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Commit b6b43fdf authored by Peter Eastman's avatar Peter Eastman
Browse files

Began implementing new features in AmoebaVdwForce

parent eec9cd69
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Showing with 556 additions and 145 deletions
plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h
View file @ b6b43fdf
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -39,11 +39,24 @@
namespace OpenMM {
/**
* This class implements a buffered 14-7 potential used to model van der Waals forces.
* This class models van der Waals forces in the AMOEBA force field. It can use
* either buffered 14-7 potential or a Lennard-Jones 12-6 potential.
*
* To use it, create an AmoebaVdwForce object then call addParticle() once for each particle. After
* a particle has been added, you can modify its force field parameters by calling setParticleParameters().
* This will have no effect on Contexts that already exist unless you call updateParametersInContext().
* This class can operate in two different modes. In one mode, force field parameters
* are defined for each particle. When two particles interact, a combining rule is
* used to calculate the interaction parameters based on the parameters for the two
* particles. To use the class in this mode, call the version of addParticle() that
* takes sigma and epsilon values. It should be called once for each particle in the
* System.
*
* In the other mode, each particle has a type index, and parameters are specified for
* each type rather than each individual particle. By default this mode also uses a
* combining rule, but you can override it by defining alternate parameters to use for
* specific pairs of particle types. To use the class in this mode, call the version of
* addParticle() that takes a type index. It should be called once for each particle
* in the System. You also must call addParticleType() once for each type. If you
* wish to override the combining for particular pairs of types, do so by calling
* addTypePair().
*
* A unique feature of this class is that the interaction site for a particle does not need to be
* exactly at the particle's location. Instead, it can be placed a fraction of the distance from that
......@@ -91,6 +104,20 @@ public:
CutoffPeriodic = 1,
};
/**
* This is an enumeration of the different potential functions that can be used.
*/
enum PotentialFunction {
/**
* Use a buffered 14-7 potential. This is the default.
*/
Buffered147 = 0,
/**
* Use a Lennard-Jones 12-6 potential.
*/
LennardJones = 1,
};
/**
* This is an enumeration of the different alchemical methods used when applying softcore interactions.
*/
......@@ -121,6 +148,20 @@ public:
return parameters.size();
}
/**
* Get the number of particle types.
*/
int getNumParticleTypes() const {
return types.size();
}
/**
* Get the number of type pairs.
*/
int getNumTypePairs() const {
return pairs.size();
}
/**
* Set the force field parameters for a vdw particle.
*
......@@ -131,9 +172,10 @@ public:
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed
* @param isAlchemical if true, this vdW particle is undergoing an alchemical change.
* @param typeIndex the index of the particle type for this particle
*/
void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon,
double reductionFactor, bool isAlchemical = false);
double reductionFactor, bool isAlchemical=false, int typeIndex=-1);
/**
* Get the force field parameters for a vdw particle.
......@@ -145,13 +187,14 @@ public:
* @param[out] reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed
* @param[out] isAlchemical if true, this vdW particle is undergoing an alchemical change.
* @param[out] typeIndex the index of the particle type for this particle
*/
void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon,
double& reductionFactor, bool& isAlchemical) const;
double& reductionFactor, bool& isAlchemical, int& typeIndex) const;
/**
* Add the force field parameters for a vdw particle.
* Add the force field parameters for a vdw particle. This version is used when parameters
* are defined for each particle.
*
* @param parentIndex the index of the parent particle
* @param sigma vdw sigma
......@@ -163,6 +206,82 @@ public:
*/
int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor, bool isAlchemical = false);
/**
* Add the force field parameters for a vdw particle. This version is used when parameters
* are defined by particle type.
*
* @param parentIndex the index of the parent particle
* @param typeIndex the index of the particle type for this particle
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed
* @param isAlchemical if true, this vdW particle is undergoing an alchemical change.
* @return index of added particle
*/
int addParticle(int parentIndex, int typeIndex, double reductionFactor, bool isAlchemical = false);
/**
* Add a particle type.
*
* @param sigma the sigma value for particles of this type
* @param epsilon the epsilon value for particles of this type
* @return the index of the particle type that was just added.
*/
int addParticleType(double sigma, double epsilon);
/**
* Get the force field parameters for a particle type.
*
* @param typeIndex the index of the particle type
* @param[out] sigma the sigma value for particles of this type
* @param[out] epsilon the epsilon value for particles of this type
*/
void getParticleTypeParameters(int typeIndex, double& sigma, double& epsilon) const;
/**
* Set the force field parameters for a particle type.
*
* @param typeIndex the index of the particle type
* @param sigma the sigma value for particles of this type
* @param epsilon the epsilon value for particles of this type
*/
void setParticleTypeParameters(int typeIndex, double sigma, double epsilon);
/**
* Add a type pair. This overrides the standard combining rule for interactions
* between particles of two particular types.
*
* @param type1 the index of the first particle type
* @param type2 the index of the second particle type
* @param sigma the sigma value for interactions between particles of these two types
* @param epsilon the epsilon value for interactions between particles of these two types
* @return the index of the type pair that was just added.
*/
int addTypePair(int type1, int type2, double sigma, double epsilon);
/**
* Get the force field parameters for a type pair. This overrides the standard
* combining rule for interactions between particles of two particular types.
*
* @param pairIndex the index of the type pair
* @param[out] type1 the index of the first particle type
* @param[out] type2 the index of the second particle type
* @param[out] sigma the sigma value for interactions between particles of these two types
* @param[out] epsilon the epsilon value for interactions between particles of these two types
*/
void getTypePairParameters(int pairIndex, int& type1, int& type2, double& sigma, double& epsilon) const;
/**
* Set the force field parameters for a type pair. This overrides the standard
* combining rule for interactions between particles of two particular types.
*
* @param pairIndex the index of the type pair
* @param type1 the index of the first particle type
* @param type2 the index of the second particle type
* @param sigma the sigma value for interactions between particles of these two types
* @param epsilon the epsilon value for interactions between particles of these two types
*/
void setTypePairParameters(int pairIndex, int type1, int type2, double sigma, double epsilon);
/**
* Set sigma combining rule
*
......@@ -211,6 +330,13 @@ public:
useDispersionCorrection = useCorrection;
}
/**
* Get whether parameters were specified by particle or by particle type.
*/
bool getUseParticleTypes() const {
return useTypes;
}
/**
* Set exclusions for specified particle
*
......@@ -268,6 +394,20 @@ public:
*/
void setNonbondedMethod(NonbondedMethod method);
/**
* Get the potential function to use.
*/
PotentialFunction getPotentialFunction() const {
return potentialFunction;
}
/**
* Set the potential function to use.
*/
void setPotentialFunction(PotentialFunction potential) {
potentialFunction = potential;
}
/**
* Set the softcore power on lambda (default = 5).
*/
......@@ -322,9 +462,12 @@ protected:
private:
class VdwInfo;
class ParticleTypeInfo;
class TypePairInfo;
NonbondedMethod nonbondedMethod;
PotentialFunction potentialFunction;
double cutoff;
bool useDispersionCorrection;
bool useDispersionCorrection, useTypes;
AlchemicalMethod alchemicalMethod;
int n;
double alpha;
......@@ -334,7 +477,8 @@ private:
std::vector< std::vector<int> > exclusions;
std::vector<VdwInfo> parameters;
std::vector< std::vector< std::vector<double> > > sigEpsTable;
std::vector<ParticleTypeInfo> types;
std::vector<TypePairInfo> pairs;
};
/**
......@@ -343,7 +487,7 @@ private:
*/
class AmoebaVdwForce::VdwInfo {
public:
int parentIndex;
int parentIndex, typeIndex;
double reductionFactor, sigma, epsilon, cutoff;
bool isAlchemical;
VdwInfo() {
......@@ -353,8 +497,36 @@ public:
epsilon = 0.0;
isAlchemical = false;
}
VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor, bool isAlchemical) :
parentIndex(parentIndex), reductionFactor(reductionFactor), sigma(sigma), epsilon(epsilon), isAlchemical(isAlchemical) {
VdwInfo(int parentIndex, double sigma, double epsilon, int typeIndex, double reductionFactor, bool isAlchemical) :
parentIndex(parentIndex), reductionFactor(reductionFactor), sigma(sigma), epsilon(epsilon), typeIndex(typeIndex), isAlchemical(isAlchemical) {
}
};
/**
* This is an internal class used to record information about a particle type.
* @private
*/
class AmoebaVdwForce::ParticleTypeInfo {
public:
double sigma, epsilon;
ParticleTypeInfo() : sigma(1.0), epsilon(0.0) {
}
ParticleTypeInfo(double sigma, double epsilon) : sigma(sigma), epsilon(epsilon) {
}
};
/**
* This is an internal class used to record information about a type pair.
* @private
*/
class AmoebaVdwForce::TypePairInfo {
public:
int type1, type2;
double sigma, epsilon;
TypePairInfo() : type1(-1), type2(-1), sigma(1.0), epsilon(0.0) {
}
TypePairInfo(int type1, int type2, double sigma, double epsilon) :
type1(type1), type2(type2), sigma(sigma), epsilon(epsilon) {
}
};
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaVdwForceImpl.h
View file @ b6b43fdf
......@@ -65,6 +65,18 @@ public:
return parameters;
}
std::vector<std::string> getKernelNames();
/**
* Compute the matrix of sigma and epsilon to use between every pair of particle types.
*
* @param force the force for which to calculate it
* @param[out] type on exit, this contains the type index of every particle
* @param[out] sigmaMatrix on exit, sigma[i][j] contains the value to use for interactions between particles
* of types i and j
* @param[out] epsilonMatrix on exit, epsilon[i][j] contains the value to use for interactions between particles
* of types i and j
*/
static void createParameterMatrix(const AmoebaVdwForce& force, std::vector<int>& type,
std::vector<std::vector<double> >& sigmaMatrix, std::vector<std::vector<double> >& epsilonMatrix);
/**
* Compute the coefficient which, when divided by the periodic box volume, gives the
* long range dispersion correction to the energy.
......
plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp
View file @ b6b43fdf
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -33,35 +33,90 @@
#include "openmm/OpenMMException.h"
#include "openmm/AmoebaVdwForce.h"
#include "openmm/internal/AmoebaVdwForceImpl.h"
#include "openmm/internal/AssertionUtilities.h"
using namespace OpenMM;
using std::string;
using std::vector;
AmoebaVdwForce::AmoebaVdwForce() : nonbondedMethod(NoCutoff), sigmaCombiningRule("CUBIC-MEAN"), epsilonCombiningRule("HHG"), cutoff(1.0e+10), useDispersionCorrection(true), alchemicalMethod(None), n(5), alpha(0.7) {
AmoebaVdwForce::AmoebaVdwForce() : nonbondedMethod(NoCutoff), potentialFunction(Buffered147),
sigmaCombiningRule("CUBIC-MEAN"), epsilonCombiningRule("HHG"), cutoff(1.0e+10), useDispersionCorrection(true),
useTypes(false), alchemicalMethod(None), n(5), alpha(0.7) {
}
int AmoebaVdwForce::addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor, bool isAlchemical) {
parameters.push_back(VdwInfo(parentIndex, sigma, epsilon, reductionFactor, isAlchemical));
if (useTypes)
throw OpenMMException("AmoebaVdwForce: must use the same version of addParticle() for all particles");
parameters.push_back(VdwInfo(parentIndex, sigma, epsilon, -1, reductionFactor, isAlchemical));
return parameters.size()-1;
}
int AmoebaVdwForce::addParticle(int parentIndex, int typeIndex, double reductionFactor, bool isAlchemical) {
if (parameters.size() > 0 && !useTypes)
throw OpenMMException("AmoebaVdwForce: must use the same version of addParticle() for all particles");
useTypes = true;
parameters.push_back(VdwInfo(parentIndex, 1.0, 0.0, typeIndex, reductionFactor, isAlchemical));
return parameters.size()-1;
}
void AmoebaVdwForce::getParticleParameters(int particleIndex, int& parentIndex,
double& sigma, double& epsilon, double& reductionFactor, bool& isAlchemical) const {
double& sigma, double& epsilon, double& reductionFactor, bool& isAlchemical, int& typeIndex) const {
ASSERT_VALID_INDEX(particleIndex, parameters);
parentIndex = parameters[particleIndex].parentIndex;
sigma = parameters[particleIndex].sigma;
epsilon = parameters[particleIndex].epsilon;
reductionFactor = parameters[particleIndex].reductionFactor;
isAlchemical = parameters[particleIndex].isAlchemical;
typeIndex = parameters[particleIndex].typeIndex;
}
void AmoebaVdwForce::setParticleParameters(int particleIndex, int parentIndex,
double sigma, double epsilon, double reductionFactor, bool isAlchemical) {
double sigma, double epsilon, double reductionFactor, bool isAlchemical, int typeIndex) {
ASSERT_VALID_INDEX(particleIndex, parameters);
parameters[particleIndex].parentIndex = parentIndex;
parameters[particleIndex].sigma = sigma;
parameters[particleIndex].epsilon = epsilon;
parameters[particleIndex].reductionFactor = reductionFactor;
parameters[particleIndex].isAlchemical = isAlchemical;
parameters[particleIndex].typeIndex = typeIndex;
}
int AmoebaVdwForce::addParticleType(double sigma, double epsilon) {
types.push_back(ParticleTypeInfo(sigma, epsilon));
return types.size()-1;
}
void AmoebaVdwForce::getParticleTypeParameters(int typeIndex, double& sigma, double& epsilon) const {
ASSERT_VALID_INDEX(typeIndex, types);
sigma = pairs[typeIndex].sigma;
epsilon = pairs[typeIndex].epsilon;
}
void AmoebaVdwForce::setParticleTypeParameters(int typeIndex, double sigma, double epsilon) {
ASSERT_VALID_INDEX(typeIndex, types);
pairs[typeIndex].sigma = sigma;
pairs[typeIndex].epsilon = epsilon;
}
int AmoebaVdwForce::addTypePair(int type1, int type2, double sigma, double epsilon) {
pairs.push_back(TypePairInfo(type1, type2, sigma, epsilon));
return pairs.size()-1;
}
void AmoebaVdwForce::getTypePairParameters(int pairIndex, int& type1, int& type2, double& sigma, double& epsilon) const {
ASSERT_VALID_INDEX(pairIndex, pairs);
type1 = pairs[pairIndex].type1;
type2 = pairs[pairIndex].type2;
sigma = pairs[pairIndex].sigma;
epsilon = pairs[pairIndex].epsilon;
}
void AmoebaVdwForce::setTypePairParameters(int pairIndex, int type1, int type2, double sigma, double epsilon) {
ASSERT_VALID_INDEX(pairIndex, pairs);
pairs[pairIndex].type1 = type1;
pairs[pairIndex].type2 = type2;
pairs[pairIndex].sigma = sigma;
pairs[pairIndex].epsilon = epsilon;
}
void AmoebaVdwForce::setSigmaCombiningRule(const std::string& inputSigmaCombiningRule) {
......
plugins/amoeba/openmmapi/src/AmoebaVdwForceImpl.cpp
View file @ b6b43fdf
......@@ -41,10 +41,6 @@
using namespace OpenMM;
using namespace std;
using std::pair;
using std::vector;
using std::set;
AmoebaVdwForceImpl::AmoebaVdwForceImpl(const AmoebaVdwForce& owner) : owner(owner) {
}
......@@ -77,6 +73,131 @@ double AmoebaVdwForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includ
return 0.0;
}
void AmoebaVdwForceImpl::createParameterMatrix(const AmoebaVdwForce& force, vector<int>& type,
vector<vector<double> >& sigmaMatrix, vector<vector<double> >& epsilonMatrix) {
int numParticles = force.getNumParticles();
type.resize(numParticles);
int numTypes;
vector<double> typeSigma, typeEpsilon;
if (force.getUseParticleTypes()) {
// We get the types directly from the particles.
double sigma, epsilon, reduction;
int parent;
bool isAlchemical;
for (int i = 0; i < numParticles; i++)
force.getParticleParameters(i, parent, sigma, epsilon, reduction, isAlchemical, type[i]);
numTypes = force.getNumParticleTypes();
typeSigma.resize(numTypes);
typeEpsilon.resize(numTypes);
for (int i = 0; i < numTypes; i++)
force.getParticleTypeParameters(i, typeSigma[i], typeEpsilon[i]);
}
else {
// Identify types by finding every unique sigma/epsilon pair.
map<pair<double, double>, int> typeForParams;
for (int i = 0; i < numParticles; i++) {
double sigma, epsilon, reduction;
int parent, typeIndex;
bool isAlchemical;
force.getParticleParameters(i, parent, sigma, epsilon, reduction, isAlchemical, typeIndex);
pair<double, double> params = make_pair(sigma, epsilon);
map<pair<double, double>, int>::iterator entry = typeForParams.find(params);
if (entry == typeForParams.end())
typeForParams[params] = typeForParams.size();
type[i] = typeForParams[params];
}
numTypes = typeForParams.size();
for (auto params : typeForParams) {
typeSigma[params.second] = params.first.first;
typeEpsilon[params.second] = params.first.second;
}
}
// Build the matrices by applying combining rules.
sigmaMatrix.clear();
epsilonMatrix.clear();
sigmaMatrix.resize(numTypes, vector<double>(numTypes));
epsilonMatrix.resize(numTypes, vector<double>(numTypes));
string sigmaCombiningRule = force.getSigmaCombiningRule();
string epsilonCombiningRule = force.getEpsilonCombiningRule();
for (int i = 0; i < numTypes; i++) {
double iSigma = typeSigma[i];
double iEpsilon = typeEpsilon[i];
for (int j = 0; j < numTypes; j++) {
double jSigma = typeSigma[j];
double jEpsilon = typeEpsilon[j];
double sigma, epsilon;
// ARITHMETIC = 1
// GEOMETRIC = 2
// CUBIC-MEAN = 3
if (sigmaCombiningRule == "ARITHMETIC")
sigma = iSigma+jSigma;
else if (sigmaCombiningRule == "GEOMETRIC")
sigma = 2*sqrt(iSigma*jSigma);
else {
double iSigma2 = iSigma*iSigma;
double jSigma2 = jSigma*jSigma;
if ((iSigma2+jSigma2) != 0.0)
sigma = 2*(iSigma2*iSigma + jSigma2*jSigma) / (iSigma2+jSigma2);
else
sigma = 0.0;
}
sigmaMatrix[i][j] = sigma;
sigmaMatrix[j][i] = sigma;
// ARITHMETIC = 1
// GEOMETRIC = 2
// HARMONIC = 3
// W-H = 4
// HHG = 5
if (epsilonCombiningRule == "ARITHMETIC")
epsilon = 0.5*(iEpsilon+jEpsilon);
else if (epsilonCombiningRule == "GEOMETRIC")
epsilon = sqrt(iEpsilon*jEpsilon);
else if (epsilonCombiningRule == "HARMONIC") {
if ((iEpsilon+jEpsilon) != 0.0)
epsilon = 2*(iEpsilon*jEpsilon) / (iEpsilon+jEpsilon);
else
epsilon = 0.0;
}
else if (epsilonCombiningRule == "W-H") {
double iSigma3 = iSigma * iSigma * iSigma;
double jSigma3 = jSigma * jSigma * jSigma;
double iSigma6 = iSigma3 * iSigma3;
double jSigma6 = jSigma3 * jSigma3;
double eps_s = sqrt(iEpsilon*jEpsilon);
epsilon = (eps_s == 0.0 ? 0.0 : 2*eps_s*iSigma3*jSigma3/(iSigma6+jSigma6));
}
else {
double epsilonS = sqrt(iEpsilon)+sqrt(jEpsilon);
if (epsilonS != 0.0)
epsilon = 4*(iEpsilon*jEpsilon) / (epsilonS*epsilonS);
else
epsilon = 0.0;
}
epsilonMatrix[i][j] = epsilon;
epsilonMatrix[j][i] = epsilon;
}
}
// Record any type pairs that override the combining rules.
if (force.getUseParticleTypes()) {
for (int i = 0; i < force.getNumTypePairs(); i++) {
int type1, type2;
double sigma, epsilon;
force.getTypePairParameters(i, type1, type2, sigma, epsilon);
sigmaMatrix[type1][type2] = sigma;
sigmaMatrix[type2][type1] = sigma;
epsilonMatrix[type1][type2] = epsilon;
epsilonMatrix[type2][type1] = epsilon;
}
}
}
double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const AmoebaVdwForce& force) {
// Amoeba VdW dispersion correction implemented by LPW
......@@ -84,24 +205,17 @@ double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const
if (force.getNonbondedMethod() == AmoebaVdwForce::NoCutoff)
return 0.0;
// Identify all particle classes (defined by sigma and epsilon and reduction), and count the number of
// Identify all particle classes (defined by sigma and epsilon), and count the number of
// particles in each class.
map<pair<double, double>, int> classCounts;
for (int i = 0; i < force.getNumParticles(); i++) {
double sigma, epsilon, reduction;
bool isAlchemical;
// The variables reduction, ivindex and isAlchemical are not used.
int ivindex;
// Get the sigma and epsilon parameters, ignoring everything else.
force.getParticleParameters(i, ivindex, sigma, epsilon, reduction, isAlchemical);
pair<double, double> key = make_pair(sigma, epsilon);
map<pair<double, double>, int>::iterator entry = classCounts.find(key);
if (entry == classCounts.end())
classCounts[key] = 1;
else
entry->second++;
}
vector<int> type;
vector<vector<double> > sigmaMatrix;
vector<vector<double> > epsilonMatrix;
createParameterMatrix(force, type, sigmaMatrix, epsilonMatrix);
int numTypes = type.size();
vector<int> typeCounts(numTypes, 0);
for (int i = 0; i < force.getNumParticles(); i++)
typeCounts[type[i]]++;
// Compute the VdW tapering coefficients. Mostly copied from amoebaCudaGpu.cpp.
double cutoff = force.getCutoffDistance();
......@@ -143,7 +257,7 @@ double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const
c4 = 15.0 * (vdwCut + vdwTaperCut) * denom;
c5 = -6.0 * denom;
// Loop over all pairs of classes to compute the coefficient.
// Loop over all pairs of types to compute the coefficient.
// Copied over from TINKER - numerical integration.
double range = 20.0;
double cut = vdwTaperCut; // This is where tapering BEGINS
......@@ -159,67 +273,18 @@ double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const
double elrc = 0.0; // This number is incremented and passed out at the end
double e = 0.0;
double sigma, epsilon; // The pairwise sigma and epsilon parameters.
int i = 0, k = 0; // Loop counters.
// Double loop over different atom types.
std::string sigmaCombiningRule = force.getSigmaCombiningRule();
std::string epsilonCombiningRule = force.getEpsilonCombiningRule();
for (auto& class1 : classCounts) {
k = 0;
for (auto& class2 : classCounts) {
// AMOEBA combining rules, copied over from the CUDA code.
double iSigma = class1.first.first;
double jSigma = class2.first.first;
double iEpsilon = class1.first.second;
double jEpsilon = class2.first.second;
// ARITHMETIC = 1
// GEOMETRIC = 2
// CUBIC-MEAN = 3
if (sigmaCombiningRule == "ARITHMETIC") {
sigma = iSigma + jSigma;
} else if (sigmaCombiningRule == "GEOMETRIC") {
sigma = 2.0f * std::sqrt(iSigma * jSigma);
} else {
double iSigma2 = iSigma*iSigma;
double jSigma2 = jSigma*jSigma;
if ((iSigma2 + jSigma2) != 0.0) {
sigma = 2.0f * (iSigma2 * iSigma + jSigma2 * jSigma) / (iSigma2 + jSigma2);
} else {
sigma = 0.0;
}
}
// ARITHMETIC = 1
// GEOMETRIC = 2
// HARMONIC = 3
// W-H = 4
// HHG = 5
if (epsilonCombiningRule == "ARITHMETIC") {
epsilon = 0.5f * (iEpsilon + jEpsilon);
} else if (epsilonCombiningRule == "GEOMETRIC") {
epsilon = std::sqrt(iEpsilon * jEpsilon);
} else if (epsilonCombiningRule == "HARMONIC") {
if ((iEpsilon + jEpsilon) != 0.0) {
epsilon = 2.0f * (iEpsilon * jEpsilon) / (iEpsilon + jEpsilon);
} else {
epsilon = 0.0;
}
} else if (epsilonCombiningRule == "W-H") {
double iSigma3 = iSigma * iSigma * iSigma;
double jSigma3 = jSigma * jSigma * jSigma;
double iSigma6 = iSigma3 * iSigma3;
double jSigma6 = jSigma3 * jSigma3;
double eps_s = std::sqrt(iEpsilon*jEpsilon);
epsilon = (eps_s == 0.0 ? 0.0 : 2.0f*eps_s*iSigma3*jSigma3/(iSigma6 + jSigma6));
} else {
double epsilonS = std::sqrt(iEpsilon) + std::sqrt(jEpsilon);
if (epsilonS != 0.0) {
epsilon = 4.0f * (iEpsilon * jEpsilon) / (epsilonS * epsilonS);
} else {
epsilon = 0.0;
}
}
int count = class1.second * class2.second;
for (int i = 0; i < numTypes; i++) {
for (int j = 0; j <= i; j++) {
double sigma = sigmaMatrix[i][j];
double epsilon = epsilonMatrix[i][j];
int count;
if (i == j)
count = typeCounts[i]*(typeCounts[i]+1)/2;
else
count = typeCounts[i]*typeCounts[j];
// Below is an exact copy of stuff from the previous block.
double rv = sigma;
double termik = 2.0 * M_PI * count; // termik is equivalent to 2 * pi * count.
......@@ -255,9 +320,7 @@ double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const
etot = etot + e * rdelta * r2;
}
elrc = elrc + termik * etot;
k++;
}
i++;
}
return elrc;
}
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ b6b43fdf
......@@ -2341,12 +2341,12 @@ public:
ForceInfo(const AmoebaVdwForce& force) : force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
int iv1, iv2;
int iv1, iv2, type1, type2;
double sigma1, sigma2, epsilon1, epsilon2, reduction1, reduction2;
bool isAlchemical1, isAlchemical2;
force.getParticleParameters(particle1, iv1, sigma1, epsilon1, reduction1, isAlchemical1);
force.getParticleParameters(particle2, iv2, sigma2, epsilon2, reduction2, isAlchemical2);
return (sigma1 == sigma2 && epsilon1 == epsilon2 && reduction1 == reduction2 && isAlchemical1 == isAlchemical2);
force.getParticleParameters(particle1, iv1, sigma1, epsilon1, reduction1, isAlchemical1, type1);
force.getParticleParameters(particle2, iv2, sigma2, epsilon2, reduction2, isAlchemical2, type2);
return (sigma1 == sigma2 && epsilon1 == epsilon2 && reduction1 == reduction2 && isAlchemical1 == isAlchemical2 && type1 == type2);
}
private:
const AmoebaVdwForce& force;
......
plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp
View file @ b6b43fdf
......@@ -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) 2010-2016 Stanford University and the Authors. *
* Portions copyright (c) 2010-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,8 +42,9 @@ AmoebaVdwForceProxy::AmoebaVdwForceProxy() : SerializationProxy("AmoebaVdwForce"
}
void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 3);
node.setIntProperty("version", 4);
const AmoebaVdwForce& force = *reinterpret_cast<const AmoebaVdwForce*>(object);
bool useTypes = force.getUseParticleTypes();
node.setIntProperty("forceGroup", force.getForceGroup());
node.setStringProperty("SigmaCombiningRule", force.getSigmaCombiningRule());
......@@ -54,31 +55,49 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
node.setDoubleProperty("n", force.getSoftcorePower());
node.setDoubleProperty("alpha", force.getSoftcoreAlpha());
node.setIntProperty("alchemicalMethod", (int) force.getAlchemicalMethod());
node.setIntProperty("potentialFunction", (int) force.getPotentialFunction());
node.setBoolProperty("useTypes", useTypes);
SerializationNode& particles = node.createChildNode("VdwParticles");
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
int ivIndex;
for (int i = 0; i < force.getNumParticles(); i++) {
int ivIndex, typeIndex;
double sigma, epsilon, reductionFactor;
bool isAlchemical;
force.getParticleParameters(ii, ivIndex, sigma, epsilon, reductionFactor, isAlchemical);
force.getParticleParameters(i, ivIndex, sigma, epsilon, reductionFactor, isAlchemical, typeIndex);
SerializationNode& particle = particles.createChildNode("Particle");
particle.setIntProperty("ivIndex", ivIndex).setDoubleProperty("sigma", sigma).setDoubleProperty("epsilon", epsilon).setDoubleProperty("reductionFactor", reductionFactor).setBoolProperty("isAlchemical",isAlchemical);
if (useTypes)
particle.setIntProperty("ivIndex", ivIndex).setIntProperty("type", typeIndex).setDoubleProperty("reductionFactor", reductionFactor).setBoolProperty("isAlchemical", isAlchemical);
else
particle.setIntProperty("ivIndex", ivIndex).setDoubleProperty("sigma", sigma).setDoubleProperty("epsilon", epsilon).setDoubleProperty("reductionFactor", reductionFactor).setBoolProperty("isAlchemical", isAlchemical);
std::vector< int > exclusions;
force.getParticleExclusions(ii, exclusions);
force.getParticleExclusions(i, exclusions);
SerializationNode& particleExclusions = particle.createChildNode("ParticleExclusions");
for (unsigned int jj = 0; jj < exclusions.size(); jj++) {
particleExclusions.createChildNode("excl").setIntProperty("index", exclusions[jj]);
for (int j = 0; j < exclusions.size(); j++)
particleExclusions.createChildNode("excl").setIntProperty("index", exclusions[j]);
}
if (useTypes) {
SerializationNode& types = node.createChildNode("ParticleTypes");
for (int i = 0; i < force.getNumParticleTypes(); i++) {
double sigma, epsilon;
force.getParticleTypeParameters(i, sigma, epsilon);
SerializationNode& type = types.createChildNode("Type");
type.setDoubleProperty("sigma", sigma).setDoubleProperty("epsilon", epsilon);
}
SerializationNode& pairs = node.createChildNode("TypePairs");
for (int i = 0; i < force.getNumParticleTypes(); i++) {
int type1, type2;
double sigma, epsilon;
force.getTypePairParameters(i, type1, type2, sigma, epsilon);
SerializationNode& pair = pairs.createChildNode("Pair");
pair.setIntProperty("type1", type1).setIntProperty("type2", type2).setDoubleProperty("sigma", sigma).setDoubleProperty("epsilon", epsilon);
}
}
}
void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
int version = node.getIntProperty("version");
if (version < 1 || version > 3)
if (version < 1 || version > 4)
throw OpenMMException("Unsupported version number");
AmoebaVdwForce* force = new AmoebaVdwForce();
try {
......@@ -95,13 +114,22 @@ void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
force->setSoftcoreAlpha(node.getDoubleProperty("alpha"));
}
bool useTypes = false;
if (version > 3) {
useTypes = node.getBoolProperty("useTypes");
force->setPotentialFunction((AmoebaVdwForce::PotentialFunction) node.getIntProperty("potentialFunction"));
}
const SerializationNode& particles = node.getChildNode("VdwParticles");
for (unsigned int ii = 0; ii < particles.getChildren().size(); ii++) {
const SerializationNode& particle = particles.getChildren()[ii];
for (int i = 0; i < particles.getChildren().size(); i++) {
const SerializationNode& particle = particles.getChildren()[i];
if (version < 3)
force->addParticle(particle.getIntProperty("ivIndex"), particle.getDoubleProperty("sigma"),
particle.getDoubleProperty("epsilon"), particle.getDoubleProperty("reductionFactor"));
else if (useTypes)
force->addParticle(particle.getIntProperty("ivIndex"), particle.getIntProperty("type"),
particle.getDoubleProperty("reductionFactor"), particle.getBoolProperty("isAlchemical"));
else
force->addParticle(particle.getIntProperty("ivIndex"), particle.getDoubleProperty("sigma"),
particle.getDoubleProperty("epsilon"), particle.getDoubleProperty("reductionFactor"),
......@@ -110,13 +138,19 @@ void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
// exclusions
const SerializationNode& particleExclusions = particle.getChildNode("ParticleExclusions");
std::vector< int > exclusions;
for (unsigned int jj = 0; jj < particleExclusions.getChildren().size(); jj++) {
exclusions.push_back(particleExclusions.getChildren()[jj].getIntProperty("index"));
std::vector<int> exclusions;
for (int j = 0; j < particleExclusions.getChildren().size(); j++)
exclusions.push_back(particleExclusions.getChildren()[j].getIntProperty("index"));
force->setParticleExclusions(i, exclusions);
}
force->setParticleExclusions(ii, exclusions);
if (useTypes) {
const SerializationNode& types = node.getChildNode("ParticleTypes");
for (const auto& type : types.getChildren())
force->addParticleType(type.getDoubleProperty("sigma"), type.getDoubleProperty("epsilon"));
const SerializationNode& pairs = node.getChildNode("TypePairs");
for (const auto& pair : pairs.getChildren())
force->addTypePair(pair.getIntProperty("type1"), pair.getIntProperty("type2"), pair.getDoubleProperty("sigma"), pair.getDoubleProperty("epsilon"));
}
}
catch (...) {
delete force;
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp
View file @ b6b43fdf
......@@ -51,16 +51,17 @@ void testSerialization() {
force1.setCutoff(0.9);
force1.setNonbondedMethod(AmoebaVdwForce::CutoffPeriodic);
force1.setAlchemicalMethod(AmoebaVdwForce::None);
force1.setPotentialFunction(AmoebaVdwForce::Buffered147);
force1.addParticle(0, 1.0, 2.0, 0.9, false);
force1.addParticle(1, 1.1, 2.1, 0.9, true);
force1.addParticle(2, 1.3, 4.1, 0.9, false);
for (unsigned int ii = 0; ii < 3; ii++) {
for (int i = 0; i < 3; i++) {
std::vector< int > exclusions;
exclusions.push_back(ii);
exclusions.push_back(ii + 1);
exclusions.push_back(ii + 10);
force1.setParticleExclusions(ii, exclusions);
exclusions.push_back(i);
exclusions.push_back(i + 1);
exclusions.push_back(i + 10);
force1.setParticleExclusions(i, exclusions);
}
// Serialize and then deserialize it.
......@@ -78,13 +79,14 @@ void testSerialization() {
ASSERT_EQUAL(force1.getCutoff(), force2.getCutoff());
ASSERT_EQUAL(force1.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force1.getAlchemicalMethod(), force2.getAlchemicalMethod());
ASSERT_EQUAL(force1.getPotentialFunction(), force2.getPotentialFunction());
ASSERT_EQUAL(force1.getNumParticles(), force2.getNumParticles());
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumParticles()); ii++) {
for (int i = 0; i < force1.getNumParticles(); i++) {
int ivIndex1;
int ivIndex2;
int ivIndex1, type1;
int ivIndex2, type2;
double sigma1, epsilon1, reductionFactor1;
double sigma2, epsilon2, reductionFactor2;
......@@ -92,38 +94,111 @@ void testSerialization() {
bool isAlchemical1;
bool isAlchemical2;
force1.getParticleParameters(ii, ivIndex1, sigma1, epsilon1, reductionFactor1, isAlchemical1);
force2.getParticleParameters(ii, ivIndex2, sigma2, epsilon2, reductionFactor2, isAlchemical2);
force1.getParticleParameters(i, ivIndex1, sigma1, epsilon1, reductionFactor1, isAlchemical1, type1);
force2.getParticleParameters(i, ivIndex2, sigma2, epsilon2, reductionFactor2, isAlchemical2, type2);
ASSERT_EQUAL(ivIndex1, ivIndex2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
ASSERT_EQUAL(reductionFactor1, reductionFactor2);
ASSERT_EQUAL(isAlchemical1, isAlchemical2);
ASSERT_EQUAL(type1, type2);
}
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumParticles()); ii++) {
for (int i = 0; i < force1.getNumParticles(); i++) {
std::vector< int > exclusions1;
std::vector< int > exclusions2;
force1.getParticleExclusions(ii, exclusions1);
force2.getParticleExclusions(ii, exclusions2);
force1.getParticleExclusions(i, exclusions1);
force2.getParticleExclusions(i, exclusions2);
ASSERT_EQUAL(exclusions1.size(), exclusions2.size());
for (unsigned int jj = 0; jj < exclusions1.size(); jj++) {
for (int j = 0; j < exclusions1.size(); j++) {
int hit = 0;
for (unsigned int kk = 0; kk < exclusions2.size(); kk++) {
if (exclusions2[jj] == exclusions1[kk])hit++;
for (int kk = 0; kk < exclusions2.size(); kk++) {
if (exclusions2[j] == exclusions1[kk])hit++;
}
ASSERT_EQUAL(hit, 1);
}
}
}
void testSerializeTypes() {
// Create a Force that specifies parameters by type.
AmoebaVdwForce force1;
force1.setPotentialFunction(AmoebaVdwForce::LennardJones);
force1.addParticle(0, 2, 1.0, false);
force1.addParticle(1, 2, 0.9, true);
force1.addParticle(2, 0, 1.0, false);
force1.addParticle(3, 1, 0.9, false);
force1.addParticleType(1.1, 2.0);
force1.addParticleType(1.2, 2.1);
force1.addParticleType(1.3, 2.2);
force1.addTypePair(0, 2, 1.5, 2.5);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<AmoebaVdwForce>(&force1, "Force", buffer);
AmoebaVdwForce* copy = XmlSerializer::deserialize<AmoebaVdwForce>(buffer);
// Compare the two forces to see if they are identical.
AmoebaVdwForce& force2 = *copy;
ASSERT_EQUAL(force1.getPotentialFunction(), force2.getPotentialFunction());
ASSERT_EQUAL(force1.getNumParticles(), force2.getNumParticles());
ASSERT_EQUAL(force1.getNumParticleTypes(), force2.getNumParticleTypes());
ASSERT_EQUAL(force1.getNumTypePairs(), force2.getNumTypePairs());
for (int i = 0; i < force1.getNumParticles(); i++) {
int ivIndex1, type1;
int ivIndex2, type2;
double sigma1, epsilon1, reductionFactor1;
double sigma2, epsilon2, reductionFactor2;
bool isAlchemical1;
bool isAlchemical2;
force1.getParticleParameters(i, ivIndex1, sigma1, epsilon1, reductionFactor1, isAlchemical1, type1);
force2.getParticleParameters(i, ivIndex2, sigma2, epsilon2, reductionFactor2, isAlchemical2, type2);
ASSERT_EQUAL(ivIndex1, ivIndex2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
ASSERT_EQUAL(reductionFactor1, reductionFactor2);
ASSERT_EQUAL(isAlchemical1, isAlchemical2);
ASSERT_EQUAL(type1, type2);
}
for (int i = 0; i < force1.getNumParticleTypes(); i++) {
double sigma1, epsilon1;
double sigma2, epsilon2;
force1.getParticleTypeParameters(i, sigma1, epsilon1);
force2.getParticleTypeParameters(i, sigma2, epsilon2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
for (int i = 0; i < force1.getNumTypePairs(); i++) {
int type11, type21;
int type12, type22;
double sigma1, epsilon1;
double sigma2, epsilon2;
force1.getTypePairParameters(i, type11, type21, sigma1, epsilon1);
force2.getTypePairParameters(i, type12, type22, sigma2, epsilon2);
ASSERT_EQUAL(type11, type12);
ASSERT_EQUAL(type21, type22);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
}
int main() {
try {
registerAmoebaSerializationProxies();
testSerialization();
testSerializeTypes();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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