProperty("cutoffDistance"));
force->setAEwald(node.getDoubleProperty("aEwald"));
force->setMutualInducedTargetEpsilon(node.getDoubleProperty("mutualInducedTargetEpsilon"));
//force->setElectricConstant(node.getDoubleProperty("electricConstant"));
force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldErrorTolerance"));
std::vector<int> gridDimensions;
const SerializationNode& gridDimensionsNode = node.getChildNode("MultipoleParticleGridDimension");
gridDimensions.push_back(gridDimensionsNode.getIntProperty("d0"));
gridDimensions.push_back(gridDimensionsNode.getIntProperty("d1"));
gridDimensions.push_back(gridDimensionsNode.getIntProperty("d2"));
force->setPmeGridDimensions(gridDimensions);
force->setPMEParameters(node.getDoubleProperty("aEwald"), gridDimensionsNode.getIntProperty("d0"), gridDimensionsNode.getIntProperty("d1"), gridDimensionsNode.getIntProperty("d2"));
if (version >= 3) {
const SerializationNode& coefficients = node.getChildNode("ExtrapolationCoefficients");
......
plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp
View file @ 01f9e415
......@@ -48,7 +48,7 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
node.setIntProperty("forceGroup", force.getForceGroup());
node.setStringProperty("SigmaCombiningRule", force.getSigmaCombiningRule());
node.setStringProperty("EpsilonCombiningRule", force.getEpsilonCombiningRule());
node.setDoubleProperty("VdwCutoff", force.getCutoff());
node.setDoubleProperty("VdwCutoff", force.getCutoffDistance());
node.setIntProperty("method", (int) force.getNonbondedMethod());
......@@ -82,7 +82,7 @@ void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setSigmaCombiningRule(node.getStringProperty("SigmaCombiningRule"));
force->setEpsilonCombiningRule(node.getStringProperty("EpsilonCombiningRule"));
force->setCutoff(node.getDoubleProperty("VdwCutoff"));
force->setCutoffDistance(node.getDoubleProperty("VdwCutoff"));
force->setNonbondedMethod((AmoebaVdwForce::NonbondedMethod) node.getIntProperty("method"));
const SerializationNode& particles = node.getChildNode("VdwParticles");
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp
View file @ 01f9e415
......@@ -116,11 +116,8 @@ void testSerialization() {
ASSERT_EQUAL(force1.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force1.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force1.getAEwald(), force2.getAEwald());
//ASSERT_EQUAL(force1.getPmeBSplineOrder(), force2.getPmeBSplineOrder());
//ASSERT_EQUAL(force1.getMutualInducedIterationMethod(), force2.getMutualInducedIterationMethod());
ASSERT_EQUAL(force1.getMutualInducedMaxIterations(), force2.getMutualInducedMaxIterations());
ASSERT_EQUAL(force1.getMutualInducedTargetEpsilon(), force2.getMutualInducedTargetEpsilon());
//ASSERT_EQUAL(force1.getElectricConstant(), force2.getElectricConstant());
ASSERT_EQUAL(force1.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
......
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