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Commit b245e772 authored by peastman's avatar peastman
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GBSAOBCForce adds an offset to the energy to reduce the discontinuity at the cutoff

parent e59e6f93
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platforms/cuda/src/kernels/gbsaObc1.cu
View file @ b245e772
...@@ -468,11 +468,16 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo ...@@ -468,11 +468,16 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
real expTerm = EXP(-D_ij); real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm; real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2); real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator); real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2); real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij); real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm); real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2; force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
if (atom1 != y*TILE_SIZE+j)
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += 0.5f*tempEnergy; energy += 0.5f*tempEnergy;
delta *= dEdR; delta *= dEdR;
force.x -= delta.x; force.x -= delta.x;
...@@ -520,11 +525,15 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo ...@@ -520,11 +525,15 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
real expTerm = EXP(-D_ij); real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm; real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2); real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator); real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2); real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij); real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm); real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2; force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy; energy += tempEnergy;
delta *= dEdR; delta *= dEdR;
force.x -= delta.x; force.x -= delta.x;
...@@ -670,11 +679,15 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo ...@@ -670,11 +679,15 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
real expTerm = EXP(-D_ij); real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm; real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2); real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator); real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2); real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij); real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm); real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2; force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy; energy += tempEnergy;
delta *= dEdR; delta *= dEdR;
force.x -= delta.x; force.x -= delta.x;
...@@ -717,11 +730,15 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo ...@@ -717,11 +730,15 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
real expTerm = EXP(-D_ij); real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm; real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2); real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator); real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2); real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij); real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm); real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2; force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy; energy += tempEnergy;
delta *= dEdR; delta *= dEdR;
force.x -= delta.x; force.x -= delta.x;
......
platforms/cuda/tests/TestCudaCustomGBForce.cpp
View file @ b245e772
...@@ -56,6 +56,7 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe ...@@ -56,6 +56,7 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
const int numMolecules = 70; const int numMolecules = 70;
const int numParticles = numMolecules*2; const int numParticles = numMolecules*2;
const double boxSize = 10.0; const double boxSize = 10.0;
const double cutoff = 2.0;
// Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction. // Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
...@@ -69,8 +70,8 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe ...@@ -69,8 +70,8 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
customSystem.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(); GBSAOBCForce* obc = new GBSAOBCForce();
CustomGBForce* custom = new CustomGBForce(); CustomGBForce* custom = new CustomGBForce();
obc->setCutoffDistance(2.0); obc->setCutoffDistance(cutoff);
custom->setCutoffDistance(2.0); custom->setCutoffDistance(cutoff);
custom->addPerParticleParameter("q"); custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius"); custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale"); custom->addPerParticleParameter("scale");
...@@ -86,7 +87,13 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe ...@@ -86,7 +87,13 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);" custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle); "psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle); custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;" string invCutoffString = "";
if (obcMethod != GBSAOBCForce::NoCutoff) {
stringstream s;
s<<(1.0/cutoff);
invCutoffString = s.str();
}
custom->addEnergyTerm("138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*("+invCutoffString+"-1/f);"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions); "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles); vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles); vector<Vec3> velocities(numParticles);
......
platforms/opencl/src/kernels/gbsaObc.cl
View file @ b245e772
...@@ -444,11 +444,16 @@ __kernel void computeGBSAForce1( ...@@ -444,11 +444,16 @@ __kernel void computeGBSAForce1(
real expTerm = EXP(-D_ij); real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm; real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2); real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator); real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2); real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij); real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm); real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2; force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
if (atom1 != y*TILE_SIZE+j)
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += 0.5f*tempEnergy; energy += 0.5f*tempEnergy;
delta.xyz *= dEdR; delta.xyz *= dEdR;
force.xyz -= delta.xyz; force.xyz -= delta.xyz;
...@@ -494,11 +499,15 @@ __kernel void computeGBSAForce1( ...@@ -494,11 +499,15 @@ __kernel void computeGBSAForce1(
real expTerm = EXP(-D_ij); real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm; real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2); real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator); real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2); real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij); real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm); real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2; force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy; energy += tempEnergy;
delta.xyz *= dEdR; delta.xyz *= dEdR;
force.xyz -= delta.xyz; force.xyz -= delta.xyz;
...@@ -657,11 +666,15 @@ __kernel void computeGBSAForce1( ...@@ -657,11 +666,15 @@ __kernel void computeGBSAForce1(
real expTerm = EXP(-D_ij); real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm; real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2); real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator); real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2); real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij); real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm); real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2; force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy; energy += tempEnergy;
delta.xyz *= dEdR; delta.xyz *= dEdR;
force.xyz -= delta.xyz; force.xyz -= delta.xyz;
...@@ -701,11 +714,15 @@ __kernel void computeGBSAForce1( ...@@ -701,11 +714,15 @@ __kernel void computeGBSAForce1(
real expTerm = EXP(-D_ij); real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm; real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2); real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator); real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2); real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij); real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm); real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2; force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy; energy += tempEnergy;
delta.xyz *= dEdR; delta.xyz *= dEdR;
force.xyz -= delta.xyz; force.xyz -= delta.xyz;
......
platforms/opencl/tests/TestOpenCLCustomGBForce.cpp
View file @ b245e772
...@@ -56,6 +56,7 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe ...@@ -56,6 +56,7 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
const int numMolecules = 70; const int numMolecules = 70;
const int numParticles = numMolecules*2; const int numParticles = numMolecules*2;
const double boxSize = 10.0; const double boxSize = 10.0;
const double cutoff = 2.0;
// Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction. // Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
...@@ -69,8 +70,8 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe ...@@ -69,8 +70,8 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
customSystem.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(); GBSAOBCForce* obc = new GBSAOBCForce();
CustomGBForce* custom = new CustomGBForce(); CustomGBForce* custom = new CustomGBForce();
obc->setCutoffDistance(2.0); obc->setCutoffDistance(cutoff);
custom->setCutoffDistance(2.0); custom->setCutoffDistance(cutoff);
custom->addPerParticleParameter("q"); custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius"); custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale"); custom->addPerParticleParameter("scale");
...@@ -86,7 +87,13 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe ...@@ -86,7 +87,13 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);" custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle); "psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle); custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;" string invCutoffString = "";
if (obcMethod != GBSAOBCForce::NoCutoff) {
stringstream s;
s<<(1.0/cutoff);
invCutoffString = s.str();
}
custom->addEnergyTerm("138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*("+invCutoffString+"-1/f);"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions); "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles); vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles); vector<Vec3> velocities(numParticles);
......
platforms/reference/include/ObcParameters.h
View file @ b245e772
...@@ -305,7 +305,7 @@ class ObcParameters { ...@@ -305,7 +305,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
bool getUseCutoff(); bool getUseCutoff() const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -313,7 +313,7 @@ class ObcParameters { ...@@ -313,7 +313,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM getCutoffDistance(); RealOpenMM getCutoffDistance() const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/src/gbsa/CpuObc.cpp
View file @ b245e772
...@@ -308,23 +308,18 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat ...@@ -308,23 +308,18 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
static const RealOpenMM fourth = static_cast<RealOpenMM>( 0.25 ); static const RealOpenMM fourth = static_cast<RealOpenMM>( 0.25 );
static const RealOpenMM eighth = static_cast<RealOpenMM>( 0.125 ); static const RealOpenMM eighth = static_cast<RealOpenMM>( 0.125 );
// ---------------------------------------------------------------------------------------
const ObcParameters* obcParameters = getObcParameters();
const int numberOfAtoms = obcParameters->getNumberOfAtoms();
// ---------------------------------------------------------------------------------------
// constants // constants
const int numberOfAtoms = _obcParameters->getNumberOfAtoms();
const RealOpenMM dielectricOffset = _obcParameters->getDielectricOffset();
const RealOpenMM cutoffDistance = _obcParameters->getCutoffDistance();
const RealOpenMM soluteDielectric = _obcParameters->getSoluteDielectric();
const RealOpenMM solventDielectric = _obcParameters->getSolventDielectric();
RealOpenMM preFactor; RealOpenMM preFactor;
if( obcParameters->getSoluteDielectric() != zero && obcParameters->getSolventDielectric() != zero ){ if (soluteDielectric != zero && solventDielectric != zero)
preFactor = two*obcParameters->getElectricConstant()*( (one/obcParameters->getSoluteDielectric()) - (one/obcParameters->getSolventDielectric()) ); preFactor = two*_obcParameters->getElectricConstant()*((one/soluteDielectric) - (one/solventDielectric));
} else { else
preFactor = zero; preFactor = zero;
}
const RealOpenMM dielectricOffset = obcParameters->getDielectricOffset();
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -343,7 +338,7 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat ...@@ -343,7 +338,7 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
// compute the nonpolar solvation via ACE approximation // compute the nonpolar solvation via ACE approximation
if( includeAceApproximation() ){ if( includeAceApproximation() ){
computeAceNonPolarForce( obcParameters, bornRadii, &obcEnergy, bornForces ); computeAceNonPolarForce( _obcParameters, bornRadii, &obcEnergy, bornForces );
} }
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -360,7 +355,7 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat ...@@ -360,7 +355,7 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR ); ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
else else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR ); ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance()) if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > cutoffDistance)
continue; continue;
RealOpenMM r2 = deltaR[ReferenceForce::R2Index]; RealOpenMM r2 = deltaR[ReferenceForce::R2Index];
...@@ -379,9 +374,14 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat ...@@ -379,9 +374,14 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
RealOpenMM dGpol_dr = -Gpol*( one - fourth*expTerm )/denominator2; RealOpenMM dGpol_dr = -Gpol*( one - fourth*expTerm )/denominator2;
RealOpenMM dGpol_dalpha2_ij = -half*Gpol*expTerm*( one + D_ij )/denominator2; RealOpenMM dGpol_dalpha2_ij = -half*Gpol*expTerm*( one + D_ij )/denominator2;
RealOpenMM energy = Gpol;
if( atomI != atomJ ){ if( atomI != atomJ ){
if (_obcParameters->getUseCutoff())
energy -= partialChargeI*partialCharges[atomJ]/cutoffDistance;
bornForces[atomJ] += dGpol_dalpha2_ij*bornRadii[atomI]; bornForces[atomJ] += dGpol_dalpha2_ij*bornRadii[atomI];
deltaX *= dGpol_dr; deltaX *= dGpol_dr;
...@@ -397,10 +397,10 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat ...@@ -397,10 +397,10 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
inputForces[atomJ][2] -= deltaZ; inputForces[atomJ][2] -= deltaZ;
} else { } else {
Gpol *= half; energy *= half;
} }
obcEnergy += Gpol; obcEnergy += energy;
bornForces[atomI] += dGpol_dalpha2_ij*bornRadii[atomJ]; bornForces[atomI] += dGpol_dalpha2_ij*bornRadii[atomJ];
} }
...@@ -411,12 +411,12 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat ...@@ -411,12 +411,12 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
// second main loop // second main loop
const RealOpenMMVector& obcChain = getObcChain(); const RealOpenMMVector& obcChain = getObcChain();
const RealOpenMMVector& atomicRadii = obcParameters->getAtomicRadii(); const RealOpenMMVector& atomicRadii = _obcParameters->getAtomicRadii();
const RealOpenMM alphaObc = obcParameters->getAlphaObc(); const RealOpenMM alphaObc = _obcParameters->getAlphaObc();
const RealOpenMM betaObc = obcParameters->getBetaObc(); const RealOpenMM betaObc = _obcParameters->getBetaObc();
const RealOpenMM gammaObc = obcParameters->getGammaObc(); const RealOpenMM gammaObc = _obcParameters->getGammaObc();
const RealOpenMMVector& scaledRadiusFactor = obcParameters->getScaledRadiusFactors(); const RealOpenMMVector& scaledRadiusFactor = _obcParameters->getScaledRadiusFactors();
// compute factor that depends only on the outer loop index // compute factor that depends only on the outer loop index
...@@ -440,7 +440,7 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat ...@@ -440,7 +440,7 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR ); ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
else else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR ); ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance()) if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > cutoffDistance)
continue; continue;
RealOpenMM deltaX = deltaR[ReferenceForce::XIndex]; RealOpenMM deltaX = deltaR[ReferenceForce::XIndex];
......
platforms/reference/src/gbsa/ObcParameters.cpp
View file @ b245e772
...@@ -351,7 +351,7 @@ void ObcParameters::setUseCutoff( RealOpenMM distance ) { ...@@ -351,7 +351,7 @@ void ObcParameters::setUseCutoff( RealOpenMM distance ) {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
bool ObcParameters::getUseCutoff() { bool ObcParameters::getUseCutoff() const {
return _cutoff; return _cutoff;
} }
...@@ -361,7 +361,7 @@ bool ObcParameters::getUseCutoff() { ...@@ -361,7 +361,7 @@ bool ObcParameters::getUseCutoff() {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getCutoffDistance() { RealOpenMM ObcParameters::getCutoffDistance() const {
return _cutoffDistance; return _cutoffDistance;
} }
......
platforms/reference/tests/TestReferenceCustomGBForce.cpp
View file @ b245e772
...@@ -57,6 +57,7 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe ...@@ -57,6 +57,7 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
const int numMolecules = 70; const int numMolecules = 70;
const int numParticles = numMolecules*2; const int numParticles = numMolecules*2;
const double boxSize = 10.0; const double boxSize = 10.0;
const double cutoff = 2.0;
ReferencePlatform platform; ReferencePlatform platform;
// Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction. // Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
...@@ -71,8 +72,8 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe ...@@ -71,8 +72,8 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
customSystem.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(); GBSAOBCForce* obc = new GBSAOBCForce();
CustomGBForce* custom = new CustomGBForce(); CustomGBForce* custom = new CustomGBForce();
obc->setCutoffDistance(2.0); obc->setCutoffDistance(cutoff);
custom->setCutoffDistance(2.0); custom->setCutoffDistance(cutoff);
custom->addPerParticleParameter("q"); custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius"); custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale"); custom->addPerParticleParameter("scale");
...@@ -88,7 +89,13 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe ...@@ -88,7 +89,13 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);" custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle); "psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle); custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
custom->addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;" string invCutoffString = "";
if (obcMethod != GBSAOBCForce::NoCutoff) {
stringstream s;
s<<(1.0/cutoff);
invCutoffString = s.str();
}
custom->addEnergyTerm("138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*("+invCutoffString+"-1/f);"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions); "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
vector<Vec3> positions(numParticles); vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles); vector<Vec3> velocities(numParticles);
......
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