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Commit 1f7866ad authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #1547 from peastman/paramderivs 

Energy derivatives with respect to global parameters
parents 37787af9 7851bad8
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Showing with 208 additions and 160 deletions
platforms/opencl/src/kernels/customCentroidBond.cl
View file @ 1f7866ad
...@@ -116,10 +116,12 @@ __kernel void computeGroupForces(__global long* restrict groupForce, __global mi ...@@ -116,10 +116,12 @@ __kernel void computeGroupForces(__global long* restrict groupForce, __global mi
__global const int* restrict bondGroups, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ __global const int* restrict bondGroups, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ
EXTRA_ARGS) { EXTRA_ARGS) {
mixed energy = 0; mixed energy = 0;
INIT_PARAM_DERIVS
for (int index = get_global_id(0); index < NUM_BONDS; index += get_global_size(0)) { for (int index = get_global_id(0); index < NUM_BONDS; index += get_global_size(0)) {
COMPUTE_FORCE COMPUTE_FORCE
} }
energyBuffer[get_global_id(0)] += energy; energyBuffer[get_global_id(0)] += energy;
SAVE_PARAM_DERIVS
} }
/** /**
......
platforms/opencl/src/kernels/customGBEnergyN2.cl
View file @ 1f7866ad
...@@ -32,6 +32,7 @@ __kernel void computeN2Energy( ...@@ -32,6 +32,7 @@ __kernel void computeN2Energy(
const unsigned int tgx = get_local_id(0) & (TILE_SIZE-1); const unsigned int tgx = get_local_id(0) & (TILE_SIZE-1);
const unsigned int tbx = get_local_id(0) - tgx; const unsigned int tbx = get_local_id(0) - tgx;
mixed energy = 0; mixed energy = 0;
INIT_PARAM_DERIVS
// First loop: process tiles that contain exclusions. // First loop: process tiles that contain exclusions.
...@@ -73,6 +74,7 @@ __kernel void computeN2Energy( ...@@ -73,6 +74,7 @@ __kernel void computeN2Energy(
atom2 = y*TILE_SIZE+j; atom2 = y*TILE_SIZE+j;
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 0.5f;
#ifdef USE_EXCLUSIONS #ifdef USE_EXCLUSIONS
bool isExcluded = !(excl & 0x1); bool isExcluded = !(excl & 0x1);
#endif #endif
...@@ -123,6 +125,7 @@ __kernel void computeN2Energy( ...@@ -123,6 +125,7 @@ __kernel void computeN2Energy(
atom2 = y*TILE_SIZE+tj; atom2 = y*TILE_SIZE+tj;
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
#ifdef USE_EXCLUSIONS #ifdef USE_EXCLUSIONS
bool isExcluded = !(excl & 0x1); bool isExcluded = !(excl & 0x1);
#endif #endif
...@@ -281,6 +284,7 @@ __kernel void computeN2Energy( ...@@ -281,6 +284,7 @@ __kernel void computeN2Energy(
atom2 = atomIndices[tbx+tj]; atom2 = atomIndices[tbx+tj];
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) { if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
COMPUTE_INTERACTION COMPUTE_INTERACTION
dEdR /= -r; dEdR /= -r;
...@@ -319,6 +323,7 @@ __kernel void computeN2Energy( ...@@ -319,6 +323,7 @@ __kernel void computeN2Energy(
atom2 = atomIndices[tbx+tj]; atom2 = atomIndices[tbx+tj];
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) { if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
COMPUTE_INTERACTION COMPUTE_INTERACTION
dEdR /= -r; dEdR /= -r;
...@@ -373,4 +378,5 @@ __kernel void computeN2Energy( ...@@ -373,4 +378,5 @@ __kernel void computeN2Energy(
pos++; pos++;
} }
energyBuffer[get_global_id(0)] += energy; energyBuffer[get_global_id(0)] += energy;
SAVE_PARAM_DERIVS
} }
platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl
View file @ 1f7866ad
...@@ -28,6 +28,7 @@ __kernel void computeN2Energy( ...@@ -28,6 +28,7 @@ __kernel void computeN2Energy(
#endif #endif
PARAMETER_ARGUMENTS) { PARAMETER_ARGUMENTS) {
mixed energy = 0; mixed energy = 0;
INIT_PARAM_DERIVS
// First loop: process tiles that contain exclusions. // First loop: process tiles that contain exclusions.
...@@ -74,6 +75,7 @@ __kernel void computeN2Energy( ...@@ -74,6 +75,7 @@ __kernel void computeN2Energy(
atom2 = y*TILE_SIZE+j; atom2 = y*TILE_SIZE+j;
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 0.5f;
#ifdef USE_EXCLUSIONS #ifdef USE_EXCLUSIONS
bool isExcluded = !(excl & 0x1); bool isExcluded = !(excl & 0x1);
#endif #endif
...@@ -140,6 +142,7 @@ __kernel void computeN2Energy( ...@@ -140,6 +142,7 @@ __kernel void computeN2Energy(
atom2 = y*TILE_SIZE+j; atom2 = y*TILE_SIZE+j;
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
#ifdef USE_EXCLUSIONS #ifdef USE_EXCLUSIONS
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1)); bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
if (!isExcluded) { if (!isExcluded) {
...@@ -291,6 +294,7 @@ __kernel void computeN2Energy( ...@@ -291,6 +294,7 @@ __kernel void computeN2Energy(
atom2 = atomIndices[j]; atom2 = atomIndices[j];
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION COMPUTE_INTERACTION
dEdR /= -r; dEdR /= -r;
energy += tempEnergy; energy += tempEnergy;
...@@ -347,6 +351,7 @@ __kernel void computeN2Energy( ...@@ -347,6 +351,7 @@ __kernel void computeN2Energy(
atom2 = atomIndices[j]; atom2 = atomIndices[j];
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION COMPUTE_INTERACTION
dEdR /= -r; dEdR /= -r;
energy += tempEnergy; energy += tempEnergy;
...@@ -400,4 +405,5 @@ __kernel void computeN2Energy( ...@@ -400,4 +405,5 @@ __kernel void computeN2Energy(
pos++; pos++;
} }
energyBuffer[get_global_id(0)] += energy; energyBuffer[get_global_id(0)] += energy;
SAVE_PARAM_DERIVS
} }
platforms/opencl/src/kernels/customGBEnergyPerParticle.cl
View file @ 1f7866ad
...@@ -12,6 +12,7 @@ ...@@ -12,6 +12,7 @@
__kernel void computePerParticleEnergy(int bufferSize, int numBuffers, __global real4* restrict forceBuffers, __global mixed* restrict energyBuffer, __global const real4* restrict posq __kernel void computePerParticleEnergy(int bufferSize, int numBuffers, __global real4* restrict forceBuffers, __global mixed* restrict energyBuffer, __global const real4* restrict posq
PARAMETER_ARGUMENTS) { PARAMETER_ARGUMENTS) {
mixed energy = 0; mixed energy = 0;
INIT_PARAM_DERIVS
unsigned int index = get_global_id(0); unsigned int index = get_global_id(0);
while (index < NUM_ATOMS) { while (index < NUM_ATOMS) {
// Reduce the derivatives // Reduce the derivatives
...@@ -27,4 +28,5 @@ __kernel void computePerParticleEnergy(int bufferSize, int numBuffers, __global ...@@ -27,4 +28,5 @@ __kernel void computePerParticleEnergy(int bufferSize, int numBuffers, __global
index += get_global_size(0); index += get_global_size(0);
} }
energyBuffer[get_global_id(0)] += energy; energyBuffer[get_global_id(0)] += energy;
SAVE_PARAM_DERIVS
} }
platforms/opencl/src/kernels/customGBGradientChainRule.cl
View file @ 1f7866ad
...@@ -4,6 +4,7 @@ ...@@ -4,6 +4,7 @@
__kernel void computeGradientChainRuleTerms(__global real4* restrict forceBuffers, __global const real4* restrict posq __kernel void computeGradientChainRuleTerms(__global real4* restrict forceBuffers, __global const real4* restrict posq
PARAMETER_ARGUMENTS) { PARAMETER_ARGUMENTS) {
INIT_PARAM_DERIVS
unsigned int index = get_global_id(0); unsigned int index = get_global_id(0);
while (index < NUM_ATOMS) { while (index < NUM_ATOMS) {
real4 pos = posq[index]; real4 pos = posq[index];
...@@ -12,4 +13,5 @@ __kernel void computeGradientChainRuleTerms(__global real4* restrict forceBuffer ...@@ -12,4 +13,5 @@ __kernel void computeGradientChainRuleTerms(__global real4* restrict forceBuffer
forceBuffers[index] = force; forceBuffers[index] = force;
index += get_global_size(0); index += get_global_size(0);
} }
SAVE_PARAM_DERIVS
} }
platforms/opencl/src/kernels/customGBValueN2.cl
View file @ 1f7866ad
...@@ -74,6 +74,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -74,6 +74,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
COMPUTE_VALUE COMPUTE_VALUE
} }
value += tempValue1; value += tempValue1;
ADD_TEMP_DERIVS1
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
} }
#endif #endif
...@@ -123,6 +124,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -123,6 +124,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
} }
value += tempValue1; value += tempValue1;
local_value[tbx+tj] += tempValue2; local_value[tbx+tj] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
} }
#endif #endif
...@@ -137,18 +140,23 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -137,18 +140,23 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
// Write results. // Write results.
#ifdef SUPPORTS_64_BIT_ATOMICS #ifdef SUPPORTS_64_BIT_ATOMICS
unsigned int offset = x*TILE_SIZE + tgx; unsigned int offset1 = x*TILE_SIZE + tgx;
atom_add(&global_value[offset], (long) (value*0x100000000)); atom_add(&global_value[offset1], (long) (value*0x100000000));
STORE_PARAM_DERIVS1
if (x != y) { if (x != y) {
offset = y*TILE_SIZE + tgx; unsigned int offset2 = y*TILE_SIZE + tgx;
atom_add(&global_value[offset], (long) (local_value[get_local_id(0)]*0x100000000)); atom_add(&global_value[offset2], (long) (local_value[get_local_id(0)]*0x100000000));
STORE_PARAM_DERIVS2
} }
#else #else
unsigned int offset1 = x*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS; unsigned int offset1 = x*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS;
unsigned int offset2 = y*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS; unsigned int offset2 = y*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS;
global_value[offset1] += value; global_value[offset1] += value;
if (x != y) STORE_PARAM_DERIVS1
if (x != y) {
global_value[offset2] += local_value[get_local_id(0)]; global_value[offset2] += local_value[get_local_id(0)];
STORE_PARAM_DERIVS2
}
#endif #endif
} }
...@@ -259,6 +267,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -259,6 +267,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
} }
value += tempValue1; value += tempValue1;
local_value[tbx+tj] += tempValue2; local_value[tbx+tj] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
} }
tj = (tj + 1) & (TILE_SIZE - 1); tj = (tj + 1) & (TILE_SIZE - 1);
SYNC_WARPS; SYNC_WARPS;
...@@ -292,6 +302,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -292,6 +302,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
} }
value += tempValue1; value += tempValue1;
local_value[tbx+tj] += tempValue2; local_value[tbx+tj] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
} }
#endif #endif
...@@ -308,15 +320,23 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -308,15 +320,23 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
unsigned int atom2 = y*TILE_SIZE + tgx; unsigned int atom2 = y*TILE_SIZE + tgx;
#endif #endif
#ifdef SUPPORTS_64_BIT_ATOMICS #ifdef SUPPORTS_64_BIT_ATOMICS
atom_add(&global_value[atom1], (long) (value*0x100000000)); unsigned int offset1 = atom1;
if (atom2 < PADDED_NUM_ATOMS) atom_add(&global_value[offset1], (long) (value*0x100000000));
atom_add(&global_value[atom2], (long) (local_value[get_local_id(0)]*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 #else
unsigned int offset1 = atom1 + warp*PADDED_NUM_ATOMS; unsigned int offset1 = atom1 + warp*PADDED_NUM_ATOMS;
unsigned int offset2 = atom2 + warp*PADDED_NUM_ATOMS;
global_value[offset1] += value; 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)]; global_value[offset2] += local_value[get_local_id(0)];
STORE_PARAM_DERIVS2
}
#endif #endif
} }
pos++; pos++;
......
platforms/opencl/src/kernels/customGBValueN2_cpu.cl
View file @ 1f7866ad
...@@ -75,6 +75,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -75,6 +75,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
COMPUTE_VALUE COMPUTE_VALUE
} }
value += tempValue1; value += tempValue1;
ADD_TEMP_DERIVS1
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
} }
#endif #endif
...@@ -86,11 +87,13 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -86,11 +87,13 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
// Write results. // Write results.
#ifdef SUPPORTS_64_BIT_ATOMICS #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 #else
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS; unsigned int offset1 = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value; global_value[offset1] += value;
#endif #endif
STORE_PARAM_DERIVS1
} }
} }
else { else {
...@@ -133,6 +136,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -133,6 +136,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
} }
value += tempValue1; value += tempValue1;
local_value[j] += tempValue2; local_value[j] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
} }
#endif #endif
...@@ -144,23 +149,26 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -144,23 +149,26 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
// Write results for atom1. // Write results for atom1.
#ifdef SUPPORTS_64_BIT_ATOMICS #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 #else
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS; unsigned int offset1 = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value; global_value[offset1] += value;
#endif #endif
STORE_PARAM_DERIVS1
} }
// Write results. // Write results.
for (int tgx = 0; tgx < TILE_SIZE; tgx++) { for (int tgx = 0; tgx < TILE_SIZE; tgx++) {
#ifdef SUPPORTS_64_BIT_ATOMICS #ifdef SUPPORTS_64_BIT_ATOMICS
unsigned int offset = y*TILE_SIZE+tgx; unsigned int offset2 = y*TILE_SIZE+tgx;
atom_add(&global_value[offset], (long) (local_value[tgx]*0x100000000)); atom_add(&global_value[offset2], (long) (local_value[tgx]*0x100000000));
#else #else
unsigned int offset = y*TILE_SIZE+tgx + get_group_id(0)*PADDED_NUM_ATOMS; unsigned int offset2 = y*TILE_SIZE+tgx + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += local_value[tgx]; global_value[offset2] += local_value[tgx];
#endif #endif
STORE_PARAM_DERIVS2
} }
} }
} }
...@@ -260,17 +268,21 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -260,17 +268,21 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
COMPUTE_VALUE COMPUTE_VALUE
value += tempValue1; value += tempValue1;
local_value[j] += tempValue2; local_value[j] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
} }
} }
// Write results for atom1. // Write results for atom1.
#ifdef SUPPORTS_64_BIT_ATOMICS #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 #else
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS; unsigned int offset1 = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value; global_value[offset1] += value;
#endif #endif
STORE_PARAM_DERIVS1
} }
} }
else else
...@@ -305,17 +317,21 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -305,17 +317,21 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
COMPUTE_VALUE COMPUTE_VALUE
value += tempValue1; value += tempValue1;
local_value[j] += tempValue2; local_value[j] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
} }
} }
// Write results for atom1. // Write results for atom1.
#ifdef SUPPORTS_64_BIT_ATOMICS #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 #else
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS; unsigned int offset1 = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value; global_value[offset1] += value;
#endif #endif
STORE_PARAM_DERIVS1
} }
} }
...@@ -329,11 +345,13 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -329,11 +345,13 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
#endif #endif
if (atom2 < PADDED_NUM_ATOMS) { if (atom2 < PADDED_NUM_ATOMS) {
#ifdef SUPPORTS_64_BIT_ATOMICS #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 #else
unsigned int offset = atom2 + get_group_id(0)*PADDED_NUM_ATOMS; unsigned int offset2 = atom2 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += local_value[tgx]; global_value[offset2] += local_value[tgx];
#endif #endif
STORE_PARAM_DERIVS2
} }
} }
} }
......
platforms/opencl/src/kernels/customGBValuePerParticle.cl
View file @ 1f7866ad
...@@ -21,6 +21,7 @@ __kernel void computePerParticleValues(int bufferSize, int numBuffers, __global ...@@ -21,6 +21,7 @@ __kernel void computePerParticleValues(int bufferSize, int numBuffers, __global
for (int i = index+bufferSize; i < totalSize; i += bufferSize) for (int i = index+bufferSize; i < totalSize; i += bufferSize)
sum += valueBuffers[i]; sum += valueBuffers[i];
#endif #endif
REDUCE_PARAM0_DERIV
// Now calculate other values // Now calculate other values
......
platforms/opencl/src/kernels/customIntegratorPerDof.cl
View file @ 1f7866ad
...@@ -25,7 +25,8 @@ void storePos(__global real4* restrict posq, __global real4* restrict posqCorrec ...@@ -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, __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 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) { PARAMETER_ARGUMENTS) {
mixed stepSize = dt[0].y; mixed stepSize = dt[0].y;
int index = get_global_id(0); int index = get_global_id(0);
......
platforms/opencl/src/kernels/customNonbonded.cl
View file @ 1f7866ad
...@@ -4,15 +4,18 @@ if (!isExcluded && r2 < CUTOFF_SQUARED) { ...@@ -4,15 +4,18 @@ if (!isExcluded && r2 < CUTOFF_SQUARED) {
if (!isExcluded) { if (!isExcluded) {
#endif #endif
real tempForce = 0.0f; real tempForce = 0.0f;
COMPUTE_FORCE real switchValue = 1, switchDeriv = 0;
#if USE_SWITCH #if USE_SWITCH
if (r > SWITCH_CUTOFF) { if (r > SWITCH_CUTOFF) {
real x = r-SWITCH_CUTOFF; real x = r-SWITCH_CUTOFF;
real switchValue = 1+x*x*x*(SWITCH_C3+x*(SWITCH_C4+x*SWITCH_C5)); 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)); switchDeriv = x*x*(3*SWITCH_C3+x*(4*SWITCH_C4+x*5*SWITCH_C5));
tempForce = tempForce*switchValue - tempEnergy*switchDeriv;
tempEnergy *= switchValue;
} }
#endif
COMPUTE_FORCE
#if USE_SWITCH
tempForce = tempForce*switchValue - tempEnergy*switchDeriv;
tempEnergy *= switchValue;
#endif #endif
dEdR += tempForce*invR; dEdR += tempForce*invR;
} }
platforms/opencl/src/kernels/nonbonded.cl
View file @ 1f7866ad
...@@ -35,6 +35,7 @@ __kernel void computeNonbonded( ...@@ -35,6 +35,7 @@ __kernel void computeNonbonded(
const unsigned int tgx = get_local_id(0) & (TILE_SIZE-1); const unsigned int tgx = get_local_id(0) & (TILE_SIZE-1);
const unsigned int tbx = get_local_id(0) - tgx; const unsigned int tbx = get_local_id(0) - tgx;
mixed energy = 0; mixed energy = 0;
INIT_DERIVATIVES
__local AtomData localData[FORCE_WORK_GROUP_SIZE]; __local AtomData localData[FORCE_WORK_GROUP_SIZE];
// First loop: process tiles that contain exclusions. // First loop: process tiles that contain exclusions.
...@@ -85,6 +86,7 @@ __kernel void computeNonbonded( ...@@ -85,6 +86,7 @@ __kernel void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1)); bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
#endif #endif
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 0.5f;
COMPUTE_INTERACTION COMPUTE_INTERACTION
energy += 0.5f*tempEnergy; energy += 0.5f*tempEnergy;
#ifdef INCLUDE_FORCES #ifdef INCLUDE_FORCES
...@@ -144,6 +146,7 @@ __kernel void computeNonbonded( ...@@ -144,6 +146,7 @@ __kernel void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1)); bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
#endif #endif
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION COMPUTE_INTERACTION
energy += tempEnergy; energy += tempEnergy;
#ifdef INCLUDE_FORCES #ifdef INCLUDE_FORCES
...@@ -320,6 +323,7 @@ __kernel void computeNonbonded( ...@@ -320,6 +323,7 @@ __kernel void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS); bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS);
#endif #endif
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION COMPUTE_INTERACTION
energy += tempEnergy; energy += tempEnergy;
#ifdef INCLUDE_FORCES #ifdef INCLUDE_FORCES
...@@ -374,6 +378,7 @@ __kernel void computeNonbonded( ...@@ -374,6 +378,7 @@ __kernel void computeNonbonded(
bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS); bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS);
#endif #endif
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
COMPUTE_INTERACTION COMPUTE_INTERACTION
energy += tempEnergy; energy += tempEnergy;
#ifdef INCLUDE_FORCES #ifdef INCLUDE_FORCES
...@@ -429,4 +434,5 @@ __kernel void computeNonbonded( ...@@ -429,4 +434,5 @@ __kernel void computeNonbonded(
#ifdef INCLUDE_ENERGY #ifdef INCLUDE_ENERGY
energyBuffer[get_global_id(0)] += energy; energyBuffer[get_global_id(0)] += energy;
#endif #endif
SAVE_DERIVATIVES
} }
platforms/reference/include/ReferenceAngleBondIxn.h
View file @ 1f7866ad
/* Portions copyright (c) 2006 Stanford University and Simbios. /* Portions copyright (c) 2006-2016 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -94,7 +94,7 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn { ...@@ -94,7 +94,7 @@ class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const; RealOpenMM* totalEnergy, double* energyParamDerivs);
}; };
......
platforms/reference/include/ReferenceBondIxn.h
View file @ 1f7866ad
/* Portions copyright (c) 2006 Stanford University and Simbios. /* Portions copyright (c) 2006-2016 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -67,7 +67,7 @@ class OPENMM_EXPORT ReferenceBondIxn { ...@@ -67,7 +67,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
virtual void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates, virtual void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const; RealOpenMM* totalEnergy, double* energyParamDerivs);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCMAPTorsionIxn.h
View file @ 1f7866ad
/* Portions copyright (c) 2010 Stanford University and Simbios. /* Portions copyright (c) 2010-2016 Stanford University and Simbios.
* Contributors: Peter Eastman * Contributors: Peter Eastman
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -97,7 +97,7 @@ public: ...@@ -97,7 +97,7 @@ public:
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const; RealOpenMM* totalEnergy, double* energyParamDerivs);
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomAngleIxn.h
View file @ 1f7866ad
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#define __ReferenceCustomAngleIxn_H__ #define __ReferenceCustomAngleIxn_H__
#include "ReferenceBondIxn.h" #include "ReferenceBondIxn.h"
#include "lepton/CompiledExpression.h" #include "openmm/internal/CompiledExpressionSet.h"
namespace OpenMM { namespace OpenMM {
...@@ -34,10 +34,10 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn { ...@@ -34,10 +34,10 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
private: private:
Lepton::CompiledExpression energyExpression; Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression; Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams; std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<double*> forceParams; CompiledExpressionSet expressionSet;
double* energyTheta; std::vector<int> angleParamIndex;
double* forceTheta; int thetaIndex;
int numParameters; int numParameters;
bool usePeriodic; bool usePeriodic;
RealVec boxVectors[3]; RealVec boxVectors[3];
...@@ -51,7 +51,8 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn { ...@@ -51,7 +51,8 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCustomAngleIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression, 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 { ...@@ -85,7 +86,7 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const; RealOpenMM* totalEnergy, double* energyParamDerivs);
}; };
......
platforms/reference/include/ReferenceCustomBondIxn.h
View file @ 1f7866ad
...@@ -26,7 +26,7 @@ ...@@ -26,7 +26,7 @@
#define __ReferenceCustomBondIxn_H__ #define __ReferenceCustomBondIxn_H__
#include "ReferenceBondIxn.h" #include "ReferenceBondIxn.h"
#include "lepton/CompiledExpression.h" #include "openmm/internal/CompiledExpressionSet.h"
namespace OpenMM { namespace OpenMM {
...@@ -35,10 +35,10 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn { ...@@ -35,10 +35,10 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
private: private:
Lepton::CompiledExpression energyExpression; Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression; Lepton::CompiledExpression forceExpression;
std::vector<double*> energyParams; std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<double*> forceParams; CompiledExpressionSet expressionSet;
double* energyR; std::vector<int> bondParamIndex;
double* forceR; int rIndex;
int numParameters; int numParameters;
bool usePeriodic; bool usePeriodic;
RealVec boxVectors[3]; RealVec boxVectors[3];
...@@ -52,7 +52,8 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn { ...@@ -52,7 +52,8 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression, 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 { ...@@ -86,7 +87,7 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates, void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const; RealOpenMM* totalEnergy, double* energyParamDerivs);
}; };
......
platforms/reference/include/ReferenceCustomCentroidBondIxn.h
View file @ 1f7866ad
...@@ -26,7 +26,7 @@ ...@@ -26,7 +26,7 @@
#define __ReferenceCustomCentroidBondIxn_H__ #define __ReferenceCustomCentroidBondIxn_H__
#include "ReferenceBondIxn.h" #include "ReferenceBondIxn.h"
#include "lepton/ExpressionProgram.h" #include "openmm/internal/CompiledExpressionSet.h"
#include "lepton/ParsedExpression.h" #include "lepton/ParsedExpression.h"
#include <map> #include <map>
#include <vector> #include <vector>
...@@ -44,12 +44,15 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn { ...@@ -44,12 +44,15 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
std::vector<std::vector<int> > groupAtoms; std::vector<std::vector<int> > groupAtoms;
std::vector<std::vector<double> > normalizedWeights; std::vector<std::vector<double> > normalizedWeights;
std::vector<std::vector<int> > bondGroups; std::vector<std::vector<int> > bondGroups;
Lepton::ExpressionProgram energyExpression; CompiledExpressionSet expressionSet;
std::vector<std::string> bondParamNames; Lepton::CompiledExpression energyExpression;
std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
std::vector<int> bondParamIndex;
std::vector<PositionTermInfo> positionTerms; std::vector<PositionTermInfo> positionTerms;
std::vector<DistanceTermInfo> distanceTerms; std::vector<DistanceTermInfo> distanceTerms;
std::vector<AngleTermInfo> angleTerms; std::vector<AngleTermInfo> angleTerms;
std::vector<DihedralTermInfo> dihedralTerms; std::vector<DihedralTermInfo> dihedralTerms;
int numParameters;
bool usePeriodic; bool usePeriodic;
RealVec boxVectors[3]; RealVec boxVectors[3];
...@@ -60,15 +63,13 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn { ...@@ -60,15 +63,13 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
@param bond the index of the bond @param bond the index of the bond
@param groupCenters group center coordinates @param groupCenters group center coordinates
@param variables the values of variables that may appear in expressions
@param forces force array (forces added) @param forces force array (forces added)
@param totalEnergy total energy @param totalEnergy total energy
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateOneIxn(int bond, std::vector<OpenMM::RealVec>& groupCenters, void calculateOneIxn(int bond, std::vector<OpenMM::RealVec>& groupCenters,
std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces, std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs);
RealOpenMM* totalEnergy) const;
void computeDelta(int group1, int group2, RealOpenMM* delta, std::vector<OpenMM::RealVec>& groupCenters) const; void computeDelta(int group1, int group2, RealOpenMM* delta, std::vector<OpenMM::RealVec>& groupCenters) const;
...@@ -86,7 +87,8 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn { ...@@ -86,7 +87,8 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
ReferenceCustomCentroidBondIxn(int numGroupsPerBond, const std::vector<std::vector<int> >& groupAtoms, 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::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::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 { ...@@ -130,7 +132,7 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
void calculatePairIxn(std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** bondParameters, void calculatePairIxn(std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** bondParameters,
const std::map<std::string, double>& globalParameters, 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 { ...@@ -139,9 +141,9 @@ class ReferenceCustomCentroidBondIxn : public ReferenceBondIxn {
class ReferenceCustomCentroidBondIxn::PositionTermInfo { class ReferenceCustomCentroidBondIxn::PositionTermInfo {
public: public:
std::string name; std::string name;
int group, component; int group, component, index;
Lepton::ExpressionProgram forceExpression; Lepton::CompiledExpression forceExpression;
PositionTermInfo(const std::string& name, int group, int component, const Lepton::ExpressionProgram& forceExpression) : PositionTermInfo(const std::string& name, int group, int component, const Lepton::CompiledExpression& forceExpression) :
name(name), group(group), component(component), forceExpression(forceExpression) { name(name), group(group), component(component), forceExpression(forceExpression) {
} }
}; };
...@@ -149,10 +151,10 @@ public: ...@@ -149,10 +151,10 @@ public:
class ReferenceCustomCentroidBondIxn::DistanceTermInfo { class ReferenceCustomCentroidBondIxn::DistanceTermInfo {
public: public:
std::string name; std::string name;
int g1, g2; int g1, g2, index;
Lepton::ExpressionProgram forceExpression; Lepton::CompiledExpression forceExpression;
mutable RealOpenMM delta[ReferenceForce::LastDeltaRIndex]; 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) { name(name), g1(groups[0]), g2(groups[1]), forceExpression(forceExpression) {
} }
}; };
...@@ -160,11 +162,11 @@ public: ...@@ -160,11 +162,11 @@ public:
class ReferenceCustomCentroidBondIxn::AngleTermInfo { class ReferenceCustomCentroidBondIxn::AngleTermInfo {
public: public:
std::string name; std::string name;
int g1, g2, g3; int g1, g2, g3, index;
Lepton::ExpressionProgram forceExpression; Lepton::CompiledExpression forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex]; mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[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) { name(name), g1(groups[0]), g2(groups[1]), g3(groups[2]), forceExpression(forceExpression) {
} }
}; };
...@@ -172,14 +174,14 @@ public: ...@@ -172,14 +174,14 @@ public:
class ReferenceCustomCentroidBondIxn::DihedralTermInfo { class ReferenceCustomCentroidBondIxn::DihedralTermInfo {
public: public:
std::string name; std::string name;
int g1, g2, g3, g4; int g1, g2, g3, g4, index;
Lepton::ExpressionProgram forceExpression; Lepton::CompiledExpression forceExpression;
mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex]; mutable RealOpenMM delta1[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex]; mutable RealOpenMM delta2[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM delta3[ReferenceForce::LastDeltaRIndex]; mutable RealOpenMM delta3[ReferenceForce::LastDeltaRIndex];
mutable RealOpenMM cross1[3]; mutable RealOpenMM cross1[3];
mutable RealOpenMM cross2[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) { name(name), g1(groups[0]), g2(groups[1]), g3(groups[2]), g4(groups[3]), forceExpression(forceExpression) {
} }
}; };
......
platforms/reference/include/ReferenceCustomDynamics.h
View file @ 1f7866ad
...@@ -41,6 +41,7 @@ namespace OpenMM { ...@@ -41,6 +41,7 @@ namespace OpenMM {
class ReferenceCustomDynamics : public ReferenceDynamics { class ReferenceCustomDynamics : public ReferenceDynamics {
private: private:
class DerivFunction;
const OpenMM::CustomIntegrator& integrator; const OpenMM::CustomIntegrator& integrator;
std::vector<RealOpenMM> inverseMasses; std::vector<RealOpenMM> inverseMasses;
std::vector<OpenMM::RealVec> sumBuffer, oldPos; std::vector<OpenMM::RealVec> sumBuffer, oldPos;
...@@ -51,6 +52,7 @@ private: ...@@ -51,6 +52,7 @@ private:
std::vector<bool> invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy; std::vector<bool> invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy;
std::vector<int> forceGroupFlags, blockEnd; std::vector<int> forceGroupFlags, blockEnd;
RealOpenMM energy; RealOpenMM energy;
std::map<std::string, double> energyParamDerivs;
Lepton::CompiledExpression kineticEnergyExpression; Lepton::CompiledExpression kineticEnergyExpression;
bool kineticEnergyNeedsForce; bool kineticEnergyNeedsForce;
CompiledExpressionSet expressionSet; CompiledExpressionSet expressionSet;
...@@ -59,6 +61,8 @@ private: ...@@ -59,6 +61,8 @@ private:
void initialize(OpenMM::ContextImpl& context, std::vector<RealOpenMM>& masses, std::map<std::string, RealOpenMM>& globals); 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, 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<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); const std::vector<std::vector<OpenMM::RealVec> >& perDof, const Lepton::CompiledExpression& expression, int forceIndex);
......
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