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Unverified Commit ed569c1d authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2378 from leucinw/master 

Added the W-H combining rule for AMOEBA+ VdW
parents c2cb6421 31786496
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Showing with 124 additions and 22 deletions
plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h
View file @ ed569c1d
......@@ -180,14 +180,14 @@ public:
/**
* Set epsilon combining rule
*
* @param epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
* @param epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'W-H', 'HHG'
*/
void setEpsilonCombiningRule(const std::string& epsilonCombiningRule);
/**
* Get epsilon combining rule
*
* @return epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
* @return epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'W-H', 'HHG'
*/
const std::string& getEpsilonCombiningRule(void) const;
......
plugins/amoeba/openmmapi/src/AmoebaVdwForceImpl.cpp
View file @ ed569c1d
......@@ -192,7 +192,8 @@ double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const
// ARITHMETIC = 1
// GEOMETRIC = 2
// HARMONIC = 3
// HHG = 4
// W-H = 4
// HHG = 5
if (epsilonCombiningRule == "ARITHMETIC") {
epsilon = 0.5f * (iEpsilon + jEpsilon);
} else if (epsilonCombiningRule == "GEOMETRIC") {
......@@ -203,6 +204,13 @@ double AmoebaVdwForceImpl::calcDispersionCorrection(const System& system, const
} 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) {
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ ed569c1d
......@@ -2442,8 +2442,10 @@ void CudaCalcAmoebaVdwForceKernel::initialize(const System& system, const Amoeba
replacements["EPSILON_COMBINING_RULE"] = "2";
else if (epsilonCombiningRule =="HARMONIC")
replacements["EPSILON_COMBINING_RULE"] = "3";
else if (epsilonCombiningRule == "HHG")
else if (epsilonCombiningRule == "W-H")
replacements["EPSILON_COMBINING_RULE"] = "4";
else if (epsilonCombiningRule == "HHG")
replacements["EPSILON_COMBINING_RULE"] = "5";
else
throw OpenMMException("Illegal combining rule for sigma: "+sigmaCombiningRule);
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaVdwForce2.cu
View file @ ed569c1d
......@@ -22,6 +22,13 @@
#elif EPSILON_COMBINING_RULE == 3
real epssum = sigmaEpsilon1.y+sigmaEpsilon2.y;
real epsilon = (epssum == 0.0f ? (real) 0 : 2*(sigmaEpsilon1.y*sigmaEpsilon2.y)/(sigmaEpsilon1.y+sigmaEpsilon2.y));
#elif EPSILON_COMBINING_RULE == 4
real sigma1_3 = sigmaEpsilon1.x*sigmaEpsilon1.x*sigmaEpsilon1.x;
real sigma2_3 = sigmaEpsilon2.x*sigmaEpsilon2.x*sigmaEpsilon2.x;
real sigma1_6 = sigma1_3*sigma1_3;
real sigma2_6 = sigma2_3*sigma2_3;
real eps_s = SQRT(sigmaEpsilon1.y*sigmaEpsilon2.y);
real epsilon = (eps_s == 0.0f ? (real) 0 : 2*eps_s*sigma1_3*sigma2_3/(sigma1_6 + sigma2_6));
#else
real epsilon_s = SQRT(sigmaEpsilon1.y) + SQRT(sigmaEpsilon2.y);
real epsilon = (epsilon_s == 0.0f ? (real) 0 : 4*sigmaEpsilon1.y*sigmaEpsilon2.y/(epsilon_s*epsilon_s));
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaVdwForce.cpp
View file @ ed569c1d
......@@ -396,11 +396,12 @@ void testVdwAmmoniaCubicMeanHhg() {
compareForcesEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance);
}
// test alchemical VDW
void testVdwAlchemical(int power, double alpha, double lambda, AmoebaVdwForce::AlchemicalMethod method) {
// test VDW w/ sigmaRule=CubicMean and epsilonRule=W-H
std::string testName = "testVdwAlchemical";
void testVdwAmmoniaCubicMeanWH() {
std::string testName = "testVdwAmmoniaCubicMeanWH";
int numberOfParticles = 8;
double boxDimension = -1.0;
......@@ -408,6 +409,32 @@ void testVdwAlchemical(int power, double alpha, double lambda, AmoebaVdwForce::A
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia("CUBIC-MEAN", "W-H", cutoff, boxDimension, forces, energy);
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 3.771794e+00;
expectedForces[0] = Vec3( 2.3979839e+02, -1.1829842e-02, -5.3258772e+00);
expectedForces[1] = Vec3(-1.9942459e+00, 4.3142144e-01, -1.7290171e-01);
expectedForces[2] = Vec3(-1.9935442e+00, -4.2937965e-01, -1.7369876e-01);
expectedForces[3] = Vec3(-8.9050582e-01, -4.8659920e-04, 2.2190848e-01);
expectedForces[4] = Vec3(-5.2306326e+01, 1.4895040e-03, -3.3588483e-01);
expectedForces[5] = Vec3( 1.4153288e+00, -2.7130186e-01, -1.5480591e-01);
expectedForces[6] = Vec3(-1.8544507e+02, 8.4027272e-03, 6.0950274e+00);
expectedForces[7] = Vec3( 1.4159723e+00, 2.7168386e-01, -1.5376786e-01);
double tolerance = 1.0e-04;
compareForcesEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance);
}
// test alchemical VDW
void testVdwAlchemical(int power, double alpha, double lambda, AmoebaVdwForce::AlchemicalMethod method) {
std::string testName = "testVdwAlchemical";
setupAndGetForcesEnergyVdwAmmonia2("CUBIC-MEAN", "HHG", cutoff, boxDimension, forces, energy,
method, power, alpha, lambda);
std::vector<Vec3> expectedForces(numberOfParticles);
......@@ -2090,6 +2117,10 @@ int main(int argc, char* argv[]) {
testVdwAmmoniaCubicMeanHhg();
// test VDW w/ sigmaRule=CubicMean and epsilonRule=HHG
testVdwAmmoniaCubicMeanWH();
// test VDW w/ sigmaRule=Arithmetic and epsilonRule=Arithmetic
testVdwAmmoniaArithmeticArithmetic();
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceVdwForce.cpp
View file @ ed569c1d
......@@ -155,6 +155,8 @@ void AmoebaReferenceVdwForce::setEpsilonCombiningRule(const std::string& epsilon
_combineEpsilons = &AmoebaReferenceVdwForce::arithmeticEpsilonCombiningRule;
} else if (_epsilonCombiningRule == "HARMONIC") {
_combineEpsilons = &AmoebaReferenceVdwForce::harmonicEpsilonCombiningRule;
} else if (_epsilonCombiningRule == "W-H") {
_combineEpsilons = &AmoebaReferenceVdwForce::whEpsilonCombiningRule;
} else if (_epsilonCombiningRule == "HHG") {
_combineEpsilons = &AmoebaReferenceVdwForce::hhgEpsilonCombiningRule;
} else {
......@@ -166,19 +168,27 @@ std::string AmoebaReferenceVdwForce::getEpsilonCombiningRule() const {
return _epsilonCombiningRule;
}
double AmoebaReferenceVdwForce::arithmeticEpsilonCombiningRule(double epsilonI, double epsilonJ) const {
double AmoebaReferenceVdwForce::arithmeticEpsilonCombiningRule(double epsilonI, double epsilonJ, double sigmaI, double sigmaJ) const {
return 0.5*(epsilonI + epsilonJ);
}
double AmoebaReferenceVdwForce::geometricEpsilonCombiningRule(double epsilonI, double epsilonJ) const {
double AmoebaReferenceVdwForce::geometricEpsilonCombiningRule(double epsilonI, double epsilonJ, double sigmaI, double sigmaJ) const {
return sqrt(epsilonI*epsilonJ);
}
double AmoebaReferenceVdwForce::harmonicEpsilonCombiningRule(double epsilonI, double epsilonJ) const {
double AmoebaReferenceVdwForce::harmonicEpsilonCombiningRule(double epsilonI, double epsilonJ, double sigmaI, double sigmaJ) const {
return (epsilonI != 0.0 && epsilonJ != 0.0) ? 2.0*(epsilonI*epsilonJ)/(epsilonI + epsilonJ) : 0.0;
}
double AmoebaReferenceVdwForce::whEpsilonCombiningRule(double epsilonI, double epsilonJ, double sigmaI, double sigmaJ) const {
double sigmaI3 = sigmaI * sigmaI * sigmaI;
double sigmaJ3 = sigmaJ * sigmaJ * sigmaJ;
double sigmaI6 = sigmaI3 * sigmaI3;
double sigmaJ6 = sigmaJ3 * sigmaJ3;
double eps_s = sqrt(epsilonI*epsilonJ);
return (epsilonI != 0.0 && epsilonJ != 0.0) ? 2.0*eps_s*sigmaI3*sigmaJ3/(sigmaI6+sigmaJ6) : 0.0;
}
double AmoebaReferenceVdwForce::hhgEpsilonCombiningRule(double epsilonI, double epsilonJ) const {
double AmoebaReferenceVdwForce::hhgEpsilonCombiningRule(double epsilonI, double epsilonJ, double sigmaI, double sigmaJ) const {
double denominator = sqrt(epsilonI) + sqrt(epsilonJ);
return (epsilonI != 0.0 && epsilonJ != 0.0) ? 4.0*(epsilonI*epsilonJ)/(denominator*denominator) : 0.0;
}
......@@ -310,7 +320,10 @@ double AmoebaReferenceVdwForce::calculateForceAndEnergy(int numParticles, double
if (exclusions[jj] == 0) {
double combinedSigma = (this->*_combineSigmas)(sigmaI, sigmas[jj]);
double combinedEpsilon = (this->*_combineEpsilons)(epsilonI, epsilons[jj]);
double combinedEpsilon = (this->*_combineEpsilons)(epsilonI, epsilons[jj], sigmaI, sigmas[jj]);
double softcore = 0.0;
if (this->_alchemicalMethod == Decouple && (isAlchemicalI != isAlchemical[jj])) {
......@@ -321,6 +334,7 @@ double AmoebaReferenceVdwForce::calculateForceAndEnergy(int numParticles, double
softcore = this->_alpha * pow(1.0 - lambda, 2);
}
Vec3 force;
energy += calculatePairIxn(combinedSigma, combinedEpsilon, softcore,
reducedPositions[ii], reducedPositions[jj], force);
......@@ -379,7 +393,9 @@ double AmoebaReferenceVdwForce::calculateForceAndEnergy(int numParticles, double
int siteJ = pair.second;
double combinedSigma = (this->*_combineSigmas)(sigmas[siteI], sigmas[siteJ]);
double combinedEpsilon = (this->*_combineEpsilons)(epsilons[siteI], epsilons[siteJ]);
double combinedEpsilon = (this->*_combineEpsilons)(epsilons[siteI], epsilons[siteJ], sigmas[siteI], sigmas[siteJ]);
double softcore = 0.0;
int isAlchemicalI = isAlchemical[siteI];
int isAlchemicalJ = isAlchemical[siteJ];
......@@ -392,6 +408,7 @@ double AmoebaReferenceVdwForce::calculateForceAndEnergy(int numParticles, double
softcore = this->_alpha * pow(1.0 - lambda, 2);
}
Vec3 force;
energy += calculatePairIxn(combinedSigma, combinedEpsilon, softcore,
reducedPositions[siteI], reducedPositions[siteJ], force);
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceVdwForce.h
View file @ ed569c1d
......@@ -34,6 +34,7 @@ namespace OpenMM {
class AmoebaReferenceVdwForce;
typedef double (AmoebaReferenceVdwForce::*CombiningFunction)(double x, double y) const;
typedef double (AmoebaReferenceVdwForce::*CombiningFunctionEpsilon)(double x, double y, double z, double w) const;
// ---------------------------------------------------------------------------------------
......@@ -333,13 +334,16 @@ private:
Vec3 _periodicBoxVectors[3];
CombiningFunction _combineSigmas;
double arithmeticSigmaCombiningRule(double sigmaI, double sigmaJ) const;
double geometricSigmaCombiningRule(double sigmaI, double sigmaJ) const;
double cubicMeanSigmaCombiningRule(double sigmaI, double sigmaJ) const;
CombiningFunction _combineEpsilons;
double arithmeticEpsilonCombiningRule(double epsilonI, double epsilonJ) const;
double geometricEpsilonCombiningRule(double epsilonI, double epsilonJ) const;
double harmonicEpsilonCombiningRule(double epsilonI, double epsilonJ) const;
double hhgEpsilonCombiningRule(double epsilonI, double epsilonJ) const;
double geometricSigmaCombiningRule(double sigmaI, double sigmaJ) const;
double cubicMeanSigmaCombiningRule(double sigmaI, double sigmaJ) const;
CombiningFunctionEpsilon _combineEpsilons;
double arithmeticEpsilonCombiningRule(double epsilonI, double epsilonJ, double sigmaI, double sigmaJ) const;
double geometricEpsilonCombiningRule(double epsilonI, double epsilonJ, double sigmaI, double sigmaJ) const;
double harmonicEpsilonCombiningRule(double epsilonI, double epsilonJ, double sigmaI, double sigmaJ) const;
double whEpsilonCombiningRule(double epsilonI, double epsilonJ, double sigmaI, double sigmaJ) const;
double hhgEpsilonCombiningRule(double epsilonI, double epsilonJ, double sigmaI, double sigmaJ) const;
/**---------------------------------------------------------------------------------------
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaVdwForce.cpp
View file @ ed569c1d
......@@ -405,6 +405,36 @@ void testVdwAmmoniaCubicMeanHhg() {
compareForcesEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance);
}
// test VDW w/ sigmaRule=CubicMean and epsilonRule=W-H
void testVdwAmmoniaCubicMeanWH() {
std::string testName = "testVdwAmmoniaCubicMeanWH";
int numberOfParticles = 8;
double boxDimension = -1.0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia("CUBIC-MEAN", "W-H", cutoff, boxDimension, forces, energy);
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 3.771794e+00;
expectedForces[0] = Vec3( 2.3979839e+02, -1.1829842e-02, -5.3258772e+00);
expectedForces[1] = Vec3(-1.9942459e+00, 4.3142144e-01, -1.7290171e-01);
expectedForces[2] = Vec3(-1.9935442e+00, -4.2937965e-01, -1.7369876e-01);
expectedForces[3] = Vec3(-8.9050582e-01, -4.8659920e-04, 2.2190848e-01);
expectedForces[4] = Vec3(-5.2306326e+01, 1.4895040e-03, -3.3588483e-01);
expectedForces[5] = Vec3( 1.4153288e+00, -2.7130186e-01, -1.5480591e-01);
expectedForces[6] = Vec3(-1.8544507e+02, 8.4027272e-03, 6.0950274e+00);
expectedForces[7] = Vec3( 1.4159723e+00, 2.7168386e-01, -1.5376786e-01);
double tolerance = 1.0e-04;
compareForcesEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance);
}
// test alchemical VDW
void testVdwAlchemical(int power, double alpha, double lambda, AmoebaVdwForce::AlchemicalMethod method) {
......@@ -441,7 +471,6 @@ void testVdwAlchemical(int power, double alpha, double lambda, AmoebaVdwForce::A
compareForcesEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance);
}
// test VDW w/ sigmaRule=Arithmetic and epsilonRule=Arithmetic
void testVdwAmmoniaArithmeticArithmetic() {
......@@ -2100,6 +2129,10 @@ int main(int numberOfArguments, char* argv[]) {
testVdwAmmoniaCubicMeanHhg();
// test VDW w/ sigmaRule=CubicMean and epsilonRule=W-H
testVdwAmmoniaCubicMeanWH();
// test VDW w/ sigmaRule=Arithmetic and epsilonRule=Arithmetic
testVdwAmmoniaArithmeticArithmetic();
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ ed569c1d
......@@ -4431,7 +4431,7 @@ class AmoebaVdwGenerator(object):
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
sigmaMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'CUBIC-MEAN':1}
epsilonMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'HARMONIC':1, 'HHG':1}
epsilonMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'HARMONIC':1, 'W-H':1, 'HHG':1}
force = mm.AmoebaVdwForce()
sys.addForce(force)
......
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