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Commit a741138b authored by Andy Simmonett's avatar Andy Simmonett
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Initial fast reciprocal space LJPME implementation, with test.

parent 40a7363d
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plugins/cpupme/src/CpuPmeKernels.cpp
View file @ a741138b
...@@ -36,6 +36,7 @@ ...@@ -36,6 +36,7 @@
#include "SimTKOpenMMRealType.h" #include "SimTKOpenMMRealType.h"
#include "openmm/internal/hardware.h" #include "openmm/internal/hardware.h"
#include "openmm/internal/vectorize.h" #include "openmm/internal/vectorize.h"
#include "openmm/OpenMMException.h"
#include <cmath> #include <cmath>
#include <algorithm> #include <algorithm>
#include <cstring> #include <cstring>
...@@ -50,7 +51,7 @@ static const int PME_ORDER = 5; ...@@ -50,7 +51,7 @@ static const int PME_ORDER = 5;
bool CpuCalcPmeReciprocalForceKernel::hasInitializedThreads = false; bool CpuCalcPmeReciprocalForceKernel::hasInitializedThreads = false;
int CpuCalcPmeReciprocalForceKernel::numThreads = 0; int CpuCalcPmeReciprocalForceKernel::numThreads = 0;
static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors, gmx_atomic_t& atomicCounter) { static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors, gmx_atomic_t& atomicCounter, const float epsilonFactor) {
float temp[4]; float temp[4];
fvec4 boxSize((float) periodicBoxVectors[0][0], (float) periodicBoxVectors[1][1], (float) periodicBoxVectors[2][2], 0); fvec4 boxSize((float) periodicBoxVectors[0][0], (float) periodicBoxVectors[1][1], (float) periodicBoxVectors[2][2], 0);
fvec4 invBoxSize((float) recipBoxVectors[0][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[2][2], 0); fvec4 invBoxSize((float) recipBoxVectors[0][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[2][2], 0);
...@@ -62,7 +63,6 @@ static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gri ...@@ -62,7 +63,6 @@ static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gri
fvec4 one(1); fvec4 one(1);
fvec4 scale(1.0f/(PME_ORDER-1)); fvec4 scale(1.0f/(PME_ORDER-1));
float posInBox[4] = {0,0,0,0}; float posInBox[4] = {0,0,0,0};
const float epsilonFactor = sqrt(ONE_4PI_EPS0);
memset(grid, 0, sizeof(float)*gridx*gridy*gridz); memset(grid, 0, sizeof(float)*gridx*gridy*gridz);
while (true) { while (true) {
...@@ -154,6 +154,46 @@ static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gri ...@@ -154,6 +154,46 @@ static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gri
} }
} }
static void computeReciprocalDispersionEterm(int start, int end, int gridx, int gridy, int gridz, vector<float>& recipEterm, double alpha, vector<float>* bsplineModuli, Vec3* periodicBoxVectors, Vec3* recipBoxVectors) {
const unsigned int zsize = gridz/2+1;
const unsigned int yzsize = gridy*zsize;
const float scaleFactor = (float) M_PI*sqrtf(M_PI) / (6.0*periodicBoxVectors[0][0]*periodicBoxVectors[1][1]*periodicBoxVectors[2][2]);
float bfac = M_PI / alpha;
float fac1 = 2.0f*M_PI*M_PI*M_PI*sqrtf(M_PI);
float fac2 = alpha*alpha*alpha;
float fac3 = -2.0f*alpha*M_PI*M_PI;
float b, m, m3, expfac, expterm, erfcterm;
for (int kx = start; kx < end; kx++) {
int mx = (kx < (gridx+1)/2) ? kx : kx-gridx;
float mhx = mx*(float)recipBoxVectors[0][0];
float bx = bsplineModuli[0][kx];
for (int ky = 0; ky < gridy; ky++) {
int my = (ky < (gridy+1)/2) ? ky : ky-gridy;
float mhy = mx*(float)recipBoxVectors[1][0] + my*(float)recipBoxVectors[1][1];
float mhx2y2 = mhx*mhx + mhy*mhy;
float bxby = bx*bsplineModuli[1][ky];
for (int kz = 0; kz < zsize; kz++) {
int index = kx*yzsize + ky*zsize + kz;
int mz = (kz < (gridz+1)/2) ? kz : kz-gridz;
float mhz = mx*(float)recipBoxVectors[2][0] + my*(float)recipBoxVectors[2][1] + mz*(float)recipBoxVectors[2][2];
float bz = bsplineModuli[2][kz];
float m2 = mhx2y2 + mhz*mhz;
float denom = scaleFactor/(bxby*bz);
m = sqrtf(m2);
m3 = m*m2;
b = bfac*m;
expfac = -b*b;
erfcterm = erfc(b);
expterm = exp(expfac);
recipEterm[index] = -2.0f*(fac1*erfcterm*m3 + expterm*(fac2 + fac3*m2)) * denom;
}
}
}
}
static void computeReciprocalEterm(int start, int end, int gridx, int gridy, int gridz, vector<float>& recipEterm, double alpha, vector<float>* bsplineModuli, Vec3* periodicBoxVectors, Vec3* recipBoxVectors) { static void computeReciprocalEterm(int start, int end, int gridx, int gridy, int gridz, vector<float>& recipEterm, double alpha, vector<float>* bsplineModuli, Vec3* periodicBoxVectors, Vec3* recipBoxVectors) {
const unsigned int zsize = gridz/2+1; const unsigned int zsize = gridz/2+1;
const unsigned int yzsize = gridy*zsize; const unsigned int yzsize = gridy*zsize;
...@@ -230,6 +270,63 @@ static double reciprocalEnergy(int start, int end, fftwf_complex* grid, int grid ...@@ -230,6 +270,63 @@ static double reciprocalEnergy(int start, int end, fftwf_complex* grid, int grid
return 0.5*energy; return 0.5*energy;
} }
static double reciprocalDispersionEnergy(int start, int end, fftwf_complex* grid, int gridx, int gridy, int gridz, double alpha, vector<float>* bsplineModuli, Vec3* periodicBoxVectors, Vec3* recipBoxVectors) {
const unsigned int zsizeHalf = gridz/2+1;
const unsigned int yzsizeHalf = gridy*zsizeHalf;
const float scaleFactor = (float) M_PI*sqrtf(M_PI) / (6.0*periodicBoxVectors[0][0]*periodicBoxVectors[1][1]*periodicBoxVectors[2][2]);
float bfac = M_PI / alpha;
float fac1 = 2.0f*M_PI*M_PI*M_PI*sqrtf(M_PI);
float fac2 = alpha*alpha*alpha;
float fac3 = -2.0f*alpha*M_PI*M_PI;
float b, m, m3, expfac, expterm, erfcterm;
double energy = 0.0;
for (int kx = start; kx < end; kx++) {
int mx = (kx < (gridx+1)/2) ? kx : kx-gridx;
float mhx = mx*(float)recipBoxVectors[0][0];
float bx = bsplineModuli[0][kx];
for (int ky = 0; ky < gridy; ky++) {
int my = (ky < (gridy+1)/2) ? ky : ky-gridy;
float mhy = mx*(float)recipBoxVectors[1][0] + my*(float)recipBoxVectors[1][1];
float mhx2y2 = mhx*mhx + mhy*mhy;
float bxby = bx*bsplineModuli[1][ky];
for (int kz = 0; kz < gridz; kz++) {
int mz = (kz < (gridz+1)/2) ? kz : kz-gridz;
float mhz = mx*(float)recipBoxVectors[2][0] + my*(float)recipBoxVectors[2][1] + mz*(float)recipBoxVectors[2][2];
float bz = bsplineModuli[2][kz];
float m2 = mhx2y2 + mhz*mhz;
float denom = scaleFactor/(bxby*bz);
m = sqrtf(m2);
m3 = m*m2;
b = bfac*m;
expfac = -b*b;
erfcterm = erfc(b);
expterm = exp(expfac);
float eterm = (fac1*erfcterm*m3 + expterm*(fac2 + fac3*m2)) * denom;
int kx1, ky1, kz1;
if (kz >= gridz/2+1) {
kx1 = (kx == 0 ? kx : gridx-kx);
ky1 = (ky == 0 ? ky : gridy-ky);
kz1 = gridz-kz;
}
else {
kx1 = kx;
ky1 = ky;
kz1 = kz;
}
int index = kx1*yzsizeHalf + ky1*zsizeHalf + kz1;
float gridReal = grid[index][0];
float gridImag = grid[index][1];
energy += eterm*(gridReal*gridReal+gridImag*gridImag);
}
}
}
return -energy;
}
static void reciprocalConvolution(int start, int end, fftwf_complex* grid, vector<float>& recipEterm) { static void reciprocalConvolution(int start, int end, fftwf_complex* grid, vector<float>& recipEterm) {
for (int index = start; index < end; index++) { for (int index = start; index < end; index++) {
float eterm = recipEterm[index]; float eterm = recipEterm[index];
...@@ -238,7 +335,7 @@ static void reciprocalConvolution(int start, int end, fftwf_complex* grid, vecto ...@@ -238,7 +335,7 @@ static void reciprocalConvolution(int start, int end, fftwf_complex* grid, vecto
} }
} }
static void interpolateForces(float* posq, float* force, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors, gmx_atomic_t& atomicCounter) { static void interpolateForces(float* posq, float* force, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors, gmx_atomic_t& atomicCounter, const float epsilonFactor) {
fvec4 boxSize((float) periodicBoxVectors[0][0], (float) periodicBoxVectors[1][1], (float) periodicBoxVectors[2][2], 0); fvec4 boxSize((float) periodicBoxVectors[0][0], (float) periodicBoxVectors[1][1], (float) periodicBoxVectors[2][2], 0);
fvec4 invBoxSize((float) recipBoxVectors[0][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[2][2], 0); fvec4 invBoxSize((float) recipBoxVectors[0][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[2][2], 0);
fvec4 recipBoxVec0((float) recipBoxVectors[0][0], (float) recipBoxVectors[0][1], (float) recipBoxVectors[0][2], 0); fvec4 recipBoxVec0((float) recipBoxVectors[0][0], (float) recipBoxVectors[0][1], (float) recipBoxVectors[0][2], 0);
...@@ -248,7 +345,6 @@ static void interpolateForces(float* posq, float* force, float* grid, int gridx, ...@@ -248,7 +345,6 @@ static void interpolateForces(float* posq, float* force, float* grid, int gridx,
ivec4 gridSizeInt(gridx, gridy, gridz, 0); ivec4 gridSizeInt(gridx, gridy, gridz, 0);
fvec4 one(1); fvec4 one(1);
fvec4 scale(1.0f/(PME_ORDER-1)); fvec4 scale(1.0f/(PME_ORDER-1));
const float epsilonFactor = sqrt(ONE_4PI_EPS0);
while (true) { while (true) {
int i = gmx_atomic_fetch_add(&atomicCounter, 1); int i = gmx_atomic_fetch_add(&atomicCounter, 1);
if (i >= numParticles) if (i >= numParticles)
...@@ -524,7 +620,8 @@ void CpuCalcPmeReciprocalForceKernel::runWorkerThread(ThreadPool& threads, int i ...@@ -524,7 +620,8 @@ void CpuCalcPmeReciprocalForceKernel::runWorkerThread(ThreadPool& threads, int i
int complexSize = gridx*gridy*(gridz/2+1); int complexSize = gridx*gridy*(gridz/2+1);
int complexStart = std::max(1, ((index*complexSize)/numThreads)); int complexStart = std::max(1, ((index*complexSize)/numThreads));
int complexEnd = (((index+1)*complexSize)/numThreads); int complexEnd = (((index+1)*complexSize)/numThreads);
spreadCharge(posq, tempGrid[index], gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors, atomicCounter); const float epsilonFactor = calculationType==Electrostatic ? sqrt(ONE_4PI_EPS0) : 1.0f;
spreadCharge(posq, tempGrid[index], gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors, atomicCounter, epsilonFactor);
threads.syncThreads(); threads.syncThreads();
int numGrids = tempGrid.size(); int numGrids = tempGrid.size();
for (int i = gridStart; i < gridEnd; i += 4) { for (int i = gridStart; i < gridEnd; i += 4) {
...@@ -534,17 +631,38 @@ void CpuCalcPmeReciprocalForceKernel::runWorkerThread(ThreadPool& threads, int i ...@@ -534,17 +631,38 @@ void CpuCalcPmeReciprocalForceKernel::runWorkerThread(ThreadPool& threads, int i
sum.store(&realGrid[i]); sum.store(&realGrid[i]);
} }
threads.syncThreads(); threads.syncThreads();
if (lastBoxVectors[0] != periodicBoxVectors[0] || lastBoxVectors[1] != periodicBoxVectors[1] || lastBoxVectors[2] != periodicBoxVectors[2]) { switch(calculationType){
computeReciprocalEterm(gridxStart, gridxEnd, gridx, gridy, gridz, recipEterm, alpha, bsplineModuli, periodicBoxVectors, recipBoxVectors); case Electrostatic:
if (lastBoxVectors[0] != periodicBoxVectors[0] || lastBoxVectors[1] != periodicBoxVectors[1] || lastBoxVectors[2] != periodicBoxVectors[2]) {
computeReciprocalEterm(gridxStart, gridxEnd, gridx, gridy, gridz, recipEterm, alpha, bsplineModuli, periodicBoxVectors, recipBoxVectors);
threads.syncThreads();
}
if (includeEnergy) {
threadEnergy[index] = reciprocalEnergy(gridxStart, gridxEnd, complexGrid, gridx, gridy, gridz, alpha, bsplineModuli, periodicBoxVectors, recipBoxVectors);
threads.syncThreads();
}
reciprocalConvolution(complexStart, complexEnd, complexGrid, recipEterm);
threads.syncThreads(); threads.syncThreads();
} break;
if (includeEnergy) { case Dispersion:
threadEnergy[index] = reciprocalEnergy(gridxStart, gridxEnd, complexGrid, gridx, gridy, gridz, alpha, bsplineModuli, periodicBoxVectors, recipBoxVectors); if (lastBoxVectors[0] != periodicBoxVectors[0] || lastBoxVectors[1] != periodicBoxVectors[1] || lastBoxVectors[2] != periodicBoxVectors[2]) {
computeReciprocalDispersionEterm(gridxStart, gridxEnd, gridx, gridy, gridz, recipEterm, alpha, bsplineModuli, periodicBoxVectors, recipBoxVectors);
threads.syncThreads();
}
if (includeEnergy) {
threadEnergy[index] = reciprocalDispersionEnergy(gridxStart, gridxEnd, complexGrid, gridx, gridy, gridz, alpha, bsplineModuli, periodicBoxVectors, recipBoxVectors);
threads.syncThreads();
}
// For dispersion, we include the {0,0,0} term, so the start point needs to be redefined
complexStart = std::max(0, ((index*complexSize)/numThreads));
reciprocalConvolution(complexStart, complexEnd, complexGrid, recipEterm);
threads.syncThreads(); threads.syncThreads();
break;
default:
throw OpenMMException("Unimplemented convolution type");
} }
reciprocalConvolution(complexStart, complexEnd, complexGrid, recipEterm);
threads.syncThreads(); interpolateForces(posq, &force[0], realGrid, gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors, atomicCounter, epsilonFactor);
interpolateForces(posq, &force[0], realGrid, gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors, atomicCounter);
} }
void CpuCalcPmeReciprocalForceKernel::beginComputation(IO& io, const Vec3* periodicBoxVectors, bool includeEnergy) { void CpuCalcPmeReciprocalForceKernel::beginComputation(IO& io, const Vec3* periodicBoxVectors, bool includeEnergy) {
......
plugins/cpupme/src/CpuPmeKernels.h
View file @ a741138b
...@@ -51,8 +51,10 @@ namespace OpenMM { ...@@ -51,8 +51,10 @@ namespace OpenMM {
class OPENMM_EXPORT_PME CpuCalcPmeReciprocalForceKernel : public CalcPmeReciprocalForceKernel { class OPENMM_EXPORT_PME CpuCalcPmeReciprocalForceKernel : public CalcPmeReciprocalForceKernel {
public: public:
enum CalculationType { Electrostatic=0, Dispersion=1 };
CpuCalcPmeReciprocalForceKernel(std::string name, const Platform& platform) : CalcPmeReciprocalForceKernel(name, platform), CpuCalcPmeReciprocalForceKernel(std::string name, const Platform& platform) : CalcPmeReciprocalForceKernel(name, platform),
hasCreatedPlan(false), isDeleted(false), realGrid(NULL), complexGrid(NULL) { hasCreatedPlan(false), isDeleted(false), realGrid(NULL), complexGrid(NULL), calculationType(Electrostatic) {
} }
/** /**
* Initialize the kernel. * Initialize the kernel.
...@@ -101,6 +103,11 @@ public: ...@@ -101,6 +103,11 @@ public:
* @param nz the number of grid points along the Z axis * @param nz the number of grid points along the Z axis
*/ */
void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const; void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
/**
* Sets the type of reciprocal space computation to perform (Electrostatic or Dispersion).
* @param type The type of computation
*/
void setCalculationType(CalculationType type) { calculationType = type; }
private: private:
class ComputeTask; class ComputeTask;
/** /**
...@@ -131,6 +138,7 @@ private: ...@@ -131,6 +138,7 @@ private:
float* posq; float* posq;
Vec3 periodicBoxVectors[3], recipBoxVectors[3]; Vec3 periodicBoxVectors[3], recipBoxVectors[3];
bool includeEnergy; bool includeEnergy;
CalculationType calculationType;
gmx_atomic_t atomicCounter; gmx_atomic_t atomicCounter;
}; };
......
plugins/cpupme/tests/TestCpuPme.cpp
View file @ a741138b
...@@ -40,6 +40,7 @@ ...@@ -40,6 +40,7 @@
#include "openmm/System.h" #include "openmm/System.h"
#include "openmm/VerletIntegrator.h" #include "openmm/VerletIntegrator.h"
#include "openmm/internal/ContextImpl.h" #include "openmm/internal/ContextImpl.h"
#include "openmm/Units.h"
#include "../src/CpuPmeKernels.h" #include "../src/CpuPmeKernels.h"
#include "SimTKOpenMMRealType.h" #include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h" #include "sfmt/SFMT.h"
...@@ -61,6 +62,510 @@ public: ...@@ -61,6 +62,510 @@ public:
} }
}; };
void make_waterbox(int natoms, double boxEdgeLength, NonbondedForce *forceField, vector<Vec3> &positions, vector<double>& eps, vector<double>& sig,
vector<pair<int, int> >& bonds, System &system, bool do_electrostatics) {
const int RESSIZE = 3;
const double masses[RESSIZE] = { 8.0, 1.0, 1.0 };
const double charges[RESSIZE] = { -0.834, 0.417, 0.417 };
// Values from the CHARMM force field, in AKMA units
const double epsilons[RESSIZE] = { -0.1521, -0.046, -0.046 };
const double halfrmins[RESSIZE] = { 1.7682, 0.2245, 0.2245 };
positions.clear();
if(natoms == 6){
const double coords[6][3] = {
{ 2.000000, 2.000000, 2.000000},
{ 2.500000, 2.000000, 3.000000},
{ 1.500000, 2.000000, 3.000000},
{ 0.000000, 0.000000, 0.000000},
{ 0.500000, 0.000000, 1.000000},
{ -0.500000, 0.000000, 1.000000}
};
for(int atom = 0; atom < natoms; ++atom)
positions.push_back(Vec3(coords[atom][0], coords[atom][1], coords[atom][2])*OpenMM::NmPerAngstrom);
}else if(natoms == 375){
const double coords[375][3] = {
{ -6.22, -6.25, -6.24 },
{ -5.32, -6.03, -6.00 },
{ -6.75, -5.56, -5.84 },
{ -3.04, -6.23, -6.19 },
{ -3.52, -5.55, -5.71 },
{ -3.59, -6.43, -6.94 },
{ 0.02, -6.23, -6.14 },
{ -0.87, -5.97, -6.37 },
{ 0.53, -6.03, -6.93 },
{ 3.10, -6.20, -6.27 },
{ 3.87, -6.35, -5.72 },
{ 2.37, -6.11, -5.64 },
{ 6.18, -6.14, -6.20 },
{ 6.46, -6.66, -5.44 },
{ 6.26, -6.74, -6.94 },
{ -6.21, -3.15, -6.24 },
{ -6.23, -3.07, -5.28 },
{ -6.02, -2.26, -6.55 },
{ -3.14, -3.07, -6.16 },
{ -3.38, -3.63, -6.90 },
{ -2.18, -3.05, -6.17 },
{ -0.00, -3.16, -6.23 },
{ -0.03, -2.30, -6.67 },
{ 0.05, -2.95, -5.29 },
{ 3.08, -3.11, -6.14 },
{ 2.65, -2.55, -6.79 },
{ 3.80, -3.53, -6.62 },
{ 6.16, -3.14, -6.16 },
{ 7.04, -3.32, -6.51 },
{ 5.95, -2.27, -6.51 },
{ -6.20, -0.04, -6.15 },
{ -5.43, 0.32, -6.59 },
{ -6.95, 0.33, -6.62 },
{ -3.10, -0.06, -6.19 },
{ -3.75, 0.42, -6.69 },
{ -2.46, 0.60, -5.93 },
{ 0.05, -0.01, -6.17 },
{ -0.10, 0.02, -7.12 },
{ -0.79, 0.16, -5.77 },
{ 3.03, 0.00, -6.19 },
{ 3.54, 0.08, -7.01 },
{ 3.69, -0.22, -5.53 },
{ 6.17, 0.05, -6.19 },
{ 5.78, -0.73, -6.57 },
{ 7.09, -0.17, -6.04 },
{ -6.20, 3.15, -6.25 },
{ -6.59, 3.18, -5.37 },
{ -5.87, 2.25, -6.33 },
{ -3.09, 3.04, -6.17 },
{ -3.88, 3.58, -6.26 },
{ -2.41, 3.54, -6.63 },
{ 0.00, 3.06, -6.26 },
{ -0.71, 3.64, -6.00 },
{ 0.65, 3.15, -5.55 },
{ 3.14, 3.06, -6.23 },
{ 3.11, 3.31, -5.30 },
{ 2.38, 3.49, -6.63 },
{ 6.19, 3.14, -6.25 },
{ 6.82, 3.25, -5.54 },
{ 5.76, 2.30, -6.07 },
{ -6.22, 6.26, -6.19 },
{ -6.22, 5.74, -7.00 },
{ -5.89, 5.67, -5.52 },
{ -3.04, 6.24, -6.20 },
{ -3.08, 5.28, -6.17 },
{ -3.96, 6.52, -6.25 },
{ -0.05, 6.21, -6.16 },
{ 0.82, 6.58, -6.06 },
{ 0.01, 5.64, -6.93 },
{ 3.10, 6.25, -6.15 },
{ 3.64, 5.47, -6.31 },
{ 2.46, 6.24, -6.87 },
{ 6.22, 6.20, -6.27 },
{ 5.37, 6.42, -5.88 },
{ 6.80, 6.07, -5.51 },
{ -6.19, -6.15, -3.13 },
{ -6.37, -7.01, -3.51 },
{ -6.25, -6.29, -2.18 },
{ -3.10, -6.27, -3.11 },
{ -2.29, -5.77, -2.99 },
{ -3.80, -5.62, -2.98 },
{ -0.03, -6.18, -3.15 },
{ -0.07, -7.05, -2.75 },
{ 0.68, -5.74, -2.70 },
{ 3.10, -6.14, -3.07 },
{ 2.35, -6.72, -3.23 },
{ 3.86, -6.65, -3.37 },
{ 6.22, -6.20, -3.16 },
{ 6.82, -6.36, -2.43 },
{ 5.35, -6.13, -2.75 },
{ -6.26, -3.13, -3.12 },
{ -6.16, -2.27, -2.70 },
{ -5.36, -3.47, -3.18 },
{ -3.11, -3.05, -3.14 },
{ -3.31, -3.96, -3.34 },
{ -2.77, -3.06, -2.24 },
{ 0.00, -3.13, -3.16 },
{ 0.48, -2.37, -2.81 },
{ -0.57, -3.40, -2.44 },
{ 3.09, -3.09, -3.16 },
{ 2.41, -3.19, -2.49 },
{ 3.91, -3.07, -2.67 },
{ 6.19, -3.04, -3.08 },
{ 5.64, -3.61, -3.61 },
{ 6.93, -3.58, -2.82 },
{ -6.18, -0.00, -3.04 },
{ -6.00, -0.59, -3.78 },
{ -6.79, 0.64, -3.39 },
{ -3.05, -0.03, -3.07 },
{ -2.95, 0.80, -3.52 },
{ -4.00, -0.20, -3.07 },
{ -0.03, 0.03, -3.06 },
{ -0.33, -0.37, -3.87 },
{ 0.89, -0.21, -2.99 },
{ 3.13, -0.05, -3.10 },
{ 3.44, 0.81, -3.34 },
{ 2.21, 0.07, -2.86 },
{ 6.20, -0.05, -3.13 },
{ 6.89, 0.60, -3.20 },
{ 5.58, 0.30, -2.49 },
{ -6.23, 3.09, -3.16 },
{ -5.62, 3.79, -2.94 },
{ -6.33, 2.60, -2.33 },
{ -3.10, 3.08, -3.04 },
{ -3.84, 3.47, -3.51 },
{ -2.40, 3.01, -3.69 },
{ 0.01, 3.04, -3.11 },
{ -0.56, 3.59, -3.64 },
{ 0.28, 3.60, -2.38 },
{ 3.04, 3.11, -3.09 },
{ 3.49, 2.30, -2.87 },
{ 3.70, 3.66, -3.51 },
{ 6.15, 3.14, -3.11 },
{ 6.52, 2.52, -3.74 },
{ 6.72, 3.06, -2.34 },
{ -6.22, 6.15, -3.13 },
{ -5.49, 6.21, -2.51 },
{ -6.56, 7.04, -3.18 },
{ -3.11, 6.24, -3.05 },
{ -3.76, 5.83, -3.62 },
{ -2.26, 5.92, -3.37 },
{ 0.03, 6.25, -3.07 },
{ 0.34, 5.63, -3.73 },
{ -0.87, 6.00, -2.91 },
{ 3.07, 6.15, -3.08 },
{ 3.29, 6.92, -2.56 },
{ 3.39, 6.35, -3.96 },
{ 6.22, 6.14, -3.12 },
{ 5.79, 6.38, -2.29 },
{ 6.25, 6.96, -3.62 },
{ -6.21, -6.20, -0.06 },
{ -5.79, -6.87, 0.48 },
{ -6.43, -5.50, 0.54 },
{ -3.16, -6.21, -0.02 },
{ -2.50, -6.87, 0.20 },
{ -2.77, -5.37, 0.23 },
{ -0.00, -6.14, -0.00 },
{ 0.68, -6.72, -0.33 },
{ -0.64, -6.73, 0.38 },
{ 3.03, -6.20, -0.01 },
{ 3.77, -6.56, -0.51 },
{ 3.43, -5.85, 0.78 },
{ 6.25, -6.16, -0.00 },
{ 5.36, -6.09, -0.36 },
{ 6.24, -6.97, 0.49 },
{ -6.24, -3.05, -0.01 },
{ -6.35, -3.64, 0.73 },
{ -5.42, -3.33, -0.42 },
{ -3.09, -3.06, 0.05 },
{ -2.44, -3.62, -0.38 },
{ -3.90, -3.21, -0.43 },
{ 0.05, -3.10, 0.02 },
{ -0.31, -2.35, -0.43 },
{ -0.63, -3.77, 0.01 },
{ 3.05, -3.09, -0.04 },
{ 3.28, -3.90, 0.41 },
{ 3.65, -2.43, 0.30 },
{ 6.20, -3.04, -0.03 },
{ 5.66, -3.31, 0.71 },
{ 6.78, -3.79, -0.19 },
{ -6.18, 0.04, -0.04 },
{ -6.73, -0.73, -0.15 },
{ -5.98, 0.06, 0.89 },
{ -3.11, -0.04, -0.04 },
{ -3.36, -0.08, 0.87 },
{ -2.70, 0.81, -0.14 },
{ -0.02, -0.02, -0.05 },
{ -0.45, 0.28, 0.75 },
{ 0.90, 0.15, 0.07 },
{ 3.04, 0.02, -0.01 },
{ 3.26, -0.82, 0.38 },
{ 3.89, 0.45, -0.13 },
{ 6.19, 0.05, -0.03 },
{ 5.52, -0.56, 0.25 },
{ 7.01, -0.29, 0.32 },
{ -6.14, 3.08, 0.00 },
{ -6.83, 2.82, 0.61 },
{ -6.59, 3.64, -0.64 },
{ -3.05, 3.09, -0.04 },
{ -3.79, 2.50, 0.09 },
{ -3.18, 3.80, 0.59 },
{ 0.02, 3.14, 0.04 },
{ -0.89, 3.04, -0.19 },
{ 0.49, 2.57, -0.57 },
{ 3.14, 3.15, 0.00 },
{ 3.28, 2.28, 0.37 },
{ 2.30, 3.08, -0.45 },
{ 6.27, 3.08, -0.00 },
{ 5.55, 2.54, -0.33 },
{ 5.83, 3.87, 0.34 },
{ -6.18, 6.15, -0.03 },
{ -6.45, 6.21, 0.88 },
{ -6.26, 7.05, -0.36 },
{ -3.06, 6.19, -0.05 },
{ -2.84, 6.64, 0.76 },
{ -3.99, 5.96, 0.03 },
{ -0.00, 6.20, 0.06 },
{ -0.67, 5.99, -0.59 },
{ 0.76, 6.46, -0.44 },
{ 3.10, 6.26, -0.03 },
{ 3.57, 6.09, 0.78 },
{ 2.57, 5.47, -0.18 },
{ 6.26, 6.18, 0.02 },
{ 5.53, 5.64, -0.29 },
{ 5.95, 7.08, -0.06 },
{ -6.26, -6.21, 3.07 },
{ -5.98, -6.38, 3.97 },
{ -5.46, -5.94, 2.62 },
{ -3.10, -6.24, 3.04 },
{ -2.69, -6.51, 3.87 },
{ -3.43, -5.35, 3.21 },
{ -0.03, -6.16, 3.06 },
{ 0.83, -6.00, 3.42 },
{ -0.30, -6.99, 3.45 },
{ 3.15, -6.25, 3.11 },
{ 2.77, -5.60, 3.72 },
{ 2.68, -6.10, 2.28 },
{ 6.20, -6.21, 3.16 },
{ 5.75, -6.73, 2.50 },
{ 6.69, -5.56, 2.66 },
{ -6.17, -3.10, 3.04 },
{ -6.82, -2.44, 3.28 },
{ -6.12, -3.69, 3.80 },
{ -3.08, -3.04, 3.11 },
{ -3.59, -3.56, 3.72 },
{ -2.97, -3.61, 2.34 },
{ 0.01, -3.04, 3.11 },
{ -0.86, -3.41, 3.20 },
{ 0.56, -3.78, 2.86 },
{ 3.07, -3.07, 3.15 },
{ 3.81, -3.68, 3.13 },
{ 2.80, -2.98, 2.23 },
{ 6.20, -3.04, 3.13 },
{ 5.48, -3.64, 2.92 },
{ 6.98, -3.49, 2.81 },
{ -6.18, -0.05, 3.12 },
{ -6.41, 0.66, 3.69 },
{ -6.33, 0.28, 2.23 },
{ -3.05, 0.03, 3.10 },
{ -3.46, -0.42, 3.83 },
{ -3.57, -0.19, 2.33 },
{ 0.03, -0.02, 3.15 },
{ 0.23, -0.08, 2.21 },
{ -0.81, 0.41, 3.18 },
{ 3.09, 0.00, 3.03 },
{ 2.48, -0.29, 3.71 },
{ 3.91, 0.16, 3.51 },
{ 6.19, -0.06, 3.11 },
{ 6.05, 0.47, 2.33 },
{ 6.59, 0.52, 3.74 },
{ -6.20, 3.05, 3.05 },
{ -6.87, 3.73, 3.17 },
{ -5.55, 3.24, 3.73 },
{ -3.11, 3.06, 3.15 },
{ -3.64, 3.74, 2.71 },
{ -2.32, 3.00, 2.62 },
{ 0.02, 3.05, 3.06 },
{ -0.87, 3.14, 3.38 },
{ 0.48, 3.82, 3.42 },
{ 3.07, 3.10, 3.16 },
{ 3.95, 3.44, 2.97 },
{ 2.76, 2.73, 2.32 },
{ 6.19, 3.07, 3.16 },
{ 7.02, 3.30, 2.72 },
{ 5.52, 3.27, 2.51 },
{ -6.19, 6.24, 3.15 },
{ -5.56, 5.88, 2.52 },
{ -7.05, 5.96, 2.83 },
{ -3.10, 6.14, 3.08 },
{ -2.34, 6.69, 3.27 },
{ -3.86, 6.69, 3.29 },
{ -0.04, 6.24, 3.13 },
{ 0.63, 6.54, 2.53 },
{ 0.08, 5.29, 3.18 },
{ 3.12, 6.24, 3.14 },
{ 3.57, 5.82, 2.40 },
{ 2.23, 5.90, 3.12 },
{ 6.25, 6.19, 3.06 },
{ 5.55, 5.59, 3.32 },
{ 6.08, 6.99, 3.55 },
{ -6.20, -6.16, 6.15 },
{ -6.29, -5.99, 7.09 },
{ -6.09, -7.11, 6.09 },
{ -3.09, -6.19, 6.27 },
{ -2.56, -5.90, 5.52 },
{ -3.80, -6.69, 5.87 },
{ 0.02, -6.25, 6.24 },
{ -0.70, -5.70, 6.51 },
{ 0.25, -5.93, 5.36 },
{ 3.11, -6.18, 6.14 },
{ 3.76, -6.54, 6.74 },
{ 2.29, -6.20, 6.64 },
{ 6.22, -6.17, 6.15 },
{ 6.61, -6.98, 6.47 },
{ 5.56, -5.94, 6.81 },
{ -6.21, -3.10, 6.14 },
{ -6.76, -2.66, 6.78 },
{ -5.51, -3.50, 6.65 },
{ -3.13, -3.05, 6.18 },
{ -2.19, -3.14, 6.34 },
{ -3.50, -3.89, 6.43 },
{ 0.01, -3.06, 6.15 },
{ -0.06, -2.81, 7.07 },
{ -0.25, -3.98, 6.13 },
{ 3.04, -3.09, 6.17 },
{ 3.84, -3.51, 5.84 },
{ 3.25, -2.85, 7.08 },
{ 6.26, -3.13, 6.19 },
{ 6.01, -2.20, 6.09 },
{ 5.47, -3.55, 6.54 },
{ -6.20, 0.01, 6.27 },
{ -5.79, -0.70, 5.78 },
{ -6.67, 0.51, 5.60 },
{ -3.13, 0.01, 6.14 },
{ -3.53, -0.35, 6.94 },
{ -2.21, 0.17, 6.39 },
{ -0.04, -0.04, 6.20 },
{ 0.26, 0.47, 5.46 },
{ 0.51, 0.22, 6.93 },
{ 3.10, -0.05, 6.23 },
{ 2.33, 0.44, 5.95 },
{ 3.85, 0.45, 5.92 },
{ 6.19, -0.01, 6.26 },
{ 7.05, 0.16, 5.88 },
{ 5.58, 0.02, 5.52 },
{ -6.22, 3.04, 6.17 },
{ -5.45, 3.57, 5.95 },
{ -6.62, 3.50, 6.92 },
{ -3.09, 3.16, 6.21 },
{ -3.71, 2.75, 5.61 },
{ -2.60, 2.43, 6.59 },
{ -0.02, 3.10, 6.26 },
{ 0.89, 3.27, 6.05 },
{ -0.44, 2.94, 5.41 },
{ 3.12, 3.04, 6.23 },
{ 2.31, 3.53, 6.43 },
{ 3.59, 3.60, 5.60 },
{ 6.23, 3.05, 6.24 },
{ 5.92, 3.91, 6.54 },
{ 6.02, 3.03, 5.30 },
{ -6.15, 6.21, 6.24 },
{ -6.27, 6.46, 5.32 },
{ -7.00, 5.85, 6.51 },
{ -3.07, 6.15, 6.22 },
{ -3.98, 6.27, 5.94 },
{ -2.66, 7.01, 6.10 },
{ 0.04, 6.20, 6.25 },
{ -0.38, 5.50, 5.75 },
{ -0.36, 7.00, 5.93 },
{ 3.12, 6.15, 6.24 },
{ 3.66, 6.88, 5.93 },
{ 2.25, 6.33, 5.86 },
{ 6.20, 6.27, 6.19 },
{ 5.46, 5.65, 6.19 },
{ 6.97, 5.73, 6.39 }
};
for(int atom = 0; atom < natoms; ++atom)
positions.push_back(Vec3(coords[atom][0], coords[atom][1], coords[atom][2])*OpenMM::NmPerAngstrom);
}else{
throw exception();
}
system.setDefaultPeriodicBoxVectors(Vec3(boxEdgeLength, 0, 0),
Vec3(0, boxEdgeLength, 0),
Vec3(0, 0, boxEdgeLength));
sig.clear();
eps.clear();
bonds.clear();
for(int atom = 0; atom < natoms; ++atom){
system.addParticle(masses[atom%RESSIZE]);
double sigma = 2.0*pow(2.0, -1.0/6.0)*halfrmins[atom%RESSIZE]*OpenMM::NmPerAngstrom;
double epsilon = fabs(epsilons[atom%RESSIZE])*OpenMM::KJPerKcal;
sig.push_back(0.5*sigma);
eps.push_back(2.0*sqrt(epsilon));
if(atom%RESSIZE == 0){
bonds.push_back(pair<int, int>(atom, atom+1));
bonds.push_back(pair<int, int>(atom, atom+2));
}
double charge = do_electrostatics ? charges[atom] : 0;
forceField->addParticle(charge, sigma, epsilon);
}
}
void test_water2_dpme_energies_forces_no_exclusions() {
const double cutoff = 7.0*OpenMM::NmPerAngstrom;
const double dalpha = 4.0124063605;
const int grid = 32;
NonbondedForce* forceField = new NonbondedForce();
vector<Vec3> positions;
vector<double> epsvals;
vector<double> sigvals;
vector<pair<int, int> > bonds;
System system;
const int NATOMS = 6;
double boxEdgeLength = 25*OpenMM::NmPerAngstrom;
make_waterbox(NATOMS, boxEdgeLength, forceField, positions, epsvals, sigvals, bonds, system, false);
forceField->setNonbondedMethod(OpenMM::NonbondedForce::LJPME);
forceField->setPMEParameters(0.0f, grid, grid, grid);
forceField->setReciprocalSpaceForceGroup(1);
forceField->setLJPMEParameters(dalpha, grid, grid, grid);
forceField->setCutoffDistance(cutoff);
forceField->setReactionFieldDielectric(1.0);
system.addForce(forceField);
// Reference calculation
VerletIntegrator integrator(0.01);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy, false, 1<<1);
double refenergy = state.getPotentialEnergy();
const vector<Vec3>& refforces = state.getForces();
// Optimized CPU calculation
CpuCalcPmeReciprocalForceKernel pme(CalcPmeReciprocalForceKernel::Name(), platform);
pme.setCalculationType(CpuCalcPmeReciprocalForceKernel::Dispersion);
IO io;
double selfEwaldEnergy = 0;
double dalpha6 = pow(dalpha, 6.0);
for (int i = 0; i < NATOMS; i++) {
io.posq.push_back((float)positions[i][0]);
io.posq.push_back((float)positions[i][1]);
io.posq.push_back((float)positions[i][2]);
double c6 = 8.0f * pow(sigvals[i], 3) * epsvals[i];
io.posq.push_back(c6);
selfEwaldEnergy += dalpha6 * c6 * c6 / 12.0;
}
pme.initialize(grid, grid, grid, NATOMS, dalpha);
Vec3 boxVectors[3];
system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
pme.beginComputation(io, boxVectors, true);
double recenergy = pme.finishComputation(io);
ASSERT_EQUAL_TOL(recenergy, -2.179629087, 1e-5);
ASSERT_EQUAL_TOL(selfEwaldEnergy, 1.731404285, 1e-5);
std::vector<Vec3> knownforces(6);
knownforces[0] = Vec3( -1.890360546, -1.890723915, -1.879662698);
knownforces[1] = Vec3( -0.003161352455, -0.000922244929, -0.005391616425);
knownforces[2] = Vec3( 0.0009199035545, -0.001453894176, -0.006188087146);
knownforces[3] = Vec3( 1.887108856, 1.887241446, 1.89644647);
knownforces[4] = Vec3( 0.0008242336483, 0.003778910089, -0.002116131106);
knownforces[5] = Vec3( 0.004912763044, 0.002324059399, -0.002844482646);
for (int i = 0; i < NATOMS; i++)
ASSERT_EQUAL_VEC(refforces[i], knownforces[i], 1e-5);
recenergy += selfEwaldEnergy;
// See if they match.
ASSERT_EQUAL_TOL(refenergy, recenergy, 1e-5);
for (int i = 0; i < NATOMS; i++)
ASSERT_EQUAL_VEC(refforces[i], Vec3(io.force[4*i], io.force[4*i+1], io.force[4*i+2]), 1e-5);
}
void testPME(bool triclinic) { void testPME(bool triclinic) {
// Create a cloud of random point charges. // Create a cloud of random point charges.
...@@ -125,7 +630,7 @@ void testPME(bool triclinic) { ...@@ -125,7 +630,7 @@ void testPME(bool triclinic) {
pme.initialize(gridx, gridy, gridz, numParticles, alpha); pme.initialize(gridx, gridy, gridz, numParticles, alpha);
pme.beginComputation(io, boxVectors, true); pme.beginComputation(io, boxVectors, true);
double energy = pme.finishComputation(io); double energy = pme.finishComputation(io);
// See if they match. // See if they match.
ASSERT_EQUAL_TOL(refState.getPotentialEnergy(), energy+ewaldSelfEnergy, 1e-3); ASSERT_EQUAL_TOL(refState.getPotentialEnergy(), energy+ewaldSelfEnergy, 1e-3);
...@@ -141,6 +646,7 @@ int main(int argc, char* argv[]) { ...@@ -141,6 +646,7 @@ int main(int argc, char* argv[]) {
} }
testPME(false); testPME(false);
testPME(true); testPME(true);
test_water2_dpme_energies_forces_no_exclusions();
} }
catch(const exception& e) { catch(const exception& e) {
cout << "exception: " << e.what() << endl; cout << "exception: " << e.what() << endl;
......
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