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Commit 776f6f22 authored by Peter Eastman's avatar Peter Eastman
Browse files

Continuing to convert AmoebaMultipoleForce

parent b186314c
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Showing with 1399 additions and 126 deletions
plugins/amoeba/platforms/cuda2/src/AmoebaCudaKernels.cpp
View file @ 776f6f22
......@@ -865,7 +865,7 @@ private:
CudaCalcAmoebaMultipoleForceKernel::CudaCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
CalcAmoebaMultipoleForceKernel(name, platform), cu(cu), system(system), hasInitializedScaleFactors(false),
multipoleParticles(NULL), torqueBufferIndices(NULL), molecularDipoles(NULL), molecularQuadrupoles(NULL),
multipoleParticles(NULL), molecularDipoles(NULL), molecularQuadrupoles(NULL),
labFrameDipoles(NULL), labFrameQuadrupoles(NULL), field(NULL), fieldPolar(NULL), dampingAndThole(NULL),
inducedDipole(NULL), inducedDipolePolar(NULL), currentEpsilon(NULL), polarizability(NULL), covalentFlags(NULL), polarizationGroupFlags(NULL),
pmeGrid(NULL) {
......@@ -875,8 +875,6 @@ CudaCalcAmoebaMultipoleForceKernel::~CudaCalcAmoebaMultipoleForceKernel() {
cu.setAsCurrent();
if (multipoleParticles != NULL)
delete multipoleParticles;
if (torqueBufferIndices != NULL)
delete torqueBufferIndices;
if (molecularDipoles != NULL)
delete molecularDipoles;
if (molecularQuadrupoles != NULL)
......@@ -933,8 +931,11 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
multipoleParticlesVec.push_back(make_int4(atomX, atomY, atomZ, axisType));
for (int j = 0; j < 3; j++)
molecularDipolesVec.push_back((float) dipole[j]);
for (int j = 0; j < 9; j++)
molecularQuadrupolesVec.push_back((float) quadrupole[j]);
molecularQuadrupolesVec.push_back((float) quadrupole[0]);
molecularQuadrupolesVec.push_back((float) quadrupole[1]);
molecularQuadrupolesVec.push_back((float) quadrupole[2]);
molecularQuadrupolesVec.push_back((float) quadrupole[4]);
molecularQuadrupolesVec.push_back((float) quadrupole[5]);
}
int paddedNumAtoms = cu.getPaddedNumAtoms();
for (int i = numMultipoles; i < paddedNumAtoms; i++) {
......@@ -943,14 +944,14 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
multipoleParticlesVec.push_back(make_int4(0, 0, 0, 0));
for (int j = 0; j < 3; j++)
molecularDipolesVec.push_back(0);
for (int j = 0; j < 9; j++)
for (int j = 0; j < 5; j++)
molecularQuadrupolesVec.push_back(0);
}
dampingAndThole = CudaArray::create<float2>(cu, paddedNumAtoms, "dampingAndThole");
polarizability = CudaArray::create<float>(cu, paddedNumAtoms, "polarizability");
multipoleParticles = CudaArray::create<int4>(cu, paddedNumAtoms, "multipoleParticles");
molecularDipoles = CudaArray::create<float>(cu, 3*paddedNumAtoms, "molecularDipoles");
molecularQuadrupoles = CudaArray::create<float>(cu, 9*paddedNumAtoms, "molecularQuadrupoles");
molecularQuadrupoles = CudaArray::create<float>(cu, 5*paddedNumAtoms, "molecularQuadrupoles");
dampingAndThole->upload(dampingAndTholeVec);
polarizability->upload(polarizabilityVec);
multipoleParticles->upload(multipoleParticlesVec);
......@@ -962,7 +963,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
int elementSize = (cu.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
labFrameDipoles = new CudaArray(cu, 3*paddedNumAtoms, elementSize, "labFrameDipoles");
labFrameQuadrupoles = new CudaArray(cu, 9*paddedNumAtoms, elementSize, "labFrameQuadrupoles");
labFrameQuadrupoles = new CudaArray(cu, 5*paddedNumAtoms, elementSize, "labFrameQuadrupoles");
field = new CudaArray(cu, 3*paddedNumAtoms, sizeof(long long), "field");
fieldPolar = new CudaArray(cu, 3*paddedNumAtoms, sizeof(long long), "fieldPolar");
inducedDipole = new CudaArray(cu, 3*paddedNumAtoms, elementSize, "inducedDipole");
......@@ -999,6 +1000,15 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
polarizationFlagValues.push_back(make_int2(i, atoms[j]));
}
// Record other options.
if (force.getPolarizationType() == AmoebaMultipoleForce::Mutual) {
maxInducedIterations = force.getMutualInducedMaxIterations();
inducedEpsilon = force.getMutualInducedTargetEpsilon();
}
else
maxInducedIterations == 0;
// Create the kernels.
......@@ -1007,13 +1017,29 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
map<string, string> defines;
defines["NUM_ATOMS"] = cu.intToString(numMultipoles);
defines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
defines["SCALING_DISTANCE_CUTOFF"] = cu.doubleToString(50.0);
defines["THREAD_BLOCK_SIZE"] = cu.intToString(cu.getNonbondedUtilities().getForceThreadBlockSize());
defines["NUM_BLOCKS"] = cu.intToString(cu.getNumAtomBlocks());
defines["ENERGY_SCALE_FACTOR"] = cu.doubleToString(138.9354558456); // DIVIDE BY INNER DIELECTRIC!!!
if (force.getPolarizationType() == AmoebaMultipoleForce::Direct)
defines["DIRECT_POLARIZATION"] = "";
CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaAmoebaKernelSources::multipoles, defines);
computeMomentsKernel = cu.getKernel(module, "computeLabFrameMoments");
recordInducedDipolesKernel = cu.getKernel(module, "recordInducedDipoles");
module = cu.createModule(CudaKernelSources::vectorOps+CudaAmoebaKernelSources::multipoleFixedField, defines);
computeFixedFieldKernel = cu.getKernel(module, "computeFixedField");
stringstream electrostaticsSource;
electrostaticsSource << CudaKernelSources::vectorOps;
electrostaticsSource << CudaAmoebaKernelSources::multipoleElectrostatics;
electrostaticsSource << "#define F1\n";
electrostaticsSource << CudaAmoebaKernelSources::electrostaticPairForce;
electrostaticsSource << "#undef F1\n";
electrostaticsSource << "#define T1\n";
electrostaticsSource << CudaAmoebaKernelSources::electrostaticPairForce;
electrostaticsSource << "#undef T1\n";
electrostaticsSource << "#define T2\n";
electrostaticsSource << CudaAmoebaKernelSources::electrostaticPairForce;
module = cu.createModule(electrostaticsSource.str(), defines);
electrostaticsKernel = cu.getKernel(module, "computeElectrostatics");
// Set up PME.
......@@ -1389,30 +1415,34 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
void* computeMomentsArgs[] = {&cu.getPosq().getDevicePointer(), &multipoleParticles->getDevicePointer(),
&molecularDipoles->getDevicePointer(), &molecularQuadrupoles->getDevicePointer(),
&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer()};
cu.executeKernel(computeMomentsKernel, computeMomentsArgs, cu.getPaddedNumAtoms());
vector<float> d, q;
labFrameDipoles->download(d);
labFrameQuadrupoles->download(q);
for (int i = 0; i < cu.getNumAtoms(); i++)
printf("%d %g %g %g\n", i, d[3*i], d[3*i+1], d[3*i+2]);
for (int i = 0; i < cu.getNumAtoms(); i++)
printf("%d %g %g %g %g %g %g %g %g %g\n", i, q[9*i], q[9*i+1], q[9*i+2], q[9*i+3], q[9*i+4], q[9*i+5], q[9*i+6], q[9*i+7], q[9*i+8]);
cu.executeKernel(computeMomentsKernel, computeMomentsArgs, cu.getNumAtoms());
int startTileIndex = nb.getStartTileIndex();
int numTileIndices = nb.getNumTiles();
int numForceThreadBlocks = nb.getNumForceThreadBlocks();
int forceThreadBlockSize = nb.getForceThreadBlockSize();
if (pmeGrid == NULL) {
// Compute induced dipoles.
void* computeFixedFieldArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(), &cu.getPosq().getDevicePointer(),
&nb.getExclusions().getDevicePointer(), &nb.getExclusionIndices().getDevicePointer(), &nb.getExclusionRowIndices().getDevicePointer(),
&nb.getExclusionIndices().getDevicePointer(), &nb.getExclusionRowIndices().getDevicePointer(),
&covalentFlags->getDevicePointer(), &polarizationGroupFlags->getDevicePointer(), &startTileIndex, &numTileIndices,
&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(), &dampingAndThole->getDevicePointer()};
cu.executeKernel(computeFixedFieldKernel, computeFixedFieldArgs, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
vector<unsigned long long> f;
field->download(f);
int pad = cu.getPaddedNumAtoms();
for (int i = 0; i < cu.getNumAtoms(); i++) {
printf("%d %g %g %g\n", i, f[i]/(double)0xFFFFFFFF, f[i+pad]/(double)0xFFFFFFFF, f[i+pad*2]/(double)0xFFFFFFFF);
void* recordInducedDipolesArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(),
&inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(), &polarizability->getDevicePointer()};
cu.executeKernel(recordInducedDipolesKernel, recordInducedDipolesArgs, cu.getNumAtoms());
for (int i = 0; i < maxInducedIterations; i++) {
}
// Compute electrostatic force.
void* electrostaticsArgs[] = {&cu.getForce().getDevicePointer(), &cu.getEnergyBuffer().getDevicePointer(),
&cu.getPosq().getDevicePointer(), &nb.getExclusionIndices().getDevicePointer(), &nb.getExclusionRowIndices().getDevicePointer(),
&covalentFlags->getDevicePointer(), &polarizationGroupFlags->getDevicePointer(), &startTileIndex, &numTileIndices,
&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(), &inducedDipole->getDevicePointer(),
&inducedDipolePolar->getDevicePointer(), &dampingAndThole->getDevicePointer()};
cu.executeKernel(electrostaticsKernel, electrostaticsArgs, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
}
return 0.0;
}
......@@ -1598,28 +1628,22 @@ void CudaCalcAmoebaVdwForceKernel::initialize(const System& system, const Amoeba
throw OpenMMException("Illegal combining rule for sigma: "+sigmaCombiningRule);
string epsilonCombiningRule = force.getEpsilonCombiningRule();
if (epsilonCombiningRule == "ARITHMETIC")
replacements["EPILON_COMBINING_RULE"] = "1";
replacements["EPSILON_COMBINING_RULE"] = "1";
else if (epsilonCombiningRule == "GEOMETRIC")
replacements["EPILON_COMBINING_RULE"] = "2";
replacements["EPSILON_COMBINING_RULE"] = "2";
else if (epsilonCombiningRule == "HARMONIC")
replacements["EPILON_COMBINING_RULE"] = "3";
replacements["EPSILON_COMBINING_RULE"] = "3";
else if (epsilonCombiningRule == "HHG")
replacements["EPILON_COMBINING_RULE"] = "4";
replacements["EPSILON_COMBINING_RULE"] = "4";
else
throw OpenMMException("Illegal combining rule for sigma: "+sigmaCombiningRule);
double cutoff = force.getCutoff();
double taperCutoff = cutoff*0.9;
replacements["CUTOFF_DISTANCE"] = cu.doubleToString(force.getCutoff());
replacements["TAPER_CUTOFF"] = cu.doubleToString(taperCutoff);
double cutoff2 = cutoff*cutoff;
double taperCutoff2 = taperCutoff*taperCutoff;
double denom = pow(cutoff-taperCutoff, -5.0);
replacements["TAPER_C0"] = cu.doubleToString(cutoff*cutoff2 * (cutoff2-5.0*cutoff*taperCutoff+10.0*taperCutoff2)*denom);
replacements["TAPER_C1"] = cu.doubleToString(-30.0*cutoff2*taperCutoff2*denom);
replacements["TAPER_C2"] = cu.doubleToString(30.0*(cutoff2*taperCutoff+cutoff*taperCutoff2)*denom);
replacements["TAPER_C3"] = cu.doubleToString(-10.0*(cutoff2+4.0*cutoff*taperCutoff+taperCutoff2)*denom);
replacements["TAPER_C4"] = cu.doubleToString(15.0*(cutoff+taperCutoff)*denom);
replacements["TAPER_C5"] = cu.doubleToString(-6.0*denom);
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));
nonbonded->addInteraction(force.getUseNeighborList(), force.getPBC(), true, force.getCutoff(), exclusions,
cu.replaceStrings(CudaAmoebaKernelSources::amoebaVdwForce2, replacements), force.getForceGroup());
......
plugins/amoeba/platforms/cuda2/src/AmoebaCudaKernels.h
View file @ 776f6f22
......@@ -374,14 +374,14 @@ public:
private:
class ForceInfo;
void initializeScaleFactors();
int numMultipoles;
int numMultipoles, maxInducedIterations;
double inducedEpsilon;
bool hasInitializedScaleFactors;
CudaContext& cu;
System& system;
std::vector<int3> covalentFlagValues;
std::vector<int2> polarizationFlagValues;
CudaArray* multipoleParticles;
CudaArray* torqueBufferIndices;
CudaArray* molecularDipoles;
CudaArray* molecularQuadrupoles;
CudaArray* labFrameDipoles;
......@@ -412,7 +412,7 @@ private:
CudaArray* pmeAtomGridIndex;
CudaSort* sort;
cufftHandle fft;
CUfunction computeMomentsKernel, computeFixedFieldKernel;
CUfunction computeMomentsKernel, recordInducedDipolesKernel, computeFixedFieldKernel, electrostaticsKernel;
};
/**
......
plugins/amoeba/platforms/cuda2/src/kernels/amoebaVdwForce2.cu
View file @ 776f6f22
......@@ -15,13 +15,11 @@
real sigma = 2*(sigmaEpsilon1.x*sigma1_2 + sigmaEpsilon2.x*sigma2_2)/(sigma1_2+sigma2_2);
#endif
#if EPSILON_COMBINING_RULE == 1
real epsilon = sigmaEpsilon1.y + sigmaEpsilon2.y;
real epsilon = 0.5f*(sigmaEpsilon1.y + sigmaEpsilon2.y);
#elif EPSILON_COMBINING_RULE == 2
real epsilon = 2*SQRT(sigmaEpsilon1.y*sigmaEpsilon2.y);
real epsilon = SQRT(sigmaEpsilon1.y*sigmaEpsilon2.y);
#elif EPSILON_COMBINING_RULE == 3
real epsilon1_2 = sigmaEpsilon1.x*sigmaEpsilon1.x;
real epsilon2_2 = sigmaEpsilon2.x*sigmaEpsilon2.x;
real epsilon = 2*(sigmaEpsilon1.x*epsilon1_2 + sigmaEpsilon2.x*epsilon2_2)/(epsilon1_2+epsilon2_2);
real epsilon = 2*(sigmaEpsilon1.y*sigmaEpsilon2.y)/(sigmaEpsilon1.y+sigmaEpsilon2.y);
#else
real epsilon_s = SQRT(sigmaEpsilon1.y) + SQRT(sigmaEpsilon2.y);
real epsilon = 4*sigmaEpsilon1.y*sigmaEpsilon2.y/(epsilon_s*epsilon_s);
......@@ -39,13 +37,14 @@
real tmp = sigma7*invRho;
real gTau = epsilon*tau7*r6*1.12f*tmp*tmp;
real termEnergy = epsilon*sigma7*tau7*((sigma7*1.12f*invRho)-2.0f);
real deltaE = (-7.0f*(dTau*termEnergy+gTau))*invR;
real deltaE = -7.0f*(dTau*termEnergy+gTau);
if (r > TAPER_CUTOFF) {
real taper = TAPER_C0+r*(TAPER_C1+r*(TAPER_C2+r*(TAPER_C3+r*(TAPER_C4+r*TAPER_C5))));
real dtaper = TAPER_C1+r*(2*TAPER_C2+r*(3*TAPER_C3+r*(4*TAPER_C4+r*5*TAPER_C5)));
real x = r-TAPER_CUTOFF;
real taper = 1+x*x*x*(TAPER_C3+x*(TAPER_C4+x*TAPER_C5));
real dtaper = x*x*(3*TAPER_C3+x*(4*TAPER_C4+x*5*TAPER_C5));
deltaE = termEnergy*dtaper + deltaE*taper;
termEnergy *= taper;
}
tempEnergy += (includeInteraction ? termEnergy : 0);
dEdR -= (includeInteraction ? deltaE : 0);
dEdR -= (includeInteraction ? deltaE*invR : 0);
}
plugins/amoeba/platforms/cuda2/src/kernels/multipoleFixedField.cu
View file @ 776f6f22
......@@ -14,12 +14,12 @@ inline __device__ void loadAtomData(AtomData& data, int atom, const real4* __res
data.dipole.x = labFrameDipole[atom*3];
data.dipole.y = labFrameDipole[atom*3+1];
data.dipole.z = labFrameDipole[atom*3+2];
data.quadrupoleXX = labFrameQuadrupole[atom*9];
data.quadrupoleXY = labFrameQuadrupole[atom*9+1];
data.quadrupoleXZ = labFrameQuadrupole[atom*9+2];
data.quadrupoleYY = labFrameQuadrupole[atom*9+4];
data.quadrupoleYZ = labFrameQuadrupole[atom*9+5];
data.quadrupoleZZ = labFrameQuadrupole[atom*9+8];
data.quadrupoleXX = labFrameQuadrupole[atom*5];
data.quadrupoleXY = labFrameQuadrupole[atom*5+1];
data.quadrupoleXZ = labFrameQuadrupole[atom*5+2];
data.quadrupoleYY = labFrameQuadrupole[atom*5+3];
data.quadrupoleYZ = labFrameQuadrupole[atom*5+4];
data.quadrupoleZZ = 1-data.quadrupoleXX-data.quadrupoleYY;
float2 temp = dampingAndThole[atom];
data.damp = temp.x;
data.thole = temp.y;
......@@ -38,7 +38,7 @@ __device__ void computeOneInteraction(AtomData& atom1, AtomData& atom2, real3 de
float damp = atom1.damp*atom2.damp;
real dampExp;
if (damp != 0 && r < SCALING_DISTANCE_CUTOFF) {
if (damp != 0) {
// get scaling factors
......@@ -83,7 +83,7 @@ __device__ real computeDScaleFactor(unsigned int polarizationGroup) {
return (polarizationGroup & 1 ? 0 : 1);
}
__device__ float computeDScaleFactor(uint2 covalent) {
__device__ float computeMScaleFactor(uint2 covalent) {
// int f1 = (value == 0 || value == 1 ? 1 : 0);
// int f2 = (value == 0 || value == 2 ? 1 : 0);
// 0 = 12 or 13: x and y: 0
......@@ -106,7 +106,7 @@ __device__ float computePScaleFactor(uint2 covalent, unsigned int polarizationGr
*/
extern "C" __global__ void computeFixedField(
unsigned long long* __restrict__ fieldBuffers, unsigned long long* __restrict__ fieldPolarBuffers, const real4* __restrict__ posq,
const unsigned int* __restrict__ exclusions, const unsigned int* __restrict__ exclusionIndices, const unsigned int* __restrict__ exclusionRowIndices,
const unsigned int* __restrict__ exclusionIndices, const unsigned int* __restrict__ exclusionRowIndices,
const uint2* __restrict__ covalentFlags, const unsigned int* __restrict__ polarizationGroupFlags, unsigned int startTileIndex, unsigned int numTileIndices,
#ifdef USE_CUTOFF
const ushort2* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, unsigned int maxTiles, const unsigned int* __restrict__ interactionFlags,
......@@ -185,11 +185,9 @@ extern "C" __global__ void computeFixedField(
localData[localAtomIndex].quadrupoleZZ = data.quadrupoleZZ;
localData[localAtomIndex].thole = data.thole; // IS THIS CORRECT?
localData[localAtomIndex].damp = data.damp; // IS THIS CORRECT?
unsigned int excl = exclusions[exclusionIndex[localGroupIndex]+tgx];
uint2 covalent = covalentFlags[exclusionIndex[localGroupIndex]+tgx];
unsigned int polarizationGroup = polarizationGroupFlags[exclusionIndex[localGroupIndex]+tgx];
for (unsigned int j = 0; j < TILE_SIZE; j++) {
bool isExcluded = !(excl & 0x1);
int atom2 = tbx+j;
real3 delta = make_real3(localData[atom2].posq.x-data.posq.x, localData[atom2].posq.y-data.posq.y, localData[atom2].posq.z-data.posq.z);
#ifdef USE_PERIODIC
......@@ -200,13 +198,13 @@ extern "C" __global__ void computeFixedField(
real3 field1;
real3 field2;
computeOneInteraction(data, localData[atom2], delta, field1, field2);
if (!isExcluded) {
float d = computeDScaleFactor(covalent);
atom2 = y*TILE_SIZE+j;
if (atom1 != atom2 && atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
float d = computeDScaleFactor(polarizationGroup);
data.field += d*field1;
float p = computePScaleFactor(covalent, polarizationGroup);
data.fieldPolar += p*field1;
}
excl >>= 1;
covalent.x >>= 1;
covalent.y >>= 1;
polarizationGroup >>= 1;
......@@ -231,7 +229,6 @@ extern "C" __global__ void computeFixedField(
for (j = 0; j < TILE_SIZE; j++) {
if ((flags&(1<<j)) != 0) {
bool isExcluded = false;
int atom2 = tbx+j;
int bufferIndex = 3*threadIdx.x;
real3 dEdR1 = make_real3(0);
......@@ -298,16 +295,13 @@ extern "C" __global__ void computeFixedField(
{
// Compute the full set of interactions in this tile.
unsigned int excl = (hasExclusions ? exclusions[exclusionIndex[localGroupIndex]+tgx] : 0xFFFFFFFF);
uint2 covalent = (hasExclusions ? covalentFlags[exclusionIndex[localGroupIndex]+tgx] : make_uint2(0, 0));
unsigned int polarizationGroup = (hasExclusions ? polarizationGroupFlags[exclusionIndex[localGroupIndex]+tgx] : 0);
excl = (excl >> tgx) | (excl << (TILE_SIZE - tgx));
covalent.x = (covalent.x >> tgx) | (covalent.x << (TILE_SIZE - tgx));
covalent.y = (covalent.y >> tgx) | (covalent.y << (TILE_SIZE - tgx));
polarizationGroup = (polarizationGroup >> tgx) | (polarizationGroup << (TILE_SIZE - tgx));
unsigned int tj = tgx;
for (j = 0; j < TILE_SIZE; j++) {
bool isExcluded = !(excl & 0x1);
int atom2 = tbx+tj;
real3 delta = make_real3(localData[atom2].posq.x-data.posq.x, localData[atom2].posq.y-data.posq.y, localData[atom2].posq.z-data.posq.z);
#ifdef USE_PERIODIC
......@@ -318,15 +312,14 @@ extern "C" __global__ void computeFixedField(
real3 field1;
real3 field2;
computeOneInteraction(data, localData[atom2], delta, field1, field2);
if (!isExcluded) {
float d = computeDScaleFactor(covalent);
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
float d = computeDScaleFactor(polarizationGroup);
data.field += d*field1;
localData[atom2].field += d*field2;
float p = computePScaleFactor(covalent, polarizationGroup);
data.fieldPolar += p*field1;
localData[atom2].fieldPolar += p*field2;
}
excl >>= 1;
covalent.x >>= 1;
covalent.y >>= 1;
polarizationGroup >>= 1;
......
plugins/amoeba/platforms/cuda2/src/kernels/multipoles.cu
View file @ 776f6f22
......@@ -8,10 +8,10 @@ extern "C" __global__ void computeLabFrameMoments(real4* __restrict__ posq, int4
// code common to ZThenX and Bisector
for (int particleIndex = blockIdx.x*blockDim.x+threadIdx.x; particleIndex < NUM_ATOMS; particleIndex += gridDim.x*blockDim.x) {
int4 particles = multipoleParticles[particleIndex];
for (int atom = blockIdx.x*blockDim.x+threadIdx.x; atom < NUM_ATOMS; atom += gridDim.x*blockDim.x) {
int4 particles = multipoleParticles[atom];
if (particles.x >= 0 && particles.z >= 0) {
real4 thisParticlePos = posq[particleIndex];
real4 thisParticlePos = posq[atom];
real4 posZ = posq[particles.z];
real3 vectorZ = make_real3(posZ.x-thisParticlePos.x, posZ.y-thisParticlePos.y, posZ.z-thisParticlePos.z);
real4 posX = posq[particles.x];
......@@ -149,7 +149,7 @@ extern "C" __global__ void computeLabFrameMoments(real4* __restrict__ posq, int4
// Transform the dipole
unsigned int offset = 3*particleIndex;
unsigned int offset = 3*atom;
real molDipole[3];
molDipole[0] = molecularDipoles[offset];
molDipole[1] = molecularDipoles[offset+1];
......@@ -164,55 +164,47 @@ extern "C" __global__ void computeLabFrameMoments(real4* __restrict__ posq, int4
// Transform the quadrupole
real mPole[3][3];
offset = 9*particleIndex;
mPole[0][0] = molecularQuadrupoles[offset];
mPole[0][1] = molecularQuadrupoles[offset+1];
mPole[0][2] = molecularQuadrupoles[offset+2];
mPole[1][0] = molecularQuadrupoles[offset+3];
mPole[1][1] = molecularQuadrupoles[offset+4];
mPole[1][2] = molecularQuadrupoles[offset+5];
mPole[2][0] = molecularQuadrupoles[offset+6];
mPole[2][1] = molecularQuadrupoles[offset+7];
mPole[2][2] = molecularQuadrupoles[offset+8];
offset = 5*atom;
real mPoleXX = molecularQuadrupoles[offset];
real mPoleXY = molecularQuadrupoles[offset+1];
real mPoleXZ = molecularQuadrupoles[offset+2];
real mPoleYY = molecularQuadrupoles[offset+3];
real mPoleYZ = molecularQuadrupoles[offset+4];
real mPoleZZ = 1-mPoleXX-mPoleYY;
if (reverse) {
mPole[0][1] *= -1;
mPole[1][0] *= -1;
mPole[1][2] *= -1;
mPole[2][1] *= -1;
mPoleXY *= -1;
mPoleYZ *= -1;
}
labFrameQuadrupoles[offset+8] = vectorX.z*(vectorX.z*mPole[0][0] + vectorY.z*mPole[0][1] + vectorZ.z*mPole[0][2]);
labFrameQuadrupoles[offset+8] += vectorY.z*(vectorX.z*mPole[1][0] + vectorY.z*mPole[1][1] + vectorZ.z*mPole[1][2]);
labFrameQuadrupoles[offset+8] += vectorZ.z*(vectorX.z*mPole[2][0] + vectorY.z*mPole[2][1] + vectorZ.z*mPole[2][2]);
labFrameQuadrupoles[offset+4] = vectorX.y*(vectorX.y*mPole[0][0] + vectorY.y*mPole[0][1] + vectorZ.y*mPole[0][2]);
labFrameQuadrupoles[offset+4] += vectorY.y*(vectorX.y*mPole[1][0] + vectorY.y*mPole[1][1] + vectorZ.y*mPole[1][2]);
labFrameQuadrupoles[offset+4] += vectorZ.y*(vectorX.y*mPole[2][0] + vectorY.y*mPole[2][1] + vectorZ.y*mPole[2][2]);
labFrameQuadrupoles[offset+5] = vectorX.y*(vectorX.z*mPole[0][0] + vectorY.z*mPole[0][1] + vectorZ.z*mPole[0][2]);
labFrameQuadrupoles[offset+5] += vectorY.y*(vectorX.z*mPole[1][0] + vectorY.z*mPole[1][1] + vectorZ.z*mPole[1][2]);
labFrameQuadrupoles[offset+5] += vectorZ.y*(vectorX.z*mPole[2][0] + vectorY.z*mPole[2][1] + vectorZ.z*mPole[2][2]);
labFrameQuadrupoles[offset] = vectorX.x*(vectorX.x*mPole[0][0] + vectorY.x*mPole[0][1] + vectorZ.x*mPole[0][2]);
labFrameQuadrupoles[offset] += vectorY.x*(vectorX.x*mPole[1][0] + vectorY.x*mPole[1][1] + vectorZ.x*mPole[1][2]);
labFrameQuadrupoles[offset] += vectorZ.x*(vectorX.x*mPole[2][0] + vectorY.x*mPole[2][1] + vectorZ.x*mPole[2][2]);
labFrameQuadrupoles[offset+1] = vectorX.x*(vectorX.y*mPole[0][0] + vectorY.y*mPole[0][1] + vectorZ.y*mPole[0][2]);
labFrameQuadrupoles[offset+1] += vectorY.x*(vectorX.y*mPole[1][0] + vectorY.y*mPole[1][1] + vectorZ.y*mPole[1][2]);
labFrameQuadrupoles[offset+1] += vectorZ.x*(vectorX.y*mPole[2][0] + vectorY.y*mPole[2][1] + vectorZ.y*mPole[2][2]);
labFrameQuadrupoles[offset+2] = vectorX.x*(vectorX.z*mPole[0][0] + vectorY.z*mPole[0][1] + vectorZ.z*mPole[0][2]);
labFrameQuadrupoles[offset+2] += vectorY.x*(vectorX.z*mPole[1][0] + vectorY.z*mPole[1][1] + vectorZ.z*mPole[1][2]);
labFrameQuadrupoles[offset+2] += vectorZ.x*(vectorX.z*mPole[2][0] + vectorY.z*mPole[2][1] + vectorZ.z*mPole[2][2]);
labFrameQuadrupoles[offset+3] = labFrameQuadrupoles[offset+1];
labFrameQuadrupoles[offset+6] = labFrameQuadrupoles[offset+2];
labFrameQuadrupoles[offset+7] = labFrameQuadrupoles[offset+5];
labFrameQuadrupoles[offset] = vectorX.x*(vectorX.x*mPoleXX + vectorY.x*mPoleXY + vectorZ.x*mPoleXZ);
+ vectorY.x*(vectorX.x*mPoleXY + vectorY.x*mPoleYY + vectorZ.x*mPoleYZ);
+ vectorZ.x*(vectorX.x*mPoleXZ + vectorY.x*mPoleYZ + vectorZ.x*mPoleZZ);
labFrameQuadrupoles[offset+1] = vectorX.x*(vectorX.y*mPoleXX + vectorY.y*mPoleXY + vectorZ.y*mPoleXZ);
+ vectorY.x*(vectorX.y*mPoleXY + vectorY.y*mPoleYY + vectorZ.y*mPoleYZ);
+ vectorZ.x*(vectorX.y*mPoleXZ + vectorY.y*mPoleYZ + vectorZ.y*mPoleZZ);
labFrameQuadrupoles[offset+2] = vectorX.x*(vectorX.z*mPoleXX + vectorY.z*mPoleXY + vectorZ.z*mPoleXZ);
+ vectorY.x*(vectorX.z*mPoleXY + vectorY.z*mPoleYY + vectorZ.z*mPoleYZ);
+ vectorZ.x*(vectorX.z*mPoleXZ + vectorY.z*mPoleYZ + vectorZ.z*mPoleZZ);
labFrameQuadrupoles[offset+3] = vectorX.y*(vectorX.y*mPoleXX + vectorY.y*mPoleXY + vectorZ.y*mPoleXZ);
+ vectorY.y*(vectorX.y*mPoleXY + vectorY.y*mPoleYY + vectorZ.y*mPoleYZ);
+ vectorZ.y*(vectorX.y*mPoleXZ + vectorY.y*mPoleYZ + vectorZ.y*mPoleZZ);
labFrameQuadrupoles[offset+4] = vectorX.y*(vectorX.z*mPoleXX + vectorY.z*mPoleXY + vectorZ.z*mPoleXZ);
+ vectorY.y*(vectorX.z*mPoleXY + vectorY.z*mPoleYY + vectorZ.z*mPoleYZ);
+ vectorZ.y*(vectorX.z*mPoleXZ + vectorY.z*mPoleYZ + vectorZ.z*mPoleZZ);
}
}
}
extern "C" __global__ void recordInducedDipoles(const long long* __restrict__ fieldBuffers, const long long* __restrict__ fieldPolarBuffers,
real* __restrict__ inducedDipole, real* __restrict__ inducedDipolePolar, const float* __restrict__ polarizability) {
for (int atom = blockIdx.x*blockDim.x+threadIdx.x; atom < NUM_ATOMS; atom += gridDim.x*blockDim.x) {
real scale = polarizability[atom]/(real) 0xFFFFFFFF;
inducedDipole[3*atom] = scale*fieldBuffers[atom];
inducedDipole[3*atom+1] = scale*fieldBuffers[atom+PADDED_NUM_ATOMS];
inducedDipole[3*atom+2] = scale*fieldBuffers[atom+PADDED_NUM_ATOMS*2];
inducedDipolePolar[3*atom] = scale*fieldPolarBuffers[atom];
inducedDipolePolar[3*atom+1] = scale*fieldPolarBuffers[atom+PADDED_NUM_ATOMS];
inducedDipolePolar[3*atom+2] = scale*fieldPolarBuffers[atom+PADDED_NUM_ATOMS*2];
}
}
\ No newline at end of file
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaVdwForce.cpp
View file @ 776f6f22
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Authors: Mark Friedrichs *
* Contributors: *
* *
......@@ -42,6 +42,13 @@
#include "openmm/LangevinIntegrator.h"
#include <iostream>
#include <vector>
#include <stdlib.h>
#include <stdio.h>
#define ASSERT_EQUAL_TOL_MOD(expected, found, tol, testname) {double _scale_ = std::abs(expected) > 1.0 ? std::abs(expected) : 1.0; if (!(std::abs((expected)-(found))/_scale_ <= (tol))) {std::stringstream details; details << testname << " Expected "<<(expected)<<", found "<<(found); throwException(__FILE__, __LINE__, details.str());}};
#define ASSERT_EQUAL_VEC_MOD(expected, found, tol,testname) {ASSERT_EQUAL_TOL_MOD((expected)[0], (found)[0], (tol),(testname)); ASSERT_EQUAL_TOL_MOD((expected)[1], (found)[1], (tol),(testname)); ASSERT_EQUAL_TOL_MOD((expected)[2], (found)[2], (tol),(testname));};
using namespace OpenMM;
const double TOL = 1e-4;
......@@ -56,22 +63,20 @@ void testVdw( FILE* log ) {
std::string epsilonCombiningRule = std::string("HHG");
amoebaVdwForce->setEpsilonCombiningRule( epsilonCombiningRule );
int classIndex = 0;
for( int ii = 0; ii < numberOfParticles; ii++ ){
int indexIV, indexClass;
int indexIV;
double mass, sigma, epsilon, reduction;
std::vector< int > exclusions;
if( ii == 0 || ii == 3 ){
mass = 16.0;
indexIV = ii;
indexClass = 70;
sigma = 1.70250E+00;
epsilon = 1.10000E-01;
reduction = 0.0;
} else {
mass = 1.0;
indexIV = ii < 3 ? 0 : 3;
indexClass = 71;
sigma = 1.32750E+00;
epsilon = 1.35000E-02;
reduction = 0.91;
......@@ -89,7 +94,7 @@ void testVdw( FILE* log ) {
exclusions.push_back ( 5 );
}
system.addParticle(mass);
amoebaVdwForce->addParticle( indexIV, indexClass, sigma, epsilon, reduction );
amoebaVdwForce->addParticle( indexIV, classIndex, sigma, epsilon, reduction );
amoebaVdwForce->setParticleExclusions( ii, exclusions );
}
LangevinIntegrator integrator(0.0, 0.1, 0.01);
......@@ -130,12 +135,13 @@ void testVdw( FILE* log ) {
positions[ii][2] *= AngstromToNm;
}
for( int ii = 0; ii < amoebaVdwForce->getNumParticles(); ii++ ){
int indexIV, indexClass;
int indexIV;
int classIndex;
double sigma, epsilon, reduction;
amoebaVdwForce->getParticleParameters( ii, indexIV, indexClass, sigma, epsilon, reduction );
amoebaVdwForce->getParticleParameters( ii, indexIV, classIndex, sigma, epsilon, reduction );
sigma *= AngstromToNm;
epsilon *= CalToJoule;
amoebaVdwForce->setParticleParameters( ii, indexIV, indexClass, sigma, epsilon, reduction );
amoebaVdwForce->setParticleParameters( ii, indexIV, classIndex, sigma, epsilon, reduction );
}
platformName = "CUDA";
Context context(system, integrator, Platform::getPlatformByName( platformName ) );
......@@ -170,6 +176,342 @@ void testVdw( FILE* log ) {
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void setupAndGetForcesEnergyVdwAmmonia( const std::string& sigmaCombiningRule, const std::string& epsilonCombiningRule, double cutoff,
double boxDimension, std::vector<Vec3>& forces, double& energy, FILE* log ){
// beginning of Vdw setup
System system;
AmoebaVdwForce* amoebaVdwForce = new AmoebaVdwForce();;
int numberOfParticles = 8;
amoebaVdwForce->setSigmaCombiningRule( sigmaCombiningRule );
amoebaVdwForce->setEpsilonCombiningRule( epsilonCombiningRule );
amoebaVdwForce->setUseNeighborList( 1 );
amoebaVdwForce->setCutoff( cutoff );
if( boxDimension > 0.0 ){
Vec3 a( boxDimension, 0.0, 0.0 );
Vec3 b( 0.0, boxDimension, 0.0 );
Vec3 c( 0.0, 0.0, boxDimension );
system.setDefaultPeriodicBoxVectors( a, b, c );
amoebaVdwForce->setPBC( 1 );
} else {
amoebaVdwForce->setPBC( 0 );
}
// addParticle: ivIndex, radius, epsilon, reductionFactor
int classIndex = 0;
system.addParticle( 1.4007000e+01 );
amoebaVdwForce->addParticle( 0, classIndex, 1.8550000e-01, 4.3932000e-01, 0.0000000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaVdwForce->addParticle( 0, classIndex, 1.3500000e-01, 8.3680000e-02, 9.1000000e-01 );
system.addParticle( 1.0080000e+00 );
amoebaVdwForce->addParticle( 0, classIndex, 1.3500000e-01, 8.3680000e-02, 9.1000000e-01 );
system.addParticle( 1.0080000e+00 );
amoebaVdwForce->addParticle( 0, classIndex, 1.3500000e-01, 8.3680000e-02, 9.1000000e-01 );
system.addParticle( 1.4007000e+01 );
amoebaVdwForce->addParticle( 4, classIndex, 1.8550000e-01, 4.3932000e-01, 0.0000000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaVdwForce->addParticle( 4, classIndex, 1.3500000e-01, 8.3680000e-02, 9.1000000e-01 );
system.addParticle( 1.0080000e+00 );
amoebaVdwForce->addParticle( 4, classIndex, 1.3500000e-01, 8.3680000e-02, 9.1000000e-01 );
system.addParticle( 1.0080000e+00 );
amoebaVdwForce->addParticle( 4, classIndex, 1.3500000e-01, 8.3680000e-02, 9.1000000e-01 );
// ParticleExclusions
std::vector< int > exclusions;
exclusions.resize(0);
exclusions.push_back( 0 );
exclusions.push_back( 1 );
exclusions.push_back( 2 );
exclusions.push_back( 3 );
amoebaVdwForce->setParticleExclusions( 0, exclusions );
exclusions.resize(0);
exclusions.push_back( 1 );
exclusions.push_back( 0 );
exclusions.push_back( 2 );
exclusions.push_back( 3 );
amoebaVdwForce->setParticleExclusions( 1, exclusions );
exclusions.resize(0);
exclusions.push_back( 2 );
exclusions.push_back( 0 );
exclusions.push_back( 1 );
exclusions.push_back( 3 );
amoebaVdwForce->setParticleExclusions( 2, exclusions );
exclusions.resize(0);
exclusions.push_back( 3 );
exclusions.push_back( 0 );
exclusions.push_back( 1 );
exclusions.push_back( 2 );
amoebaVdwForce->setParticleExclusions( 3, exclusions );
exclusions.resize(0);
exclusions.push_back( 4 );
exclusions.push_back( 5 );
exclusions.push_back( 6 );
exclusions.push_back( 7 );
amoebaVdwForce->setParticleExclusions( 4, exclusions );
exclusions.resize(0);
exclusions.push_back( 5 );
exclusions.push_back( 4 );
exclusions.push_back( 6 );
exclusions.push_back( 7 );
amoebaVdwForce->setParticleExclusions( 5, exclusions );
exclusions.resize(0);
exclusions.push_back( 6 );
exclusions.push_back( 4 );
exclusions.push_back( 5 );
exclusions.push_back( 7 );
amoebaVdwForce->setParticleExclusions( 6, exclusions );
exclusions.resize(0);
exclusions.push_back( 7 );
exclusions.push_back( 4 );
exclusions.push_back( 5 );
exclusions.push_back( 6 );
amoebaVdwForce->setParticleExclusions( 7, exclusions );
// end of Vdw setup
std::vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3( 1.5927280e-01, 1.7000000e-06, 1.6491000e-03 );
positions[1] = Vec3( 2.0805540e-01, -8.1258800e-02, 3.7282500e-02 );
positions[2] = Vec3( 2.0843610e-01, 8.0953200e-02, 3.7462200e-02 );
positions[3] = Vec3( 1.7280780e-01, 2.0730000e-04, -9.8741700e-02 );
positions[4] = Vec3( -1.6743680e-01, 1.5900000e-05, -6.6149000e-03 );
positions[5] = Vec3( -2.0428260e-01, 8.1071500e-02, 4.1343900e-02 );
positions[6] = Vec3( -6.7308300e-02, 1.2800000e-05, 1.0623300e-02 );
positions[7] = Vec3( -2.0426290e-01, -8.1231400e-02, 4.1033500e-02 );
system.addForce(amoebaVdwForce);
std::string platformName;
platformName = "CUDA";
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName( platformName ) );
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
forces = state.getForces();
energy = state.getPotentialEnergy();
}
void compareForcesEnergy( std::string& testName, double expectedEnergy, double energy,
std::vector<Vec3>& expectedForces,
std::vector<Vec3>& forces, double tolerance, FILE* log ) {
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "%s: expected energy=%14.7e %14.7e\n", testName.c_str(), expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC_MOD( expectedForces[ii], forces[ii], tolerance, testName );
}
ASSERT_EQUAL_TOL_MOD( expectedEnergy, energy, tolerance, testName );
}
// test VDW w/ sigmaRule=CubicMean and epsilonRule=HHG
void testVdwAmmoniaCubicMeanHhg( FILE* log ) {
std::string testName = "testVdwAmmoniaCubicMeanHhg";
int numberOfParticles = 8;
double boxDimension = -1.0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HHG", cutoff, boxDimension, forces, energy, log );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 4.8012258e+00;
expectedForces[0] = Vec3( 2.9265247e+02, -1.4507808e-02, -6.9562123e+00 );
expectedForces[1] = Vec3( -2.2451693e+00, 4.8143073e-01, -2.0041494e-01 );
expectedForces[2] = Vec3( -2.2440698e+00, -4.7905450e-01, -2.0125284e-01 );
expectedForces[3] = Vec3( -1.0840394e+00, -5.8531253e-04, 2.6934135e-01 );
expectedForces[4] = Vec3( -5.6305662e+01, 1.4733908e-03, -1.8083306e-01 );
expectedForces[5] = Vec3( 1.6750145e+00, -3.2448374e-01, -1.8030914e-01 );
expectedForces[6] = Vec3( -2.3412420e+02, 1.0754069e-02, 7.6287492e+00 );
expectedForces[7] = Vec3( 1.6756544e+00, 3.2497316e-01, -1.7906832e-01 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
}
// test VDW w/ sigmaRule=Arithmetic and epsilonRule=Arithmetic
void testVdwAmmoniaArithmeticArithmetic( FILE* log ) {
std::string testName = "testVdwAmmoniaArithmeticArithmetic";
int numberOfParticles = 8;
double boxDimension = -1.0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "ARITHMETIC", "ARITHMETIC", cutoff, boxDimension, forces, energy, log );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 4.2252403e+00;
expectedForces[0] = Vec3( 3.0603839e+02, -1.5550310e-02, -7.2661707e+00 );
expectedForces[1] = Vec3( -2.7801357e+00, 5.8805051e-01, -2.5907269e-01 );
expectedForces[2] = Vec3( -2.7753968e+00, -5.8440732e-01, -2.5969111e-01 );
expectedForces[3] = Vec3( -2.2496416e+00, -1.1797440e-03, 5.5501757e-01 );
expectedForces[4] = Vec3( -5.5077629e+01, 8.3417114e-04, -3.3668921e-01 );
expectedForces[5] = Vec3( 2.3752452e+00, -4.6788669e-01, -2.4907764e-01 );
expectedForces[6] = Vec3( -2.4790697e+02, 1.1419770e-02, 8.0629999e+00 );
expectedForces[7] = Vec3( 2.3761408e+00, 4.6871961e-01, -2.4731607e-01 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
}
// test VDW w/ sigmaRule=Geometric and epsilonRule=Geometric
void testVdwAmmoniaGeometricGeometric( FILE* log ) {
std::string testName = "testVdwAmmoniaGeometricGeometric";
int numberOfParticles = 8;
double boxDimension = -1.0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "GEOMETRIC", "GEOMETRIC", cutoff, boxDimension, forces, energy, log );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 2.5249914e+00;
expectedForces[0] = Vec3( 2.1169631e+02, -1.0710925e-02, -4.3728025e+00 );
expectedForces[1] = Vec3( -2.2585621e+00, 4.8409995e-01, -2.0188344e-01 );
expectedForces[2] = Vec3( -2.2551351e+00, -4.8124855e-01, -2.0246986e-01 );
expectedForces[3] = Vec3( -1.7178028e+00, -9.0851787e-04, 4.2466975e-01 );
expectedForces[4] = Vec3( -4.8302147e+01, 9.6603376e-04, -5.7972068e-01 );
expectedForces[5] = Vec3( 1.8100634e+00, -3.5214093e-01, -1.9357207e-01 );
expectedForces[6] = Vec3( -1.6078365e+02, 7.2117601e-03, 5.3180261e+00 );
expectedForces[7] = Vec3( 1.8109211e+00, 3.5273117e-01, -1.9224723e-01 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
}
void testVdwAmmoniaCubicMeanHarmonic( FILE* log ) {
std::string testName = "testVdwAmmoniaCubicMeanHarmonic";
int numberOfParticles = 8;
double boxDimension = -1.0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HARMONIC", cutoff, boxDimension, forces, energy, log );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 4.1369069e+00;
expectedForces[0] = Vec3( 2.5854436e+02, -1.2779529e-02, -5.9041148e+00 );
expectedForces[1] = Vec3( -2.0832419e+00, 4.4915831e-01, -1.8266000e-01 );
expectedForces[2] = Vec3( -2.0823991e+00, -4.4699804e-01, -1.8347141e-01 );
expectedForces[3] = Vec3( -9.5914714e-01, -5.2162026e-04, 2.3873165e-01 );
expectedForces[4] = Vec3( -5.3724787e+01, 1.4838241e-03, -2.8089191e-01 );
expectedForces[5] = Vec3( 1.5074325e+00, -2.9016397e-01, -1.6385118e-01 );
expectedForces[6] = Vec3( -2.0271029e+02, 9.2367947e-03, 6.6389988e+00 );
expectedForces[7] = Vec3( 1.5080748e+00, 2.9058422e-01, -1.6274118e-01 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
}
// test w/ cutoff=0.25 nm; single ixn between two particles (0 and 6); force nonzero on
// particle 4 due to reduction applied to NH
// the distance between 0 and 6 is ~ 0.235 so the ixn is in the tapered region
void testVdwTaper( FILE* log ) {
std::string testName = "testVdwTaper";
int numberOfParticles = 8;
double boxDimension = -1.0;
double cutoff = 0.25;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HHG", cutoff, boxDimension, forces, energy, log );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 3.5478444e+00;
expectedForces[0] = Vec3( 5.6710779e+02, -2.7391004e-02, -1.7867730e+01 );
expectedForces[1] = Vec3( -0.0000000e+00, -0.0000000e+00, -0.0000000e+00 );
expectedForces[2] = Vec3( -0.0000000e+00, -0.0000000e+00, -0.0000000e+00 );
expectedForces[3] = Vec3( -0.0000000e+00, -0.0000000e+00, -0.0000000e+00 );
expectedForces[4] = Vec3( -5.1039701e+01, 2.4651903e-03, 1.6080957e+00 );
expectedForces[5] = Vec3( -0.0000000e+00, -0.0000000e+00, -0.0000000e+00 );
expectedForces[6] = Vec3( -5.1606809e+02, 2.4925813e-02, 1.6259634e+01 );
expectedForces[7] = Vec3( -0.0000000e+00, -0.0000000e+00, -0.0000000e+00 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
}
// test PBC
void testVdwPBC( FILE* log ) {
std::string testName = "testVdwPBC";
int numberOfParticles = 8;
double boxDimension = 0.6;
double cutoff = 0.25;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HHG", cutoff, boxDimension, forces, energy, log );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 8.4385405e+00;
expectedForces[0] = Vec3( 5.1453069e+02, 4.9751912e-01, -1.2759570e+01 );
expectedForces[1] = Vec3( -2.5622586e+02, -4.6524265e+01, 2.4281465e+01 );
expectedForces[2] = Vec3( -2.7538705e+02, 5.1831690e+01, 2.7367710e+01 );
expectedForces[3] = Vec3( -0.0000000e+00, -0.0000000e+00, -0.0000000e+00 );
expectedForces[4] = Vec3( 3.0883034e+02, -5.8876974e+00, -5.8286122e+01 );
expectedForces[5] = Vec3( 1.1319359e+02, -3.2047069e-01, 1.6181231e+00 );
expectedForces[6] = Vec3( -5.1606809e+02, 2.4925813e-02, 1.6259634e+01 );
expectedForces[7] = Vec3( 1.1112638e+02, 3.7829857e-01, 1.5187587e+00 );
// tolerance is higher here due to interpolation used in setting tapering coefficients;
// if tapering turned off, then absolute difference < 2.0e-05
double tolerance = 5.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
}
int main( int numberOfArguments, char* argv[] ) {
......@@ -178,7 +520,37 @@ int main( int numberOfArguments, char* argv[] ) {
registerAmoebaCudaKernelFactories();
FILE* log = NULL;
testVdw( log );
// tests using two ammonia molecules
// test VDW w/ sigmaRule=CubicMean and epsilonRule=HHG
testVdwAmmoniaCubicMeanHhg( log );
// test VDW w/ sigmaRule=Arithmetic and epsilonRule=Arithmetic
testVdwAmmoniaArithmeticArithmetic( log );
// test VDW w/ sigmaRule=Geometric and epsilonRule=Geometric
testVdwAmmoniaGeometricGeometric( log );
// test VDW w/ sigmaRule=CubicMean and epsilonRule=Harmonic
testVdwAmmoniaCubicMeanHarmonic( log );
// test w/ cutoff=0.25 nm; single ixn between two particles (0 and 6); force nonzero on
// particle 4 due to reduction applied to NH
// the distance between 0 and 6 is ~ 0.235 so the ixn is in the tapered region
testVdwTaper( log );
// test PBC
testVdwPBC( log );
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
......
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