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Commit 73183c61 authored by ChayaSt's avatar ChayaSt
Browse files

resolved conflict

parents 0e218233 32e08b87
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Showing with 303 additions and 137 deletions
platforms/opencl/src/kernels/gbsaObc_cpu.cl
View file @ 73183c61
......@@ -178,6 +178,8 @@ __kernel void computeBornSum(
#ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else
......@@ -196,35 +198,31 @@ __kernel void computeBornSum(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
includeTile = (nextToSkip != pos);
else
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
#endif
if (includeTile) {
// Load the data for this tile.
......@@ -593,6 +591,8 @@ __kernel void computeGBSAForce1(
#ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else
......@@ -611,35 +611,31 @@ __kernel void computeGBSAForce1(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
includeTile = (nextToSkip != pos);
else
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/opencl/src/kernels/nonbonded.cl
View file @ 73183c61
......@@ -200,6 +200,8 @@ __kernel void computeNonbonded(
#ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long)numTileIndices/totalWarps : warp*(long)numTiles/totalWarps);
int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long)numTileIndices/totalWarps : (warp+1)*(long)numTiles/totalWarps);
#else
......@@ -223,42 +225,38 @@ __kernel void computeNonbonded(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
}
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/opencl/src/kernels/nonbonded_cpu.cl
View file @ 73183c61
......@@ -214,6 +214,8 @@ __kernel void computeNonbonded(
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? (unsigned int) (startTileIndex+get_group_id(0)*(long)numTileIndices/get_num_groups(0)) : get_group_id(0)*(long)numTiles/get_num_groups(0));
int end = (int) (numTiles > maxTiles ? (unsigned int) (startTileIndex+(get_group_id(0)+1)*(long)numTileIndices/get_num_groups(0)) : (get_group_id(0)+1)*(long)numTiles/get_num_groups(0));
#else
......@@ -234,35 +236,31 @@ __kernel void computeNonbonded(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
}
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
includeTile = (nextToSkip != pos);
else
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/opencl/src/kernels/pme.cl
View file @ 73183c61
__kernel void updateBsplines(__global const real4* restrict posq, __global real4* restrict pmeBsplineTheta, __local real4* restrict bsplinesCache,
__global int2* restrict pmeAtomGridIndex, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
__global int2* restrict pmeAtomGridIndex, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
const real4 scale = 1/(real) (PME_ORDER-1);
for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
__local real4* data = &bsplinesCache[get_local_id(0)*PME_ORDER];
real4 pos = posq[i];
APPLY_PERIODIC_TO_POS(pos)
real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
pos.z*recipBoxVecZ.z);
......@@ -83,7 +85,8 @@ __kernel void recordZIndex(__global int2* restrict pmeAtomGridIndex, __global co
#pragma OPENCL EXTENSION cl_khr_int64_base_atomics : enable
__kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
__global long* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
__global long* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
const real scale = 1/(real) (PME_ORDER-1);
real4 data[PME_ORDER];
......@@ -93,9 +96,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
int atom = pmeAtomGridIndex[i].x;
real4 pos = posq[atom];
pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
APPLY_PERIODIC_TO_POS(pos)
real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
pos.z*recipBoxVecZ.z);
......@@ -165,7 +166,8 @@ __kernel void finishSpreadCharge(__global long* restrict fixedGrid, __global rea
}
#elif defined(DEVICE_IS_CPU)
__kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
__global real* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
__global real* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
const int firstx = get_global_id(0)*GRID_SIZE_X/get_global_size(0);
const int lastx = (get_global_id(0)+1)*GRID_SIZE_X/get_global_size(0);
if (firstx == lastx)
......@@ -179,9 +181,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
for (int i = 0; i < NUM_ATOMS; i++) {
int atom = i;//pmeAtomGridIndex[i].x;
real4 pos = posq[atom];
pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
APPLY_PERIODIC_TO_POS(pos)
real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
pos.z*recipBoxVecZ.z);
......@@ -370,7 +370,8 @@ __kernel void gridEvaluateEnergy(__global real2* restrict pmeGrid, __global mixe
}
__kernel void gridInterpolateForce(__global const real4* restrict posq, __global real4* restrict forceBuffers, __global const real* restrict pmeGrid,
real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, __global int2* restrict pmeAtomGridIndex) {
real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real4 recipBoxVecX,
real4 recipBoxVecY, real4 recipBoxVecZ, __global int2* restrict pmeAtomGridIndex) {
const real scale = 1/(real) (PME_ORDER-1);
real4 data[PME_ORDER];
real4 ddata[PME_ORDER];
......@@ -382,9 +383,7 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
int atom = pmeAtomGridIndex[i].x;
real4 force = 0.0f;
real4 pos = posq[atom];
pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
APPLY_PERIODIC_TO_POS(pos)
real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
pos.z*recipBoxVecZ.z);
......
platforms/opencl/src/kernels/torsionForce.cl
View file @ 73183c61
......@@ -2,6 +2,11 @@ const real PI = 3.14159265358979323846f;
real4 v0 = (real4) (pos1.xyz-pos2.xyz, 0.0f);
real4 v1 = (real4) (pos3.xyz-pos2.xyz, 0.0f);
real4 v2 = (real4) (pos3.xyz-pos4.xyz, 0.0f);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(v0)
APPLY_PERIODIC_TO_DELTA(v1)
APPLY_PERIODIC_TO_DELTA(v2)
#endif
real4 cp0 = cross(v0, v1);
real4 cp1 = cross(v1, v2);
real cosangle = dot(normalize(cp0), normalize(cp1));
......
platforms/opencl/tests/OpenCLTests.h
View file @ 73183c61
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2015 Stanford University and the Authors. *
* Portions copyright (c) 2015-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -39,9 +39,9 @@ OpenMM::OpenCLPlatform platform;
void initializeTests(int argc, char* argv[]) {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", std::string(argv[1]));
platform.setPropertyDefaultValue("Precision", std::string(argv[1]));
if (argc > 2)
platform.setPropertyDefaultValue("OpenCLPlatformIndex", std::string(argv[2]));
if (argc > 3)
platform.setPropertyDefaultValue("OpenCLDeviceIndex", std::string(argv[3]));
platform.setPropertyDefaultValue("DeviceIndex", std::string(argv[3]));
}
platforms/reference/include/ReferenceAngleBondIxn.h
View file @ 73183c61
......@@ -33,6 +33,9 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
public:
/**---------------------------------------------------------------------------------------
......@@ -51,6 +54,16 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
~ReferenceAngleBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Get dEdR and energy term for angle bond
......
platforms/reference/include/ReferenceCMAPTorsionIxn.h
View file @ 73183c61
......@@ -38,6 +38,8 @@ private:
std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
std::vector<int> torsionMaps;
std::vector<std::vector<int> > torsionIndices;
bool usePeriodic;
RealVec boxVectors[3];
/**---------------------------------------------------------------------------------------
......@@ -65,6 +67,16 @@ public:
const std::vector<int>& torsionMaps,
const std::vector<std::vector<int> >& torsionIndices);
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate torsion interaction
......
platforms/reference/include/ReferenceCustomAngleIxn.h
View file @ 73183c61
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,6 +39,8 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
double* energyTheta;
double* forceTheta;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
public:
......@@ -59,6 +61,16 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
~ReferenceCustomAngleIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Custom Angle Ixn
......
platforms/reference/include/ReferenceCustomBondIxn.h
View file @ 73183c61
/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -40,6 +40,8 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
double* energyR;
double* forceR;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
public:
......@@ -60,6 +62,16 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
~ReferenceCustomBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Custom Bond Ixn
......
platforms/reference/include/ReferenceCustomCentroidBondIxn.h
View file @ 73183c61
/* Portions copyright (c) 2009-2015 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -50,6 +50,8 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
std::vector<DistanceTermInfo> distanceTerms;
std::vector<AngleTermInfo> angleTerms;
std::vector<DihedralTermInfo> dihedralTerms;
bool usePeriodic;
RealVec boxVectors[3];
/**---------------------------------------------------------------------------------------
......@@ -94,6 +96,16 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
~ReferenceCustomCentroidBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Get the list of groups in each bond.
......
platforms/reference/include/ReferenceCustomCompoundBondIxn.h
View file @ 73183c61
/* Portions copyright (c) 2009-2012 Stanford University and Simbios.
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -48,6 +48,8 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
std::vector<DistanceTermInfo> distanceTerms;
std::vector<AngleTermInfo> angleTerms;
std::vector<DihedralTermInfo> dihedralTerms;
bool usePeriodic;
RealVec boxVectors[3];
/**---------------------------------------------------------------------------------------
......@@ -91,6 +93,16 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
~ReferenceCustomCompoundBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Get the list atoms in each bond.
......
platforms/reference/include/ReferenceCustomDynamics.h
View file @ 73183c61
/* Portions copyright (c) 2011-2015 Stanford University and Simbios.
/* Portions copyright (c) 2011-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -29,7 +29,8 @@
#include "openmm/CustomIntegrator.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/CustomIntegratorUtilities.h"
#include "lepton/ExpressionProgram.h"
#include "openmm/internal/CompiledExpressionSet.h"
#include "lepton/CompiledExpression.h"
#include <map>
#include <string>
......@@ -44,23 +45,27 @@ private:
std::vector<RealOpenMM> inverseMasses;
std::vector<OpenMM::RealVec> sumBuffer, oldPos;
std::vector<OpenMM::CustomIntegrator::ComputationType> stepType;
std::vector<std::string> stepVariable, forceName, energyName;
std::vector<std::vector<Lepton::ExpressionProgram> > stepExpressions;
std::vector<std::string> stepVariable;
std::vector<std::vector<Lepton::CompiledExpression> > stepExpressions;
std::vector<CustomIntegratorUtilities::Comparison> comparisons;
std::vector<bool> invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy;
std::vector<int> forceGroupFlags, blockEnd;
RealOpenMM energy;
Lepton::ExpressionProgram kineticEnergyExpression;
Lepton::CompiledExpression kineticEnergyExpression;
bool kineticEnergyNeedsForce;
CompiledExpressionSet expressionSet;
int xIndex, vIndex, mIndex, fIndex, energyIndex, gaussianIndex, uniformIndex;
std::vector<int> forceVariableIndex, energyVariableIndex, perDofVariableIndex, stepVariableIndex;
void initialize(OpenMM::ContextImpl& context, std::vector<RealOpenMM>& masses, std::map<std::string, RealOpenMM>& globals);
void computePerDof(int numberOfAtoms, std::vector<OpenMM::RealVec>& results, const std::vector<OpenMM::RealVec>& atomCoordinates,
const std::vector<OpenMM::RealVec>& velocities, const std::vector<OpenMM::RealVec>& forces, const std::vector<RealOpenMM>& masses,
const std::map<std::string, RealOpenMM>& globals, const std::vector<std::vector<OpenMM::RealVec> >& perDof,
const Lepton::ExpressionProgram& expression, const std::string& forceName);
const std::vector<std::vector<OpenMM::RealVec> >& perDof, const Lepton::CompiledExpression& expression, int forceIndex);
void recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, RealOpenMM>& globals);
bool evaluateCondition(int step, std::map<std::string, RealOpenMM>& globals);
bool evaluateCondition(int step);
public:
......
platforms/reference/include/ReferenceCustomTorsionIxn.h
View file @ 73183c61
/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,6 +39,8 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
double* energyTheta;
double* forceTheta;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
public:
......@@ -59,6 +61,16 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
~ReferenceCustomTorsionIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Custom Torsion Ixn
......
platforms/reference/include/ReferenceForce.h
View file @ 73183c61
......@@ -83,6 +83,19 @@ class OPENMM_EXPORT ReferenceForce {
static void getDeltaR(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
RealOpenMM* deltaR);
/**---------------------------------------------------------------------------------------
Get deltaR between atomI and atomJ (static method)
deltaR: j - i
@param atomCoordinatesI atom i coordinates
@param atomCoordinatesI atom j coordinates
@return the displacement
--------------------------------------------------------------------------------------- */
static RealVec getDeltaR(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ);
/**---------------------------------------------------------------------------------------
Get deltaR and distance and distance**2 between atomI and atomJ, assuming periodic
......@@ -113,6 +126,21 @@ class OPENMM_EXPORT ReferenceForce {
static void getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
const OpenMM::RealVec* boxVectors, RealOpenMM* deltaR);
/**---------------------------------------------------------------------------------------
Get deltaR between atomI and atomJ, assuming periodic boundary conditions (static method);
deltaR: j - i
@param atomCoordinatesI atom i coordinates
@param atomCoordinatesI atom j coordinates
@param boxVectors the vectors defining the periodic box
@return the displacement
--------------------------------------------------------------------------------------- */
static RealVec getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
const OpenMM::RealVec* boxVectors);
/**
* Get a pointer to the memory for setting a variable in a CompiledExpression. If the expression
* does not use the specified variable, return NULL.
......
platforms/reference/include/ReferenceHarmonicBondIxn.h
View file @ 73183c61
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -32,6 +32,9 @@ namespace OpenMM {
class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
public:
......@@ -51,6 +54,16 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
~ReferenceHarmonicBondIxn();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Harmonic Bond Ixn
......
platforms/reference/include/ReferenceKernels.h
View file @ 73183c61
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -172,7 +172,7 @@ public:
* @param b the vector defining the second edge of the periodic box
* @param c the vector defining the third edge of the periodic box
*/
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const;
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
/**
* Create a checkpoint recording the current state of the Context.
*
......@@ -280,6 +280,7 @@ private:
int numBonds;
int **bondIndexArray;
RealOpenMM **bondParamArray;
bool usePeriodic;
};
/**
......@@ -319,6 +320,7 @@ private:
RealOpenMM **bondParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
bool usePeriodic;
};
/**
......@@ -356,6 +358,7 @@ private:
int numAngles;
int **angleIndexArray;
RealOpenMM **angleParamArray;
bool usePeriodic;
};
/**
......@@ -395,6 +398,7 @@ private:
RealOpenMM **angleParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
bool usePeriodic;
};
/**
......@@ -432,6 +436,7 @@ private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
bool usePeriodic;
};
/**
......@@ -469,6 +474,7 @@ private:
int numTorsions;
int **torsionIndexArray;
RealOpenMM **torsionParamArray;
bool usePeriodic;
};
/**
......@@ -505,6 +511,7 @@ private:
std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
std::vector<int> torsionMaps;
std::vector<std::vector<int> > torsionIndices;
bool usePeriodic;
};
/**
......@@ -544,6 +551,7 @@ private:
RealOpenMM **torsionParamArray;
Lepton::CompiledExpression energyExpression, forceExpression;
std::vector<std::string> parameterNames, globalParameterNames;
bool usePeriodic;
};
/**
......@@ -860,6 +868,7 @@ private:
RealOpenMM **bondParamArray;
ReferenceCustomCentroidBondIxn* ixn;
std::vector<std::string> globalParameterNames;
bool usePeriodic;
};
/**
......@@ -898,6 +907,7 @@ private:
RealOpenMM **bondParamArray;
ReferenceCustomCompoundBondIxn* ixn;
std::vector<std::string> globalParameterNames;
bool usePeriodic;
};
/**
......
platforms/reference/include/ReferenceProperDihedralBond.h
View file @ 73183c61
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -33,6 +33,9 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
public:
/**---------------------------------------------------------------------------------------
......@@ -51,6 +54,16 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
~ReferenceProperDihedralBond();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate proper dihedral bond ixn
......
platforms/reference/include/ReferenceRbDihedralBond.h
View file @ 73183c61
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -33,6 +33,9 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
public:
/**---------------------------------------------------------------------------------------
......@@ -51,6 +54,16 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
~ReferenceRbDihedralBond();
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions.
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
Calculate Ryckaert-Bellemans bond ixn
......
platforms/reference/include/ReferenceTabulatedFunction.h
View file @ 73183c61
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2014 Stanford University and the Authors. *
* Portions copyright (c) 2014-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -55,6 +55,7 @@ public:
double evaluateDerivative(const double* arguments, const int* derivOrder) const;
CustomFunction* clone() const;
private:
ReferenceContinuous1DFunction(const ReferenceContinuous1DFunction& other);
const Continuous1DFunction& function;
double min, max;
std::vector<double> x, values, derivs;
......@@ -71,6 +72,7 @@ public:
double evaluateDerivative(const double* arguments, const int* derivOrder) const;
CustomFunction* clone() const;
private:
ReferenceContinuous2DFunction(const ReferenceContinuous2DFunction& other);
const Continuous2DFunction& function;
int xsize, ysize;
double xmin, xmax, ymin, ymax;
......@@ -89,6 +91,7 @@ public:
double evaluateDerivative(const double* arguments, const int* derivOrder) const;
CustomFunction* clone() const;
private:
ReferenceContinuous3DFunction(const ReferenceContinuous3DFunction& other);
const Continuous3DFunction& function;
int xsize, ysize, zsize;
double xmin, xmax, ymin, ymax, zmin, zmax;
......
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