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Commit 7a36f461 authored by Mark Friedrichs's avatar Mark Friedrichs
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dded GB/VI to Cuda platform 

Free energy plugin added
Plugin will not run w/ Obc or GB/VI forces unless line 2004 of gpu.cpp (gpu->sim.totalNonbondOutputBuffers  = 2*gpu->sim.nonbondOutputBuffers;) is commented in -- working on removing this constraint
Also unit tests for GB/VI currently fail
parent 43ebedfb
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plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateGBVISoftcoreBornSum.h 0 → 100644
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This file contains the kernel for calculating Born sums. It is included
* several times in kCalculateGBVIBornSum.cu with different #defines to generate
* different versions of the kernels.
*/
#include "kCalculateGBVIAux.h"
__global__ void METHOD_NAME(kCalculateGBVISoftcore, BornSum_kernel)(unsigned int* workUnit)
{
extern __shared__ Atom sA[];
unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID;
unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
unsigned int numWorkUnits = cSim.pInteractionCount[0];
unsigned int pos = warp*numWorkUnits/totalWarps;
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
// int end = workUnits / gridDim.x;
// int pos = end - (threadIdx.x >> GRIDBITS) - 1;
#ifdef USE_CUTOFF
float* tempBuffer = (float*) &sA[cSim.nonbond_threads_per_block];
#endif
while ( pos < end )
{
// Extract cell coordinates from appropriate work unit
unsigned int x = workUnit[pos];
unsigned int y = ((x >> 2) & 0x7fff) << GRIDBITS;
x = (x >> 17) << GRIDBITS;
float dx;
float dy;
float dz;
float r2;
float r;
// forces tgx into interval [0,31]
// forces tbx 0
unsigned int tgx = threadIdx.x & (GRID - 1);
unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx;
Atom* psA = &sA[tbx];
if (x == y) // Handle diagonals uniquely at 50% efficiency
{
// Read fixed atom data into registers and GRF
unsigned int i = x + tgx;
float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum
float4 ar = cSim.pGBVIData[i]; // Local atom vr, sr
sA[threadIdx.x].x = apos.x;
sA[threadIdx.x].y = apos.y;
sA[threadIdx.x].z = apos.z;
sA[threadIdx.x].r = ar.x;
sA[threadIdx.x].sr = ar.y;
sA[threadIdx.x].bornRadiusScaleFactor = ar.w;
apos.w = 0.0f;
for (unsigned int j = 0; j < GRID; j++)
{
dx = psA[j].x - apos.x;
dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#if defined USE_PERIODIC
if (i < cSim.atoms && x+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#endif
{
r = sqrt(r2);
if ((j != tgx) )
{
apos.w += psA[j].bornRadiusScaleFactor*getGBVI_Volume( r, ar.x, psA[j].sr );
}
}
}
// Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
cSim.pBornSum[offset] += apos.w;
#else
unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = apos.w;
#endif
}
else // 100% utilization
{
// Read fixed atom data into registers and GRF
unsigned int j = y + tgx;
unsigned int i = x + tgx;
float4 temp = cSim.pPosq[j];
float4 temp1 = cSim.pGBVIData[j];
float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum
float4 ar = cSim.pGBVIData[i]; // Local atom vr, sr
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
sA[threadIdx.x].r = temp1.x;
sA[threadIdx.x].sr = temp1.y;
sA[threadIdx.x].bornRadiusScaleFactor = temp1.w;
sA[threadIdx.x].sum = apos.w = 0.0f;
#ifdef USE_CUTOFF
//unsigned int flags = cSim.pInteractionFlag[pos + (blockIdx.x*workUnits)/gridDim.x];
unsigned int flags = cSim.pInteractionFlag[pos];
if (flags == 0)
{
// No interactions in this block.
}
else if (flags == 0xFFFFFFFF)
#endif
{
// Compute all interactions within this block.
for (unsigned int j = 0; j < GRID; j++)
{
dx = psA[tj].x - apos.x;
dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_PERIODIC
if (i < cSim.atoms && y+tj < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#endif
{
r = sqrt(r2);
// psA[tj].sr = Sj
// ar.x = Ri
apos.w += psA[tj].bornRadiusScaleFactor*getGBVI_Volume( r, ar.x, psA[tj].sr );
psA[tj].sum += ar.w*getGBVI_Volume( r, psA[tj].r, ar.y );
}
tj = (tj - 1) & (GRID - 1);
}
}
#ifdef USE_CUTOFF
else
{
// Compute only a subset of the interactions in this block.
for (unsigned int j = 0; j < GRID; j++)
{
if ((flags&(1<<j)) != 0)
{
tempBuffer[threadIdx.x] = 0.0f;
dx = psA[j].x - apos.x;
dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_PERIODIC
if (i < cSim.atoms && y+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#endif
{
r = sqrt(r2);
tempBuffer[threadIdx.x] = ar.w*getGBVI_Volume( r, psA[tj].r, ar.y );
}
// Sum the terms.
if (tgx % 2 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1];
if (tgx % 4 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+2];
if (tgx % 8 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+4];
if (tgx % 16 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0)
psA[j].sum += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16];
}
}
}
#endif
// Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
cSim.pBornSum[offset] += apos.w;
offset = y + tgx + warp*cSim.stride;
cSim.pBornSum[offset] += sA[threadIdx.x].sum;
#else
unsigned int offset = x + tgx + (y >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = apos.w;
offset = y + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = sA[threadIdx.x].sum;
#endif
}
pos++;
}
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateLocalSoftcoreForces.cu 0 → 100755
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "gputypes.h"
#include "GpuLJ14Softcore.h"
#include <cuda.h>
extern __shared__ Vectors sV[];
static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaFreeEnergySimulationNonbonded14 feSim;
/* Cuda compiler on Windows does not recognized "static const float" values */
#define LOCAL_HACK_PI 3.1415926535897932384626433832795
#define DOT3(v1, v2) (v1.x * v2.x + v1.y * v2.y + v1.z * v2.z)
#define GETNORMEDDOTPRODUCT(v1, v2, dp) \
{ \
dp = DOT3(v1, v2); \
float norm1 = DOT3(v1, v1); \
float norm2 = DOT3(v2, v2); \
dp /= sqrt(norm1 * norm2); \
dp = min(dp, 1.0f); \
dp = max(dp, -1.0f); \
}
#define CROSS_PRODUCT(v1, v2, c) \
c.x = v1.y * v2.z - v1.z * v2.y; \
c.y = v1.z * v2.x - v1.x * v2.z; \
c.z = v1.x * v2.y - v1.y * v2.x;
#define GETPREFACTORSGIVENANGLECOSINE(cosine, param, dEdR) \
{ \
float angle = acos(cosine); \
float deltaIdeal = angle - (param.x * (LOCAL_HACK_PI / 180.0f)); \
dEdR = param.y * deltaIdeal; \
}
#define GETENERGYGIVENANGLECOSINE(cosine, param, dEdR) \
{ \
float angle = acos(cosine); \
float deltaIdeal = angle - (param.x * (LOCAL_HACK_PI / 180.0f)); \
dEdR = param.y * deltaIdeal * deltaIdeal; \
}
#define GETANGLEBETWEENTWOVECTORS(v1, v2, angle) \
{ \
float dp; \
GETNORMEDDOTPRODUCT(v1, v2, dp); \
angle = acos(dp); \
}
#define GETANGLECOSINEBETWEENTWOVECTORS(v1, v2, angle, cosine) \
{ \
GETNORMEDDOTPRODUCT(v1, v2, cosine); \
angle = acos(cosine); \
}
#define GETDIHEDRALANGLEBETWEENTHREEVECTORS(vector1, vector2, vector3, signVector, cp0, cp1, angle) \
{ \
CROSS_PRODUCT(vector1, vector2, cp0); \
CROSS_PRODUCT(vector2, vector3, cp1); \
GETANGLEBETWEENTWOVECTORS(cp0, cp1, angle); \
float dp = DOT3(signVector, cp1); \
angle = (dp >= 0) ? angle : -angle; \
}
#define GETDIHEDRALANGLECOSINEBETWEENTHREEVECTORS(vector1, vector2, vector3, signVector, cp0, cp1, angle, cosine) \
{ \
CROSS_PRODUCT(vector1, vector2, cp0); \
CROSS_PRODUCT(vector2, vector3, cp1); \
GETANGLECOSINEBETWEENTWOVECTORS(cp0, cp1, angle, cosine); \
float dp = DOT3(signVector, cp1); \
angle = (dp >= 0) ? angle : -angle; \
}
extern "C"
void SetCalculateLocalSoftcoreGpuSim(gpuContext gpu)
{
(void) fprintf( stderr, "SetCalculateLocalSoftcoreForcesSim called\n" );
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateLocalSoftcoreForcesSim copy to cSim failed");
}
static void SetCalculateLocalSoftcoreSim( GpuLJ14Softcore* gpuLJ14Softcore)
{
cudaError_t status;
(void) fprintf( stderr, "SetCalculateLocalSoftcoreSim called\n" );
status = cudaMemcpyToSymbol(feSim, &gpuLJ14Softcore->feSim, sizeof(cudaFreeEnergySimulationNonbonded14));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateLocalSoftcoreSim copy to cSim failed");
}
void GetCalculateLocalSoftcoreForcesSim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyFromSymbol: SetSim copy from cSim failed");
}
#define USE_SOFTCORE_LJ
#ifdef USE_SOFTCORE_LJ
#include "kSoftcoreLJ.h"
#endif
//__global__ void METHOD_NAME(kCalculateLocalSoftcore, Forces_kernel)()
__global__ void kCalculateLocalSoftcoreForces_kernel()
{
unsigned int pos = blockIdx.x * blockDim.x + threadIdx.x;
//Vectors* A = &sV[threadIdx.x];
float energy = 0.0f;
#if 0
while (pos < cSim.bond_offset)
{
if (pos < cSim.bonds)
{
int4 atom = cSim.pBondID[pos];
float4 atomA = cSim.pPosq[atom.x];
float4 atomB = cSim.pPosq[atom.y];
float2 bond = cSim.pBondParameter[pos];
float dx = atomB.x - atomA.x;
float dy = atomB.y - atomA.y;
float dz = atomB.z - atomA.z;
float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2);
float deltaIdeal = r - bond.x;
/* E */ energy += 0.5f * bond.y * deltaIdeal * deltaIdeal;
float dEdR = bond.y * deltaIdeal;
dEdR = (r > 0.0f) ? (dEdR / r) : 0.0f;
// printf("D: %11.4f %11.4f %11.4f %11.4f %11.4f %11.4f\n", dx, dy, dz, r, deltaIdeal, dEdR);
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
unsigned int offsetA = atom.x + atom.z * cSim.stride;
unsigned int offsetB = atom.y + atom.w * cSim.stride;
float4 forceA = cSim.pForce4[offsetA];
float4 forceB = cSim.pForce4[offsetB];
forceA.x += dx;
forceA.y += dy;
forceA.z += dz;
forceB.x -= dx;
forceB.y -= dy;
forceB.z -= dz;
cSim.pForce4[offsetA] = forceA;
cSim.pForce4[offsetB] = forceB;
}
pos += blockDim.x * gridDim.x;
}
while (pos < cSim.bond_angle_offset)
{
unsigned int pos1 = pos - cSim.bond_offset;
if (pos1 < cSim.bond_angles)
{
int4 atom1 = cSim.pBondAngleID1[pos1];
float2 bond_angle = cSim.pBondAngleParameter[pos1];
float4 a1 = cSim.pPosq[atom1.x];
float4 a2 = cSim.pPosq[atom1.y];
float4 a3 = cSim.pPosq[atom1.z];
A->v0.x = a2.x - a1.x;
A->v0.y = a2.y - a1.y;
A->v0.z = a2.z - a1.z;
A->v1.x = a2.x - a3.x;
A->v1.y = a2.y - a3.y;
A->v1.z = a2.z - a3.z;
float3 cp;
CROSS_PRODUCT(A->v0, A->v1, cp);
float rp = DOT3(cp, cp); //cx * cx + cy * cy + cz * cz;
rp = max(sqrt(rp), 1.0e-06f);
float r21 = DOT3(A->v0, A->v0); // dx1 * dx1 + dy1 * dy1 + dz1 * dz1;
float r23 = DOT3(A->v1, A->v1); // dx2 * dx2 + dy2 * dy2 + dz2 * dz2;
float dot = DOT3(A->v0, A->v1); // dx1 * dx2 + dy1 * dy2 + dz1 * dz2;
float cosine = dot / sqrt(r21 * r23);
float angle_energy;
/* E */ GETENERGYGIVENANGLECOSINE(cosine, bond_angle, angle_energy);
energy += 0.5f*angle_energy;
float dEdR;
GETPREFACTORSGIVENANGLECOSINE(cosine, bond_angle, dEdR);
//printf("%11.4f %11.4f\n", cosine, dEdR);
float termA = dEdR / (r21 * rp);
float termC = -dEdR / (r23 * rp);
float3 c21;
float3 c23;
CROSS_PRODUCT(A->v0, cp, c21);
CROSS_PRODUCT(A->v1, cp, c23);
c21.x *= termA;
c21.y *= termA;
c21.z *= termA;
c23.x *= termC;
c23.y *= termC;
c23.z *= termC;
int2 atom2 = cSim.pBondAngleID2[pos1];
unsigned int offset = atom1.x + atom1.w * cSim.stride;
float4 force = cSim.pForce4[offset];
force.x += c21.x;
force.y += c21.y;
force.z += c21.z;
cSim.pForce4[offset] = force;
offset = atom1.y + atom2.x * cSim.stride;
force = cSim.pForce4[offset];
force.x -= (c21.x + c23.x);
force.y -= (c21.y + c23.y);
force.z -= (c21.z + c23.z);
cSim.pForce4[offset] = force;
offset = atom1.z + atom2.y * cSim.stride;
force = cSim.pForce4[offset];
force.x += c23.x;
force.y += c23.y;
force.z += c23.z;
cSim.pForce4[offset] = force;
}
pos += blockDim.x * gridDim.x;
}
while (pos < cSim.dihedral_offset)
{
unsigned int pos1 = pos - cSim.bond_angle_offset;
if (pos1 < cSim.dihedrals)
{
int4 atom1 = cSim.pDihedralID1[pos1];
float4 atomA = cSim.pPosq[atom1.x];
float4 atomB = cSim.pPosq[atom1.y];
float4 atomC = cSim.pPosq[atom1.z];
float4 atomD = cSim.pPosq[atom1.w];
A->v0.x = atomA.x - atomB.x;
A->v0.y = atomA.y - atomB.y;
A->v0.z = atomA.z - atomB.z;
A->v1.x = atomC.x - atomB.x;
A->v1.y = atomC.y - atomB.y;
A->v1.z = atomC.z - atomB.z;
A->v2.x = atomC.x - atomD.x;
A->v2.y = atomC.y - atomD.y;
A->v2.z = atomC.z - atomD.z;
float3 cp0, cp1;
float dihedralAngle;
GETDIHEDRALANGLEBETWEENTHREEVECTORS(A->v0, A->v1, A->v2, A->v0, cp0, cp1, dihedralAngle);
float4 dihedral = cSim.pDihedralParameter[pos1];
float deltaAngle = dihedral.z * dihedralAngle - (dihedral.y * PI / 180.0f);
// ATTENTION: This section leads to a divergent deltaAngle values wrt
// forces and energies. We separate the case dihedral.z = n = 0, which
// is treated by the calculation of energies via a harmonic potential
/* E */ if (dihedral.z) energy += dihedral.x * (1.0f + cos(deltaAngle));
/* E */ else
{
float deltaAngle = dihedralAngle - dihedral.y;
if (deltaAngle < -PI) deltaAngle += 2.0f * PI;
else if (deltaAngle > PI) deltaAngle -= 2.0f * PI;
energy += dihedral.x * deltaAngle * deltaAngle;
}
float sinDeltaAngle = sin(deltaAngle);
float dEdAngle = -dihedral.x * dihedral.z * sinDeltaAngle;
float normCross1 = DOT3(cp0, cp0);
float normBC = sqrt(DOT3(A->v1, A->v1));
float4 ff;
ff.x = (-dEdAngle * normBC) / normCross1;
float normCross2 = DOT3(cp1, cp1);
ff.w = (dEdAngle * normBC) / normCross2;
float dp = 1.0f / DOT3(A->v1, A->v1);
ff.y = DOT3(A->v0, A->v1) * dp;
ff.z = DOT3(A->v2, A->v1) * dp;
int4 atom2 = cSim.pDihedralID2[pos1];
float3 internalF0;
float3 internalF3;
float3 s;
// printf("%4d: %9.4f %9.4f %9.4f %9.4f\n", pos1, ff.x, ff.y, ff.z, ff.w);
unsigned int offset = atom1.x + atom2.x * cSim.stride;
float4 force = cSim.pForce4[offset];
internalF0.x = ff.x * cp0.x;
force.x += internalF0.x;
internalF0.y = ff.x * cp0.y;
force.y += internalF0.y;
internalF0.z = ff.x * cp0.z;
force.z += internalF0.z;
cSim.pForce4[offset] = force;
//printf("%4d - 0: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
offset = atom1.w + atom2.w * cSim.stride;
force = cSim.pForce4[offset];
internalF3.x = ff.w * cp1.x;
force.x += internalF3.x;
internalF3.y = ff.w * cp1.y;
force.y += internalF3.y;
internalF3.z = ff.w * cp1.z;
force.z += internalF3.z;
cSim.pForce4[offset] = force;
// printf("%4d - 3: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
s.x = ff.y * internalF0.x - ff.z * internalF3.x;
s.y = ff.y * internalF0.y - ff.z * internalF3.y;
s.z = ff.y * internalF0.z - ff.z * internalF3.z;
offset = atom1.y + atom2.y * cSim.stride;
force = cSim.pForce4[offset];
force.x += -internalF0.x + s.x;
force.y += -internalF0.y + s.y;
force.z += -internalF0.z + s.z;
cSim.pForce4[offset] = force;
//printf("%4d - 1: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
offset = atom1.z + atom2.z * cSim.stride;
force = cSim.pForce4[offset];
force.x += -internalF3.x - s.x;
force.y += -internalF3.y - s.y;
force.z += -internalF3.z - s.z;
cSim.pForce4[offset] = force;
//printf("%4d - 2: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
}
pos += blockDim.x * gridDim.x;
}
// Ryckaert Bellemans dihedrals
while (pos < cSim.rb_dihedral_offset)
{
unsigned int pos1 = pos - cSim.dihedral_offset;
if (pos1 < cSim.rb_dihedrals)
{
int4 atom1 = cSim.pRbDihedralID1[pos1];
float4 atomA = cSim.pPosq[atom1.x];
float4 atomB = cSim.pPosq[atom1.y];
float4 atomC = cSim.pPosq[atom1.z];
float4 atomD = cSim.pPosq[atom1.w];
A->v0.x = atomA.x - atomB.x;
A->v0.y = atomA.y - atomB.y;
A->v0.z = atomA.z - atomB.z;
A->v1.x = atomC.x - atomB.x;
A->v1.y = atomC.y - atomB.y;
A->v1.z = atomC.z - atomB.z;
A->v2.x = atomC.x - atomD.x;
A->v2.y = atomC.y - atomD.y;
A->v2.z = atomC.z - atomD.z;
float3 cp0, cp1;
float dihedralAngle, cosPhi;
// printf("%4d - 0 : %9.4f %9.4f %9.4f\n", pos1, A->v0.x, A->v0.y, A->v0.z);
// printf("%4d - 1 : %9.4f %9.4f %9.4f\n", pos1, A->v1.x, A->v1.y, A->v1.z);
// printf("%4d - 2 : %9.4f %9.4f %9.4f\n", pos1, A->v2.x, A->v2.y, A->v2.z);
GETDIHEDRALANGLECOSINEBETWEENTHREEVECTORS(A->v0, A->v1, A->v2, A->v0, cp0, cp1, dihedralAngle, cosPhi);
if (dihedralAngle < 0.0f )
{
dihedralAngle += PI;
}
else
{
dihedralAngle -= PI;
}
cosPhi = -cosPhi;
// printf("%4d: %9.4f %9.4f\n", pos1, dihedralAngle, cosPhi);
float4 dihedral1 = cSim.pRbDihedralParameter1[pos1];
float2 dihedral2 = cSim.pRbDihedralParameter2[pos1];
float cosFactor = cosPhi;
float dEdAngle = -dihedral1.y;
/* E */ float rb_energy = dihedral1.x;
rb_energy += dihedral1.y * cosFactor;
// printf("%4d - 1: %9.4f %9.4f\n", pos1, dEdAngle, 1.0f);
dEdAngle -= 2.0f * dihedral1.z * cosFactor;
// printf("%4d - 2: %9.4f %9.4f\n", pos1, dEdAngle, cosFactor);
cosFactor *= cosPhi;
dEdAngle -= 3.0f * dihedral1.w * cosFactor;
rb_energy += dihedral1.z * cosFactor;
// printf("%4d - 3: %9.4f %9.4f\n", pos1, dEdAngle, cosFactor);
cosFactor *= cosPhi;
dEdAngle -= 4.0f * dihedral2.x * cosFactor;
rb_energy += dihedral1.w * cosFactor;
// printf("%4d - 4: %9.4f %9.4f\n", pos1, dEdAngle, cosFactor);
cosFactor *= cosPhi;
dEdAngle -= 5.0f * dihedral2.y * cosFactor;
rb_energy += dihedral2.x * cosFactor;
rb_energy += dihedral2.y * cosFactor * cosPhi;
/* E */ energy += rb_energy;
// printf("%4d - 5: %9.4f %9.4f\n", pos1, dEdAngle, cosFactor);
dEdAngle *= sin(dihedralAngle);
// printf("%4d - f: %9.4f\n", pos1, dEdAngle);
float normCross1 = DOT3(cp0, cp0);
float normBC = sqrt(DOT3(A->v1, A->v1));
float4 ff;
ff.x = (-dEdAngle * normBC) / normCross1;
float normCross2 = DOT3(cp1, cp1);
ff.w = (dEdAngle * normBC) / normCross2;
float dp = 1.0f / DOT3(A->v1, A->v1);
ff.y = DOT3(A->v0, A->v1) * dp;
ff.z = DOT3(A->v2, A->v1) * dp;
int4 atom2 = cSim.pRbDihedralID2[pos1];
float3 internalF0;
float3 internalF3;
float3 s;
// printf("%4d: %9.4f %9.4f %9.4f %9.4f\n", pos1, ff.x, ff.y, ff.z, ff.w);
unsigned int offset = atom1.x + atom2.x * cSim.stride;
float4 force = cSim.pForce4[offset];
internalF0.x = ff.x * cp0.x;
force.x += internalF0.x;
internalF0.y = ff.x * cp0.y;
force.y += internalF0.y;
internalF0.z = ff.x * cp0.z;
force.z += internalF0.z;
cSim.pForce4[offset] = force;
// printf("%4d - 0: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
offset = atom1.w + atom2.w * cSim.stride;
force = cSim.pForce4[offset];
internalF3.x = ff.w * cp1.x;
force.x += internalF3.x;
internalF3.y = ff.w * cp1.y;
force.y += internalF3.y;
internalF3.z = ff.w * cp1.z;
force.z += internalF3.z;
cSim.pForce4[offset] = force;
// printf("%4d - 3: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
s.x = ff.y * internalF0.x - ff.z * internalF3.x;
s.y = ff.y * internalF0.y - ff.z * internalF3.y;
s.z = ff.y * internalF0.z - ff.z * internalF3.z;
offset = atom1.y + atom2.y * cSim.stride;
force = cSim.pForce4[offset];
force.x += -internalF0.x + s.x;
force.y += -internalF0.y + s.y;
force.z += -internalF0.z + s.z;
cSim.pForce4[offset] = force;
// printf("%4d - 1: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
offset = atom1.z + atom2.z * cSim.stride;
force = cSim.pForce4[offset];
force.x += -internalF3.x - s.x;
force.y += -internalF3.y - s.y;
force.z += -internalF3.z - s.z;
cSim.pForce4[offset] = force;
// printf("%4d - 2: %9.4f %9.4f %9.4f\n", pos1, cSim.pForce[offset], cSim.pForce[offset + cSim.stride], cSim.pForce[offset + cSim.stride2]);
}
pos += blockDim.x * gridDim.x;
}
#endif
if (cSim.nonbondedMethod == NO_CUTOFF)
{
while (pos < feSim.LJ14_offset)
{
//unsigned int pos1 = pos - feSim.rb_dihedral_offset;
unsigned int pos1 = pos;
if (pos1 < feSim.LJ14s)
{
int4 atom = feSim.pLJ14ID[pos1];
float4 LJ14 = feSim.pLJ14Parameter[pos1];
float4 a1 = cSim.pPosq[atom.x];
float4 a2 = cSim.pPosq[atom.y];
float3 d;
d.x = a1.x - a2.x;
d.y = a1.y - a2.y;
d.z = a1.z - a2.z;
float r2 = DOT3(d, d);
float inverseR = 1.0f / sqrt(r2);
#ifdef USE_SOFTCORE_LJ
float CDLJ_energy = 0.0f;
float dEdR = getSoftCoreLJ( r2, LJ14.y, LJ14.x, LJ14.w, LJ14.w, &CDLJ_energy );
energy += CDLJ_energy;
#else
float sig2 = inverseR * LJ14.y;
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
float dEdR = LJ14.x * (12.0f * sig6 - 6.0f) * sig6;
energy += LJ14.x * (sig6 - 1.0f) * sig6;
#endif
energy += LJ14.z * inverseR;
dEdR += LJ14.z * inverseR;
dEdR *= inverseR * inverseR;
unsigned int offsetA = atom.x + atom.z * cSim.stride;
unsigned int offsetB = atom.y + atom.w * cSim.stride;
float4 forceA = cSim.pForce4[offsetA];
float4 forceB = cSim.pForce4[offsetB];
d.x *= dEdR;
d.y *= dEdR;
d.z *= dEdR;
forceA.x += d.x;
forceA.y += d.y;
forceA.z += d.z;
forceB.x -= d.x;
forceB.y -= d.y;
forceB.z -= d.z;
cSim.pForce4[offsetA] = forceA;
cSim.pForce4[offsetB] = forceB;
}
pos += blockDim.x * gridDim.x;
}
}
else if (cSim.nonbondedMethod == CUTOFF)
{
float LJ14_energy;
while (pos < feSim.LJ14_offset)
{
//unsigned int pos1 = pos - feSim.rb_dihedral_offset;
unsigned int pos1 = pos;
if (pos1 < feSim.LJ14s)
{
int4 atom = feSim.pLJ14ID[pos1];
float4 LJ14 = feSim.pLJ14Parameter[pos1];
float4 a1 = cSim.pPosq[atom.x];
float4 a2 = cSim.pPosq[atom.y];
float3 d;
d.x = a1.x - a2.x;
d.y = a1.y - a2.y;
d.z = a1.z - a2.z;
float r2 = DOT3(d, d);
float inverseR = 1.0f / sqrt(r2);
#ifdef USE_SOFTCORE_LJ
float dEdR = getSoftCoreLJ( r2, LJ14.y, LJ14.x, LJ14.w, LJ14.w, &LJ14_energy);
#else
float sig2 = inverseR * LJ14.y;
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
float dEdR = LJ14.x * (12.0f * sig6 - 6.0f) * sig6;
/* E */
LJ14_energy = LJ14.x * (sig6 - 1.0f) * sig6;
#endif
LJ14_energy += LJ14.z * (inverseR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
dEdR += LJ14.z * (inverseR - 2.0f * cSim.reactionFieldK * r2);
dEdR *= inverseR * inverseR;
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
LJ14_energy = 0.0f;
}
/* E */
energy += LJ14_energy;
unsigned int offsetA = atom.x + atom.z * cSim.stride;
unsigned int offsetB = atom.y + atom.w * cSim.stride;
float4 forceA = cSim.pForce4[offsetA];
float4 forceB = cSim.pForce4[offsetB];
d.x *= dEdR;
d.y *= dEdR;
d.z *= dEdR;
forceA.x += d.x;
forceA.y += d.y;
forceA.z += d.z;
forceB.x -= d.x;
forceB.y -= d.y;
forceB.z -= d.z;
cSim.pForce4[offsetA] = forceA;
cSim.pForce4[offsetB] = forceB;
}
pos += blockDim.x * gridDim.x;
}
}
else if (cSim.nonbondedMethod == PERIODIC)
{
float LJ14_energy;
while (pos < feSim.LJ14_offset)
{
//unsigned int pos1 = pos - feSim.rb_dihedral_offset;
unsigned int pos1 = pos;
if (pos1 < feSim.LJ14s)
{
int4 atom = feSim.pLJ14ID[pos1];
float4 LJ14 = feSim.pLJ14Parameter[pos1];
float4 a1 = cSim.pPosq[atom.x];
float4 a2 = cSim.pPosq[atom.y];
float3 d;
d.x = a1.x - a2.x;
d.y = a1.y - a2.y;
d.z = a1.z - a2.z;
d.x -= floor(d.x/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
d.y -= floor(d.y/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
d.z -= floor(d.z/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
float r2 = DOT3(d, d);
float inverseR = 1.0f / sqrt(r2);
#ifdef USE_SOFTCORE_LJ
float dEdR = getSoftCoreLJ( r2, LJ14.y, LJ14.x, LJ14.w, LJ14.w, &LJ14_energy);
#else
float sig2 = inverseR * LJ14.y;
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
float dEdR = LJ14.x * (12.0f * sig6 - 6.0f) * sig6;
/* E */
LJ14_energy = LJ14.x * (sig6 - 1.0f) * sig6;
#endif
LJ14_energy += LJ14.z * (inverseR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
dEdR += LJ14.z * (inverseR - 2.0f * cSim.reactionFieldK * r2);
dEdR *= inverseR * inverseR;
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
LJ14_energy = 0.0f;
}
/* E */
energy += LJ14_energy;
unsigned int offsetA = atom.x + atom.z * cSim.stride;
unsigned int offsetB = atom.y + atom.w * cSim.stride;
float4 forceA = cSim.pForce4[offsetA];
float4 forceB = cSim.pForce4[offsetB];
d.x *= dEdR;
d.y *= dEdR;
d.z *= dEdR;
forceA.x += d.x;
forceA.y += d.y;
forceA.z += d.z;
forceB.x -= d.x;
forceB.y -= d.y;
forceB.z -= d.z;
cSim.pForce4[offsetA] = forceA;
cSim.pForce4[offsetB] = forceB;
}
pos += blockDim.x * gridDim.x;
}
}
cSim.pEnergy[blockIdx.x * blockDim.x + threadIdx.x] += energy;
}
extern "C"
GpuLJ14Softcore* gpuSetLJ14SoftcoreParameters(gpuContext gpu, float epsfac, float fudge, const std::vector<int>& atom1, const std::vector<int>& atom2,
const std::vector<float>& c6, const std::vector<float>& c12, const std::vector<float>& q1,
const std::vector<float>& q2, const std::vector<float>& softcoreLJLambdaArray)
{
int LJ14s = atom1.size();
float scale = epsfac * fudge;
GpuLJ14Softcore* gpuLJ14Softcore = new GpuLJ14Softcore();
gpuLJ14Softcore->feSim.LJ14s = LJ14s;
CUDAStream<int4>* psLJ14ID = new CUDAStream<int4>(LJ14s, 1, "LJ14SoftcoreID");
gpuLJ14Softcore->psLJ14SoftcoreID = psLJ14ID;
gpuLJ14Softcore->feSim.pLJ14ID = psLJ14ID->_pDevStream[0];
CUDAStream<float4>* psLJ14Parameter = new CUDAStream<float4>(LJ14s, 1, "LJ14SoftcoreParameter");
gpuLJ14Softcore->psLJ14SoftcoreParameter = psLJ14Parameter;
gpuLJ14Softcore->feSim.pLJ14Parameter = psLJ14Parameter->_pDevStream[0];
gpuLJ14Softcore->feSim.LJ14_offset = LJ14s;
for (int i = 0; i < LJ14s; i++)
{
(*psLJ14ID)[i].x = atom1[i];
(*psLJ14ID)[i].y = atom2[i];
psLJ14ID->_pSysData[i].z = gpu->pOutputBufferCounter[psLJ14ID->_pSysData[i].x]++;
psLJ14ID->_pSysData[i].w = gpu->pOutputBufferCounter[psLJ14ID->_pSysData[i].y]++;
float p0, p1, p2, p3;
if (c12[i] == 0.0f)
{
p0 = 0.0f;
p1 = 1.0f;
}
else
{
p0 = c6[i] * c6[i] / c12[i];
p1 = pow(c12[i] / c6[i], 1.0f / 6.0f);
}
p2 = scale * q1[i] * q2[i];
p3 = softcoreLJLambdaArray[i];
(*psLJ14Parameter)[i].x = p0;
(*psLJ14Parameter)[i].y = p1;
(*psLJ14Parameter)[i].z = p2;
(*psLJ14Parameter)[i].w = p3;
}
#if (DUMP_PARAMETERS == 1)
cout <<
i << " " <<
(*psLJ14ID)[i].x << " " <<
(*psLJ14ID)[i].y << " " <<
(*psLJ14ID)[i].z << " " <<
(*psLJ14ID)[i].w << " " <<
(*psLJ14Parameter)[i].x << " " <<
(*psLJ14Parameter)[i].y << " " <<
(*psLJ14Parameter)[i].z << " " <<
(*psLJ14Parameter)[i].w << " " <<
p0 << " " <<
p1 << " " <<
p2 << " " <<
p3 << " " <<
endl;
#endif
psLJ14ID->Upload();
psLJ14Parameter->Upload();
SetCalculateLocalSoftcoreSim( gpuLJ14Softcore );
return gpuLJ14Softcore;
}
void kCalculateLocalSoftcoreForces(gpuContext gpu)
{
// printf("kCalculateLocalForces\n");
// fprintf( stderr, "kCalculateLocalSoftcoreForces blks=%u localForces_threads_per_block=%u szVector=%u total=%u\n", gpu->sim.blocks, gpu->sim.localForces_threads_per_block, sizeof(Vectors),
// gpu->sim.localForces_threads_per_block * sizeof(Vectors) ); fflush( stderr );
kCalculateLocalSoftcoreForces_kernel<<<gpu->sim.blocks, gpu->sim.localForces_threads_per_block, gpu->sim.localForces_threads_per_block * sizeof(Vectors)>>>();
LAUNCHERROR("kCalculateLocalSoftcoreForces");
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateNonbondedSoftcore.cu 0 → 100755
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "GpuNonbondedSoftcore.h"
#include "GpuFreeEnergyCudaKernels.h"
// structure containing array of softcore lambdas
struct cudaFreeEnergySimulationNonBonded {
float* pParticleSoftCoreLJLambda;
};
struct cudaFreeEnergySimulationNonBonded feSim;
// device handles
static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaFreeEnergySimulationNonBonded feSimDev;
// write address of structs to devices
void SetCalculateCDLJSoftcoreGpuSim( gpuContext gpu )
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed");
(void) fprintf( stderr, "SetCalculateCDLJSoftcoreGpuSim gpu=%p cSim=%p sizeof=%u\n", gpu, &gpu->sim, sizeof(cudaGmxSimulation) ); fflush( stderr );
}
void SetCalculateCDLJSoftcoreSupplementarySim( float* gpuParticleSoftCoreLJLambda)
{
cudaError_t status;
feSim.pParticleSoftCoreLJLambda = gpuParticleSoftCoreLJLambda;
status = cudaMemcpyToSymbol(feSimDev, &feSim, sizeof(cudaFreeEnergySimulationNonBonded));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateCDLJSoftcoreSupplementarySim");
(void) fprintf( stderr, "SetCalculateCDLJSoftcoreSupplementarySim\n" );
}
void GetCalculateCDLJSoftcoreForcesSim(float* gpuParticleSoftCoreLJLambda)
{
// cudaError_t status;
// status = cudaMemcpyFromSymbol(gpuParticleSoftCoreLJLambda, particleSoftCoreLJLambdaDev, sizeof(float*));
// RTERROR(status, "cudaMemcpyFromSymbol: GetCalculateCDLJSoftcoreForcesSim failed");
}
// create, initialize and entrt SoftCoreLJLambda values
// return handle to GpuNonbondedSoftcore object
extern "C"
GpuNonbondedSoftcore* gpuSetNonbondedSoftcoreParameters(gpuContext gpu, float epsfac, const std::vector<int>& atom, const std::vector<float>& c6,
const std::vector<float>& c12, const std::vector<float>& q,
const std::vector<float>& softcoreLJLambdaArray, const std::vector<char>& symbol,
const std::vector<std::vector<int> >& exclusions, CudaNonbondedMethod method)
{
unsigned int numberOfParticles = c6.size();
gpu->sim.epsfac = epsfac;
gpu->sim.nonbondedMethod = method;
if (numberOfParticles > 0)
setExclusions(gpu, exclusions);
// create gpuNonbondedSoftcore
GpuNonbondedSoftcore* gpuNonbondedSoftcore = new GpuNonbondedSoftcore();
gpuNonbondedSoftcore->initializeParticleSoftCoreLJLambda( numberOfParticles );
float minSoftcore = 1.0e+10;
for (unsigned int i = 0; i < numberOfParticles; i++)
{
float p0 = q[i];
// track min softcore value
float softcoreLJLambda = softcoreLJLambdaArray[i];
if( minSoftcore > softcoreLJLambda ){
minSoftcore = softcoreLJLambda;
}
gpuNonbondedSoftcore->setParticleSoftCoreLJLambda( i, softcoreLJLambda );
float p1 = 0.5f, p2 = 0.0f;
if ((c6[i] > 0.0f) && (c12[i] > 0.0f))
{
p1 = 0.5f * pow(c12[i] / c6[i], 1.0f / 6.0f);
p2 = c6[i] * sqrt(1.0f / c12[i]);
}
if (symbol.size() > 0)
gpu->pAtomSymbol[i] = symbol[i];
(*gpu->psPosq4)[i].w = p0;
(*gpu->psSigEps2)[i].x = p1;
(*gpu->psSigEps2)[i].y = p2;
}
gpuNonbondedSoftcore->setSoftCoreLJLambda( minSoftcore );
// Dummy out extra atom data
for (unsigned int i = numberOfParticles; i < gpu->sim.paddedNumberOfAtoms; i++)
{
(*gpu->psPosq4)[i].x = 100000.0f + i * 10.0f;
(*gpu->psPosq4)[i].y = 100000.0f + i * 10.0f;
(*gpu->psPosq4)[i].z = 100000.0f + i * 10.0f;
(*gpu->psPosq4)[i].w = 0.0f;
(*gpu->psSigEps2)[i].x = 0.0f;
(*gpu->psSigEps2)[i].y = 0.0f;
}
#undef DUMP_PARAMETERS
#define DUMP_PARAMETERS 1
#if (DUMP_PARAMETERS == 1)
(void) fprintf( stderr,"gpuSetNonbondedSoftcoreParameters: %5u epsfac=%14.7e method=%d\n", numberOfParticles, gpu->sim.paddedNumberOfAtoms, epsfac, method );
int maxPrint = 31;
for (unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++){
(void) fprintf( stderr,"%6u x[%14.7e %14.7e %14.7e %14.7e] sig[%14.7e %14.7e]\n",
ii, (*gpu->psPosq4)[ii].x, (*gpu->psPosq4)[ii].y, (*gpu->psPosq4)[ii].z, (*gpu->psPosq4)[ii].w,
(*gpu->psSigEps2)[ii].x, (*gpu->psSigEps2)[ii].y );
if( ii == maxPrint && ii < gpu->sim.paddedNumberOfAtoms - maxPrint ){
ii = gpu->sim.paddedNumberOfAtoms - maxPrint;
}
}
#endif
// upload data to board
gpuNonbondedSoftcore->upload( gpu );
gpu->psPosq4->Upload();
gpu->psSigEps2->Upload();
return gpuNonbondedSoftcore;
}
// delete gpuNonbondedSoftcore
extern "C"
void gpuDeleteNonbondedSoftcoreParameters( void* gpuNonbondedSoftcore)
{
GpuNonbondedSoftcore* internalGNonbondedSoftcore = static_cast<GpuNonbondedSoftcore*>(gpuNonbondedSoftcore);
delete internalGNonbondedSoftcore;
}
struct Atom {
float x;
float y;
float z;
float q;
float sig;
float eps;
float softCoreLJLambda;
float fx;
float fy;
float fz;
};
#if 0
texture<float, 1, cudaReadModeElementType> tabulatedErfcRef;
__device__ float fastErfc(float r)
{
float normalized = cSim.tabulatedErfcScale*r;
int index = (int) normalized;
float fract2 = normalized-index;
float fract1 = 1.0f-fract2;
return fract1*tex1Dfetch(tabulatedErfcRef, index) + fract2*tex1Dfetch(tabulatedErfcRef, index+1);
}
// Include versions of the kernels for N^2 calculations.
#define METHOD_NAME(a, b) a##N2##b
#include "kCalculateNonbondedSoftcore.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##N2ByWarp##b
#include "kCalculateNonbondedSoftcore.h"
#endif
// Include versions of the kernels for N^2 calculations with softcore LJ.
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##N2SoftcoreLJ##b
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_SOFTCORE_LJ
#include "kCalculateNonbondedSoftcore.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##N2SoftcoreLJByWarp##b
#include "kCalculateNonbondedSoftcore.h"
#undef USE_SOFTCORE_LJ
// Include versions of the kernels with cutoffs.
#if 0
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_CUTOFF
#define METHOD_NAME(a, b) a##Cutoff##b
#include "kCalculateNonbondedSoftcore.h"
#include "kFindInteractingBlocks.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##CutoffByWarp##b
#include "kCalculateNonbondedSoftcore.h"
// Include versions of the kernels with periodic boundary conditions.
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_PERIODIC
#define METHOD_NAME(a, b) a##Periodic##b
#include "kCalculateNonbondedSoftcore.h"
#include "kFindInteractingBlocks.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateNonbondedSoftcore.h"
// Include versions of the kernels for Ewald
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_PERIODIC
#define USE_EWALD
#define METHOD_NAME(a, b) a##Ewald##b
#include "kCalculateNonbondedSoftcore.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##EwaldByWarp##b
#include "kCalculateNonbondedSoftcore.h"
// Reciprocal Space Ewald summation is in a separate kernel
#include "kCalculateCDLJEwaldFastReciprocal.h"
void kCalculatePME(gpuContext gpu);
#endif
void kCalculateCDLJSoftcoreForces(gpuContext gpu )
{
//printf("kCalculateCDLJCutoffForces %d\n", gpu->sim.nonbondedMethod); fflush( stdout );
switch (gpu->sim.nonbondedMethod)
{
case NO_CUTOFF:
if (gpu->bOutputBufferPerWarp)
kCalculateCDLJSoftcoreN2SoftcoreLJByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit);
else
kCalculateCDLJSoftcoreN2SoftcoreLJForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit );
//(gpu->sim.pWorkUnit, gpuNonbondedSoftcore->getGpuParticleSoftCoreLJLambda());
LAUNCHERROR("kCalculateCDLJSoftcoreN2Forces");
#if 0
int maxPrint = 31;
gpu->psWorkUnit->Download();
fprintf( stderr, "kCalculateCDLJSoftcoreForces: bOutputBufferPerWarp=%u blks=%u th/blk=%u wu=%u %u shrd=%u\n", gpu->bOutputBufferPerWarp,
gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block, gpu->sim.workUnits, gpu->psWorkUnit->_pSysStream[0][0],
sizeof(Atom)*gpu->sim.nonbond_threads_per_block );
gpu->psPosq4->Download();
(void) fprintf( stderr, "\nkCalculateGBVISoftcoreBornSum: pre BornSum %s Born radii & params\n",
(gpu->bIncludeGBVI ? "GBVI" : "Obc") );
for( int ii = 0; ii < gpu->natoms; ii++ ){
(void) fprintf( stderr, "%6d bSum=%14.6e param[%14.6e %14.6e %14.6e] x[%14.6f %14.6f %14.6f %14.6f]\n",
ii,
gpu->psBornSum->_pSysStream[0][ii],
gpu->psGBVIData->_pSysStream[0][ii].x,
gpu->psGBVIData->_pSysStream[0][ii].y,
gpu->psGBVIData->_pSysStream[0][ii].z,
gpu->psPosq4->_pSysStream[0][ii].x, gpu->psPosq4->_pSysStream[0][ii].y,
gpu->psPosq4->_pSysStream[0][ii].z, gpu->psPosq4->_pSysStream[0][ii].w
);
if( (ii == maxPrint) && ( ii < (gpu->natoms - maxPrint)) ){
ii = gpu->natoms - maxPrint;
}
}
#endif
#undef GBVI
break;
#if 0
case CUTOFF:
kFindBlockBoundsCutoff_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsCutoff");
kFindBlocksWithInteractionsCutoff_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
LAUNCHERROR("kFindBlocksWithInteractionsCutoff");
compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
kFindInteractionsWithinBlocksCutoff_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
#if 0
static int iteration = 0;
if (iteration >= 0)
{
gpu->psInteractingWorkUnit->Download();
gpu->psInteractionCount->Download();
/*
unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID;
unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
unsigned int numWorkUnits = cSim.pInteractionCount[0];
unsigned int pos = warp*numWorkUnits/totalWarps;
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
*/
printf("# Post kCalculateCDLJCutoffForces %d atoms warps=%d cnt=%u bOutputBufferPerWarp=%d zC=%d\n",
gpu->natoms, ((gpu->sim.nonbond_blocks*gpu->sim.nonbond_threads_per_block)/GRID),
gpu->psInteractionCount->_pSysStream[0][0], gpu->bOutputBufferPerWarp,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block);
fflush( stdout );
for (int i = 0; i < gpu->psInteractingWorkUnit->_stride; i++)
{
printf("%5d %u\n", i, gpu->psInteractingWorkUnit->_pSysStream[0][i] );
fflush( stdout );
}
}
iteration++;
#endif
if (gpu->bOutputBufferPerWarp)
kCalculateCDLJCutoffByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateCDLJCutoffForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
LAUNCHERROR("kCalculateCDLJCutoffForces");
break;
case PERIODIC:
kFindBlockBoundsPeriodic_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsPeriodic");
kFindBlocksWithInteractionsPeriodic_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
LAUNCHERROR("kFindBlocksWithInteractionsPeriodic");
compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
kFindInteractionsWithinBlocksPeriodic_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
if (gpu->bOutputBufferPerWarp)
kCalculateCDLJPeriodicByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateCDLJPeriodicForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
LAUNCHERROR("kCalculateCDLJPeriodicForces");
break;
case EWALD:
case PARTICLE_MESH_EWALD:
kFindBlockBoundsPeriodic_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
LAUNCHERROR("kFindBlockBoundsPeriodic");
kFindBlocksWithInteractionsPeriodic_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
LAUNCHERROR("kFindBlocksWithInteractionsPeriodic");
compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
kFindInteractionsWithinBlocksPeriodic_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
LAUNCHERROR("kFindInteractionsWithinBlocksPeriodic");
cudaChannelFormatDesc channelDesc = cudaCreateChannelDesc<float>();
cudaBindTexture(NULL, &tabulatedErfcRef, gpu->psTabulatedErfc->_pDevData, &channelDesc, gpu->psTabulatedErfc->_length*sizeof(float));
if (gpu->bOutputBufferPerWarp)
kCalculateCDLJEwaldByWarpForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateCDLJEwaldForces_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
LAUNCHERROR("kCalculateCDLJEwaldForces");
if (gpu->sim.nonbondedMethod == EWALD)
{
kCalculateEwaldFastCosSinSums_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block>>>();
LAUNCHERROR("kCalculateEwaldFastCosSinSums");
kCalculateEwaldFastForces_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>();
LAUNCHERROR("kCalculateEwaldFastForces");
}
else
kCalculatePME(gpu);
#endif
}
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateNonbondedSoftcore.h 0 → 100644
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
/**
* This file contains the kernels for evalauating nonbonded forces. It is included
* several times in kCalculateCDLJForces.cu with different #defines to generate
* different versions of the kernels.
*/
#ifdef USE_SOFTCORE_LJ
#include "kSoftcoreLJ.h"
#endif
/* Cuda compiler on Windows does not recognized "static const float" values */
#define LOCAL_HACK_PI 3.1415926535897932384626433832795f
//__global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit, float* softCoreLJLambdaArray)
__global__ void METHOD_NAME(kCalculateCDLJSoftcore, Forces_kernel)(unsigned int* workUnit )
{
extern __shared__ Atom sA[];
unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID;
unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
unsigned int numWorkUnits = cSim.pInteractionCount[0];
unsigned int pos = warp*numWorkUnits/totalWarps;
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
float CDLJ_energy;
float energy = 0.0f;
#ifdef USE_CUTOFF
float3* tempBuffer = (float3*) &sA[cSim.nonbond_threads_per_block];
#endif
#ifdef USE_EWALD
const float TWO_OVER_SQRT_PI = 2.0f/sqrt(LOCAL_HACK_PI);
#endif
unsigned int lasty = 0xFFFFFFFF;
while (pos < end)
{
// Extract cell coordinates from appropriate work unit
unsigned int x = workUnit[pos];
unsigned int y = ((x >> 2) & 0x7fff) << GRIDBITS;
bool bExclusionFlag = (x & 0x1);
x = (x >> 17) << GRIDBITS;
float4 apos; // Local atom x, y, z, q
float3 af; // Local atom fx, fy, fz
float dx;
float dy;
float dz;
float r2;
float invR;
float sig;
float eps;
float dEdR;
unsigned int tgx = threadIdx.x & (GRID - 1);
unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx;
Atom* psA = &sA[tbx];
unsigned int i = x + tgx;
apos = cSim.pPosq[i];
float2 a = cSim.pAttr[i];
//float softCoreLJLambda = cSim.pSoftCoreLJLambda[i];
//float softCoreLJLambda = softCoreLJLambdaArray[i];
float softCoreLJLambda = feSimDev.pParticleSoftCoreLJLambda[i];
af.x = 0.0f;
af.y = 0.0f;
af.z = 0.0f;
if (x == y) // Handle diagonals uniquely at 50% efficiency
{
// Read fixed atom data into registers and GRF
sA[threadIdx.x].x = apos.x;
sA[threadIdx.x].y = apos.y;
sA[threadIdx.x].z = apos.z;
sA[threadIdx.x].q = apos.w;
sA[threadIdx.x].sig = a.x;
sA[threadIdx.x].eps = a.y;
sA[threadIdx.x].softCoreLJLambda = softCoreLJLambda;
apos.w *= cSim.epsfac;
if (!bExclusionFlag)
{
for (unsigned int j = 0; j < GRID; j++)
{
dx = psA[j].x - apos.x;
dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
invR = 1.0f / sqrt(r2);
sig = a.x + psA[j].sig;
eps = a.y * psA[j].eps;
#ifdef USE_SOFTCORE_LJ
dEdR = getSoftCoreLJ( r2, sig, eps, softCoreLJLambda, psA[j].softCoreLJLambda, &CDLJ_energy );
#else
float sig2 = invR * sig;
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI );
/* E */
CDLJ_energy += apos.w * psA[j].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJ_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
#else
dEdR += apos.w * psA[j].q * invR;
/* E */
CDLJ_energy += apos.w * psA[j].q * invR;
#endif
dEdR *= invR * invR;
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJ_energy = 0.0f;
}
#endif
/* E */
energy += 0.5f*CDLJ_energy;
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
af.x -= dx;
af.y -= dy;
af.z -= dz;
}
}
else // bExclusion
{
unsigned int xi = x>>GRIDBITS;
unsigned int cell = xi+xi*cSim.paddedNumberOfAtoms/GRID-xi*(xi+1)/2;
unsigned int excl = cSim.pExclusion[cSim.pExclusionIndex[cell]+tgx];
for (unsigned int j = 0; j < GRID; j++)
{
dx = psA[j].x - apos.x;
dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
invR = 1.0f / sqrt(r2);
sig = a.x + psA[j].sig;
eps = a.y * psA[j].eps;
#ifdef USE_SOFTCORE_LJ
dEdR = getSoftCoreLJ( r2, sig, eps, softCoreLJLambda, psA[j].softCoreLJLambda, &CDLJ_energy );
#else
float sig2 = invR * sig;
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJ_energy += apos.w * psA[j].q * invR * erfcAlphaR;
bool needCorrection = !(excl & 0x1) && x+tgx != y+j && x+tgx < cSim.atoms && y+j < cSim.atoms;
if (needCorrection)
{
// Subtract off the part of this interaction that was included in the reciprocal space contribution.
dEdR = -apos.w * psA[j].q * invR * ((1.0f-erfcAlphaR) - alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
CDLJ_energy = -apos.w * psA[j].q * invR * (1.0f-erfcAlphaR);
}
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJ_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
#else
dEdR += apos.w * psA[j].q * invR;
/* E */
CDLJ_energy += apos.w * psA[j].q * invR;
#endif
dEdR *= invR * invR;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
if ((!(excl & 0x1) && !needCorrection) || r2 > cSim.nonbondedCutoffSqr)
#else
if (!(excl & 0x1) || r2 > cSim.nonbondedCutoffSqr)
#endif
#else
if (!(excl & 0x1))
#endif
{
dEdR = 0.0f;
/* E */
CDLJ_energy = 0.0f;
}
/* E */
energy += 0.5f*CDLJ_energy;
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
af.x -= dx;
af.y -= dy;
af.z -= dz;
excl >>= 1;
}
}
// Write results
float4 of;
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
of = cSim.pForce4a[offset];
of.x += af.x;
of.y += af.y;
of.z += af.z;
cSim.pForce4a[offset] = of;
#else
of.x = af.x;
of.y = af.y;
of.z = af.z;
of.w = 0.0f;
unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pForce4a[offset] = of;
#endif
}
else // 100% utilization
{
// Read fixed atom data into registers and GRF
if (lasty != y)
{
unsigned int j = y + tgx;
float4 temp = cSim.pPosq[j];
float2 temp1 = cSim.pAttr[j];
//float temp3 = cSim.pSoftCoreLJLambda[j];
//float temp3 = softCoreLJLambdaArray[j];
float temp3 = feSimDev.pParticleSoftCoreLJLambda[j];
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
sA[threadIdx.x].q = temp.w;
sA[threadIdx.x].sig = temp1.x;
sA[threadIdx.x].eps = temp1.y;
sA[threadIdx.x].softCoreLJLambda = temp3;
}
sA[threadIdx.x].fx = 0.0f;
sA[threadIdx.x].fy = 0.0f;
sA[threadIdx.x].fz = 0.0f;
apos.w *= cSim.epsfac;
if (!bExclusionFlag)
{
#ifdef USE_CUTOFF
unsigned int flags = cSim.pInteractionFlag[pos];
if (flags == 0)
{
// No interactions in this block.
}
else if (flags == 0xFFFFFFFF)
#endif
{
// Compute all interactions within this block.
for (unsigned int j = 0; j < GRID; j++)
{
dx = psA[tj].x - apos.x;
dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
invR = 1.0f / sqrt(r2);
sig = a.x + psA[tj].sig;
eps = a.y * psA[tj].eps;
#ifdef USE_SOFTCORE_LJ
dEdR = getSoftCoreLJ( r2, sig, eps, softCoreLJLambda, psA[tj].softCoreLJLambda, &CDLJ_energy );
#else
float sig2 = invR * sig;
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJ_energy += apos.w * psA[tj].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJ_energy += apos.w * psA[tj].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
#else
dEdR += apos.w * psA[tj].q * invR;
/* E */
CDLJ_energy += apos.w * psA[tj].q * invR;
#endif
dEdR *= invR * invR;
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJ_energy = 0.0f;
}
#endif
/* E */
energy += CDLJ_energy;
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
af.x -= dx;
af.y -= dy;
af.z -= dz;
psA[tj].fx += dx;
psA[tj].fy += dy;
psA[tj].fz += dz;
tj = (tj + 1) & (GRID - 1);
}
}
#ifdef USE_CUTOFF
else
{
// Compute only a subset of the interactions in this block.
for (unsigned int j = 0; j < GRID; j++)
{
if ((flags&(1<<j)) != 0)
{
dx = psA[j].x - apos.x;
dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
invR = 1.0f / sqrt(r2);
sig = a.x + psA[j].sig;
eps = a.y * psA[j].eps;
#ifdef USE_SOFTCORE_LJ
dEdR = getSoftCoreLJ( r2, sig, eps, softCoreLJLambda, psA[j].softCoreLJLambda, &CDLJ_energy );
#else
float sig2 = invR * sig;
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[j].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
CDLJ_energy += apos.w * psA[j].q * invR * erfcAlphaR;
#else
dEdR += apos.w * psA[j].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJ_energy += apos.w * psA[j].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
#else
dEdR += apos.w * psA[j].q * invR;
/* E */
CDLJ_energy += apos.w * psA[j].q * invR;
#endif
dEdR *= invR * invR;
#ifdef USE_CUTOFF
if (r2 > cSim.nonbondedCutoffSqr)
{
dEdR = 0.0f;
/* E */
CDLJ_energy = 0.0f;
}
#endif
/* E */
energy += CDLJ_energy;
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
af.x -= dx;
af.y -= dy;
af.z -= dz;
tempBuffer[threadIdx.x].x = dx;
tempBuffer[threadIdx.x].y = dy;
tempBuffer[threadIdx.x].z = dz;
// Sum the forces on atom j.
if (tgx % 2 == 0)
{
tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+1].x;
tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+1].y;
tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+1].z;
}
if (tgx % 4 == 0)
{
tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+2].x;
tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+2].y;
tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+2].z;
}
if (tgx % 8 == 0)
{
tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+4].x;
tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+4].y;
tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+4].z;
}
if (tgx % 16 == 0)
{
tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+8].x;
tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+8].y;
tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+8].z;
}
if (tgx == 0)
{
psA[j].fx += tempBuffer[threadIdx.x].x + tempBuffer[threadIdx.x+16].x;
psA[j].fy += tempBuffer[threadIdx.x].y + tempBuffer[threadIdx.x+16].y;
psA[j].fz += tempBuffer[threadIdx.x].z + tempBuffer[threadIdx.x+16].z;
}
}
}
}
#endif
}
else // bExclusion
{
// Read fixed atom data into registers and GRF
unsigned int xi = x>>GRIDBITS;
unsigned int yi = y>>GRIDBITS;
unsigned int cell = xi+yi*cSim.paddedNumberOfAtoms/GRID-yi*(yi+1)/2;
unsigned int excl = cSim.pExclusion[cSim.pExclusionIndex[cell]+tgx];
excl = (excl >> tgx) | (excl << (GRID - tgx));
for (unsigned int j = 0; j < GRID; j++)
{
dx = psA[tj].x - apos.x;
dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
invR = 1.0f / sqrt(r2);
sig = a.x + psA[tj].sig;
eps = a.y * psA[tj].eps;
#ifdef USE_SOFTCORE_LJ
dEdR = getSoftCoreLJ( r2, sig, eps, softCoreLJLambda, psA[tj].softCoreLJLambda, &CDLJ_energy );
#else
float sig2 = invR * sig;
sig2 *= sig2;
float sig6 = sig2 * sig2 * sig2;
dEdR = eps * (12.0f * sig6 - 6.0f) * sig6;
/* E */
CDLJ_energy = eps * (sig6 - 1.0f) * sig6;
#endif
#ifdef USE_CUTOFF
#ifdef USE_EWALD
float r = sqrt(r2);
float alphaR = cSim.alphaEwald * r;
float erfcAlphaR = fastErfc(alphaR);
dEdR += apos.w * psA[tj].q * invR * (erfcAlphaR + alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
/* E */
CDLJ_energy += apos.w * psA[tj].q * invR * erfcAlphaR;
bool needCorrection = !(excl & 0x1) && x+tgx != y+tj && x+tgx < cSim.atoms && y+tj < cSim.atoms;
if (needCorrection)
{
// Subtract off the part of this interaction that was included in the reciprocal space contribution.
dEdR = -apos.w * psA[tj].q * invR * ((1.0f-erfcAlphaR) - alphaR * exp ( - alphaR * alphaR) * TWO_OVER_SQRT_PI);
CDLJ_energy = -apos.w * psA[tj].q * invR * (1.0f-erfcAlphaR);
}
#else
dEdR += apos.w * psA[tj].q * (invR - 2.0f * cSim.reactionFieldK * r2);
/* E */
CDLJ_energy += apos.w * psA[tj].q * (invR + cSim.reactionFieldK * r2 - cSim.reactionFieldC);
#endif
#else
dEdR += apos.w * psA[tj].q * invR;
/* E */
CDLJ_energy += apos.w * psA[tj].q * invR;
#endif
dEdR *= invR * invR;
#ifdef USE_CUTOFF
#ifdef USE_EWALD
if ((!(excl & 0x1) && !needCorrection) || r2 > cSim.nonbondedCutoffSqr)
#else
if (!(excl & 0x1) || r2 > cSim.nonbondedCutoffSqr)
#endif
#else
if (!(excl & 0x1))
#endif
{
dEdR = 0.0f;
/* E */
CDLJ_energy = 0.0f;
}
/* E */
energy += CDLJ_energy;
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
af.x -= dx;
af.y -= dy;
af.z -= dz;
psA[tj].fx += dx;
psA[tj].fy += dy;
psA[tj].fz += dz;
excl >>= 1;
tj = (tj + 1) & (GRID - 1);
}
}
// Write results
float4 of;
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
of = cSim.pForce4a[offset];
of.x += af.x;
of.y += af.y;
of.z += af.z;
cSim.pForce4a[offset] = of;
offset = y + tgx + warp*cSim.stride;
of = cSim.pForce4a[offset];
of.x += sA[threadIdx.x].fx;
of.y += sA[threadIdx.x].fy;
of.z += sA[threadIdx.x].fz;
cSim.pForce4a[offset] = of;
#else
of.x = af.x;
of.y = af.y;
of.z = af.z;
of.w = 0.0f;
unsigned int offset = x + tgx + (y >> GRIDBITS) * cSim.stride;
cSim.pForce4a[offset] = of;
of.x = sA[threadIdx.x].fx;
of.y = sA[threadIdx.x].fy;
of.z = sA[threadIdx.x].fz;
offset = y + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pForce4a[offset] = of;
#endif
lasty = y;
}
pos++;
}
cSim.pEnergy[blockIdx.x*blockDim.x+threadIdx.x] += energy;
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreBornSum.cu 0 → 100755
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "gputypes.h"
#include "cudaKernels.h"
#include "GpuObcGbsaSoftcore.h"
#include <cuda.h>
#include <string>
struct Atom {
float x;
float y;
float z;
float r;
float sr;
float sum;
float polarScaleData;
};
struct cudaFreeEnergySimulationObcGbsaSoftcore {
float* pNonPolarScalingFactors;
};
struct cudaFreeEnergySimulationObcGbsaSoftcore gbsaSim;
static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaFreeEnergySimulationObcGbsaSoftcore gbsaSimDev;
extern "C"
void SetCalculateObcGbsaSoftcoreBornSumSim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "SetCalculateObcGbsaSoftcoreBornSumSim: cudaMemcpyToSymbol: SetSim copy to cSim failed");
}
extern "C"
void SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsSim( float* nonPolarScalingFactors )
{
cudaError_t status;
gbsaSim.pNonPolarScalingFactors = nonPolarScalingFactors;
status = cudaMemcpyToSymbol(gbsaSimDev, &gbsaSim, sizeof(cudaFreeEnergySimulationObcGbsaSoftcore));
RTERROR(status, "cudaMemcpyToSymbol: SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsSim");
(void) fprintf( stderr, "In SetCalculateObcGbsaSoftcoreNonPolarScalingFactorsSim\n" );
}
void GetCalculateObcGbsaSoftcoreBornSumSim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
RTERROR(status, "GetCalculateObcGbsaSoftcoreBornSumSim: cudaMemcpyFromSymbol: SetSim copy from cSim failed");
}
// Include versions of the kernels for N^2 calculations.
#define METHOD_NAME(a, b) a##N2##b
#include "kCalculateObcGbsaSoftcoreBornSum.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##N2ByWarp##b
#include "kCalculateObcGbsaSoftcoreBornSum.h"
// Include versions of the kernels with cutoffs.
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_CUTOFF
#define METHOD_NAME(a, b) a##Cutoff##b
#include "kCalculateObcGbsaSoftcoreBornSum.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##CutoffByWarp##b
#include "kCalculateObcGbsaSoftcoreBornSum.h"
// Include versions of the kernels with periodic boundary conditions.
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_PERIODIC
#define METHOD_NAME(a, b) a##Periodic##b
#include "kCalculateObcGbsaSoftcoreBornSum.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateObcGbsaSoftcoreBornSum.h"
#if 0
__global__ void kClearObcGbsaBornSum_kernel()
{
unsigned int pos = blockIdx.x * blockDim.x + threadIdx.x;
while (pos < cSim.stride * cSim.nonbondOutputBuffers)
{
((float*)cSim.pBornSum)[pos] = 0.0f;
pos += gridDim.x * blockDim.x;
}
}
__global__ void kReduceObcGbsaBornSum_kernel()
{
unsigned int pos = (blockIdx.x * blockDim.x + threadIdx.x);
while (pos < cSim.atoms)
{
float sum = 0.0f;
float* pSt = cSim.pBornSum + pos;
float2 atom = cSim.pObcData[pos];
// Get summed Born data
for (int i = 0; i < cSim.nonbondOutputBuffers; i++)
{
sum += *pSt;
// printf("%4d %4d A: %9.4f\n", pos, i, *pSt);
pSt += cSim.stride;
}
// Now calculate Born radius and OBC term.
sum *= 0.5f * atom.x;
float sum2 = sum * sum;
float sum3 = sum * sum2;
float tanhSum = tanh(cSim.alphaOBC * sum - cSim.betaOBC * sum2 + cSim.gammaOBC * sum3);
float nonOffsetRadii = atom.x + cSim.dielectricOffset;
float bornRadius = 1.0f / (1.0f / atom.x - tanhSum / nonOffsetRadii);
float obcChain = atom.x * (cSim.alphaOBC - 2.0f * cSim.betaOBC * sum + 3.0f * cSim.gammaOBC * sum2);
obcChain = (1.0f - tanhSum * tanhSum) * obcChain / nonOffsetRadii;
cSim.pBornRadii[pos] = bornRadius;
cSim.pObcChain[pos] = obcChain;
pos += gridDim.x * blockDim.x;
}
}
void kReduceObcGbsaBornSum(gpuContext gpu)
{
// printf("kReduceObcGbsaBornSum\n");
kReduceObcGbsaBornSum_kernel<<<gpu->sim.blocks, 384>>>();
gpu->bRecalculateBornRadii = false;
LAUNCHERROR("kReduceObcGbsaBornSum");
}
#endif
/**
* Initialize parameters for Cuda Obc softcore
*
* @param gpu gpu context
* @param innerDielectric solute dielectric
* @param solventDielectric solvent dielectric
* @param radius intrinsic Born radii
* @param scale Obc scaling factors
* @param charge atomic charges (possibly overwritten by other methods?)
* @param nonPolarScalingFactors non-polar scaling factors
*
*/
extern "C"
void gpuSetObcSoftcoreParameters(gpuContext gpu, float innerDielectric, float solventDielectric, const std::vector<float>& radius, const std::vector<float>& scale,
const std::vector<float>& charge, const std::vector<float>& nonPolarScalingFactors)
{
// ---------------------------------------------------------------------------------------
static const float dielectricOffset = 0.009f;
static const float electricConstant = -166.02691f;
static const std::string methodName = "gpuSetObcSoftcoreParameters";
// ---------------------------------------------------------------------------------------
unsigned int atoms = radius.size();
// initialize parameters
// gpu->bIncludeGBSA = true;
GpuObcGbsaSoftcore* gpuObcGbsaSoftcore = new GpuObcGbsaSoftcore();
gpuObcGbsaSoftcore->initializeNonPolarScalingFactors( gpu->sim.paddedNumberOfAtoms );
for (unsigned int i = 0; i < atoms; i++)
{
(*gpu->psObcData)[i].x = radius[i] - dielectricOffset;
(*gpu->psObcData)[i].y = scale[i] * (*gpu->psObcData)[i].x;
(*gpu->psPosq4)[i].w = charge[i];
gpuObcGbsaSoftcore->setNonPolarScalingFactors( i, nonPolarScalingFactors[i] );
}
// diagnostics
#if (DUMP_PARAMETERS == 1)
(void) fprintf( stderr, "%s %u %u\n", methodName.c_str(), gpu->natoms, gpu->sim.paddedNumberOfAtoms );
for (unsigned int i = 0; i < atoms; i++)
{
(void) fprintf( stderr, "%6u %13.6e %13.6e %8.3f %8.3f\n", i, (*gpu->psObcData)[i].x, (*gpu->psObcData)[i].y, (*gpu->psPosq4)[i].w , nonPolarScalingFactors[i] );
#endif
// dummy out extra atom data
for (unsigned int i = gpu->natoms; i < gpu->sim.paddedNumberOfAtoms; i++)
{
(*gpu->psBornRadii)[i] = 0.2f;
(*gpu->psObcData)[i].x = 0.01f;
(*gpu->psObcData)[i].y = 0.01f;
}
// load data to board
gpuObcGbsaSoftcore->upload( gpu );
gpu->psBornRadii->Upload();
gpu->psObcData->Upload();
gpu->psPosq4->Upload();
gpu->sim.preFactor = 2.0f*electricConstant*((1.0f/innerDielectric)-(1.0f/solventDielectric))*gpu->sim.forceConversionFactor;
}
void kCalculateObcGbsaSoftcoreBornSum(gpuContext gpu)
{
// printf("kCalculateObcGbsaSoftcoreBornSum\n");
kClearObcGbsaBornSum( gpu );
LAUNCHERROR("kClearBornSum from kCalculateObcGbsaSoftcoreBornSum");
switch (gpu->sim.nonbondedMethod)
{
case NO_CUTOFF:
#define GBSA 0
#if GBSA == 1
gpu->psWorkUnit->Download();
fprintf( stderr, "kCalculateObcGbsaSoftcoreBornSum: bOutputBufferPerWarp=%u blks=%u th/blk=%u wu=%u %u\n", gpu->bOutputBufferPerWarp,
gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block, gpu->sim.workUnits, gpu->psWorkUnit->_pSysData[0] );
#endif
#undef GBSA
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaN2ByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit);
else
kCalculateObcGbsaN2BornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
sizeof(Atom)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pWorkUnit);
break;
case CUTOFF:
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaCutoffByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateObcGbsaCutoffBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
break;
case PERIODIC:
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaPeriodicByWarpBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateObcGbsaPeriodicBornSum_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
(sizeof(Atom)+sizeof(float))*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
break;
}
LAUNCHERROR("kCalculateObcGbsaSoftcoreBornSum");
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreBornSum.h 0 → 100644
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
/**
* This file contains the kernel for calculating Born sums. It is included
* several times in kCalculateObcGbsaBornSum.cu with different #defines to generate
* different versions of the kernels.
*/
__global__ void METHOD_NAME(kCalculateObcGbsa, BornSum_kernel)(unsigned int* workUnit)
{
extern __shared__ Atom sA[];
unsigned int totalWarps = cSim.nonbond_blocks*cSim.nonbond_threads_per_block/GRID;
unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
unsigned int numWorkUnits = cSim.pInteractionCount[0];
unsigned int pos = warp*numWorkUnits/totalWarps;
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
#ifdef USE_CUTOFF
float* tempBuffer = (float*) &sA[cSim.nonbond_threads_per_block];
#endif
while (pos < end)
{
// Extract cell coordinates from appropriate work unit
//unsigned int x = workUnit[pos + (blockIdx.x*numWorkUnits)/gridDim.x];
unsigned int x = workUnit[pos];
unsigned int y = ((x >> 2) & 0x7fff) << GRIDBITS;
x = (x >> 17) << GRIDBITS;
float dx;
float dy;
float dz;
float r2;
float r;
unsigned int tgx = threadIdx.x & (GRID - 1);
unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx;
Atom* psA = &sA[tbx];
if (x == y) // Handle diagonals uniquely at 50% efficiency
{
// Read fixed atom data into registers and GRF
unsigned int i = x + tgx;
float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum
float2 ar = cSim.pObcData[i]; // Local atom vr, sr
float polarScaleData = gbsaSimDev.pNonPolarScalingFactors[i]; // scale contribution
sA[threadIdx.x].x = apos.x;
sA[threadIdx.x].y = apos.y;
sA[threadIdx.x].z = apos.z;
sA[threadIdx.x].r = ar.x;
sA[threadIdx.x].sr = ar.y;
sA[threadIdx.x].polarScaleData = polarScaleData;
apos.w = 0.0f;
for (unsigned int j = 0; j < GRID; j++)
{
dx = psA[j].x - apos.x;
dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#if defined USE_PERIODIC
if (i < cSim.atoms && x+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#endif
{
r = sqrt(r2);
float rInverse = 1.0f / r;
float rScaledRadiusJ = r + psA[j].sr;
if ((j != tgx) && (ar.x < rScaledRadiusJ))
{
float l_ij = 1.0f / max(ar.x, fabs(r - psA[j].sr));
float u_ij = 1.0f / rScaledRadiusJ;
float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij);
float sum = l_ij -
u_ij +
0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) +
(0.25f * psA[j].sr * psA[j].sr * rInverse) *
(l_ij2 - u_ij2);
float rj = psA[j].r;
if (ar.x < (rj - r))
{
sum += 2.0f * ((1.0f / ar.x) - l_ij);
}
apos.w += psA[j].polarScaleData*sum;
}
}
}
// Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
cSim.pBornSum[offset] += apos.w;
#else
unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = apos.w;
#endif
}
else // 100% utilization
{
// Read fixed atom data into registers and GRF
unsigned int j = y + tgx;
unsigned int i = x + tgx;
float4 temp = cSim.pPosq[j];
float2 temp1 = cSim.pObcData[j];
float polarScaleDataJ = gbsaSimDev.pNonPolarScalingFactors[j]; // scale contribution
float4 apos = cSim.pPosq[i]; // Local atom x, y, z, sum
float2 ar = cSim.pObcData[i]; // Local atom vr, sr
float polarScaleDataI = gbsaSimDev.pNonPolarScalingFactors[i]; // scale contribution
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
sA[threadIdx.x].r = temp1.x;
sA[threadIdx.x].sr = temp1.y;
sA[threadIdx.x].polarScaleData = polarScaleDataJ;
sA[threadIdx.x].sum = apos.w = 0.0f;
#ifdef USE_CUTOFF
//unsigned int flags = cSim.pInteractionFlag[pos + (blockIdx.x*numWorkUnits)/gridDim.x];
unsigned int flags = cSim.pInteractionFlag[pos];
if (flags == 0)
{
// No interactions in this block.
}
else if (flags == 0xFFFFFFFF)
#endif
{
// Compute all interactions within this block.
for (unsigned int j = 0; j < GRID; j++)
{
dx = psA[tj].x - apos.x;
dy = psA[tj].y - apos.y;
dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_PERIODIC
if (i < cSim.atoms && y+tj < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#endif
{
r = sqrt(r2);
float rInverse = 1.0f / r;
float rScaledRadiusJ = r + psA[tj].sr;
if (ar.x < rScaledRadiusJ)
{
float l_ij = 1.0f / max(ar.x, fabs(r - psA[tj].sr));
float u_ij = 1.0f / rScaledRadiusJ;
float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij);
float term = l_ij -
u_ij +
0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) +
(0.25f * psA[tj].sr * psA[tj].sr * rInverse) *
(l_ij2 - u_ij2);
float srj = psA[tj].sr;
float scale = psA[tj].polarScaleData;
if (ar.x < (srj - r))
{
term += 2.0f * ((1.0f / ar.x) - l_ij);
}
//apos.w += term;
apos.w += (scale*term);
}
float rScaledRadiusI = r + ar.y;
if (psA[tj].r < rScaledRadiusI)
{
float l_ij = 1.0f / max(psA[tj].r, fabs(r - ar.y));
float u_ij = 1.0f / rScaledRadiusI;
float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij);
float term = l_ij -
u_ij +
0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) +
(0.25f * ar.y * ar.y * rInverse) *
(l_ij2 - u_ij2);
float rj = psA[tj].r;
if (rj < (ar.y - r))
{
term += 2.0f * ((1.0f / psA[tj].r) - l_ij);
}
psA[tj].sum += polarScaleDataI*term;
}
}
tj = (tj - 1) & (GRID - 1);
}
}
#ifdef USE_CUTOFF
else
{
// Compute only a subset of the interactions in this block.
for (unsigned int j = 0; j < GRID; j++)
{
if ((flags&(1<<j)) != 0)
{
tempBuffer[threadIdx.x] = 0.0f;
dx = psA[j].x - apos.x;
dy = psA[j].y - apos.y;
dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
r2 = dx * dx + dy * dy + dz * dz;
#ifdef USE_PERIODIC
if (i < cSim.atoms && y+j < cSim.atoms && r2 < cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (r2 < cSim.nonbondedCutoffSqr)
#endif
{
r = sqrt(r2);
float rInverse = 1.0f / r;
float rScaledRadiusJ = r + psA[j].sr;
if (ar.x < rScaledRadiusJ)
{
float l_ij = 1.0f / max(ar.x, fabs(r - psA[j].sr));
float u_ij = 1.0f / rScaledRadiusJ;
float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij);
float term = l_ij -
u_ij +
0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) +
(0.25f * psA[j].sr * psA[j].sr * rInverse) *
(l_ij2 - u_ij2);
float srj = psA[j].sr;
if (ar.x < (srj - r))
{
term += 2.0f * ((1.0f / ar.x) - l_ij);
}
apos.w += psA[j].polarScaleData*term;
}
float rScaledRadiusI = r + ar.y;
if (psA[j].r < rScaledRadiusI)
{
float l_ij = 1.0f / max(psA[j].r, fabs(r - ar.y));
float u_ij = 1.0f / rScaledRadiusI;
float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij;
float ratio = log(u_ij / l_ij);
float term = l_ij -
u_ij +
0.25f * r * (u_ij2 - l_ij2) +
(0.50f * rInverse * ratio) +
(0.25f * ar.y * ar.y * rInverse) *
(l_ij2 - u_ij2);
float rj = psA[j].r;
if (rj < (ar.y - r))
{
term += 2.0f * ((1.0f / psA[j].r) - l_ij);
}
tempBuffer[threadIdx.x] = polarScaleDataI*term;
}
}
// Sum the terms.
if (tgx % 2 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+1];
if (tgx % 4 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+2];
if (tgx % 8 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+4];
if (tgx % 16 == 0)
tempBuffer[threadIdx.x] += tempBuffer[threadIdx.x+8];
if (tgx == 0)
psA[j].sum += tempBuffer[threadIdx.x] + tempBuffer[threadIdx.x+16];
}
}
}
#endif
// Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
cSim.pBornSum[offset] += apos.w;
offset = y + tgx + warp*cSim.stride;
cSim.pBornSum[offset] += sA[threadIdx.x].sum;
#else
unsigned int offset = x + tgx + (y >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = apos.w;
offset = y + tgx + (x >> GRIDBITS) * cSim.stride;
cSim.pBornSum[offset] = sA[threadIdx.x].sum;
#endif
}
pos++;
}
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreForces2.cu 0 → 100755
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include <stdio.h>
#include <cuda.h>
#include <vector_functions.h>
#include <cstdlib>
#include <string>
#include <iostream>
#include <fstream>
using namespace std;
#include "gputypes.h"
#include "cudaKernels.h"
struct Atom {
float x;
float y;
float z;
float r;
float sr;
float fx;
float fy;
float fz;
float fb;
};
static __constant__ cudaGmxSimulation cSim;
extern "C"
void SetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed");
}
void GetCalculateObcGbsaSoftcoreForces2Sim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyFromSymbol: SetSim copy from cSim failed");
}
// Include versions of the kernels for N^2 calculations.
#define METHOD_NAME(a, b) a##N2##b
#include "kCalculateObcGbsaSoftcoreForces2.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##N2ByWarp##b
#include "kCalculateObcGbsaSoftcoreForces2.h"
// Include versions of the kernels with cutoffs.
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_CUTOFF
#define METHOD_NAME(a, b) a##Cutoff##b
#include "kCalculateObcGbsaSoftcoreForces2.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##CutoffByWarp##b
#include "kCalculateObcGbsaSoftcoreForces2.h"
// Include versions of the kernels with periodic boundary conditions.
#undef METHOD_NAME
#undef USE_OUTPUT_BUFFER_PER_WARP
#define USE_PERIODIC
#define METHOD_NAME(a, b) a##Periodic##b
#include "kCalculateObcGbsaSoftcoreForces2.h"
#define USE_OUTPUT_BUFFER_PER_WARP
#undef METHOD_NAME
#define METHOD_NAME(a, b) a##PeriodicByWarp##b
#include "kCalculateObcGbsaSoftcoreForces2.h"
void kCalculateObcGbsaSoftcoreForces2(gpuContext gpu)
{
//printf("kCalculateObcGbsaSoftcoreForces2\n");
//fprintf( stderr, "kCalculateObcGbsaSoftcoreForces2 nonbondedMethod=%d warp=%d\n", gpu->sim.nonbondedMethod, gpu->bOutputBufferPerWarp);
//fprintf( stderr, "kCalculateObcGbsaSoftcoreForces2 nonbondedMethod=%d calling kReduceForces\n", gpu->sim.nonbondedMethod);
//kReduceForces(gpu);
switch (gpu->sim.nonbondedMethod)
{
case NO_CUTOFF:
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcoreN2ByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit);
else
kCalculateObcGbsaSoftcoreN2Forces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
sizeof(Atom)*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pWorkUnit);
break;
case CUTOFF:
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcoreCutoffByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateObcGbsaSoftcoreCutoffForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
break;
case PERIODIC:
if (gpu->bOutputBufferPerWarp)
kCalculateObcGbsaSoftcorePeriodicByWarpForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
else
kCalculateObcGbsaSoftcorePeriodicForces2_kernel<<<gpu->sim.bornForce2_blocks, gpu->sim.bornForce2_threads_per_block,
(sizeof(Atom)+sizeof(float3))*gpu->sim.bornForce2_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
break;
}
LAUNCHERROR("kCalculateObcGbsaSoftcoreForces2");
}
plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreForces2.h 0 → 100644
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
/**
* This file contains the kernel for evalauating the second stage of GBSA. It is included
* several times in kCalculateObcGbsaSoftcoreForces2.cu with different #defines to generate
* different versions of the kernels.
*/
__global__ void METHOD_NAME(kCalculateObcGbsaSoftcore, Forces2_kernel)(unsigned int* workUnit)
{
extern __shared__ Atom sA[];
unsigned int totalWarps = cSim.bornForce2_blocks*cSim.bornForce2_threads_per_block/GRID;
unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
unsigned int numWorkUnits = cSim.pInteractionCount[0];
unsigned int pos = warp*numWorkUnits/totalWarps;
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
#ifdef USE_CUTOFF
float3* tempBuffer = (float3*) &sA[cSim.bornForce2_threads_per_block];
#endif
unsigned int lasty = -0xFFFFFFFF;
while (pos < end)
{
// Extract cell coordinates from appropriate work unit
unsigned int x = workUnit[pos];
unsigned int y = ((x >> 2) & 0x7fff) << GRIDBITS;
x = (x >> 17) << GRIDBITS;
unsigned int tgx = threadIdx.x & (GRID - 1);
unsigned int i = x + tgx;
float4 apos = cSim.pPosq[i];
float2 a = cSim.pObcData[i];
float fb = cSim.pBornForce[i];
unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx;
Atom* psA = &sA[tbx];
float3 af;
sA[threadIdx.x].fx = af.x = 0.0f;
sA[threadIdx.x].fy = af.y = 0.0f;
sA[threadIdx.x].fz = af.z = 0.0f;
if (x == y) // Handle diagonals uniquely at 50% efficiency
{
// Read fixed atom data into registers and GRF
sA[threadIdx.x].x = apos.x;
sA[threadIdx.x].y = apos.y;
sA[threadIdx.x].z = apos.z;
sA[threadIdx.x].r = a.x;
sA[threadIdx.x].sr = a.y;
sA[threadIdx.x].fb = fb;
for (unsigned int j = (tgx+1)&(GRID-1); j != tgx; j = (j+1)&(GRID-1))
{
float dx = psA[j].x - apos.x;
float dy = psA[j].y - apos.y;
float dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2);
// Atom I Born forces and sum
float rScaledRadiusJ = r + psA[j].sr;
float l_ij = 1.0f / max(a.x, fabs(r - psA[j].sr));
float u_ij = 1.0f / rScaledRadiusJ;
float rInverse = 1.0f / r;
float l_ij2 = l_ij * l_ij;
float u_ij2 = u_ij * u_ij;
float r2Inverse = rInverse * rInverse;
float t1 = log (u_ij / l_ij);
float t2 = (l_ij2 - u_ij2);
float t3 = t2 * rInverse;
t1 *= rInverse;
// Born Forces term
float term = 0.125f *
(1.000f + psA[j].sr * psA[j].sr * r2Inverse) * t3 +
0.250f * t1 * r2Inverse;
float dE = fb * term;
#if defined USE_PERIODIC
if (a.x >= rScaledRadiusJ || i >= cSim.atoms || x+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (a.x >= rScaledRadiusJ || r2 > cSim.nonbondedCutoffSqr)
#else
if (a.x >= rScaledRadiusJ)
#endif
{
dE = 0.0f;
}
float d = dx * dE;
af.x -= d;
psA[j].fx += d;
d = dy * dE;
af.y -= d;
psA[j].fy += d;
d = dz * dE;
af.z -= d;
psA[j].fz += d;
}
// Write results
float4 of;
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
#else
unsigned int offset = x + tgx + (x >> GRIDBITS) * cSim.stride;
#endif
of = cSim.pForce4b[offset];
of.x += af.x + sA[threadIdx.x].fx;
of.y += af.y + sA[threadIdx.x].fy;
of.z += af.z + sA[threadIdx.x].fz;
of.w = 0.0f;
cSim.pForce4b[offset] = of;
}
else
{
// Read fixed atom data into registers and GRF
if (lasty != y)
{
unsigned int j = y + tgx;
float4 temp = cSim.pPosq[j];
float2 temp1 = cSim.pObcData[j];
sA[threadIdx.x].fb = cSim.pBornForce[j];
sA[threadIdx.x].x = temp.x;
sA[threadIdx.x].y = temp.y;
sA[threadIdx.x].z = temp.z;
sA[threadIdx.x].r = temp1.x;
sA[threadIdx.x].sr = temp1.y;
}
float sr2 = a.y * a.y;
#ifdef USE_CUTOFF
unsigned int flags = cSim.pInteractionFlag[pos];
if (flags == 0)
{
// No interactions in this block.
}
else if (flags == 0xFFFFFFFF)
#endif
{
// Compute all interactions within this block.
for (unsigned int j = 0; j < GRID; j++)
{
float dx = psA[tj].x - apos.x;
float dy = psA[tj].y - apos.y;
float dz = psA[tj].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2);
// Interleaved Atom I and J Born Forces and sum components
float r2Inverse = 1.0f / r2;
float rScaledRadiusJ = r + psA[tj].sr;
float rScaledRadiusI = r + a.y;
float rInverse = 1.0f / r;
float l_ijJ = 1.0f / max(a.x, fabs(r - psA[tj].sr));
float l_ijI = 1.0f / max(psA[tj].r, fabs(r - a.y));
float u_ijJ = 1.0f / rScaledRadiusJ;
float u_ijI = 1.0f / rScaledRadiusI;
float l_ij2J = l_ijJ * l_ijJ;
float l_ij2I = l_ijI * l_ijI;
float u_ij2J = u_ijJ * u_ijJ;
float u_ij2I = u_ijI * u_ijI;
float t1J = log (u_ijJ / l_ijJ);
float t1I = log (u_ijI / l_ijI);
float t2J = (l_ij2J - u_ij2J);
float t2I = (l_ij2I - u_ij2I);
float t3J = t2J * rInverse;
float t3I = t2I * rInverse;
t1J *= rInverse;
t1I *= rInverse;
// Born Forces term
float term = 0.125f *
(1.000f + psA[tj].sr * psA[tj].sr * r2Inverse) * t3J +
0.250f * t1J * r2Inverse;
float dE = fb * term;
#if defined USE_PERIODIC
if (a.x >= rScaledRadiusJ || i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (a.x >= rScaledRadiusJ || r2 > cSim.nonbondedCutoffSqr)
#else
if (a.x >= rScaledRadiusJ)
#endif
{
dE = 0.0f;
}
float d = dx * dE;
af.x -= d;
psA[tj].fx += d;
d = dy * dE;
af.y -= d;
psA[tj].fy += d;
d = dz * dE;
af.z -= d;
psA[tj].fz += d;
// Atom J Born sum term
term = 0.125f *
(1.000f + sr2 * r2Inverse) * t3I +
0.250f * t1I * r2Inverse;
dE = psA[tj].fb * term;
float rj = psA[tj].r;
#ifdef USE_PERIODIC
if (rj >= rScaledRadiusI || i >= cSim.atoms || y+tj >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (rj >= rScaledRadiusI || r2 > cSim.nonbondedCutoffSqr)
#else
if (rj >= rScaledRadiusI)
#endif
{
dE = 0.0f;
}
dx *= dE;
dy *= dE;
dz *= dE;
psA[tj].fx += dx;
psA[tj].fy += dy;
psA[tj].fz += dz;
af.x -= dx;
af.y -= dy;
af.z -= dz;
tj = (tj + 1) & (GRID - 1);
}
}
#ifdef USE_CUTOFF
else
{
// Compute only a subset of the interactions in this block.
for (unsigned int j = 0; j < GRID; j++)
{
if ((flags&(1<<j)) != 0)
{
float dx = psA[j].x - apos.x;
float dy = psA[j].y - apos.y;
float dz = psA[j].z - apos.z;
#ifdef USE_PERIODIC
dx -= floor(dx/cSim.periodicBoxSizeX+0.5f)*cSim.periodicBoxSizeX;
dy -= floor(dy/cSim.periodicBoxSizeY+0.5f)*cSim.periodicBoxSizeY;
dz -= floor(dz/cSim.periodicBoxSizeZ+0.5f)*cSim.periodicBoxSizeZ;
#endif
float r2 = dx * dx + dy * dy + dz * dz;
float r = sqrt(r2);
// Interleaved Atom I and J Born Forces and sum components
float r2Inverse = 1.0f / r2;
float rScaledRadiusJ = r + psA[j].sr;
float rScaledRadiusI = r + a.y;
float rInverse = 1.0f / r;
float l_ijJ = 1.0f / max(a.x, fabs(r - psA[j].sr));
float l_ijI = 1.0f / max(psA[j].r, fabs(r - a.y));
float u_ijJ = 1.0f / rScaledRadiusJ;
float u_ijI = 1.0f / rScaledRadiusI;
float l_ij2J = l_ijJ * l_ijJ;
float l_ij2I = l_ijI * l_ijI;
float u_ij2J = u_ijJ * u_ijJ;
float u_ij2I = u_ijI * u_ijI;
float t1J = log (u_ijJ / l_ijJ);
float t1I = log (u_ijI / l_ijI);
float t2J = (l_ij2J - u_ij2J);
float t2I = (l_ij2I - u_ij2I);
float t3J = t2J * rInverse;
float t3I = t2I * rInverse;
t1J *= rInverse;
t1I *= rInverse;
// Born Forces term
float term = 0.125f *
(1.000f + psA[j].sr * psA[j].sr * r2Inverse) * t3J +
0.250f * t1J * r2Inverse;
float dE = fb * term;
#if defined USE_PERIODIC
if (a.x >= rScaledRadiusJ || i >= cSim.atoms || y+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (a.x >= rScaledRadiusJ || r2 > cSim.nonbondedCutoffSqr)
#else
if (a.x >= rScaledRadiusJ)
#endif
{
dE = 0.0f;
}
float d = dx * dE;
af.x -= d;
tempBuffer[threadIdx.x].x = d;
d = dy * dE;
af.y -= d;
tempBuffer[threadIdx.x].y = d;
d = dz * dE;
af.z -= d;
tempBuffer[threadIdx.x].z = d;
// Atom J Born sum term
term = 0.125f *
(1.000f + sr2 * r2Inverse) * t3I +
0.250f * t1I * r2Inverse;
dE = psA[j].fb * term;
float rj = psA[j].r;
#ifdef USE_PERIODIC
if (rj >= rScaledRadiusI || i >= cSim.atoms || y+j >= cSim.atoms || r2 > cSim.nonbondedCutoffSqr)
#elif defined USE_CUTOFF
if (rj >= rScaledRadiusI || r2 > cSim.nonbondedCutoffSqr)
#else
if (rj >= rScaledRadiusI)
#endif
{
dE = 0.0f;
}
dx *= dE;
dy *= dE;
dz *= dE;
tempBuffer[threadIdx.x].x += dx;
tempBuffer[threadIdx.x].y += dy;
tempBuffer[threadIdx.x].z += dz;
af.x -= dx;
af.y -= dy;
af.z -= dz;
// Sum the forces on atom j.
if (tgx % 2 == 0)
{
tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+1].x;
tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+1].y;
tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+1].z;
}
if (tgx % 4 == 0)
{
tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+2].x;
tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+2].y;
tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+2].z;
}
if (tgx % 8 == 0)
{
tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+4].x;
tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+4].y;
tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+4].z;
}
if (tgx % 16 == 0)
{
tempBuffer[threadIdx.x].x += tempBuffer[threadIdx.x+8].x;
tempBuffer[threadIdx.x].y += tempBuffer[threadIdx.x+8].y;
tempBuffer[threadIdx.x].z += tempBuffer[threadIdx.x+8].z;
}
if (tgx == 0)
{
psA[j].fx += tempBuffer[threadIdx.x].x + tempBuffer[threadIdx.x+16].x;
psA[j].fy += tempBuffer[threadIdx.x].y + tempBuffer[threadIdx.x+16].y;
psA[j].fz += tempBuffer[threadIdx.x].z + tempBuffer[threadIdx.x+16].z;
}
}
}
}
#endif
// Write results
float4 of;
#ifdef USE_OUTPUT_BUFFER_PER_WARP
unsigned int offset = x + tgx + warp*cSim.stride;
#else
unsigned int offset = x + tgx + (y >> GRIDBITS) * cSim.stride;
#endif
of = cSim.pForce4b[offset];
of.x += af.x;
of.y += af.y;
of.z += af.z;
cSim.pForce4b[offset] = of;
#ifdef USE_OUTPUT_BUFFER_PER_WARP
offset = y + tgx + warp*cSim.stride;
#else
offset = y + tgx + (x >> GRIDBITS) * cSim.stride;
#endif
of = cSim.pForce4b[offset];
of.x += sA[threadIdx.x].fx;
of.y += sA[threadIdx.x].fy;
of.z += sA[threadIdx.x].fz;
cSim.pForce4b[offset] = of;
}
lasty = y;
pos++;
}
}
plugins/freeEnergy/platforms/cuda/src/kernels/kSoftcoreLJ.h 0 → 100644
View file @ 7a36f461
#ifndef _K_SOFTCORE_LJ__H__
#define _K_SOFTCORE_LJ__H__
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
/**
* This file contains kernel for calculating softcore LJ force prefactor
*/
#ifdef USE_SOFTCORE_LJ
__device__ float getSoftCoreLJ( float r2, float sig, float eps, float lambdaI, float lambdaJ, float* energy)
{
float r = sqrt(r2);
float lambda = lambdaI < lambdaJ ? lambdaI : lambdaJ;
eps *= lambda;
// (r/sig)
float sig2 = r/sig;
sig2 *= sig2;
float sig6 = sig2*sig2*sig2;
float softcoreLJTerm = 0.5f*( 1.0f - lambda) + sig6;
float softcoreLJInv = 1.0f/softcoreLJTerm;
float softcoreLJInv2 = softcoreLJInv*softcoreLJInv;
*energy = eps*(softcoreLJInv2 - softcoreLJInv);
return eps*softcoreLJInv2*( 12.0f*softcoreLJInv - 6.0f )*sig6;
}
#endif
#endif
plugins/freeEnergy/platforms/cuda/staticTarget/CMakeLists.txt 0 → 100644
View file @ 7a36f461
#
# Include CUDA related files.
#
SET(OPENMM_BUILD_FREE_ENERGY_PATH ${CMAKE_SOURCE_DIR}/plugins/freeEnergy)
SET(CUDA_NVCC_BUILD_FLAGS "-DCUDPP_STATIC_LIB" )
INCLUDE(${FINDCUDA_DIR}/FindCuda.cmake)
INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
LINK_DIRECTORIES(${CUDA_TARGET_LINK})
FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
FILE(GLOB src_files ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/${subdir}/src/*.cu ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/${subdir}/src/*/*.cu)
FOREACH(file ${src_files})
FILE(RELATIVE_PATH file ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda ${file})
SET(SOURCE_FILES ${SOURCE_FILES} ${file}) #append
ENDFOREACH(file)
CUDA_INCLUDE_DIRECTORIES(BEFORE ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/${subdir}/include)
CUDA_INCLUDE_DIRECTORIES(BEFORE ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/${subdir}/src)
ENDFOREACH(subdir)
#CUDA_INCLUDE_DIRECTORIES(BEFORE ${OPENMM_BUILD_FREE_ENERGY_PATH}/jama/include)
CUDA_INCLUDE_DIRECTORIES(${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/../src
${OPENMM_DIR}/platforms/cuda/src
${OPENMM_DIR}/platforms/cuda/src/kernels
${OPENMM_DIR}/openmmapi/include )
CUDA_ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
# required for getting OPENMM_EXPORT to be set correctly in 'class OPENMM_EXPORT CudaStreamFactory', ...
# see OpenMM/openmmapi/include/internal/windowsExport.h for details
SET(CUDA_STATIC_COMPILE_FLAG "-DOPENMM_BUILDING_STATIC_LIBRARY -DOPENMM_USE_STATIC_LIBRARIES -DCUDPP_STATIC_LIB")
SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES COMPILE_FLAGS ${CUDA_STATIC_COMPILE_FLAG})
TARGET_LINK_LIBRARIES(${STATIC_TARGET} optimized ${OPENMM_LIBRARY_NAME}_static)
TARGET_LINK_LIBRARIES(${STATIC_TARGET} debug ${OPENMM_LIBRARY_NAME}_static_d optimized ${OPENMM_LIBRARY_NAME}_static ${CUFFT_TARGET_LINK})
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})
plugins/freeEnergy/platforms/cuda/tests/CMakeLists.txt 0 → 100644
View file @ 7a36f461
#
# Testing
#
ENABLE_TESTING()
INCLUDE(${CMAKE_SOURCE_DIR}/platforms/cuda/cuda-cmake/FindCuda.cmake)
INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/include)
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src)
INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src/kernels)
Set( SHARED_OPENMM_TARGET OpenMMFreeEnergy)
Set( SHARED_CUDA_TARGET OpenMMCuda)
Set( STATIC_CUDA_TARGET OpenMMCuda_static)
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(SHARED_CUDA_TARGET ${SHARED_CUDA_TARGET}_d)
SET(SHARED_OPENMM_TARGET ${SHARED_OPENMM_TARGET}_d)
SET(STATIC_CUDA_TARGET ${STATIC_CUDA_TARGET}_d)
SET(STATIC_CUDA_TARGET ${STATIC_CUDA_TARGET}_d)
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
#LINK_DIRECTORIES
# Automatically create tests using files named "Test*.cpp"
FILE(GLOB TEST_PROGS "*Test*.cpp")
FOREACH(TEST_PROG ${TEST_PROGS})
GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
# Link with shared library
CUDA_ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_CUDA_TARGET})
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
# Link with static library
# SET(TEST_STATIC ${TEST_ROOT}Static)
# CUDA_ADD_EXECUTABLE(${TEST_STATIC} ${TEST_PROG})
# SET_TARGET_PROPERTIES(${TEST_STATIC}
# PROPERTIES
# COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
# )
# TARGET_LINK_LIBRARIES(${TEST_STATIC} ${STATIC_TARGET})
# ADD_TEST(${TEST_STATIC} ${EXECUTABLE_OUTPUT_PATH}/${TEST_STATIC})
ENDFOREACH(TEST_PROG ${TEST_PROGS})
# TestCudaUsingParameterFile customized w/ command-line argument (input file name used in test)
#ADD_EXECUTABLE(TestCudaUsingParameterFile TstCudaUsingParameterFile.cpp)
#TARGET_LINK_LIBRARIES(TestCudaUsingParameterFile ${SHARED_TARGET})
#ADD_TEST(TestCudaUsingParameterFile "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFile" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/lambdaSdObcParameters.txt")
#ADD_TEST(TestCudaUsingParameterFile "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFile" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfNoPbcParameters.txt")
#
#SET(TEST_ROOT TestCudaUsingParameterFile)
#SET(TEST_PROG TstCudaUsingParameterFile.cpp)
#SET(TEST_STATIC ${TEST_ROOT}Static)
#SET(INCLUDE_CUDA_STATIC 1)
#IF(INCLUDE_CUDA_STATIC)
# ADD_EXECUTABLE(${TEST_STATIC} ${TEST_PROG})
# SET_TARGET_PROPERTIES(${TEST_STATIC}
# PROPERTIES
# COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
# )
# TARGET_LINK_LIBRARIES(${TEST_STATIC} ${STATIC_TARGET} ${STATIC_BROOK_TARGET})
# ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/lambdaSdObcParameters.txt")
# ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfNoPbcParameters.txt")
# ADD_TEST(${TEST_STATIC} "${EXECUTABLE_OUTPUT_PATH}/TestCudaUsingParameterFileStatic" "-parameterFileName" "${CMAKE_CURRENT_SOURCE_DIR}/bptiMdRfPbcParameters.txt" " +checkEnergyForceConsistent -checkForces" )
#ENDIF(INCLUDE_CUDA_STATIC)
plugins/freeEnergy/platforms/cuda/tests/TestCudaGBVISoftcoreForce.cpp 0 → 100644
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the reference implementation of GBVIForce.
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "ReferencePlatform.h"
#include "openmm/GBVISoftcoreForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/NonbondedForce.h"
#include "openmm/NonbondedSoftcoreForce.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/sfmt/SFMT.h"
#include "OpenMMFreeEnergy.h"
#include "openmm/freeEnergyKernels.h"
#include "ReferenceFreeEnergyKernelFactory.h"
#include "CudaFreeEnergyKernelFactory.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
#define PRINT_ON 1
int compareForcesOfTwoStates( int numParticles, State& state1, State& state2, double relativeTolerance, double absoluteTolerance ) {
int error = 0;
for (int i = 0; i < numParticles; ++i) {
Vec3 f1 = state1.getForces()[i];
Vec3 f2 = state2.getForces()[i];
double diff = (f1[0] - f2[0])*(f1[0] - f2[0]) +
(f1[1] - f2[1])*(f1[1] - f2[1]) +
(f1[2] - f2[2])*(f1[2] - f2[2]);
double denom1 = fabs( f1[0] ) + fabs( f1[1] ) +fabs( f1[2] );
double denom2 = fabs( f2[0] ) + fabs( f2[1] ) +fabs( f2[2] );
int ok = 1;
if( (denom1 > 0.0 || denom2 > 0.0) && (sqrt( diff )/(denom1+denom2)) > relativeTolerance ){
error++;
ok = 0;
}
#if PRINT_ON == 1
(void) fprintf( stderr, "F %d [%14.6e %14.6e %14.6e] [%14.6e %14.6e %14.6e] %s\n", i,
f1[0], f1[1], f1[2], f2[0], f2[1], f2[2], (ok ? "":"XXXXXX") );
#endif
}
return error;
}
void testSingleParticle() {
CudaPlatform platform;
System system;
system.addParticle(2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBVISoftcoreForce* forceField = new GBVISoftcoreForce;
double charge = 1.0;
double radius = 0.15;
double gamma = 1.0;
forceField->addParticle(charge, radius, gamma);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Energy);
double bornRadius = radius;
double eps0 = EPSILON0;
double tau = (1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric());
double bornEnergy = (-charge*charge/(8*PI_M*eps0))*tau/bornRadius;
double nonpolarEnergy = -0.1*CAL2JOULE*gamma*tau*std::pow( radius/bornRadius, 3.0);
double expectedE = (bornEnergy+nonpolarEnergy);
double obtainedE = state.getPotentialEnergy();
double diff = fabs( obtainedE - expectedE );
#if PRINT_ON == 1
(void) fprintf( stderr, "testSingleParticle expected=%14.6e obtained=%14.6e diff=%14.6e breakdown:[%14.6e %14.6e]\n",
expectedE, obtainedE, diff, bornEnergy, nonpolarEnergy );
#endif
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
}
void testCutoffAndPeriodic() {
CudaPlatform cuda;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBVISoftcoreForce* gbsa = new GBVISoftcoreForce();
NonbondedForce* nonbonded = new NonbondedForce();
gbsa->addParticle(-1, 0.15, 1.0);
nonbonded->addParticle(-1, 1, 0);
gbsa->addParticle(1, 0.15, 1.0);
nonbonded->addParticle(1, 1, 0);
const double cutoffDistance = 3.0;
const double boxSize = 10.0;
nonbonded->setCutoffDistance(cutoffDistance);
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(gbsa);
system.addForce(nonbonded);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
// Calculate the forces for both cutoff and periodic with two different atom positions.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
Context context(system, integrator, cuda);
context.setPositions(positions);
State state1 = context.getState(State::Forces);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
context.reinitialize();
context.setPositions(positions);
State state2 = context.getState(State::Forces);
positions[1][0]+= boxSize;
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
context.reinitialize();
context.setPositions(positions);
State state3 = context.getState(State::Forces);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
context.reinitialize();
context.setPositions(positions);
State state4 = context.getState(State::Forces);
// All forces should be identical, exception state3 which should be zero.
#if PRINT_ON == 1
(void) fprintf( stderr, "testCutoffAndPeriodic\n" );
#endif
ASSERT_EQUAL_VEC(state1.getForces()[0], state2.getForces()[0], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[1], state2.getForces()[1], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[0], state4.getForces()[0], 0.01);
ASSERT_EQUAL_VEC(state1.getForces()[1], state4.getForces()[1], 0.01);
ASSERT_EQUAL_VEC(state3.getForces()[0], Vec3(0, 0, 0), 0.01);
ASSERT_EQUAL_VEC(state3.getForces()[1], Vec3(0, 0, 0), 0.01);
}
void testEnergyEthane() {
std::string methodName = "testEnergyEthane";
#if 0
CudaPlatform platform;
CudaFreeEnergyKernelFactory* factory = new CudaFreeEnergyKernelFactory();
platform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
platform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
platform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
#else
ReferencePlatform platform;
ReferenceFreeEnergyKernelFactory* referenceFactoryT = new ReferenceFreeEnergyKernelFactory();
platform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), referenceFactoryT);
platform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), referenceFactoryT);
platform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), referenceFactoryT);
#endif
ReferencePlatform referencePlatform;
ReferenceFreeEnergyKernelFactory* referenceFactory = new ReferenceFreeEnergyKernelFactory();
referencePlatform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), referenceFactory);
referencePlatform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), referenceFactory);
referencePlatform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), referenceFactory);
System system;
const int numParticles = 8;
for( int i = 0; i < numParticles; i++ ){
system.addParticle(1.0);
}
LangevinIntegrator integrator(0, 0.1, 0.01);
double C_HBondDistance = 0.1097;
double C_CBondDistance = 0.1504;
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
int AM1_BCC = 1;
H_charge = -0.053;
C_charge = -3.0*H_charge;
if( AM1_BCC ){
C_radius = 0.180;
//C_radius = 0.360;
C_gamma = -0.2863;
C_gamma = 1.0;
H_radius = 0.125;
//H_radius = 0.25;
H_gamma = 0.2437;
H_gamma = 1.0;
//H_charge = C_charge = 0.0;
//H_gamma = C_gamma = 0.0;
} else {
C_radius = 0.215;
C_gamma = -1.1087;
H_radius = 0.150;
H_gamma = 0.1237;
}
// for ethane all Coulomb forces are excluded since all atoms 3 or
// fewer bonds away from all other atoms -- is this true for H's on
// difference carbons? -- should be computed in 14 ixn
int VI = 1;
if( VI ){
//double bornRadiusScaleFactorsEven = 0.5;
double bornRadiusScaleFactorsEven = 1.0;
//double bornRadiusScaleFactorsOdd = 0.5;
double bornRadiusScaleFactorsOdd = 1.0;
#if PRINT_ON == 1
(void) fprintf( stderr, "%s: Applying GB/VI\n", methodName.c_str() );
(void) fprintf( stderr, "C[%14.7e %14.7e %14.7e] H[%14.7e %14.7e %14.7e] scale[%.1f %.1f]\n",
C_charge, C_radius, C_gamma, H_charge, H_radius, H_gamma,
bornRadiusScaleFactorsEven, bornRadiusScaleFactorsOdd);
#endif
GBVISoftcoreForce* forceField = new GBVISoftcoreForce();
for( int i = 0; i < numParticles; i++ ){
forceField->addParticle( H_charge, H_radius, H_gamma, (i%2) ? bornRadiusScaleFactorsOdd : bornRadiusScaleFactorsEven);
nonbonded->addParticle( H_charge, H_radius, 0.0);
}
forceField->setParticleParameters( 1, C_charge, C_radius, C_gamma, bornRadiusScaleFactorsOdd);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
forceField->setParticleParameters( 4, C_charge, C_radius, C_gamma, bornRadiusScaleFactorsEven);
nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
forceField->addBond( 0, 1, C_HBondDistance );
forceField->addBond( 2, 1, C_HBondDistance );
forceField->addBond( 3, 1, C_HBondDistance );
forceField->addBond( 1, 4, C_CBondDistance );
forceField->addBond( 5, 4, C_HBondDistance );
forceField->addBond( 6, 4, C_HBondDistance );
forceField->addBond( 7, 4, C_HBondDistance );
std::vector<pair<int, int> > bonds;
std::vector<double> bondDistances;
bonds.push_back(pair<int, int>(0, 1));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(2, 1));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(3, 1));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(1, 4));
bondDistances.push_back( C_CBondDistance );
bonds.push_back(pair<int, int>(5, 4));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(6, 4));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(7, 4));
bondDistances.push_back( C_HBondDistance );
nonbonded->createExceptionsFromBonds(bonds, 0.0, 0.0);
system.addForce(forceField);
} else {
#if PRINT_ON == 1
(void) fprintf( stderr, "testEnergyEthane: Applying GBSA OBC\n" );
#endif
GBSAOBCForce* forceField = new GBSAOBCForce();
double H_scale = 0.85;
double C_scale = 0.72;
for( int i = 0; i < numParticles; i++ ){
forceField->addParticle( H_charge, H_radius, H_scale );
nonbonded->addParticle( H_charge, 1, 0);
}
forceField->setParticleParameters(1, C_charge, C_radius, C_scale);
forceField->setParticleParameters(4, C_charge, C_radius, C_scale);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
system.addForce(forceField);
}
system.addForce(nonbonded);
Context referenceContext(system, integrator, referencePlatform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
positions[0] = Vec3(0.5480, 1.7661, 0.0000);
positions[1] = Vec3(0.7286, 0.8978, 0.6468);
positions[2] = Vec3(0.4974, 0.0000, 0.0588);
positions[3] = Vec3(0.0000, 0.9459, 1.4666);
positions[4] = Vec3(2.1421, 0.8746, 1.1615);
positions[5] = Vec3(2.3239, 0.0050, 1.8065);
positions[6] = Vec3(2.8705, 0.8295, 0.3416);
positions[7] = Vec3(2.3722, 1.7711, 1.7518);
context.setPositions(positions);
referenceContext.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
#if PRINT_ON == 1
(void) fprintf( stderr, "cudaE=%14.7e refE=%14.7e\n", state.getPotentialEnergy(), referenceState.getPotentialEnergy() );
#endif
// Take a small step in the direction of the energy gradient.
if( compareForcesOfTwoStates( numParticles, state, referenceState, 0.001, 0.001 ) ){
ASSERT_EQUAL_TOL(0.0, 1.0, 0.01)
}
double norm = 0.0;
double forceSum[3] = { 0.0, 0.0, 0.0 };
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
forceSum[0] += f[0];
forceSum[1] += f[1];
forceSum[2] += f[2];
}
norm = std::sqrt(norm);
#if PRINT_ON == 1
(void) fprintf( stderr, "Fsum [%14.7e %14.7e %14.7e] norm=%14.7e\n", forceSum[0], forceSum[1], forceSum[2], norm );
#endif
const double delta = 1e-3;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
double diff = (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta;
double off = fabs( diff - norm );
#if PRINT_ON == 1
(void) fprintf( stderr, "X Energies %.8e %.8e norms[%14.7e %14.7e] deltaNorms=%14.7e delta=%.2e\n",
state.getPotentialEnergy(), state2.getPotentialEnergy(), diff, norm, off, delta );
#endif
// See whether the potential energy changed by the expected amount.
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
}
void testEnergyEthaneSwitchingFunction() {
std::string methodName = "testEnergyEthaneSwitchingFunction";
#if 0
CudaPlatform platform;
CudaFreeEnergyKernelFactory* factory = new CudaFreeEnergyKernelFactory();
platform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
platform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
platform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
#else
ReferencePlatform platform;
ReferenceFreeEnergyKernelFactory* referenceFactoryT = new ReferenceFreeEnergyKernelFactory();
platform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), referenceFactoryT);
platform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), referenceFactoryT);
platform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), referenceFactoryT);
#endif
ReferencePlatform referencePlatform;
ReferenceFreeEnergyKernelFactory* referenceFactory = new ReferenceFreeEnergyKernelFactory();
referencePlatform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), referenceFactory);
referencePlatform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), referenceFactory);
referencePlatform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), referenceFactory);
System system;
const int numParticles = 9;
for( int i = 0; i < numParticles; i++ ){
system.addParticle(1.0);
}
LangevinIntegrator integrator(0, 0.1, 0.01);
double C_HBondDistance = 0.1097;
double C_CBondDistance = 0.1504;
NonbondedSoftcoreForce* nonbonded = new NonbondedSoftcoreForce();
nonbonded->setNonbondedMethod(NonbondedSoftcoreForce::NoCutoff);
double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
int AM1_BCC = 1;
H_charge = -0.053;
C_charge = -3.0*H_charge;
if( AM1_BCC ){
C_radius = 0.180;
//C_radius = 0.360;
C_gamma = -0.2863;
C_gamma = 1.0;
H_radius = 0.125;
//H_radius = 0.25;
H_gamma = 0.2437;
H_gamma = 1.0;
//H_charge = C_charge = 0.0;
//H_gamma = C_gamma = 0.0;
} else {
C_radius = 0.215;
C_gamma = -1.1087;
H_radius = 0.150;
H_gamma = 0.1237;
}
// for ethane all Coulomb forces are excluded since all atoms 3 or
// fewer bonds away from all other atoms -- is this true for H's on
// difference carbons? -- should be computed in 14 ixn
int VI = 1;
if( VI ){
//double bornRadiusScaleFactorsEven = 0.5;
double bornRadiusScaleFactorsEven = 1.0;
//double bornRadiusScaleFactorsOdd = 0.5;
double bornRadiusScaleFactorsOdd = 1.0;
#if PRINT_ON == 1
(void) fprintf( stderr, "%s: Applying GB/VI\n", methodName.c_str() );
(void) fprintf( stderr, "C[%14.7e %14.7e %14.7e] H[%14.7e %14.7e %14.7e] scale[%.1f %.1f]\n",
C_charge, C_radius, C_gamma, H_charge, H_radius, H_gamma,
bornRadiusScaleFactorsEven, bornRadiusScaleFactorsOdd);
#endif
GBVISoftcoreForce* forceField = new GBVISoftcoreForce();
for( int i = 0; i < numParticles; i++ ){
forceField->addParticle( H_charge, H_radius, H_gamma, (i%2) ? bornRadiusScaleFactorsOdd : bornRadiusScaleFactorsEven);
nonbonded->addParticle( H_charge, H_radius, 0.0);
}
forceField->setParticleParameters( 1, C_charge, C_radius, C_gamma, bornRadiusScaleFactorsOdd);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
forceField->setParticleParameters( 4, C_charge, C_radius, C_gamma, bornRadiusScaleFactorsEven);
nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
forceField->setParticleParameters( 8, C_charge, (C_radius+0.5), C_gamma, bornRadiusScaleFactorsEven);
nonbonded->setParticleParameters( 8, C_charge, C_radius, 0.0);
forceField->setBornRadiusScalingMethod( GBVISoftcoreForce::NoScaling );
// forceField->setBornRadiusScalingMethod( GBVISoftcoreForce::QuinticSpline );
forceField->addBond( 0, 1, C_HBondDistance );
forceField->addBond( 2, 1, C_HBondDistance );
forceField->addBond( 3, 1, C_HBondDistance );
forceField->addBond( 1, 4, C_CBondDistance );
forceField->addBond( 5, 4, C_HBondDistance );
forceField->addBond( 6, 4, C_HBondDistance );
forceField->addBond( 7, 4, C_HBondDistance );
std::vector<pair<int, int> > bonds;
std::vector<double> bondDistances;
bonds.push_back(pair<int, int>(0, 1));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(2, 1));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(3, 1));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(1, 4));
bondDistances.push_back( C_CBondDistance );
bonds.push_back(pair<int, int>(5, 4));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(6, 4));
bondDistances.push_back( C_HBondDistance );
bonds.push_back(pair<int, int>(7, 4));
bondDistances.push_back( C_HBondDistance );
nonbonded->createExceptionsFromBonds(bonds, 0.0, 0.0);
system.addForce(forceField);
} else {
#if PRINT_ON == 1
(void) fprintf( stderr, "testEnergyEthane: Applying GBSA OBC\n" );
#endif
GBSAOBCForce* forceField = new GBSAOBCForce();
double H_scale = 0.85;
double C_scale = 0.72;
for( int i = 0; i < numParticles; i++ ){
forceField->addParticle( H_charge, H_radius, H_scale );
nonbonded->addParticle( H_charge, 1, 0);
}
forceField->setParticleParameters(1, C_charge, C_radius, C_scale);
forceField->setParticleParameters(4, C_charge, C_radius, C_scale);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
system.addForce(forceField);
}
system.addForce(nonbonded);
Context referenceContext(system, integrator, referencePlatform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
positions[0] = Vec3(0.5480, 1.7661, 0.0000);
positions[1] = Vec3(0.7286, 0.8978, 0.6468);
positions[2] = Vec3(0.4974, 0.0000, 0.0588);
positions[3] = Vec3(0.0000, 0.9459, 1.4666);
positions[4] = Vec3(2.1421, 0.8746, 1.1615);
positions[5] = Vec3(2.3239, 0.0050, 1.8065);
positions[6] = Vec3(2.8705, 0.8295, 0.3416);
positions[7] = Vec3(2.3722, 1.7711, 1.7518);
positions[8] = Vec3(2.1421, 0.8746, 2.1615);
vector<Vec3> originalPositions(numParticles);
for( int ii = 0; ii < numParticles; ii++ ){
originalPositions[ii][0] = positions[ii][0];
originalPositions[ii][1] = positions[ii][1];
originalPositions[ii][2] = positions[ii][2];
}
int tries = 7;
double positionIncrement = 0.15;
for( int ii = 0; ii < tries; ii++ ){
context.setPositions(positions);
referenceContext.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
#if PRINT_ON == 1
(void) fprintf( stderr, "cudaE=%14.7e refE=%14.7e\n", state.getPotentialEnergy(), referenceState.getPotentialEnergy() );
#endif
// Take a small step in the direction of the energy gradient.
if( compareForcesOfTwoStates( numParticles, state, referenceState, 0.001, 0.001 ) ){
ASSERT_EQUAL_TOL(0.0, 1.0, 0.01)
}
double norm = 0.0;
double forceSum[3] = { 0.0, 0.0, 0.0 };
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
forceSum[0] += f[0];
forceSum[1] += f[1];
forceSum[2] += f[2];
}
norm = std::sqrt(norm);
#if PRINT_ON == 1
(void) fprintf( stderr, "Fsum [%14.7e %14.7e %14.7e] norm=%14.7e\n", forceSum[0], forceSum[1], forceSum[2], norm );
#endif
const double delta = 1e-03;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
double diff = (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta;
double off = fabs( diff - norm )/norm;
#if PRINT_ON == 1
(void) fprintf( stderr, "%2d Energies %.8e %.8e norms[%13.7e %13.7e] deltaNorms=%13.7e delta=%.2e\n",
ii, state.getPotentialEnergy(), state2.getPotentialEnergy(), diff, norm, off, delta );
#endif
// See whether the potential energy changed by the expected amount.
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 1e-3*abs(state.getPotentialEnergy()) );
if( ii < (tries-1) ){
for( int jj = 0; jj < numParticles; jj++ ){
positions[jj][0] = originalPositions[jj][0];
positions[jj][1] = originalPositions[jj][1];
positions[jj][2] = originalPositions[jj][2];
}
positions[8][2] -= static_cast<double>(ii+1)*0.1;
positions[8][2] -= 0.001;
(void) fprintf( stderr, "r48=%14.6e r28=%14.6e r24=%14.6e\n", positions[8][2]-positions[4][2], positions[8][2], positions[4][2] );
}
#if 0
int carbonIndex = 1;
int hydrogenIndex = 0;
while( hydrogenIndex < 8 ){
Vec3 carbonDelta;
for( int kk = 0; kk < 3; kk++ ){
positions[hydrogenIndex][kk] += positionIncrement*(positions[carbonIndex][kk] - positions[hydrogenIndex][kk] );
}
double dist = 0.0;
for( int kk = 0; kk < 3; kk++ ){
dist += (positions[carbonIndex][kk] - positions[hydrogenIndex][kk] )*(positions[carbonIndex][kk] - positions[hydrogenIndex][kk]);
}
(void) fprintf( stderr, "H=%d C=%d r=%14.6e\n", hydrogenIndex, carbonIndex, dist );
hydrogenIndex++;
if( hydrogenIndex == carbonIndex ){
hydrogenIndex++;
}
if( carbonIndex == 1 && hydrogenIndex == 4 ){
carbonIndex = 4;
hydrogenIndex = 5;
}
}
#endif
}
}
void testTwoParticleEnergyEthaneSwitchingFunction() {
std::string methodName = "testTwoParticleEnergyEthaneSwitchingFunction";
#if 0
CudaPlatform platform;
CudaFreeEnergyKernelFactory* factory = new CudaFreeEnergyKernelFactory();
platform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
platform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
platform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
#else
ReferencePlatform platform;
ReferenceFreeEnergyKernelFactory* referenceFactoryT = new ReferenceFreeEnergyKernelFactory();
platform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), referenceFactoryT);
platform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), referenceFactoryT);
platform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), referenceFactoryT);
#endif
ReferencePlatform referencePlatform;
ReferenceFreeEnergyKernelFactory* referenceFactory = new ReferenceFreeEnergyKernelFactory();
referencePlatform.registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), referenceFactory);
referencePlatform.registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), referenceFactory);
referencePlatform.registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), referenceFactory);
System system;
const int numParticles = 3;
for( int i = 0; i < numParticles; i++ ){
system.addParticle(1.0);
}
LangevinIntegrator integrator(0, 0.1, 0.01);
double C_HBondDistance = 0.1097;
double C_CBondDistance = 0.1504;
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
int AM1_BCC = 1;
H_charge = -0.053;
C_charge = -3.0*H_charge;
if( AM1_BCC ){
C_radius = 0.180;
//C_radius = 0.360;
C_gamma = -0.2863;
C_gamma = 1.0;
H_radius = 0.125;
//H_radius = 0.25;
H_gamma = 0.2437;
H_gamma = 1.0;
//H_charge = C_charge = 0.0;
//H_gamma = C_gamma = 0.0;
} else {
C_radius = 0.215;
C_gamma = -1.1087;
H_radius = 0.150;
H_gamma = 0.1237;
}
// for ethane all Coulomb forces are excluded since all atoms 3 or
// fewer bonds away from all other atoms -- is this true for H's on
// difference carbons? -- should be computed in 14 ixn
int VI = 1;
if( VI ){
//double bornRadiusScaleFactorsEven = 0.5;
double bornRadiusScaleFactorsEven = 1.0;
//double bornRadiusScaleFactorsOdd = 0.5;
double bornRadiusScaleFactorsOdd = 1.0;
#if PRINT_ON == 1
(void) fprintf( stderr, "%s: Applying GB/VI\n", methodName.c_str() );
(void) fprintf( stderr, "C[%14.7e %14.7e %14.7e] H[%14.7e %14.7e %14.7e] scale[%.1f %.1f]\n",
C_charge, C_radius, C_gamma, H_charge, H_radius, H_gamma,
bornRadiusScaleFactorsEven, bornRadiusScaleFactorsOdd);
#endif
GBVISoftcoreForce* forceField = new GBVISoftcoreForce();
for( int i = 0; i < numParticles; i++ ){
forceField->addParticle( H_charge, H_radius, H_gamma, (i%2) ? bornRadiusScaleFactorsOdd : bornRadiusScaleFactorsEven);
nonbonded->addParticle( H_charge, H_radius, 0.0);
}
forceField->setParticleParameters( 0, C_charge, C_radius, C_gamma, bornRadiusScaleFactorsOdd);
nonbonded->setParticleParameters( 0, C_charge, C_radius, 0.0);
forceField->setParticleParameters( 1, C_charge, C_radius, C_gamma, bornRadiusScaleFactorsOdd);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
forceField->setParticleParameters( 2, C_charge, C_radius, C_gamma, bornRadiusScaleFactorsOdd);
nonbonded->setParticleParameters( 2, C_charge, C_radius, 0.0);
system.addForce(forceField);
} else {
#if PRINT_ON == 1
(void) fprintf( stderr, "testEnergyEthane: Applying GBSA OBC\n" );
#endif
GBSAOBCForce* forceField = new GBSAOBCForce();
double H_scale = 0.85;
double C_scale = 0.72;
for( int i = 0; i < numParticles; i++ ){
forceField->addParticle( H_charge, H_radius, H_scale );
nonbonded->addParticle( H_charge, 1, 0);
}
forceField->setParticleParameters(1, C_charge, C_radius, C_scale);
forceField->setParticleParameters(4, C_charge, C_radius, C_scale);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
system.addForce(forceField);
}
system.addForce(nonbonded);
Context referenceContext(system, integrator, referencePlatform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
positions[0] = Vec3( 0.0000, 0.0000, 0.0000);
positions[1] = Vec3( 1.0000, 0.0000, 0.0000);
positions[2] = Vec3(-1.0000, 0.0000, 0.0000);
vector<Vec3> originalPositions(numParticles);
for( int ii = 0; ii < numParticles; ii++ ){
originalPositions[ii][0] = positions[ii][0];
originalPositions[ii][1] = positions[ii][1];
originalPositions[ii][2] = positions[ii][2];
}
int tries = 11;
double positionIncrement = 0.15;
for( int ii = 0; ii < tries; ii++ ){
context.setPositions(positions);
referenceContext.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
#if PRINT_ON == 1
(void) fprintf( stderr, "cudaE=%14.7e refE=%14.7e\n", state.getPotentialEnergy(), referenceState.getPotentialEnergy() );
#endif
// Take a small step in the direction of the energy gradient.
if( compareForcesOfTwoStates( numParticles, state, referenceState, 0.001, 0.001 ) ){
ASSERT_EQUAL_TOL(0.0, 1.0, 0.01)
}
double norm = 0.0;
double forceSum[3] = { 0.0, 0.0, 0.0 };
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
forceSum[0] += f[0];
forceSum[1] += f[1];
forceSum[2] += f[2];
}
norm = std::sqrt(norm);
#if PRINT_ON == 1
(void) fprintf( stderr, "Fsum [%14.7e %14.7e %14.7e] norm=%14.7e\n", forceSum[0], forceSum[1], forceSum[2], norm );
#endif
const double delta = 1e-3;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
double diff = (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta;
double off = fabs( diff - norm );
#if PRINT_ON == 1
(void) fprintf( stderr, "X Energies %.8e %.8e norms[%14.7e %14.7e] deltaNorms=%14.7e delta=%.2e\n",
state.getPotentialEnergy(), state2.getPotentialEnergy(), diff, norm, off, delta );
#endif
// See whether the potential energy changed by the expected amount.
// ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
for( int jj = 0; jj < numParticles; jj++ ){
positions[jj][0] = originalPositions[jj][0];
positions[jj][1] = originalPositions[jj][1];
positions[jj][2] = originalPositions[jj][2];
}
positions[1][0] -= static_cast<double>(ii+1)*0.1;
positions[2][0] += static_cast<double>(ii+1)*0.1;
positions[1][0] -= 0.001;
positions[2][0] += 0.001;
(void) fprintf( stderr, "r12=%14.6e\n", positions[1][0]);
#if 0
int carbonIndex = 1;
int hydrogenIndex = 0;
while( hydrogenIndex < 8 ){
Vec3 carbonDelta;
for( int kk = 0; kk < 3; kk++ ){
positions[hydrogenIndex][kk] += positionIncrement*(positions[carbonIndex][kk] - positions[hydrogenIndex][kk] );
}
double dist = 0.0;
for( int kk = 0; kk < 3; kk++ ){
dist += (positions[carbonIndex][kk] - positions[hydrogenIndex][kk] )*(positions[carbonIndex][kk] - positions[hydrogenIndex][kk]);
}
(void) fprintf( stderr, "H=%d C=%d r=%14.6e\n", hydrogenIndex, carbonIndex, dist );
hydrogenIndex++;
if( hydrogenIndex == carbonIndex ){
hydrogenIndex++;
}
if( carbonIndex == 1 && hydrogenIndex == 4 ){
carbonIndex = 4;
hydrogenIndex = 5;
}
}
#endif
}
}
void testEnergyTwoParticle() {
CudaPlatform platform;
const int numParticles = 2;
System system;
for( int i = 0; i < numParticles; i++ ){
system.addParticle(1.0);
}
LangevinIntegrator integrator(0, 0.1, 0.01);
//void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k)
double C_HBondDistance = 3.0;
double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
/*
H_charge = -1.0;
C_charge = 1.0;
H_gamma = 1.0;
C_gamma = 1.0;
H_radius = 1.0;
C_radius = 1.0;
*/
H_charge = -0.5;
C_charge = 0.5;
H_gamma = 0.5;
C_gamma = 0.5;
H_radius = 0.15;
C_radius = 0.15;
int VI = 1;
if( VI ){
(void) fprintf( stderr, "Applying GB/VI\n" );
GBVISoftcoreForce* forceField = new GBVISoftcoreForce();
forceField->addParticle( H_charge, H_radius, H_gamma);
forceField->addParticle( C_charge, C_radius, C_gamma);
system.addForce(forceField);
} else {
(void) fprintf( stderr, "Applying GBSA OBC\n" );
GBSAOBCForce* forceField = new GBSAOBCForce();
forceField->addParticle( H_charge, H_radius, 0.8);
forceField->addParticle( C_charge, C_radius, 0.8);
system.addForce(forceField);
}
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
double charge = i%2 == 0 ? -1 : 1;
nonbonded->addParticle( charge, 1, 0);
}
nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
positions[0] = Vec3( 0.0000, 0.0000, 0.0000);
positions[1] = Vec3(C_HBondDistance, 0.0000, 0.0000);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// Take a small step in the direction of the energy gradient.
double norm = 0.0;
double forceSum[3] = { 0.0, 0.0, 0.0 };
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
#if PRINT_ON == 1
(void) fprintf( stderr, "F %d [%14.6e %14.6e %14.6e]\n", i, f[0], f[1], f[2] );
#endif
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
forceSum[0] += f[0];
forceSum[1] += f[1];
forceSum[2] += f[2];
}
norm = std::sqrt(norm);
#if PRINT_ON == 1
(void) fprintf( stderr, "Fsum [%14.6e %14.6e %14.6e] norm=%14.6e\n", forceSum[0], forceSum[1], forceSum[2], norm );
#endif
const double delta = 1e-4;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
double diff = fabs( norm - (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta );
#if PRINT_ON == 1
(void) fprintf( stderr, "Energies %14.6e %14.6e diff=%14.6e [%14.6e %14.6e]\n",
state.getPotentialEnergy(), state2.getPotentialEnergy(), diff, norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta );
#endif
// See whether the potential energy changed by the expected amount.
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
}
void testEnergyManyParticles( int numParticles ) {
CudaPlatform platform;
System system;
for( int i = 0; i < numParticles; i++ ){
system.addParticle(1.0);
}
LangevinIntegrator integrator(0, 0.1, 0.01);
//void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k)
/*
double C_HBondDistance = 3.0;
HarmonicBondForce* bonds = new HarmonicBondForce(numParticles-1);
for( int ii = 1; ii < numParticles; ii++ ){
bonds->setBondParameters(ii-1, ii-1, ii, C_HBondDistance, 0.0);
}
system.addForce(bonds);
*/
double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
/*
H_charge = -1.0;
C_charge = 1.0;
H_gamma = 1.0;
C_gamma = 1.0;
H_radius = 1.0;
C_radius = 1.0;
*/
H_charge = -0.5;
C_charge = 0.5;
H_gamma = 0.5;
C_gamma = 0.5;
H_radius = 0.15;
C_radius = 0.15;
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
int VI = 0;
if( VI ){
#if PRINT_ON == 1
(void) fprintf( stderr, "testEnergyManyParticles: Applying GB/VI\n" );
#endif
GBVISoftcoreForce* forceField = new GBVISoftcoreForce();
for( int ii = 0; ii < numParticles; ii++ ){
forceField->addParticle( H_charge, H_radius, H_gamma);
nonbonded->addParticle( H_charge, H_radius, 0.0);
}
system.addForce(forceField);
} else {
#if PRINT_ON == 1
(void) fprintf( stderr, "testEnergyManyParticles: Applying GBSA OBC\n" );
#endif
GBSAOBCForce* forceField = new GBSAOBCForce();
for( int ii = 0; ii < numParticles; ii++ ){
forceField->addParticle(H_charge, H_radius, 0.8);
nonbonded->addParticle( H_charge, H_radius, 0.0);
}
system.addForce(forceField);
}
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for( int ii = 0; ii < numParticles; ii++ ){
positions[ii] = Vec3( (double) ii, 0.0000, 0.0000);
}
context.setPositions(positions);
//State state = context.getState(State::Forces | State::Energy);
/*
// Take a small step in the direction of the energy gradient.
double norm = 0.0;
double forceSum[3] = { 0.0, 0.0, 0.0 };
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
(void) fprintf( stderr, "F %d [%14.6e %14.6e %14.6e]\n", i, f[0], f[1], f[2] );
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
forceSum[0] += f[0];
forceSum[1] += f[1];
forceSum[2] += f[2];
}
norm = std::sqrt(norm);
(void) fprintf( stderr, "Fsum [%14.6e %14.6e %14.6e] norm=%14.6e\n", forceSum[0], forceSum[1], forceSum[2], norm );
const double delta = 1e-4;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
double diff = fabs( norm - (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta );
(void) fprintf( stderr, "Energies %14.6e %14.6e diff=%14.6e [%14.6e %14.6e]\n",
state.getPotentialEnergy(), state2.getPotentialEnergy(), diff, norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta );
// See whether the potential energy changed by the expected amount.
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
*/
}
void testForce(int numParticles, NonbondedForce::NonbondedMethod method) {
CudaPlatform cuda;
ReferencePlatform reference;
System system;
LangevinIntegrator integrator(0, 0.1, 0.01);
GBVISoftcoreForce* gbsa = new GBVISoftcoreForce();
NonbondedForce* nonbonded = new NonbondedForce();
double radius = 0.15;
double gamma = 0.0;
for (int i = 0; i < numParticles; ++i) {
system.addParticle(1.0);
double charge = i%2 == 0 ? -1 : 1;
gbsa->addParticle(charge, radius, gamma);
nonbonded->addParticle(charge, 1, 0);
}
nonbonded->setNonbondedMethod(method);
nonbonded->setCutoffDistance(3.0);
int grid = (int) floor(0.5+pow(numParticles, 1.0/3.0));
if (method == NonbondedForce::CutoffPeriodic) {
double boxSize = (grid+1)*2.0;
system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
}
system.addForce(gbsa);
system.addForce(nonbonded);
Context context(system, integrator, cuda);
Context refContext(system, integrator, reference);
// Set random (but uniformly distributed) positions for all the particles.
vector<Vec3> positions(numParticles);
init_gen_rand(0);
for (int i = 0; i < grid; i++)
for (int j = 0; j < grid; j++)
for (int k = 0; k < grid; k++)
//positions[i*grid*grid+j*grid+k] = Vec3(i*2.0, j*2.0, k*2.0);
positions[i*grid*grid+j*grid+k] = Vec3(i*0.5, j*0.5, k*0.5);
for (int i = 0; i < numParticles; ++i)
positions[i] = positions[i] + Vec3(0.5*genrand_real2(), 0.5*genrand_real2(), 0.5*genrand_real2());
context.setPositions(positions);
refContext.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
State refState = refContext.getState(State::Forces | State::Energy);
// Make sure the Cuda and Reference platforms agree.
double norm = 0.0;
double diff = 0.0;
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
Vec3 delta = f-refState.getForces()[i];
Vec3 g = refState.getForces()[i];
#if PRINT_ON == 1
fprintf( stderr, "FFF %d fcud[%14.6e %14.6e %14.6e] [%14.6e %14.6e %14.6e]\n", i, f[0], f[1], f[2], g[0], g[1], g[2] );
diff += delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2];
#endif
}
norm = std::sqrt(norm);
diff = std::sqrt(diff);
#if PRINT_ON == 1
(void) fprintf( stderr, "F norm%14.6e diff w/ ref=%14.6e\n", norm, diff );
#endif
ASSERT_EQUAL_TOL(0.0, diff, 0.001*norm);
// Take a small step in the direction of the energy gradient. (This doesn't work with cutoffs, since the energy
// changes discontinuously at the cutoff distance.)
if (method == NonbondedForce::NoCutoff)
{
const double delta = 1e-2;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
// See whether the potential energy changed by the expected amount.
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 1e-3*abs(state.getPotentialEnergy()));
}
}
int main() {
try {
// testEnergyEthane();
testEnergyEthaneSwitchingFunction();
// testTwoParticleEnergyEthaneSwitchingFunction();
// testSingleParticle();
// testCutoffAndPeriodic();
// testEnergyTwoParticle();
// for (int i = 2; i < 8; i++) {
// testForce(i*i*i, NonbondedForce::NoCutoff);
// }
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
plugins/freeEnergy/platforms/reference/include/ReferenceFreeEnergyKernelFactory.h 0 → 100644
View file @ 7a36f461
#ifndef OPENMM_REFERENCE_FREE_ENERGY_KERNEL_FACTORY_H_
#define OPENMM_REFERENCE_FREE_ENERGY_KERNEL_FACTORY_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* 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. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/KernelFactory.h"
namespace OpenMM {
/**
* This KernelFactory creates all kernels for ReferencePlatform.
*/
class ReferenceFreeEnergyKernelFactory : public KernelFactory {
public:
KernelImpl* createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const;
};
} // namespace OpenMM
#endif /*OPENMM_REFERENCE_FREE_ENERGY_KERNEL_FACTORY_H_*/
plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyKernelFactory.cpp 0 → 100644
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* 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. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ReferenceFreeEnergyKernelFactory.h"
#include "ReferenceFreeEnergyKernels.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/OpenMMException.h"
// using PluginInitializer.h and initOpenMMPlugin() does not seem to work
//#include "openmm/PluginInitializer.h"
#if defined(OPENMM_BUILDING_SHARED_LIBRARY)
#if defined(WIN32)
#include <windows.h>
extern "C" void initOpenMMReferenceFreeEnergyPlugin();
BOOL WINAPI DllMain(HANDLE hModule, DWORD ul_reason_for_call, LPVOID lpReserved) {
if (ul_reason_for_call == DLL_PROCESS_ATTACH)
initOpenMMReferenceFreeEnergyPlugin();
return TRUE;
}
#else
extern "C" void __attribute__((constructor)) initOpenMMReferenceFreeEnergyPlugin();
#endif
#endif
using namespace OpenMM;
extern "C" void initOpenMMReferenceFreeEnergyPlugin() {
ReferencePlatform* referencePlatform = new ReferencePlatform();
ReferenceFreeEnergyKernelFactory* factory = new ReferenceFreeEnergyKernelFactory();
referencePlatform->registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
referencePlatform->registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
referencePlatform->registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
Platform::registerPlatform(referencePlatform);
}
KernelImpl* ReferenceFreeEnergyKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
ReferencePlatform::PlatformData& data = *static_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
if (name == CalcNonbondedSoftcoreForceKernel::Name())
return new ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel(name, platform);
if (name == CalcGBSAOBCSoftcoreForceKernel::Name())
return new ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel(name, platform);
if (name == CalcGBVISoftcoreForceKernel::Name())
return new ReferenceFreeEnergyCalcGBVISoftcoreForceKernel(name, platform);
throw OpenMMException( (std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str() );
}
plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyKernels.cpp 0 → 100644
View file @ 7a36f461
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ReferenceFreeEnergyKernels.h"
#include "gbsa/CpuGBVISoftcore.h"
#include "gbsa/CpuObcSoftcore.h"
#include "SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.h"
#include "SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.h"
#include "ReferenceBondForce.h"
#include "openmm/System.h"
#include "openmm/internal/ContextImpl.h"
#include "SimTKUtilities/SimTKOpenMMUtilities.h"
#include <cmath>
#include <limits>
using namespace OpenMM;
static int** allocateIntArray(int length, int width) {
int** array = new int*[length];
for (int i = 0; i < length; ++i)
array[i] = new int[width];
return array;
}
static RealOpenMM** allocateRealArray(int length, int width) {
RealOpenMM** array = new RealOpenMM*[length];
for (int i = 0; i < length; ++i)
array[i] = new RealOpenMM[width];
return array;
}
static int** copyToArray(const std::vector<std::vector<int> > vec) {
if (vec.size() == 0)
return new int*[0];
int** array = allocateIntArray(vec.size(), vec[0].size());
for (size_t i = 0; i < vec.size(); ++i)
for (size_t j = 0; j < vec[i].size(); ++j)
array[i][j] = vec[i][j];
return array;
}
static RealOpenMM** copyToArray(const std::vector<std::vector<double> > vec) {
if (vec.size() == 0)
return new RealOpenMM*[0];
RealOpenMM** array = allocateRealArray(vec.size(), vec[0].size());
for (size_t i = 0; i < vec.size(); ++i)
for (size_t j = 0; j < vec[i].size(); ++j)
array[i][j] = static_cast<RealOpenMM>(vec[i][j]);
return array;
}
static void disposeIntArray(int** array, int size) {
if (array) {
for (int i = 0; i < size; ++i)
delete[] array[i];
delete[] array;
}
}
static void disposeRealArray(RealOpenMM** array, int size) {
if (array) {
for (int i = 0; i < size; ++i)
delete[] array[i];
delete[] array;
}
}
static RealOpenMM** extractPositions(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealOpenMM**) data->positions;
}
static RealOpenMM** extractVelocities(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealOpenMM**) data->velocities;
}
static RealOpenMM** extractForces(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return (RealOpenMM**) data->forces;
}
ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::~ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel() {
disposeRealArray(particleParamArray, numParticles);
disposeIntArray(exclusionArray, numParticles);
disposeIntArray(bonded14IndexArray, num14);
disposeRealArray(bonded14ParamArray, num14);
if (neighborList != NULL)
delete neighborList;
}
void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const System& system, const NonbondedSoftcoreForce& force) {
// Identify which exceptions are 1-4 interactions.
numParticles = force.getNumParticles();
exclusions.resize(numParticles);
std::vector<int> nb14s;
for (int i = 0; i < force.getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon, softcoreLJLambda;
force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon, softcoreLJLambda);
exclusions[particle1].insert(particle2);
exclusions[particle2].insert(particle1);
if (chargeProd != 0.0 || epsilon != 0.0)
nb14s.push_back(i);
}
// Build the arrays.
particleParamArray = allocateRealArray(numParticles, 4);
RealOpenMM sqrtEps = static_cast<RealOpenMM>( std::sqrt(138.935485) );
for (int i = 0; i < numParticles; ++i) {
double charge, radius, depth, softcoreLJLambda;
force.getParticleParameters(i, charge, radius, depth,softcoreLJLambda);
particleParamArray[i][0] = static_cast<RealOpenMM>(0.5*radius);
particleParamArray[i][1] = static_cast<RealOpenMM>(2.0*sqrt(depth));
particleParamArray[i][2] = static_cast<RealOpenMM>(charge*sqrtEps);
particleParamArray[i][3] = static_cast<RealOpenMM>(softcoreLJLambda);
}
this->exclusions = exclusions;
exclusionArray = new int*[numParticles];
for (int i = 0; i < numParticles; ++i) {
exclusionArray[i] = new int[exclusions[i].size()+1];
exclusionArray[i][0] = exclusions[i].size();
int index = 0;
for (std::set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
exclusionArray[i][++index] = *iter;
}
num14 = nb14s.size();
bonded14IndexArray = allocateIntArray(num14, 2);
bonded14ParamArray = allocateRealArray(num14, 4);
for (int i = 0; i < num14; ++i) {
int particle1, particle2;
double charge, radius, depth, softcoreLJLambda;
force.getExceptionParameters(nb14s[i], particle1, particle2, charge, radius, depth, softcoreLJLambda);
bonded14IndexArray[i][0] = particle1;
bonded14IndexArray[i][1] = particle2;
bonded14ParamArray[i][0] = static_cast<RealOpenMM>(radius);
bonded14ParamArray[i][1] = static_cast<RealOpenMM>(4.0*depth);
bonded14ParamArray[i][2] = static_cast<RealOpenMM>(charge*sqrtEps*sqrtEps);
bonded14ParamArray[i][3] = static_cast<RealOpenMM>(softcoreLJLambda);
}
nonbondedMethod = CalcNonbondedSoftcoreForceKernel::NonbondedSoftcoreMethod(force.getNonbondedMethod());
nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
//softCoreLJLambda = (RealOpenMM) force.getSoftCoreLJLambda();
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
if (nonbondedMethod == NoCutoff)
neighborList = NULL;
else
neighborList = new NeighborList();
#if 0
if (nonbondedMethod == Ewald || nonbondedMethod == PME) {
RealOpenMM ewaldErrorTol = (RealOpenMM) force.getEwaldErrorTolerance();
ewaldAlpha = (RealOpenMM) (std::sqrt(-std::log(ewaldErrorTol))/nonbondedCutoff);
RealOpenMM mx = periodicBoxSize[0]/nonbondedCutoff;
RealOpenMM my = periodicBoxSize[1]/nonbondedCutoff;
RealOpenMM mz = periodicBoxSize[2]/nonbondedCutoff;
RealOpenMM pi = (RealOpenMM) 3.1415926535897932385;
kmax[0] = (int)std::ceil(-(mx/pi)*std::log(ewaldErrorTol));
kmax[1] = (int)std::ceil(-(my/pi)*std::log(ewaldErrorTol));
kmax[2] = (int)std::ceil(-(mz/pi)*std::log(ewaldErrorTol));
if (kmax[0]%2 == 0)
kmax[0]++;
if (kmax[1]%2 == 0)
kmax[1]++;
if (kmax[2]%2 == 0)
kmax[2]++;
}
if (nonbondedMethod == Ewald || nonbondedMethod == PME) {
RealOpenMM ewaldErrorTol = (RealOpenMM) force.getEwaldErrorTolerance();
ewaldAlpha = (RealOpenMM) (std::sqrt(-std::log(ewaldErrorTol))/nonbondedCutoff);
RealOpenMM mx = periodicBoxSize[0]/nonbondedCutoff;
RealOpenMM my = periodicBoxSize[1]/nonbondedCutoff;
RealOpenMM mz = periodicBoxSize[2]/nonbondedCutoff;
RealOpenMM pi = (RealOpenMM) 3.1415926535897932385;
kmax[0] = (int)std::ceil(-(mx/pi)*std::log(ewaldErrorTol));
kmax[1] = (int)std::ceil(-(my/pi)*std::log(ewaldErrorTol));
kmax[2] = (int)std::ceil(-(mz/pi)*std::log(ewaldErrorTol));
if (kmax[0]%2 == 0)
kmax[0]++;
if (kmax[1]%2 == 0)
kmax[1]++;
if (kmax[2]%2 == 0)
kmax[2]++;
}
#endif
rfDielectric = (RealOpenMM)force.getReactionFieldDielectric();
}
void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
ReferenceFreeEnergyLJCoulombSoftcoreIxn clj;
//clj.setSoftCoreLJLambda( softCoreLJLambda );
bool periodic = (nonbondedMethod == CutoffPeriodic);
bool ewald = (nonbondedMethod == Ewald);
bool pme = (nonbondedMethod == PME);
if (nonbondedMethod != NoCutoff) {
computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, (periodic || ewald || pme) ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
clj.setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
}
if (periodic||ewald||pme)
clj.setPeriodic(periodicBoxSize);
if (ewald)
clj.setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
if (pme)
clj.setUsePME(ewaldAlpha);
clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, 0);
ReferenceBondForce refBondForce;
ReferenceFreeEnergyLJCoulomb14Softcore nonbonded14;
if (nonbondedMethod == CutoffNonPeriodic || nonbondedMethod == CutoffPeriodic)
nonbonded14.setUseCutoff(nonbondedCutoff, rfDielectric);
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, 0, 0, nonbonded14);
}
double ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = allocateRealArray(numParticles, 3);
RealOpenMM energy = 0;
ReferenceFreeEnergyLJCoulombSoftcoreIxn clj;
// clj.setSoftCoreLJLambda( softCoreLJLambda );
bool periodic = (nonbondedMethod == CutoffPeriodic);
bool ewald = (nonbondedMethod == Ewald);
bool pme = (nonbondedMethod == PME);
if (nonbondedMethod != NoCutoff) {
computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, (periodic || ewald || pme) ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
clj.setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
}
if (periodic || ewald || pme)
clj.setPeriodic(periodicBoxSize);
if (ewald)
clj.setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
if (pme)
clj.setUsePME(ewaldAlpha);
clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, &energy);
ReferenceBondForce refBondForce;
ReferenceFreeEnergyLJCoulomb14Softcore nonbonded14;
if (nonbondedMethod == CutoffNonPeriodic || nonbondedMethod == CutoffPeriodic)
nonbonded14.setUseCutoff(nonbondedCutoff, rfDielectric);
RealOpenMM* energyArray = new RealOpenMM[num14];
for (int i = 0; i < num14; ++i)
energyArray[i] = 0;
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, energyArray, 0, &energy, nonbonded14);
disposeRealArray(forceData, numParticles);
delete[] energyArray;
return energy;
}
ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::~ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel() {
if (obc) {
delete obc;
}
}
void ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::initialize(const System& system, const GBSAOBCSoftcoreForce& force) {
int numParticles = system.getNumParticles();
charges.resize(numParticles);
std::vector<RealOpenMM> atomicRadii(numParticles);
std::vector<RealOpenMM> scaleFactors(numParticles);
std::vector<RealOpenMM> nonPolarScaleFactors(numParticles);
for (int i = 0; i < numParticles; ++i) {
double charge, radius, scalingFactor, nonPolarScaleFactor;
force.getParticleParameters(i, charge, radius, scalingFactor, nonPolarScaleFactor);
charges[i] = static_cast<RealOpenMM>(charge);
atomicRadii[i] = static_cast<RealOpenMM>(radius);
scaleFactors[i] = static_cast<RealOpenMM>(scalingFactor);
nonPolarScaleFactors[i] = static_cast<RealOpenMM>(nonPolarScaleFactor);
}
ObcSoftcoreParameters* obcParameters = new ObcSoftcoreParameters(numParticles, ObcSoftcoreParameters::ObcTypeII);
obcParameters->setAtomicRadii(atomicRadii);
obcParameters->setScaledRadiusFactors(scaleFactors);
obcParameters->setNonPolarScaleFactors(nonPolarScaleFactors);
obcParameters->setSolventDielectric( static_cast<RealOpenMM>(force.getSolventDielectric()) );
obcParameters->setSoluteDielectric( static_cast<RealOpenMM>(force.getSoluteDielectric()) );
obcParameters->setNonPolarPrefactor( static_cast<RealOpenMM>(force.getNonPolarPrefactor()) );
// If there is a NonbondedForce in this system, use it to initialize cutoffs and periodic boundary conditions.
for (int i = 0; i < system.getNumForces(); i++) {
const NonbondedForce* nonbonded = dynamic_cast<const NonbondedForce*>(&system.getForce(i));
if (nonbonded != NULL) {
if (nonbonded->getNonbondedMethod() != NonbondedForce::NoCutoff)
obcParameters->setUseCutoff(static_cast<RealOpenMM>(nonbonded->getCutoffDistance()));
if (nonbonded->getNonbondedMethod() == NonbondedForce::CutoffPeriodic) {
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
RealOpenMM periodicBoxSize[3];
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
obcParameters->setPeriodic(periodicBoxSize);
}
break;
}
}
obc = new CpuObcSoftcore(obcParameters);
obc->setIncludeAceApproximation(true);
}
void ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
}
double ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
return obc->getEnergy();
}
ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::~ReferenceFreeEnergyCalcGBVISoftcoreForceKernel() {
if (gbviSoftcore) {
delete gbviSoftcore;
}
}
void ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::initialize(const System& system, const GBVISoftcoreForce& force, const std::vector<double> & inputScaledRadii ) {
int numParticles = system.getNumParticles();
charges.resize(numParticles);
std::vector<RealOpenMM> atomicRadii(numParticles);
std::vector<RealOpenMM> scaledRadii(numParticles);
std::vector<RealOpenMM> gammas(numParticles);
std::vector<RealOpenMM> bornRadiusScaleFactors(numParticles);
for (int i = 0; i < numParticles; ++i) {
double charge, radius, gamma, bornRadiusScaleFactor;
force.getParticleParameters(i, charge, radius, gamma, bornRadiusScaleFactor);
charges[i] = static_cast<RealOpenMM>(charge);
atomicRadii[i] = static_cast<RealOpenMM>(radius);
gammas[i] = static_cast<RealOpenMM>(gamma);
scaledRadii[i] = static_cast<RealOpenMM>(inputScaledRadii[i]);
bornRadiusScaleFactors[i] = static_cast<RealOpenMM>(bornRadiusScaleFactor);
}
GBVISoftcoreParameters* gBVIParameters = new GBVISoftcoreParameters(numParticles);
gBVIParameters->setAtomicRadii(atomicRadii);
gBVIParameters->setGammaParameters(gammas);
gBVIParameters->setBornRadiusScaleFactors(bornRadiusScaleFactors);
gBVIParameters->setScaledRadii(scaledRadii);
// switching function/scaling
// quintic spline
if( force.getBornRadiusScalingMethod() == GBVISoftcoreForce::QuinticSpline ){
gBVIParameters->setBornRadiusScalingSoftcoreMethod( GBVISoftcoreParameters::QuinticSpline );
gBVIParameters->setQuinticLowerLimitFactor( static_cast<RealOpenMM>(force.getQuinticLowerLimitFactor()) );
gBVIParameters->setQuinticUpperBornRadiusLimit( static_cast<RealOpenMM>(force.getQuinticUpperBornRadiusLimit()) );
}
gBVIParameters->setSolventDielectric( static_cast<RealOpenMM>(force.getSolventDielectric()) );
gBVIParameters->setSoluteDielectric( static_cast<RealOpenMM>(force.getSoluteDielectric()) );
if (force.getNonbondedMethod() != GBVISoftcoreForce::NoCutoff)
gBVIParameters->setUseCutoff(static_cast<RealOpenMM>(force.getCutoffDistance()));
if (force.getNonbondedMethod() == GBVISoftcoreForce::CutoffPeriodic) {
Vec3 boxVectors[3];
system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
RealOpenMM periodicBoxSize[3];
periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
gBVIParameters->setPeriodic(periodicBoxSize);
}
gbviSoftcore = new CpuGBVISoftcore(gBVIParameters);
}
void ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
RealOpenMM* bornRadii = new RealOpenMM[context.getSystem().getNumParticles()];
gbviSoftcore->computeBornRadii(posData, bornRadii, NULL );
gbviSoftcore->computeBornForces(bornRadii, posData, &charges[0], forceData);
delete[] bornRadii;
}
double ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM* bornRadii = new RealOpenMM[context.getSystem().getNumParticles()];
gbviSoftcore->computeBornRadii(posData, bornRadii, NULL );
RealOpenMM energy = gbviSoftcore->computeBornEnergy(bornRadii ,posData, &charges[0]);
delete[] bornRadii;
return static_cast<double>(energy);
}
plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyKernels.h 0 → 100644
View file @ 7a36f461
#ifndef OPENMM_REFERENCE_FREE_ENERGY_KERNELS_H_
#define OPENMM_REFERENCE_FREE_ENERGY_KERNELS_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* 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. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ReferencePlatform.h"
#include "openmm/freeEnergyKernels.h"
#include "SimTKUtilities/SimTKOpenMMRealType.h"
#include "SimTKReference/ReferenceNeighborList.h"
#include "gbsa/CpuGBVISoftcore.h"
#include "gbsa/CpuObcSoftcore.h"
namespace OpenMM {
/**
* This kernel is invoked by NonbondedSoftcoreForce to calculate the forces acting on the system.
*/
class ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel : public CalcNonbondedSoftcoreForceKernel {
public:
ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel(std::string name, const Platform& platform) : CalcNonbondedSoftcoreForceKernel(name, platform) {
}
~ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the NonbondedSoftcoreForce this kernel will be used for
*/
void initialize(const System& system, const NonbondedSoftcoreForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the NonbondedSoftcoreForce
*/
double executeEnergy(ContextImpl& context);
private:
int numParticles, num14;
int **exclusionArray, **bonded14IndexArray;
RealOpenMM **particleParamArray, **bonded14ParamArray;
RealOpenMM nonbondedCutoff, periodicBoxSize[3], rfDielectric, ewaldAlpha;
int kmax[3];
std::vector<std::set<int> > exclusions;
NonbondedSoftcoreMethod nonbondedMethod;
NeighborList* neighborList;
};
/**
* This kernel is invoked by GBSAOBCForce to calculate the forces acting on the system.
*/
class ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel : public CalcGBSAOBCSoftcoreForceKernel {
public:
ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel(std::string name, const Platform& platform) : CalcGBSAOBCSoftcoreForceKernel(name, platform) {
}
~ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the GBSAOBCSoftcoreForce this kernel will be used for
*/
void initialize(const System& system, const GBSAOBCSoftcoreForce& force);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBSAOBCSoftcoreForce
*/
double executeEnergy(ContextImpl& context);
private:
CpuObcSoftcore* obc;
std::vector<RealOpenMM> charges;
};
/**
* This kernel is invoked by GBVISoftcoreForce to calculate the forces acting on the system.
*/
class ReferenceFreeEnergyCalcGBVISoftcoreForceKernel : public CalcGBVISoftcoreForceKernel {
public:
ReferenceFreeEnergyCalcGBVISoftcoreForceKernel(std::string name, const Platform& platform) : CalcGBVISoftcoreForceKernel(name, platform) {
}
~ReferenceFreeEnergyCalcGBVISoftcoreForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the GBVISoftcoreForce this kernel will be used for
* @param scaled radii the scaled radii (Eq. 5 of Labute paper)
*/
void initialize(const System& system, const GBVISoftcoreForce& force, const std::vector<double> & scaledRadii);
/**
* Execute the kernel to calculate the forces.
*
* @param context the context in which to execute this kernel
*/
void executeForces(ContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBVISoftcoreForce
*/
double executeEnergy(ContextImpl& context);
private:
CpuGBVISoftcore* gbviSoftcore;
std::vector<RealOpenMM> charges;
};
} // namespace OpenMM
#endif /*OPENMM_REFERENCE_FREE_ENERGY_KERNELS_H_*/
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.cpp 0 → 100644
View file @ 7a36f461
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include <string.h>
#include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "ReferenceFreeEnergyLJCoulomb14Softcore.h"
#include "ReferenceForce.h"
/**---------------------------------------------------------------------------------------
ReferenceFreeEnergyLJCoulomb14Softcore constructor
--------------------------------------------------------------------------------------- */
ReferenceFreeEnergyLJCoulomb14Softcore::ReferenceFreeEnergyLJCoulomb14Softcore( ) : cutoff(false) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceFreeEnergyLJCoulomb14Softcore::ReferenceFreeEnergyLJCoulomb14Softcore";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
ReferenceFreeEnergyLJCoulomb14Softcore destructor
--------------------------------------------------------------------------------------- */
ReferenceFreeEnergyLJCoulomb14Softcore::~ReferenceFreeEnergyLJCoulomb14Softcore( ){
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceFreeEnergyLJCoulomb14Softcore::~ReferenceFreeEnergyLJCoulomb14Softcore";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
@param solventDielectric the dielectric constant of the bulk solvent
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulomb14Softcore::setUseCutoff( RealOpenMM distance, RealOpenMM solventDielectric ) {
cutoff = true;
cutoffDistance = distance;
krf = pow(cutoffDistance, -3.0f)*(solventDielectric-1.0f)/(2.0f*solventDielectric+1.0f);
crf = (1.0f/cutoffDistance)*(3.0f*solventDielectric)/(2.0f*solventDielectric+1.0f);
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate parameters for LJ 1-4 ixn
@param c6 c6
@param c12 c12
@param q1 q1 charge atom 1
@param q2 q2 charge atom 2
@param epsfac epsfac ????????????
@param parameters output parameters:
parameter[0]= c6*c6/c12
parameter[1]= (c12/c6)**1/6
parameter[2]= epsfactor*q1*q2
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulomb14Softcore::getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1,
RealOpenMM q2, RealOpenMM epsfac,
RealOpenMM* parameters ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceFreeEnergyLJCoulomb14Softcore::getDerivedParameters";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM six = 6.0;
static const RealOpenMM oneSixth = one/six;
// ---------------------------------------------------------------------------------------
if( c12 <= zero ){
parameters[0] = one;
parameters[1] = zero;
} else {
parameters[0] = (c6*c6)/c12;
parameters[1] = POW( (c12/c6), oneSixth );
}
parameters[2] = epsfac*q1*q2;
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate LJ 1-4 ixn
@param atomIndices atom indices of 4 atoms in bond
@param atomCoordinates atom coordinates
@param parameters three parameters:
parameters[0]= (c12/c6)**1/6 (sigma)
parameters[1]= c6*c6/c12 (4*epsilon)
parameters[2]= epsfac*q1*q2
@param forces force array (forces added to current values)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energiesByBond,
RealOpenMM* energiesByAtom ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn";
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn";
// constants -- reduce Visual Studio warnings regarding conversions between float & double
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM two = 2.0;
static const RealOpenMM three = 3.0;
static const RealOpenMM six = 6.0;
static const RealOpenMM twelve = 12.0;
static const RealOpenMM oneM = -1.0;
static const int threeI = 3;
// number of parameters
static const int numberOfParameters = 3;
// debug flag
static const int debug = 0;
static const int LastAtomIndex = 2;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
// ---------------------------------------------------------------------------------------
// get deltaR, R2, and R between 2 atoms
int atomAIndex = atomIndices[0];
int atomBIndex = atomIndices[1];
ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0] );
if (cutoff && deltaR[0][ReferenceForce::RIndex] > cutoffDistance)
return ReferenceForce::DefaultReturn;
RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM sig = parameters[0];
RealOpenMM eps = parameters[1];
RealOpenMM minSoftCoreLJLambda = parameters[3];
RealOpenMM energy = zero;
RealOpenMM dEdR = zero;
if( minSoftCoreLJLambda < one ){
calculateOneSoftCoreLJ14Ixn( deltaR[0][ReferenceForce::RIndex], sig, eps, minSoftCoreLJLambda, &dEdR, &energy );
} else {
calculateOneLJ14Ixn( inverseR, sig, eps, &dEdR, &energy );
}
if (cutoff)
dEdR += parameters[2]*(inverseR-2.0f*krf*r2);
else
dEdR += parameters[2]*inverseR;
dEdR *= inverseR*inverseR;
// accumulate forces
for( int ii = 0; ii < 3; ii++ ){
RealOpenMM force = dEdR*deltaR[0][ii];
forces[atomAIndex][ii] += force;
forces[atomBIndex][ii] -= force;
}
if (cutoff)
energy += parameters[2]*(inverseR+krf*r2-crf);
else
energy += parameters[2]*inverseR;
// accumulate energies
updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
// debug
if( debug ){
static bool printHeader = false;
std::stringstream message;
message << methodName;
message << std::endl;
if( !printHeader ){
printHeader = true;
message << std::endl;
message << methodName.c_str() << " a0 k [c q p s] r1 r2 angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
}
message << std::endl;
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " Atm " << atomIndices[ii] << " [" << atomCoordinates[atomIndices[ii]][0] << " " << atomCoordinates[atomIndices[ii]][1] << "] ";
}
message << std::endl << " Delta:";
for( int ii = 0; ii < (LastAtomIndex - 1); ii++ ){
message << " [";
for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
message << deltaR[ii][jj] << " ";
}
message << "]";
}
message << std::endl;
message << " p1=" << parameters[0];
message << " p2=" << parameters[1];
message << " p3=" << parameters[2];
message << std::endl << " ";
message << " dEdR=" << dEdR;
message << " E=" << energy << " force factors: ";
message << "F=compute force; f=cumulative force";
message << std::endl << " ";
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " F" << (ii+1) << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, deltaR[0], threeI, dEdR );
message << "]";
}
message << std::endl << " ";
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " f" << (ii+1) << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, forces[atomIndices[ii]], threeI );
message << "]";
}
SimTKOpenMMLog::printMessage( message );
}
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate LJ pair ixn between two atoms
@param inverseR 1/r
@param sig sigma
@param eps epsilon
@param dEdR output force factor
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulomb14Softcore::calculateOneLJ14Ixn( RealOpenMM inverseR, RealOpenMM sig, RealOpenMM eps,
RealOpenMM* dEdR, RealOpenMM* energy ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "\nReferenceLJ14CoulombIxn::calculateOneLJIxn";
// ---------------------------------------------------------------------------------------
// constants -- reduce Visual Studio warnings regarding conversions between float & double
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM six = 6.0;
static const RealOpenMM twelve = 12.0;
RealOpenMM sig2 = inverseR*sig;
sig2 *= sig2;
RealOpenMM sig6 = sig2*sig2*sig2;
*dEdR = eps*( twelve*sig6 - six )*sig6;
*energy += eps*(sig6-one)*sig6;
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate softcore LJ pair ixn between two atoms
@param r r
@param sig sigma
@param eps epsilon
@param lambda lambda
@param dEdR output force factor
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulomb14Softcore::calculateOneSoftCoreLJ14Ixn( RealOpenMM r, RealOpenMM sig, RealOpenMM eps,
RealOpenMM lambda,
RealOpenMM* dEdR, RealOpenMM* energy ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "\nReferenceFreeEnergyLJCoulomb14Softcore::calculateOneSoftCoreLJ14Ixn";
// ---------------------------------------------------------------------------------------
// constants -- reduce Visual Studio warnings regarding conversions between float & double
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM six = 6.0;
static const RealOpenMM twelve = 12.0;
static const RealOpenMM alphaLJ = 0.5;
#if 0
RealOpenMM dEdROrig = 0.0;
RealOpenMM E_Orig = 0.0;
static int maxPrint = 0;
calculateOneLJIxn( one/r, sig, eps, &dEdROrig, &E_Orig );
#endif
// soft-core LJ energy = lambda*4*eps*[ 1/{alphaLJ*(1-lambda) + (r/sig)**6}**2 - 1/{alphaLJ*(1-lambda) + (r/sig)**6} ]
eps *= lambda;
RealOpenMM sig2 = r/sig;
sig2 *= sig2;
RealOpenMM sig6 = sig2*sig2*sig2;
RealOpenMM softcoreLJTerm = alphaLJ*(one - lambda) + sig6;
RealOpenMM softcoreLJInv = one/softcoreLJTerm;
RealOpenMM softcoreLJInv2 = softcoreLJInv*softcoreLJInv;
*dEdR = eps*softcoreLJInv2*( twelve*softcoreLJInv - six )*sig6;
*energy += eps*softcoreLJInv*( softcoreLJInv - one );
#if 0
if( maxPrint++ < 5 ){
printf( "r=%14.6e sig=%14.6e eps=%14.6e lambda=%14.6e de[%14.6e %14.6e] e[%14.6e %14.6e] %14.6e %14.6e\n",
r, sig, eps/lambda, lambda, dEdROrig, *dEdR, E_Orig, *energy, softcoreLJInv, sig6 );
}
#endif
return ReferenceForce::DefaultReturn;
}
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.h 0 → 100644
View file @ 7a36f461
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __ReferenceFreeEnergyLJCoulomb14Softcore_H__
#define __ReferenceFreeEnergyLJCoulomb14Softcore_H__
#include "SimTKReference/ReferenceBondIxn.h"
// ---------------------------------------------------------------------------------------
class ReferenceFreeEnergyLJCoulomb14Softcore : public ReferenceBondIxn {
private:
bool cutoff;
RealOpenMM cutoffDistance;
RealOpenMM krf, crf;
public:
/**---------------------------------------------------------------------------------------
Constructor
--------------------------------------------------------------------------------------- */
ReferenceFreeEnergyLJCoulomb14Softcore( );
/**---------------------------------------------------------------------------------------
Destructor
--------------------------------------------------------------------------------------- */
~ReferenceFreeEnergyLJCoulomb14Softcore( );
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
@param solventDielectric the dielectric constant of the bulk solvent
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int setUseCutoff( RealOpenMM distance, RealOpenMM solventDielectric );
/**---------------------------------------------------------------------------------------
Calculate parameters for LJ 1-4 ixn
@param c6 c6
@param c12 c12
@param q1 q1 charge atom 1
@param q2 q2 charge atom 2
@param epsfac epsfac ????????????
@param parameters output parameters:
parameter[0]= c6*c6/c12
parameter[1]= (c12/c6)**1/6
parameter[2]= epsfactor*q1*q2
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1,
RealOpenMM q2, RealOpenMM epsfac,
RealOpenMM* parameters ) const;
/**---------------------------------------------------------------------------------------
Calculate Ryckaert-Bellemans bond ixn
@param atomIndices atom indices of 4 atoms in bond
@param atomCoordinates atom coordinates
@param parameters six RB parameters
@param forces force array (forces added to current values)
@param energiesByBond energies by bond: energiesByBond[bondIndex]
@param energiesByAtom energies by atom: energiesByAtom[atomIndex]
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
RealOpenMM* parameters, RealOpenMM** forces,
RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
/**---------------------------------------------------------------------------------------
Calculate LJ pair ixn between two atoms
@param inverseR 1/r
@param sig sigma
@param eps epsilon
@param dEdR output force factor
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int calculateOneLJ14Ixn( RealOpenMM inverseR, RealOpenMM sig, RealOpenMM eps,
RealOpenMM* dEdR, RealOpenMM* energy ) const;
/**---------------------------------------------------------------------------------------
Calculate softcore LJ pair ixn between two atoms
@param r r
@param sig sigma
@param eps epsilon
@param lambda lambda
@param dEdR output force factor
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int calculateOneSoftCoreLJ14Ixn( RealOpenMM r, RealOpenMM sig, RealOpenMM eps,
RealOpenMM lambda, RealOpenMM* dEdR, RealOpenMM* energy ) const;
};
// ---------------------------------------------------------------------------------------
#endif // __ReferenceFreeEnergyLJCoulomb14Softcore_H__
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.cpp 0 → 100644
View file @ 7a36f461
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include <string.h>
#include <sstream>
#include <complex>
#include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "ReferenceFreeEnergyLJCoulombSoftcoreIxn.h"
#include "ReferenceForce.h"
#include "PME.h"
// In case we're using some primitive version of Visual Studio this will
// make sure that erf() and erfc() are defined.
//#include "MSVC_erfc.h"
using std::vector;
/**---------------------------------------------------------------------------------------
ReferenceFreeEnergyLJCoulombSoftcoreIxn constructor
--------------------------------------------------------------------------------------- */
ReferenceFreeEnergyLJCoulombSoftcoreIxn::ReferenceFreeEnergyLJCoulombSoftcoreIxn( ) : cutoff(false), periodic(false), ewald(false), pme(false), softCoreLJLambda(1.0) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceFreeEnergyLJCoulombSoftcoreIxn::ReferenceFreeEnergyLJCoulombSoftcoreIxn";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
ReferenceFreeEnergyLJCoulombSoftcoreIxn destructor
--------------------------------------------------------------------------------------- */
ReferenceFreeEnergyLJCoulombSoftcoreIxn::~ReferenceFreeEnergyLJCoulombSoftcoreIxn( ){
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceFreeEnergyLJCoulombSoftcoreIxn::~ReferenceFreeEnergyLJCoulombSoftcoreIxn";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
@param neighbors the neighbor list to use
@param solventDielectric the dielectric constant of the bulk solvent
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulombSoftcoreIxn::setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors, RealOpenMM solventDielectric ) {
cutoff = true;
cutoffDistance = distance;
neighborList = &neighbors;
krf = pow(cutoffDistance, -3.0f)*(solventDielectric-1.0f)/(2.0f*solventDielectric+1.0f);
crf = (1.0f/cutoffDistance)*(3.0f*solventDielectric)/(2.0f*solventDielectric+1.0f);
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
also been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulombSoftcoreIxn::setPeriodic( RealOpenMM* boxSize ) {
assert(cutoff);
assert(boxSize[0] >= 2.0*cutoffDistance);
assert(boxSize[1] >= 2.0*cutoffDistance);
assert(boxSize[2] >= 2.0*cutoffDistance);
periodic = true;
periodicBoxSize[0] = boxSize[0];
periodicBoxSize[1] = boxSize[1];
periodicBoxSize[2] = boxSize[2];
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Set the force to use Ewald summation.
@param alpha the Ewald separation parameter
@param kmaxx the largest wave vector in the x direction
@param kmaxy the largest wave vector in the y direction
@param kmaxz the largest wave vector in the z direction
--------------------------------------------------------------------------------------- */
void ReferenceFreeEnergyLJCoulombSoftcoreIxn::setUseEwald(RealOpenMM alpha, int kmaxx, int kmaxy, int kmaxz) {
alphaEwald = alpha;
numRx = kmaxx;
numRy = kmaxy;
numRz = kmaxz;
ewald = true;
}
/**---------------------------------------------------------------------------------------
Set the force to use Particle-Mesh Ewald (PME) summation.
@param alpha the Ewald separation parameter
--------------------------------------------------------------------------------------- */
void ReferenceFreeEnergyLJCoulombSoftcoreIxn::setUsePME(RealOpenMM alpha) {
alphaEwald = alpha;
pme = true;
}
/**---------------------------------------------------------------------------------------
Set the soft core LJ lambda
@param lambda the soft core LJ lambda
--------------------------------------------------------------------------------------- */
void ReferenceFreeEnergyLJCoulombSoftcoreIxn::setSoftCoreLJLambda(RealOpenMM lambda) {
softCoreLJLambda = lambda;
}
/**---------------------------------------------------------------------------------------
Calculate parameters for LJ Coulomb ixn
@param c6 c6
@param c12 c12
@param q1 q1 charge atom 1
@param epsfac epsfacSqrt ????????????
@param parameters output parameters:
parameter[SigIndex] = 0.5*( (c12/c6)**1/6 ) (sigma/2)
parameter[EpsIndex] = sqrt(c6*c6/c12) (2*sqrt(epsilon))
parameter[QIndex] = epsfactorSqrt*q1
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulombSoftcoreIxn::getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1,
RealOpenMM epsfacSqrt,
RealOpenMM* parameters ) const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceFreeEnergyLJCoulombSoftcoreIxn::getDerivedParameters";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM six = 6.0;
static const RealOpenMM half = 0.5;
static const RealOpenMM oneSixth = one/six;
static const RealOpenMM oneTweleth = half*oneSixth;
// ---------------------------------------------------------------------------------------
if( c12 <= 0.0 ){
parameters[EpsIndex] = zero;
parameters[SigIndex] = half;
} else {
parameters[EpsIndex] = c6*SQRT( one/c12 );
parameters[SigIndex] = POW( (c12/c6), oneSixth );
parameters[SigIndex] *= half;
}
parameters[QIndex] = epsfacSqrt*q1;
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate Ewald ixn
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, RealOpenMM** forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const {
#include "../SimTKUtilities/RealTypeSimTk.h"
typedef std::complex<RealOpenMM> d_complex;
static const RealOpenMM epsilon = 1.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM six = 6.0;
static const RealOpenMM twelve = 12.0;
int kmax = (ewald ? std::max(numRx, std::max(numRy,numRz)) : 0);
RealOpenMM factorEwald = -1 / (4*alphaEwald*alphaEwald);
RealOpenMM SQRT_PI = sqrt(PI);
RealOpenMM TWO_PI = 2.0 * PI;
RealOpenMM recipCoeff = (RealOpenMM)(4*PI/(periodicBoxSize[0] * periodicBoxSize[1] * periodicBoxSize[2]) /epsilon);
RealOpenMM totalSelfEwaldEnergy = 0.0;
RealOpenMM realSpaceEwaldEnergy = 0.0;
RealOpenMM recipEnergy = 0.0;
RealOpenMM totalRecipEnergy = 0.0;
RealOpenMM vdwEnergy = 0.0;
// **************************************************************************************
// SELF ENERGY
// **************************************************************************************
for( int atomID = 0; atomID < numberOfAtoms; atomID++ ){
RealOpenMM selfEwaldEnergy = atomParameters[atomID][QIndex]*atomParameters[atomID][QIndex] * alphaEwald/SQRT_PI;
totalSelfEwaldEnergy -= selfEwaldEnergy;
if( energyByAtom ){
energyByAtom[atomID] -= selfEwaldEnergy;
}
}
if( totalEnergy ){
*totalEnergy += totalSelfEwaldEnergy;
}
// **************************************************************************************
// RECIPROCAL SPACE EWALD ENERGY AND FORCES
// **************************************************************************************
// PME
if (pme) {
pme_t pmedata; /* abstract handle for PME data */
int ngrid[3];
RealOpenMM virial[3][3];
/* PME grid dimensions.
* We typically want to set this as the spacing rather than absolute dimensions, but
* to be able to reproduce results from other programs (e.g. Gromacs) we need to be
* able to set exact grid dimenisions occasionally.
*/
ngrid[0] = 16;
ngrid[1] = 16;
ngrid[2] = 16;
pme_init(&pmedata,alphaEwald,numberOfAtoms,ngrid,4,1);
pme_exec(pmedata,atomCoordinates,forces,atomParameters,periodicBoxSize,&recipEnergy,virial);
if( totalEnergy )
*totalEnergy += recipEnergy;
if( energyByAtom )
for(int n = 0; n < numberOfAtoms; n++)
energyByAtom[n] += recipEnergy;
pme_destroy(pmedata);
}
// Ewald method
else if (ewald) {
// setup reciprocal box
RealOpenMM recipBoxSize[3] = { TWO_PI / periodicBoxSize[0], TWO_PI / periodicBoxSize[1], TWO_PI / periodicBoxSize[2]};
// setup K-vectors
#define EIR(x, y, z) eir[(x)*numberOfAtoms*3+(y)*3+z]
vector<d_complex> eir(kmax*numberOfAtoms*3);
vector<d_complex> tab_xy(numberOfAtoms);
vector<d_complex> tab_qxyz(numberOfAtoms);
if (kmax < 1) {
std::stringstream message;
message << " kmax < 1 , Aborting" << std::endl;
SimTKOpenMMLog::printError( message );
}
for(int i = 0; (i < numberOfAtoms); i++) {
for(int m = 0; (m < 3); m++)
EIR(0, i, m) = d_complex(1,0);
for(int m=0; (m<3); m++)
EIR(1, i, m) = d_complex(cos(atomCoordinates[i][m]*recipBoxSize[m]),
sin(atomCoordinates[i][m]*recipBoxSize[m]));
for(int j=2; (j<kmax); j++)
for(int m=0; (m<3); m++)
EIR(j, i, m) = EIR(j-1, i, m) * EIR(1, i, m);
}
// calculate reciprocal space energy and forces
int lowry = 0;
int lowrz = 1;
for(int rx = 0; rx < numRx; rx++) {
RealOpenMM kx = rx * recipBoxSize[0];
for(int ry = lowry; ry < numRy; ry++) {
RealOpenMM ky = ry * recipBoxSize[1];
if(ry >= 0) {
for(int n = 0; n < numberOfAtoms; n++)
tab_xy[n] = EIR(rx, n, 0) * EIR(ry, n, 1);
}
else {
for(int n = 0; n < numberOfAtoms; n++)
tab_xy[n]= EIR(rx, n, 0) * conj (EIR(-ry, n, 1));
}
for (int rz = lowrz; rz < numRz; rz++) {
if( rz >= 0) {
for( int n = 0; n < numberOfAtoms; n++)
tab_qxyz[n] = atomParameters[n][QIndex] * (tab_xy[n] * EIR(rz, n, 2));
}
else {
for( int n = 0; n < numberOfAtoms; n++)
tab_qxyz[n] = atomParameters[n][QIndex] * (tab_xy[n] * conj(EIR(-rz, n, 2)));
}
RealOpenMM cs = 0.0f;
RealOpenMM ss = 0.0f;
for( int n = 0; n < numberOfAtoms; n++) {
cs += tab_qxyz[n].real();
ss += tab_qxyz[n].imag();
}
RealOpenMM kz = rz * recipBoxSize[2];
RealOpenMM k2 = kx * kx + ky * ky + kz * kz;
RealOpenMM ak = exp(k2*factorEwald) / k2;
for(int n = 0; n < numberOfAtoms; n++) {
RealOpenMM force = ak * (cs * tab_qxyz[n].imag() - ss * tab_qxyz[n].real());
forces[n][0] += 2 * recipCoeff * force * kx ;
forces[n][1] += 2 * recipCoeff * force * ky ;
forces[n][2] += 2 * recipCoeff * force * kz ;
}
recipEnergy = recipCoeff * ak * ( cs * cs + ss * ss);
totalRecipEnergy += recipEnergy;
if( totalEnergy )
*totalEnergy += recipEnergy;
if( energyByAtom )
for(int n = 0; n < numberOfAtoms; n++)
energyByAtom[n] += recipEnergy;
lowrz = 1 - numRz;
}
lowry = 1 - numRy;
}
}
}
else {
std::stringstream message;
message << " Wrong method for Ewald summation, Aborting" << std::endl;
SimTKOpenMMLog::printError( message );
}
// **************************************************************************************
// SHORT-RANGE ENERGY AND FORCES
// **************************************************************************************
RealOpenMM totalVdwEnergy = 0.0f;
RealOpenMM totalRealSpaceEwaldEnergy = 0.0f;
for (int i = 0; i < (int) neighborList->size(); i++) {
OpenMM::AtomPair pair = (*neighborList)[i];
int ii = pair.first;
int jj = pair.second;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxSize, deltaR[0] );
RealOpenMM r = deltaR[0][ReferenceForce::RIndex];
RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM alphaR = alphaEwald * r;
RealOpenMM dEdR = atomParameters[ii][QIndex] * atomParameters[jj][QIndex] * inverseR * inverseR * inverseR;
dEdR = (RealOpenMM)(dEdR * (erfc(alphaR) + 2 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI ));
RealOpenMM sig = atomParameters[ii][SigIndex] + atomParameters[jj][SigIndex];
RealOpenMM sig2 = inverseR*sig;
sig2 *= sig2;
RealOpenMM sig6 = sig2*sig2*sig2;
RealOpenMM eps = atomParameters[ii][EpsIndex]*atomParameters[jj][EpsIndex];
dEdR += eps*( twelve*sig6 - six )*sig6*inverseR*inverseR;
// accumulate forces
for( int kk = 0; kk < 3; kk++ ){
RealOpenMM force = dEdR*deltaR[0][kk];
forces[ii][kk] += force;
forces[jj][kk] -= force;
}
// accumulate energies
realSpaceEwaldEnergy = (RealOpenMM) (atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erfc(alphaR));
vdwEnergy = eps*(sig6-one)*sig6;
totalVdwEnergy += vdwEnergy;
totalRealSpaceEwaldEnergy += realSpaceEwaldEnergy;
if( energyByAtom ){
energyByAtom[ii] += realSpaceEwaldEnergy + vdwEnergy;
energyByAtom[jj] += realSpaceEwaldEnergy + vdwEnergy;
}
}
if( totalEnergy )
*totalEnergy += totalRealSpaceEwaldEnergy + totalVdwEnergy;
// Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
RealOpenMM totalExclusionEnergy = 0.0f;
for (int i = 0; i < numberOfAtoms; i++)
for (int j = 1; j <= exclusions[i][0]; j++)
if (exclusions[i][j] > i) {
int ii = i;
int jj = exclusions[i][j];
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxSize, deltaR[0] );
RealOpenMM r = deltaR[0][ReferenceForce::RIndex];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM alphaR = alphaEwald * r;
RealOpenMM dEdR = atomParameters[ii][QIndex] * atomParameters[jj][QIndex] * inverseR * inverseR * inverseR;
dEdR = (RealOpenMM)(dEdR * (erf(alphaR) - 2 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI ));
// accumulate forces
for( int kk = 0; kk < 3; kk++ ){
RealOpenMM force = dEdR*deltaR[0][kk];
forces[ii][kk] -= force;
forces[jj][kk] += force;
}
// accumulate energies
realSpaceEwaldEnergy = (RealOpenMM) (atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erf(alphaR));
totalExclusionEnergy += realSpaceEwaldEnergy;
if( energyByAtom ){
energyByAtom[ii] -= realSpaceEwaldEnergy;
energyByAtom[jj] -= realSpaceEwaldEnergy;
}
}
if( totalEnergy )
*totalEnergy -= totalExclusionEnergy;
// ***********************************************************************
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate PME ixn
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculatePMEIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, RealOpenMM** forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const {
RealOpenMM SQRT_PI = sqrt(PI);
static const RealOpenMM one = 1.0;
RealOpenMM selfEwaldEnergy = 0.0;
RealOpenMM realSpaceEwaldEnergy = 0.0;
RealOpenMM recipEnergy = 0.0;
// **************************************************************************************
// SELF ENERGY
// **************************************************************************************
for( int atomID = 0; atomID < numberOfAtoms; atomID++ ){
selfEwaldEnergy = selfEwaldEnergy + atomParameters[atomID][QIndex]*atomParameters[atomID][QIndex];
}
selfEwaldEnergy = selfEwaldEnergy * alphaEwald/SQRT_PI ;
// **************************************************************************************
// RECIPROCAL SPACE EWALD ENERGY AND FORCES
// **************************************************************************************
pme_t pmedata; /* abstract handle for PME data */
int ngrid[3];
RealOpenMM virial[3][3];
/* PME grid dimensions.
* We typically want to set this as the spacing rather than absolute dimensions, but
* to be able to reproduce results from other programs (e.g. Gromacs) we need to be
* able to set exact grid dimenisions occasionally.
*/
ngrid[0] = 16;
ngrid[1] = 16;
ngrid[2] = 16;
pme_init(&pmedata,alphaEwald,numberOfAtoms,ngrid,4,1);
pme_exec(pmedata,atomCoordinates,forces,atomParameters,periodicBoxSize,&recipEnergy,virial);
// **************************************************************************************
// SHORT-RANGE ENERGY AND FORCES
// **************************************************************************************
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
for( int atomID1 = 0; atomID1 < numberOfAtoms; atomID1++ ){
for( int atomID2 = atomID1 + 1; atomID2 < numberOfAtoms; atomID2++ ){
ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomID2], atomCoordinates[atomID1], periodicBoxSize, deltaR[0] );
RealOpenMM r = deltaR[0][ReferenceForce::RIndex];
RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
realSpaceEwaldEnergy =
(RealOpenMM)(realSpaceEwaldEnergy + atomParameters[atomID1][QIndex]*atomParameters[atomID2][QIndex]*inverseR*erfc(alphaEwald*r));
}
}
// allocate and initialize exclusion array
vector<int> exclusionIndices(numberOfAtoms);
for( int ii = 0; ii < numberOfAtoms; ii++ ){
exclusionIndices[ii] = -1;
}
for( int ii = 0; ii < numberOfAtoms; ii++ ){
// set exclusions
for( int jj = 1; jj <= exclusions[ii][0]; jj++ ){
exclusionIndices[exclusions[ii][jj]] = ii;
}
// loop over atom pairs
for( int jj = ii+1; jj < numberOfAtoms; jj++ ){
if( exclusionIndices[jj] != ii ){
ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxSize, deltaR[0] );
RealOpenMM r = deltaR[0][ReferenceForce::RIndex];
RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM alphaR = alphaEwald * r;
realSpaceEwaldEnergy =
(RealOpenMM)(realSpaceEwaldEnergy + atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erfc(alphaR));
RealOpenMM dEdR = atomParameters[ii][QIndex] * atomParameters[jj][QIndex] * inverseR * inverseR * inverseR;
dEdR = (RealOpenMM)(dEdR * (erfc(alphaR) + 2 * alphaR * exp ( - alphaR * alphaR) / SQRT_PI ));
for( int kk = 0; kk < 3; kk++ ){
RealOpenMM force = dEdR*deltaR[0][kk];
forces[ii][kk] += force;
forces[jj][kk] -= force;
}
}
}
}
// ***********************************************************************
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate LJ Coulomb pair ixn
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculatePairIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, RealOpenMM** forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {
if (ewald || pme)
return calculateEwaldIxn(numberOfAtoms, atomCoordinates, atomParameters, exclusions, fixedParameters, forces, energyByAtom, totalEnergy);
if (cutoff) {
for (int i = 0; i < (int) neighborList->size(); i++) {
OpenMM::AtomPair pair = (*neighborList)[i];
calculateOneIxn(pair.first, pair.second, atomCoordinates, atomParameters, forces, energyByAtom, totalEnergy);
}
}
else {
// allocate and initialize exclusion array
int* exclusionIndices = new int[numberOfAtoms];
for( int ii = 0; ii < numberOfAtoms; ii++ ){
exclusionIndices[ii] = -1;
}
for( int ii = 0; ii < numberOfAtoms; ii++ ){
// set exclusions
for( int jj = 1; jj <= exclusions[ii][0]; jj++ ){
exclusionIndices[exclusions[ii][jj]] = ii;
}
// loop over atom pairs
for( int jj = ii+1; jj < numberOfAtoms; jj++ ){
if( exclusionIndices[jj] != ii ){
calculateOneIxn(ii, jj, atomCoordinates, atomParameters, forces, energyByAtom, totalEnergy);
}
}
}
delete[] exclusionIndices;
}
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate LJ Coulomb pair ixn between two atoms
@param ii the index of the first atom
@param jj the index of the second atom
@param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneIxn( int ii, int jj, RealOpenMM** atomCoordinates,
RealOpenMM** atomParameters, RealOpenMM** forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneIxn";
// ---------------------------------------------------------------------------------------
// constants -- reduce Visual Studio warnings regarding conversions between float & double
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM two = 2.0;
static const RealOpenMM three = 3.0;
static const RealOpenMM six = 6.0;
static const RealOpenMM twelve = 12.0;
static const RealOpenMM oneM = -1.0;
static const int threeI = 3;
// debug flag
static const int debug = -1;
static const int LastAtomIndex = 2;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
// get deltaR, R2, and R between 2 atoms
if (periodic)
ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxSize, deltaR[0] );
else
ReferenceForce::getDeltaR( atomCoordinates[jj], atomCoordinates[ii], deltaR[0] );
RealOpenMM r2 = deltaR[0][ReferenceForce::R2Index];
RealOpenMM inverseR = one/(deltaR[0][ReferenceForce::RIndex]);
RealOpenMM sig = atomParameters[ii][SigIndex] + atomParameters[jj][SigIndex];
RealOpenMM eps = atomParameters[ii][EpsIndex]*atomParameters[jj][EpsIndex];
RealOpenMM minSoftCoreLJLambda = atomParameters[ii][SoftCoreLJLambdaIndex] < atomParameters[jj][SoftCoreLJLambdaIndex] ?
atomParameters[ii][SoftCoreLJLambdaIndex] : atomParameters[jj][SoftCoreLJLambdaIndex];
// LJ: use soft core LJ if lambda < 1
RealOpenMM energy = zero;
RealOpenMM dEdR;
if( minSoftCoreLJLambda < one ){
calculateOneSoftCoreLJIxn( deltaR[0][ReferenceForce::RIndex], sig, eps, minSoftCoreLJLambda, &dEdR, &energy );
} else {
calculateOneLJIxn( inverseR, sig, eps, &dEdR, &energy );
}
// Coulomb
if (cutoff)
dEdR += atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR-2.0f*krf*r2);
else
dEdR += atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR;
dEdR *= inverseR*inverseR;
// accumulate forces
for( int kk = 0; kk < 3; kk++ ){
RealOpenMM force = dEdR*deltaR[0][kk];
forces[ii][kk] += force;
forces[jj][kk] -= force;
}
// accumulate energies
if( totalEnergy || energyByAtom ) {
if (cutoff)
energy += atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR+krf*r2-crf);
else
energy += atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR;
if( totalEnergy )
*totalEnergy += energy;
if( energyByAtom ){
energyByAtom[ii] += energy;
energyByAtom[jj] += energy;
}
}
// debug
if( debug == ii ){
static bool printHeader = false;
std::stringstream message;
message << methodName;
message << std::endl;
int pairArray[2] = { ii, jj };
if( !printHeader ){
printHeader = true;
message << std::endl;
message << methodName.c_str() << " a0 k [c q p s] r1 r2 angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
}
message << std::endl;
for( int kk = 0; kk < 2; kk++ ){
message << " Atm " << pairArray[kk] << " [" << atomCoordinates[pairArray[kk]][0] << " " << atomCoordinates[pairArray[kk]][1] << " " << atomCoordinates[pairArray[kk]][2] << "] ";
}
message << std::endl << " Delta:";
for( int kk = 0; kk < (LastAtomIndex - 1); kk++ ){
message << " [";
for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
message << deltaR[kk][jj] << " ";
}
message << "]";
}
message << std::endl;
for( int kk = 0; kk < 2; kk++ ){
message << " p" << pairArray[kk] << " [";
message << atomParameters[pairArray[kk]][0] << " " << atomParameters[pairArray[kk]][1] << " " << atomParameters[pairArray[kk]][2];
message << "]";
}
message << std::endl;
message << " dEdR=" << dEdR;
message << " E=" << energy << " force factors: ";
message << "F=compute force; f=cumulative force";
message << std::endl << " ";
message << " f" << ii << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, deltaR[0], threeI, dEdR );
message << "]";
for( int kk = 0; kk < 2; kk++ ){
message << " F" << pairArray[kk] << " [";
SimTKOpenMMUtilities::formatRealStringStream( message, forces[pairArray[kk]], threeI );
message << "]";
}
SimTKOpenMMLog::printMessage( message );
}
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate LJ pair ixn between two atoms
@param inverseR 1/r
@param sig sigma
@param eps epsilon
@param dEdR output force factor
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneLJIxn( RealOpenMM inverseR, RealOpenMM sig, RealOpenMM eps,
RealOpenMM* dEdR, RealOpenMM* energy ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "\nReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneLJIxn";
// ---------------------------------------------------------------------------------------
// constants -- reduce Visual Studio warnings regarding conversions between float & double
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM six = 6.0;
static const RealOpenMM twelve = 12.0;
RealOpenMM sig2 = inverseR*sig;
sig2 *= sig2;
RealOpenMM sig6 = sig2*sig2*sig2;
*dEdR = eps*( twelve*sig6 - six )*sig6;
*energy += eps*(sig6-one)*sig6;
return ReferenceForce::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Calculate softcore LJ pair ixn between two atoms
@param r r
@param sig sigma
@param eps epsilon
@param lambda lambda
@param dEdR output force factor
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneSoftCoreLJIxn( RealOpenMM r, RealOpenMM sig, RealOpenMM eps,
RealOpenMM lambda,
RealOpenMM* dEdR, RealOpenMM* energy ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "\nReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneSoftCoreLJIxn";
// ---------------------------------------------------------------------------------------
// constants -- reduce Visual Studio warnings regarding conversions between float & double
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM six = 6.0;
static const RealOpenMM twelve = 12.0;
static const RealOpenMM alphaLJ = 0.5;
#if 0
RealOpenMM dEdROrig = 0.0;
RealOpenMM E_Orig = 0.0;
static int maxPrint = 0;
calculateOneLJIxn( one/r, sig, eps, &dEdROrig, &E_Orig );
#endif
// soft-core LJ energy = lambda*4*eps*[ 1/{alphaLJ*(1-lambda) + (r/sig)**6}**2 - 1/{alphaLJ*(1-lambda) + (r/sig)**6} ]
eps *= lambda;
RealOpenMM sig2 = r/sig;
sig2 *= sig2;
RealOpenMM sig6 = sig2*sig2*sig2;
RealOpenMM softcoreLJTerm = alphaLJ*(one - lambda) + sig6;
RealOpenMM softcoreLJInv = one/softcoreLJTerm;
RealOpenMM softcoreLJInv2 = softcoreLJInv*softcoreLJInv;
*dEdR = eps*softcoreLJInv2*( twelve*softcoreLJInv - six )*sig6;
*energy += eps*softcoreLJInv*( softcoreLJInv - one );
#if 0
if( maxPrint++ < 5 ){
printf( "r=%14.6e sig=%14.6e eps=%14.6e lambda=%14.6e de[%14.6e %14.6e] e[%14.6e %14.6e] %14.6e %14.6e\n",
r, sig, eps/lambda, lambda, dEdROrig, *dEdR, E_Orig, *energy, softcoreLJInv, sig6 );
}
#endif
return ReferenceForce::DefaultReturn;
}
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.h 0 → 100644
View file @ 7a36f461
#ifndef __ReferenceFreeEnergyLJCoulombSoftcoreIxn_H__
#define __ReferenceFreeEnergyLJCoulombSoftcoreIxn_H__
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "SimTKReference/ReferencePairIxn.h"
#include "SimTKReference/ReferenceNeighborList.h"
// ---------------------------------------------------------------------------------------
class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
private:
bool cutoff;
bool periodic;
bool ewald;
bool pme;
const OpenMM::NeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance;
RealOpenMM krf, crf;
RealOpenMM softCoreLJLambda;
int numRx, numRy, numRz;
RealOpenMM alphaEwald;
// parameter indices
static const int SigIndex = 0;
static const int EpsIndex = 1;
static const int QIndex = 2;
static const int SoftCoreLJLambdaIndex = 3;
/**---------------------------------------------------------------------------------------
Calculate LJ Coulomb pair ixn between two atoms
@param atom1 the index of the first atom
@param atom2 the index of the second atom
@param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int calculateOneIxn( int atom1, int atom2, RealOpenMM** atomCoordinates,
RealOpenMM** atomParameters, RealOpenMM** forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
public:
/**---------------------------------------------------------------------------------------
Constructor
--------------------------------------------------------------------------------------- */
ReferenceFreeEnergyLJCoulombSoftcoreIxn( );
/**---------------------------------------------------------------------------------------
Destructor
--------------------------------------------------------------------------------------- */
~ReferenceFreeEnergyLJCoulombSoftcoreIxn( );
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
@param neighbors the neighbor list to use
@param solventDielectric the dielectric constant of the bulk solvent
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors, RealOpenMM solventDielectric );
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int setPeriodic( RealOpenMM* boxSize );
/**---------------------------------------------------------------------------------------
Set the force to use Ewald summation.
@param alpha the Ewald separation parameter
@param kmaxx the largest wave vector in the x direction
@param kmaxy the largest wave vector in the y direction
@param kmaxz the largest wave vector in the z direction
--------------------------------------------------------------------------------------- */
void setUseEwald(RealOpenMM alpha, int kmaxx, int kmaxy, int kmaxz);
/**---------------------------------------------------------------------------------------
Set the force to use Particle-Mesh Ewald (PME) summation.
@param alpha the Ewald separation parameter
--------------------------------------------------------------------------------------- */
void setUsePME(RealOpenMM alpha);
/**---------------------------------------------------------------------------------------
Set the soft core LJ lambda
@param lambda the soft core LJ lambda
--------------------------------------------------------------------------------------- */
void setSoftCoreLJLambda(RealOpenMM lambda);
/**---------------------------------------------------------------------------------------
Calculate parameters for LJ 1-4 ixn
@param c6 c6
@param c12 c12
@param q1 q1 charge atom
@param epsfacSqrt epsfacSqrt (what is this?)
@param parameters output parameters:
parameter[SigIndex] = sqrt(c6*c6/c12)
parameter[EpsIndex] = 0.5*( (c12/c6)**1/6 )
parameter[QIndex] = epsfactorSqrt*q1
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1,
RealOpenMM epsfacSqrt,
RealOpenMM* parameters ) const;
/**---------------------------------------------------------------------------------------
Calculate LJ Coulomb pair ixn
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int calculatePairIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, RealOpenMM** forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
private:
/**---------------------------------------------------------------------------------------
Calculate Ewald ixn
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int calculateEwaldIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, RealOpenMM** forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
/**---------------------------------------------------------------------------------------
Calculate PME ixn
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int calculatePMEIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, RealOpenMM** forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
/**---------------------------------------------------------------------------------------
Calculate LJ pair ixn between two atoms
@param inverseR 1/r
@param sig sigma
@param eps epsilon
@param dEdR output force factor
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int calculateOneLJIxn( RealOpenMM inverseR, RealOpenMM sig, RealOpenMM eps,
RealOpenMM* dEdR, RealOpenMM* energy ) const;
/**---------------------------------------------------------------------------------------
Calculate softcore LJ pair ixn between two atoms
@param r r
@param sig sigma
@param eps epsilon
@param lambda lambda
@param dEdR output force factor
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
int calculateOneSoftCoreLJIxn( RealOpenMM r, RealOpenMM sig, RealOpenMM eps,
RealOpenMM lambda, RealOpenMM* dEdR, RealOpenMM* energy ) const;
};
// ---------------------------------------------------------------------------------------
#endif // __ReferenceFreeEnergyLJCoulombSoftcoreIxn_H__
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