Skip to content

GitLab

Commit a381a3ab authored by peastman's avatar peastman
Browse files

Merge branch 'master' into gayberne

parents 5ecc8e00 1f7866ad
Show whitespace changes
Inline Side-by-side
Showing with 402 additions and 385 deletions
platforms/opencl/src/kernels/customGBGradientChainRule.cl
View file @ a381a3ab
......@@ -4,6 +4,7 @@
__kernel void computeGradientChainRuleTerms(__global real4* restrict forceBuffers, __global const real4* restrict posq
PARAMETER_ARGUMENTS) {
INIT_PARAM_DERIVS
unsigned int index = get_global_id(0);
while (index < NUM_ATOMS) {
real4 pos = posq[index];
......@@ -12,4 +13,5 @@ __kernel void computeGradientChainRuleTerms(__global real4* restrict forceBuffer
forceBuffers[index] = force;
index += get_global_size(0);
}
SAVE_PARAM_DERIVS
}
platforms/opencl/src/kernels/customGBValueN2.cl
View file @ a381a3ab
......@@ -74,6 +74,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
COMPUTE_VALUE
}
value += tempValue1;
ADD_TEMP_DERIVS1
#ifdef USE_CUTOFF
}
#endif
......@@ -123,6 +124,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
}
value += tempValue1;
local_value[tbx+tj] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
#ifdef USE_CUTOFF
}
#endif
......@@ -137,18 +140,23 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
// Write results.
#ifdef SUPPORTS_64_BIT_ATOMICS
unsigned int offset = x*TILE_SIZE + tgx;
atom_add(&global_value[offset], (long) (value*0x100000000));
unsigned int offset1 = x*TILE_SIZE + tgx;
atom_add(&global_value[offset1], (long) (value*0x100000000));
STORE_PARAM_DERIVS1
if (x != y) {
offset = y*TILE_SIZE + tgx;
atom_add(&global_value[offset], (long) (local_value[get_local_id(0)]*0x100000000));
unsigned int offset2 = y*TILE_SIZE + tgx;
atom_add(&global_value[offset2], (long) (local_value[get_local_id(0)]*0x100000000));
STORE_PARAM_DERIVS2
}
#else
unsigned int offset1 = x*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS;
unsigned int offset2 = y*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS;
global_value[offset1] += value;
if (x != y)
STORE_PARAM_DERIVS1
if (x != y) {
global_value[offset2] += local_value[get_local_id(0)];
STORE_PARAM_DERIVS2
}
#endif
}
......@@ -157,6 +165,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
#ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -178,16 +188,12 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
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
{
#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.
......@@ -213,7 +219,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......@@ -261,6 +267,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
}
value += tempValue1;
local_value[tbx+tj] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
}
tj = (tj + 1) & (TILE_SIZE - 1);
SYNC_WARPS;
......@@ -294,6 +302,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
}
value += tempValue1;
local_value[tbx+tj] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
#ifdef USE_CUTOFF
}
#endif
......@@ -310,15 +320,23 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
unsigned int atom2 = y*TILE_SIZE + tgx;
#endif
#ifdef SUPPORTS_64_BIT_ATOMICS
atom_add(&global_value[atom1], (long) (value*0x100000000));
if (atom2 < PADDED_NUM_ATOMS)
atom_add(&global_value[atom2], (long) (local_value[get_local_id(0)]*0x100000000));
unsigned int offset1 = atom1;
atom_add(&global_value[offset1], (long) (value*0x100000000));
STORE_PARAM_DERIVS1
if (atom2 < PADDED_NUM_ATOMS) {
unsigned int offset2 = atom2;
atom_add(&global_value[offset2], (long) (local_value[get_local_id(0)]*0x100000000));
STORE_PARAM_DERIVS2
}
#else
unsigned int offset1 = atom1 + warp*PADDED_NUM_ATOMS;
unsigned int offset2 = atom2 + warp*PADDED_NUM_ATOMS;
global_value[offset1] += value;
if (atom2 < PADDED_NUM_ATOMS)
STORE_PARAM_DERIVS1
if (atom2 < PADDED_NUM_ATOMS) {
unsigned int offset2 = atom2 + warp*PADDED_NUM_ATOMS;
global_value[offset2] += local_value[get_local_id(0)];
STORE_PARAM_DERIVS2
}
#endif
}
pos++;
......
platforms/opencl/src/kernels/customGBValueN2_cpu.cl
View file @ a381a3ab
......@@ -75,6 +75,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
COMPUTE_VALUE
}
value += tempValue1;
ADD_TEMP_DERIVS1
#ifdef USE_CUTOFF
}
#endif
......@@ -86,11 +87,13 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
// Write results.
#ifdef SUPPORTS_64_BIT_ATOMICS
atom_add(&global_value[atom1], (long) (value*0x100000000));
unsigned int offset1 = atom1;
atom_add(&global_value[offset1], (long) (value*0x100000000));
#else
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value;
unsigned int offset1 = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset1] += value;
#endif
STORE_PARAM_DERIVS1
}
}
else {
......@@ -133,6 +136,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
}
value += tempValue1;
local_value[j] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
#ifdef USE_CUTOFF
}
#endif
......@@ -144,23 +149,26 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
// Write results for atom1.
#ifdef SUPPORTS_64_BIT_ATOMICS
atom_add(&global_value[atom1], (long) (value*0x100000000));
unsigned int offset1 = atom1;
atom_add(&global_value[offset1], (long) (value*0x100000000));
#else
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value;
unsigned int offset1 = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset1] += value;
#endif
STORE_PARAM_DERIVS1
}
// Write results.
for (int tgx = 0; tgx < TILE_SIZE; tgx++) {
#ifdef SUPPORTS_64_BIT_ATOMICS
unsigned int offset = y*TILE_SIZE+tgx;
atom_add(&global_value[offset], (long) (local_value[tgx]*0x100000000));
unsigned int offset2 = y*TILE_SIZE+tgx;
atom_add(&global_value[offset2], (long) (local_value[tgx]*0x100000000));
#else
unsigned int offset = y*TILE_SIZE+tgx + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += local_value[tgx];
unsigned int offset2 = y*TILE_SIZE+tgx + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset2] += local_value[tgx];
#endif
STORE_PARAM_DERIVS2
}
}
}
......@@ -170,6 +178,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
#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) (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
......@@ -188,16 +198,12 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
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
{
#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.
......@@ -216,7 +222,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
}
#endif
if (includeTile) {
// Load the data for this tile.
......@@ -262,17 +268,21 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
COMPUTE_VALUE
value += tempValue1;
local_value[j] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
}
}
// Write results for atom1.
#ifdef SUPPORTS_64_BIT_ATOMICS
atom_add(&global_value[atom1], (long) (value*0x100000000));
unsigned int offset1 = atom1;
atom_add(&global_value[offset1], (long) (value*0x100000000));
#else
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value;
unsigned int offset1 = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset1] += value;
#endif
STORE_PARAM_DERIVS1
}
}
else
......@@ -307,17 +317,21 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
COMPUTE_VALUE
value += tempValue1;
local_value[j] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
}
}
// Write results for atom1.
#ifdef SUPPORTS_64_BIT_ATOMICS
atom_add(&global_value[atom1], (long) (value*0x100000000));
unsigned int offset1 = atom1;
atom_add(&global_value[offset1], (long) (value*0x100000000));
#else
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value;
unsigned int offset1 = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset1] += value;
#endif
STORE_PARAM_DERIVS1
}
}
......@@ -331,11 +345,13 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
#endif
if (atom2 < PADDED_NUM_ATOMS) {
#ifdef SUPPORTS_64_BIT_ATOMICS
atom_add(&global_value[atom2], (long) (local_value[tgx]*0x100000000));
unsigned int offset2 = atom2;
atom_add(&global_value[offset2], (long) (local_value[tgx]*0x100000000));
#else
unsigned int offset = atom2 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += local_value[tgx];
unsigned int offset2 = atom2 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset2] += local_value[tgx];
#endif
STORE_PARAM_DERIVS2
}
}
}
......
platforms/opencl/src/kernels/customGBValuePerParticle.cl
View file @ a381a3ab
......@@ -21,6 +21,7 @@ __kernel void computePerParticleValues(int bufferSize, int numBuffers, __global
for (int i = index+bufferSize; i < totalSize; i += bufferSize)
sum += valueBuffers[i];
#endif
REDUCE_PARAM0_DERIV
// Now calculate other values
......
platforms/opencl/src/kernels/customIntegratorPerDof.cl
View file @ a381a3ab
......@@ -25,7 +25,8 @@ void storePos(__global real4* restrict posq, __global real4* restrict posqCorrec
__kernel void computePerDof(__global real4* restrict posq, __global real4* restrict posqCorrection, __global mixed4* restrict posDelta,
__global mixed4* restrict velm, __global const real4* restrict force, __global const mixed2* restrict dt, __global const mixed* restrict globals,
__global mixed* restrict sum, __global const float4* restrict gaussianValues, unsigned int gaussianBaseIndex, __global const float4* restrict uniformValues, const real energy
__global mixed* restrict sum, __global const float4* restrict gaussianValues, unsigned int gaussianBaseIndex, __global const float4* restrict uniformValues,
const real energy, __global mixed* restrict energyParamDerivs
PARAMETER_ARGUMENTS) {
mixed stepSize = dt[0].y;
int index = get_global_id(0);
......
platforms/opencl/src/kernels/customNonbonded.cl
View file @ a381a3ab
......@@ -4,15 +4,18 @@ if (!isExcluded && r2 < CUTOFF_SQUARED) {
if (!isExcluded) {
#endif
real tempForce = 0.0f;
COMPUTE_FORCE
real switchValue = 1, switchDeriv = 0;
#if USE_SWITCH
if (r > SWITCH_CUTOFF) {
real x = r-SWITCH_CUTOFF;
real switchValue = 1+x*x*x*(SWITCH_C3+x*(SWITCH_C4+x*SWITCH_C5));
real switchDeriv = x*x*(3*SWITCH_C3+x*(4*SWITCH_C4+x*5*SWITCH_C5));
switchValue = 1+x*x*x*(SWITCH_C3+x*(SWITCH_C4+x*SWITCH_C5));
switchDeriv = x*x*(3*SWITCH_C3+x*(4*SWITCH_C4+x*5*SWITCH_C5));
}
#endif
COMPUTE_FORCE
#if USE_SWITCH
tempForce = tempForce*switchValue - tempEnergy*switchDeriv;
tempEnergy *= switchValue;
}
#endif
dEdR += tempForce*invR;
}
platforms/opencl/src/kernels/gbsaObc.cl
View file @ a381a3ab
......@@ -169,6 +169,8 @@ __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) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -190,16 +192,12 @@ __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
{
#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.
......@@ -225,7 +223,7 @@ __kernel void computeBornSum(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......@@ -556,6 +554,8 @@ __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) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -577,16 +577,12 @@ __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
{
#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.
......@@ -612,7 +608,7 @@ __kernel void computeGBSAForce1(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/opencl/src/kernels/gbsaObc_cpu.cl
View file @ a381a3ab
......@@ -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
......@@ -196,16 +198,12 @@ __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
{
#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.
......@@ -224,7 +222,7 @@ __kernel void computeBornSum(
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
......@@ -611,16 +611,12 @@ __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
{
#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.
......@@ -639,7 +635,7 @@ __kernel void computeGBSAForce1(
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
}
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/opencl/src/kernels/nonbonded.cl
View file @ a381a3ab
......@@ -35,6 +35,7 @@ __kernel void computeNonbonded(
const unsigned int tgx = get_local_id(0) & (TILE_SIZE-1);
const unsigned int tbx = get_local_id(0) - tgx;
mixed energy = 0;
INIT_DERIVATIVES
__local AtomData localData[FORCE_WORK_GROUP_SIZE];
// First loop: process tiles that contain exclusions.
......@@ -85,6 +86,7 @@ __kernel void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
#endif
real tempEnergy = 0;
const real interactionScale = 0.5f;
COMPUTE_INTERACTION
energy += 0.5f*tempEnergy;
#ifdef INCLUDE_FORCES
......@@ -144,6 +146,7 @@ __kernel void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
#endif
real tempEnergy = 0;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
......@@ -200,6 +203,8 @@ __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
......@@ -223,16 +228,12 @@ __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
{
#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.
......@@ -258,7 +259,7 @@ __kernel void computeNonbonded(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......@@ -322,6 +323,7 @@ __kernel void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS);
#endif
real tempEnergy = 0;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
......@@ -376,6 +378,7 @@ __kernel void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS);
#endif
real tempEnergy = 0;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION
energy += tempEnergy;
#ifdef INCLUDE_FORCES
......@@ -431,4 +434,5 @@ __kernel void computeNonbonded(
#ifdef INCLUDE_ENERGY
energyBuffer[get_global_id(0)] += energy;
#endif
SAVE_DERIVATIVES
}
platforms/opencl/src/kernels/nonbonded_cpu.cl
View file @ a381a3ab
......@@ -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
......@@ -234,16 +236,12 @@ __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
{
#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.
......@@ -262,7 +260,7 @@ __kernel void computeNonbonded(
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
}
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/reference/include/ReferenceAngleBondIxn.h
View file @ a381a3ab
/* 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
......@@ -94,7 +94,7 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
RealOpenMM* totalEnergy, double* energyParamDerivs);
};
......
platforms/reference/include/ReferenceBondIxn.h
View file @ a381a3ab
/* 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
......@@ -67,7 +67,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
virtual void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
RealOpenMM* totalEnergy, double* energyParamDerivs);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCMAPTorsionIxn.h
View file @ a381a3ab
/* Portions copyright (c) 2010 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
......@@ -97,7 +97,7 @@ public:
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
RealOpenMM* totalEnergy, double* energyParamDerivs);
// ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomAngleIxn.h
View file @ a381a3ab
......@@ -25,7 +25,7 @@
#define __ReferenceCustomAngleIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/CompiledExpression.h"
#include "openmm/internal/CompiledExpressionSet.h"
namespace OpenMM {
......@@ -34,10 +34,10 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
private:
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams;
std::vector<double*> forceParams;
double* energyTheta;
double* forceTheta;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
CompiledExpressionSet expressionSet;
std::vector<int> angleParamIndex;
int thetaIndex;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
......@@ -51,7 +51,8 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomAngleIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters,
const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions);
/**---------------------------------------------------------------------------------------
......@@ -85,7 +86,7 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
RealOpenMM* totalEnergy, double* energyParamDerivs);
};
......
platforms/reference/include/ReferenceCustomBondIxn.h
View file @ a381a3ab
......@@ -26,7 +26,7 @@
#define __ReferenceCustomBondIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/CompiledExpression.h"
#include "openmm/internal/CompiledExpressionSet.h"
namespace OpenMM {
......@@ -35,10 +35,10 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
private:
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams;
std::vector<double*> forceParams;
double* energyR;
double* forceR;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
CompiledExpressionSet expressionSet;
std::vector<int> bondParamIndex;
int rIndex;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
......@@ -52,7 +52,8 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters,
const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions);
/**---------------------------------------------------------------------------------------
......@@ -86,7 +87,7 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
RealOpenMM* totalEnergy, double* energyParamDerivs);
};
......
platforms/reference/include/ReferenceCustomCentroidBondIxn.h
View file @ a381a3ab
......@@ -26,7 +26,7 @@
#define __ReferenceCustomCentroidBondIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/ExpressionProgram.h"
#include "openmm/internal/CompiledExpressionSet.h"
#include "lepton/ParsedExpression.h"
#include <map>
#include <vector>
......@@ -44,12 +44,15 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
std::vector<std::vector<int> > groupAtoms;
std::vector<std::vector<double> > normalizedWeights;
std::vector<std::vector<int> > bondGroups;
Lepton::ExpressionProgram energyExpression;
std::vector<std::string> bondParamNames;
CompiledExpressionSet expressionSet;
Lepton::CompiledExpression energyExpression;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<int> bondParamIndex;
std::vector<PositionTermInfo> positionTerms;
std::vector<DistanceTermInfo> distanceTerms;
std::vector<AngleTermInfo> angleTerms;
std::vector<DihedralTermInfo> dihedralTerms;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
......@@ -60,15 +63,13 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
@param bond the index of the bond
@param groupCenters group center coordinates
@param variables the values of variables that may appear in expressions
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateOneIxn(int bond, std::vector<OpenMM::RealVec>& groupCenters,
std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs);
void computeDelta(int group1, int group2, RealOpenMM* delta, std::vector<OpenMM::RealVec>& groupCenters) const;
......@@ -86,7 +87,8 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
ReferenceCustomCentroidBondIxn(int numGroupsPerBond, const std::vector<std::vector<int> >& groupAtoms,
const std::vector<std::vector<double> >& normalizedWeights, const std::vector<std::vector<int> >& bondGroups, const Lepton::ParsedExpression& energyExpression,
const std::vector<std::string>& bondParameterNames, const std::map<std::string, std::vector<int> >& distances,
const std::map<std::string, std::vector<int> >& angles, const std::map<std::string, std::vector<int> >& dihedrals);
const std::map<std::string, std::vector<int> >& angles, const std::map<std::string, std::vector<int> >& dihedrals,
const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions);
/**---------------------------------------------------------------------------------------
......@@ -130,7 +132,7 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
void calculatePairIxn(std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** bondParameters,
const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy) const;
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs);
// ---------------------------------------------------------------------------------------
......@@ -139,9 +141,9 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
class ReferenceCustomCentroidBondIxn::PositionTermInfo {
public:
std::string name;
int group, component;
Lepton::ExpressionProgram forceExpression;
PositionTermInfo(const std::string& name, int group, int component, const Lepton::ExpressionProgram& forceExpression) :
int group, component, index;
Lepton::CompiledExpression forceExpression;
PositionTermInfo(const std::string& name, int group, int component, const Lepton::CompiledExpression& forceExpression) :
name(name), group(group), component(component), forceExpression(forceExpression) {
}
};
......@@ -149,10 +151,10 @@ public:
class ReferenceCustomCentroidBondIxn::DistanceTermInfo {
public:
std::string name;
int g1, g2;
Lepton::ExpressionProgram forceExpression;
int g1, g2, index;
Lepton::CompiledExpression forceExpression;
mutable RealOpenMM delta[ReferenceForce::LastDeltaRIndex];
DistanceTermInfo(const std::string& name, const std::vector<int>& groups, const Lepton::ExpressionProgram& forceExpression) :
DistanceTermInfo(const std::string& name, const std::vector<int>& groups, const Lepton::CompiledExpression& forceExpression) :
name(name), g1(groups[0]), g2(groups[1]), forceExpression(forceExpression) {
}
};
......@@ -160,11 +162,11 @@ public:
class ReferenceCustomCentroidBondIxn::AngleTermInfo {
public:
std::string name;
int g1, g2, g3;
Lepton::ExpressionProgram forceExpression;
int g1, g2, g3, index;
Lepton::CompiledExpression forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex];
AngleTermInfo(const std::string& name, const std::vector<int>& groups, const Lepton::ExpressionProgram& forceExpression) :
AngleTermInfo(const std::string& name, const std::vector<int>& groups, const Lepton::CompiledExpression& forceExpression) :
name(name), g1(groups[0]), g2(groups[1]), g3(groups[2]), forceExpression(forceExpression) {
}
};
......@@ -172,14 +174,14 @@ public:
class ReferenceCustomCentroidBondIxn::DihedralTermInfo {
public:
std::string name;
int g1, g2, g3, g4;
Lepton::ExpressionProgram forceExpression;
int g1, g2, g3, g4, index;
Lepton::CompiledExpression forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta3[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM cross1[3];
mutable RealOpenMM cross2[3];
DihedralTermInfo(const std::string& name, const std::vector<int>& groups, const Lepton::ExpressionProgram& forceExpression) :
DihedralTermInfo(const std::string& name, const std::vector<int>& groups, const Lepton::CompiledExpression& forceExpression) :
name(name), g1(groups[0]), g2(groups[1]), g3(groups[2]), g4(groups[3]), forceExpression(forceExpression) {
}
};
......
platforms/reference/include/ReferenceCustomCompoundBondIxn.h
View file @ a381a3ab
......@@ -26,7 +26,7 @@
#define __ReferenceCustomCompoundBondIxn_H__
#include "ReferenceBondIxn.h"
#include "lepton/ExpressionProgram.h"
#include "openmm/internal/CompiledExpressionSet.h"
#include "lepton/ParsedExpression.h"
#include <map>
#include <vector>
......@@ -42,12 +42,15 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
class AngleTermInfo;
class DihedralTermInfo;
std::vector<std::vector<int> > bondAtoms;
Lepton::ExpressionProgram energyExpression;
std::vector<std::string> bondParamNames;
CompiledExpressionSet expressionSet;
Lepton::CompiledExpression energyExpression;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<int> bondParamIndex;
std::vector<ParticleTermInfo> particleTerms;
std::vector<DistanceTermInfo> distanceTerms;
std::vector<AngleTermInfo> angleTerms;
std::vector<DihedralTermInfo> dihedralTerms;
int numParameters;
bool usePeriodic;
RealVec boxVectors[3];
......@@ -58,15 +61,13 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
@param bond the index of the bond
@param atomCoordinates atom coordinates
@param variables the values of variables that may appear in expressions
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateOneIxn(int bond, std::vector<OpenMM::RealVec>& atomCoordinates,
std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const;
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs);
void computeDelta(int atom1, int atom2, RealOpenMM* delta, std::vector<OpenMM::RealVec>& atomCoordinates) const;
......@@ -83,7 +84,8 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
ReferenceCustomCompoundBondIxn(int numParticlesPerBond, const std::vector<std::vector<int> >& bondAtoms, const Lepton::ParsedExpression& energyExpression,
const std::vector<std::string>& bondParameterNames, const std::map<std::string, std::vector<int> >& distances,
const std::map<std::string, std::vector<int> >& angles, const std::map<std::string, std::vector<int> >& dihedrals);
const std::map<std::string, std::vector<int> >& angles, const std::map<std::string, std::vector<int> >& dihedrals,
const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions);
/**---------------------------------------------------------------------------------------
......@@ -127,7 +129,7 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
void calculatePairIxn(std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** bondParameters,
const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy) const;
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs);
// ---------------------------------------------------------------------------------------
......@@ -136,9 +138,9 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
class ReferenceCustomCompoundBondIxn::ParticleTermInfo {
public:
std::string name;
int atom, component;
Lepton::ExpressionProgram forceExpression;
ParticleTermInfo(const std::string& name, int atom, int component, const Lepton::ExpressionProgram& forceExpression) :
int atom, component, index;
Lepton::CompiledExpression forceExpression;
ParticleTermInfo(const std::string& name, int atom, int component, const Lepton::CompiledExpression& forceExpression) :
name(name), atom(atom), component(component), forceExpression(forceExpression) {
}
};
......@@ -146,10 +148,10 @@ public:
class ReferenceCustomCompoundBondIxn::DistanceTermInfo {
public:
std::string name;
int p1, p2;
Lepton::ExpressionProgram forceExpression;
int p1, p2, index;
Lepton::CompiledExpression forceExpression;
mutable RealOpenMM delta[ReferenceForce::LastDeltaRIndex];
DistanceTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
DistanceTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::CompiledExpression& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), forceExpression(forceExpression) {
}
};
......@@ -157,11 +159,11 @@ public:
class ReferenceCustomCompoundBondIxn::AngleTermInfo {
public:
std::string name;
int p1, p2, p3;
Lepton::ExpressionProgram forceExpression;
int p1, p2, p3, index;
Lepton::CompiledExpression forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex];
AngleTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
AngleTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::CompiledExpression& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), forceExpression(forceExpression) {
}
};
......@@ -169,14 +171,14 @@ public:
class ReferenceCustomCompoundBondIxn::DihedralTermInfo {
public:
std::string name;
int p1, p2, p3, p4;
Lepton::ExpressionProgram forceExpression;
int p1, p2, p3, p4, index;
Lepton::CompiledExpression forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta3[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM cross1[3];
mutable RealOpenMM cross2[3];
DihedralTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::ExpressionProgram& forceExpression) :
DihedralTermInfo(const std::string& name, const std::vector<int>& atoms, const Lepton::CompiledExpression& forceExpression) :
name(name), p1(atoms[0]), p2(atoms[1]), p3(atoms[2]), p4(atoms[3]), forceExpression(forceExpression) {
}
};
......
platforms/reference/include/ReferenceCustomDynamics.h
View file @ a381a3ab
......@@ -41,6 +41,7 @@ namespace OpenMM {
class ReferenceCustomDynamics : public ReferenceDynamics {
private:
class DerivFunction;
const OpenMM::CustomIntegrator& integrator;
std::vector<RealOpenMM> inverseMasses;
std::vector<OpenMM::RealVec> sumBuffer, oldPos;
......@@ -51,6 +52,7 @@ private:
std::vector<bool> invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy;
std::vector<int> forceGroupFlags, blockEnd;
RealOpenMM energy;
std::map<std::string, double> energyParamDerivs;
Lepton::CompiledExpression kineticEnergyExpression;
bool kineticEnergyNeedsForce;
CompiledExpressionSet expressionSet;
......@@ -59,6 +61,8 @@ private:
void initialize(OpenMM::ContextImpl& context, std::vector<RealOpenMM>& masses, std::map<std::string, RealOpenMM>& globals);
Lepton::ExpressionTreeNode replaceDerivFunctions(const Lepton::ExpressionTreeNode& node, OpenMM::ContextImpl& context);
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::vector<std::vector<OpenMM::RealVec> >& perDof, const Lepton::CompiledExpression& expression, int forceIndex);
......
platforms/reference/include/ReferenceCustomGBIxn.h
View file @ a381a3ab
/* Portions copyright (c) 2009 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
......@@ -26,7 +26,7 @@
#define __ReferenceCustomGBIxn_H__
#include "ReferenceNeighborList.h"
#include "lepton/ExpressionProgram.h"
#include "openmm/internal/CompiledExpressionSet.h"
#include "openmm/CustomGBForce.h"
#include <map>
#include <set>
......@@ -43,18 +43,24 @@ class ReferenceCustomGBIxn {
const OpenMM::NeighborList* neighborList;
OpenMM::RealVec periodicBoxVectors[3];
RealOpenMM cutoffDistance;
std::vector<Lepton::ExpressionProgram> valueExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > valueDerivExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > valueGradientExpressions;
std::vector<std::string> valueNames;
CompiledExpressionSet expressionSet;
std::vector<Lepton::CompiledExpression> valueExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueGradientExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueParamDerivExpressions;
std::vector<OpenMM::CustomGBForce::ComputationType> valueTypes;
std::vector<Lepton::ExpressionProgram> energyExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > energyDerivExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > energyGradientExpressions;
std::vector<std::string> paramNames;
std::vector<Lepton::CompiledExpression> energyExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyGradientExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyParamDerivExpressions;
std::vector<OpenMM::CustomGBForce::ComputationType> energyTypes;
std::vector<std::string> particleParamNames;
std::vector<std::string> particleValueNames;
std::vector<int> paramIndex;
std::vector<int> valueIndex;
std::vector<int> particleParamIndex;
std::vector<int> particleValueIndex;
int rIndex, xIndex, yIndex, zIndex;
std::vector<std::vector<RealOpenMM> > values, dEdV;
std::vector<std::vector<std::vector<RealOpenMM> > > dValuedParam;
/**---------------------------------------------------------------------------------------
......@@ -63,14 +69,11 @@ class ReferenceCustomGBIxn {
@param index the index of the value to compute
@param numAtoms number of atoms
@param atomCoordinates atom coordinates
@param values the vector to store computed values into
@param globalParameters the values of global parameters
@param atomParameters atomParameters[atomIndex][paramterIndex]
--------------------------------------------------------------------------------------- */
void calculateSingleParticleValue(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<std::vector<RealOpenMM> >& values,
const std::map<std::string, double>& globalParameters, RealOpenMM** atomParameters) const;
void calculateSingleParticleValue(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters);
/**---------------------------------------------------------------------------------------
......@@ -80,17 +83,13 @@ class ReferenceCustomGBIxn {
@param numAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param values the vector to store computed values into
@param globalParameters the values of global parameters
@param exclusions exclusions[i] is the set of excluded indices for atom i
@param useExclusions specifies whether to use exclusions
--------------------------------------------------------------------------------------- */
void calculateParticlePairValue(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
std::vector<std::vector<RealOpenMM> >& values,
const std::map<std::string, double>& globalParameters,
const std::vector<std::set<int> >& exclusions, bool useExclusions) const;
const std::vector<std::set<int> >& exclusions, bool useExclusions);
/**---------------------------------------------------------------------------------------
......@@ -101,14 +100,10 @@ class ReferenceCustomGBIxn {
@param atom2 the index of the second atom in the pair
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param globalParameters the values of global parameters
@param values the vector to store computed values into
--------------------------------------------------------------------------------------- */
void calculateOnePairValue(int index, int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::map<std::string, double>& globalParameters,
std::vector<std::vector<RealOpenMM> >& values) const;
void calculateOnePairValue(int index, int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters);
/**---------------------------------------------------------------------------------------
......@@ -117,18 +112,14 @@ class ReferenceCustomGBIxn {
@param index the index of the value to compute
@param numAtoms number of atoms
@param atomCoordinates atom coordinates
@param values the vector containing computed values
@param globalParameters the values of global parameters
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param forces forces on atoms are added to this
@param totalEnergy the energy contribution is added to this
@param dEdV the derivative of energy with respect to computed values is stored in this
--------------------------------------------------------------------------------------- */
void calculateSingleParticleEnergyTerm(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, const std::vector<std::vector<RealOpenMM> >& values,
const std::map<std::string, double>& globalParameters, RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV) const;
void calculateSingleParticleEnergyTerm(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs);
/**---------------------------------------------------------------------------------------
......@@ -138,21 +129,16 @@ class ReferenceCustomGBIxn {
@param numAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param values the vector containing computed values
@param globalParameters the values of global parameters
@param exclusions exclusions[i] is the set of excluded indices for atom i
@param useExclusions specifies whether to use exclusions
@param forces forces on atoms are added to this
@param totalEnergy the energy contribution is added to this
@param dEdV the derivative of energy with respect to computed values is stored in this
--------------------------------------------------------------------------------------- */
void calculateParticlePairEnergyTerm(int index, int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::vector<std::vector<RealOpenMM> >& values,
const std::map<std::string, double>& globalParameters,
const std::vector<std::set<int> >& exclusions, bool useExclusions,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV) const;
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs);
/**---------------------------------------------------------------------------------------
......@@ -163,18 +149,13 @@ class ReferenceCustomGBIxn {
@param atom2 the index of the second atom in the pair
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param globalParameters the values of global parameters
@param values the vector containing computed values
@param forces forces on atoms are added to this
@param totalEnergy the energy contribution is added to this
@param dEdV the derivative of energy with respect to computed values is stored in this
--------------------------------------------------------------------------------------- */
void calculateOnePairEnergyTerm(int index, int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::map<std::string, double>& globalParameters,
const std::vector<std::vector<RealOpenMM> >& values,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, std::vector<std::vector<RealOpenMM> >& dEdV) const;
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs);
/**---------------------------------------------------------------------------------------
......@@ -183,19 +164,13 @@ class ReferenceCustomGBIxn {
@param numAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param values the vector containing computed values
@param globalParameters the values of global parameters
@param exclusions exclusions[i] is the set of excluded indices for atom i
@param forces forces on atoms are added to this
@param dEdV the derivative of energy with respect to computed values is stored in this
--------------------------------------------------------------------------------------- */
void calculateChainRuleForces(int numAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::vector<std::vector<RealOpenMM> >& values,
const std::map<std::string, double>& globalParameters,
const std::vector<std::set<int> >& exclusions,
std::vector<OpenMM::RealVec>& forces, std::vector<std::vector<RealOpenMM> >& dEdV) const;
const std::vector<std::set<int> >& exclusions, std::vector<OpenMM::RealVec>& forces, double* energyParamDerivs);
/**---------------------------------------------------------------------------------------
......@@ -205,19 +180,13 @@ class ReferenceCustomGBIxn {
@param atom2 the index of the second atom in the pair
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][paramterIndex]
@param globalParameters the values of global parameters
@param values the vector containing computed values
@param forces forces on atoms are added to this
@param dEdV the derivative of energy with respect to computed values is stored in this
@param isExcluded specifies whether this is an excluded pair
--------------------------------------------------------------------------------------- */
void calculateOnePairChainRule(int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const std::map<std::string, double>& globalParameters,
const std::vector<std::vector<RealOpenMM> >& values,
std::vector<OpenMM::RealVec>& forces, std::vector<std::vector<RealOpenMM> >& dEdV,
bool isExcluded) const;
std::vector<OpenMM::RealVec>& forces, bool isExcluded);
public:
......@@ -227,14 +196,16 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomGBIxn(const std::vector<Lepton::ExpressionProgram>& valueExpressions,
const std::vector<std::vector<Lepton::ExpressionProgram> > valueDerivExpressions,
const std::vector<std::vector<Lepton::ExpressionProgram> > valueGradientExpressions,
ReferenceCustomGBIxn(const std::vector<Lepton::CompiledExpression>& valueExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> > valueGradientExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> > valueParamDerivExpressions,
const std::vector<std::string>& valueNames,
const std::vector<OpenMM::CustomGBForce::ComputationType>& valueTypes,
const std::vector<Lepton::ExpressionProgram>& energyExpressions,
const std::vector<std::vector<Lepton::ExpressionProgram> > energyDerivExpressions,
const std::vector<std::vector<Lepton::ExpressionProgram> > energyGradientExpressions,
const std::vector<Lepton::CompiledExpression>& energyExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> > energyDerivExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> > energyGradientExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> > energyParamDerivExpressions,
const std::vector<OpenMM::CustomGBForce::ComputationType>& energyTypes,
const std::vector<std::string>& parameterNames);
......@@ -284,7 +255,7 @@ class ReferenceCustomGBIxn {
--------------------------------------------------------------------------------------- */
void calculateIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters, const std::vector<std::set<int> >& exclusions,
std::map<std::string, double>& globalParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy) const;
std::map<std::string, double>& globalParameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs);
// ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomNonbondedIxn.h
View file @ a381a3ab
/* 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
......@@ -27,7 +27,7 @@
#include "ReferencePairIxn.h"
#include "ReferenceNeighborList.h"
#include "lepton/CompiledExpression.h"
#include "openmm/internal/CompiledExpressionSet.h"
#include <map>
#include <set>
#include <utility>
......@@ -48,10 +48,10 @@ class ReferenceCustomNonbondedIxn {
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
std::vector<std::string> paramNames;
std::vector<double*> energyParticleParams;
std::vector<double*> forceParticleParams;
double* energyR;
double* forceR;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
CompiledExpressionSet expressionSet;
std::vector<int> particleParamIndex;
int rIndex;
std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
/**---------------------------------------------------------------------------------------
......@@ -69,7 +69,7 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
void calculateOneIxn(int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy);
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, double* energyParamDerivs);
public:
......@@ -81,7 +81,7 @@ class ReferenceCustomNonbondedIxn {
--------------------------------------------------------------------------------------- */
ReferenceCustomNonbondedIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames);
const std::vector<std::string>& parameterNames, const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions);
/**---------------------------------------------------------------------------------------
......@@ -155,7 +155,8 @@ class ReferenceCustomNonbondedIxn {
void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions,
RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy);
std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy,
double* energyParamDerivs);
// ---------------------------------------------------------------------------------------
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment