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Commit 83ed602e authored by peastman's avatar peastman
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Merge pull request #797 from peastman/triclinic 

C++ libraries support triclinic boxes
parents b51e05a8 050e1262
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Showing with 448 additions and 118 deletions
platforms/opencl/src/kernels/monteCarloBarostat.cl
View file @ 83ed602e
......@@ -2,7 +2,8 @@
* Scale the particle positions with each axis independent.
*/
__kernel void scalePositions(float scaleX, float scaleY, float scaleZ, int numMolecules, real4 periodicBoxSize, real4 invPeriodicBoxSize, __global real4* restrict posq,
__kernel void scalePositions(float scaleX, float scaleY, float scaleZ, int numMolecules, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, __global real4* restrict posq,
__global const int* restrict moleculeAtoms, __global const int* restrict moleculeStartIndex) {
for (int index = get_global_id(0); index < numMolecules; index += get_global_size(0)) {
int first = moleculeStartIndex[index];
......@@ -11,19 +12,17 @@ __kernel void scalePositions(float scaleX, float scaleY, float scaleZ, int numMo
// Find the center of each molecule.
real4 center = (real4) 0;
real3 center = (real3) 0;
for (int atom = first; atom < last; atom++)
center += posq[moleculeAtoms[atom]];
center += posq[moleculeAtoms[atom]].xyz;
center /= (real) numAtoms;
// Move it into the first periodic box.
int xcell = (int) floor(center.x*invPeriodicBoxSize.x);
int ycell = (int) floor(center.y*invPeriodicBoxSize.y);
int zcell = (int) floor(center.z*invPeriodicBoxSize.z);
real4 delta = (real4) (xcell*periodicBoxSize.x, ycell*periodicBoxSize.y, zcell*periodicBoxSize.z, 0);
real4 scaleXYZ = (real4) (scaleX, scaleY, scaleZ, 1);
center -= delta;
real3 oldCenter = center;
APPLY_PERIODIC_TO_POS(center)
real3 delta = oldCenter-center;;
real3 scaleXYZ = (real3) (scaleX, scaleY, scaleZ);
// Now scale the position of the molecule center.
......
platforms/opencl/src/kernels/nonbonded.cl
View file @ 83ed602e
......@@ -26,7 +26,8 @@ __kernel void computeNonbonded(
__global const ushort2* restrict exclusionTiles, unsigned int startTileIndex, unsigned int numTileIndices
#ifdef USE_CUTOFF
, __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
unsigned int maxTiles, __global const real4* restrict blockCenter, __global const real4* restrict blockSize, __global const int* restrict interactingAtoms
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, __global const real4* restrict blockCenter,
__global const real4* restrict blockSize, __global const int* restrict interactingAtoms
#endif
PARAMETER_ARGUMENTS) {
const unsigned int totalWarps = get_global_size(0)/TILE_SIZE;
......@@ -67,7 +68,7 @@ __kernel void computeNonbonded(
real4 posq2 = (real4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
real invR = RSQRT(r2);
......@@ -121,7 +122,7 @@ __kernel void computeNonbonded(
real4 posq2 = (real4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
#ifdef PRUNE_BY_CUTOFF
......@@ -289,10 +290,8 @@ __kernel void computeNonbonded(
// box, then skip having to apply periodic boundary conditions later.
real4 blockCenterX = blockCenter[x];
posq1.xyz -= floor((posq1.xyz-blockCenterX.xyz)*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
localData[localAtomIndex].x -= floor((localData[localAtomIndex].x-blockCenterX.x)*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
localData[localAtomIndex].y -= floor((localData[localAtomIndex].y-blockCenterX.y)*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
localData[localAtomIndex].z -= floor((localData[localAtomIndex].z-blockCenterX.z)*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
APPLY_PERIODIC_TO_POS_WITH_CENTER(posq1, blockCenterX)
APPLY_PERIODIC_TO_POS_WITH_CENTER(localData[localAtomIndex], blockCenterX)
SYNC_WARPS;
unsigned int tj = tgx;
for (j = 0; j < TILE_SIZE; j++) {
......@@ -349,7 +348,7 @@ __kernel void computeNonbonded(
real4 posq2 = (real4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
real4 delta = (real4) (posq2.xyz - posq1.xyz, 0);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
#ifdef PRUNE_BY_CUTOFF
......
platforms/opencl/src/kernels/pme.cl
View file @ 83ed602e
__kernel void updateBsplines(__global const real4* restrict posq, __global real4* restrict pmeBsplineTheta, __local real4* restrict bsplinesCache,
__global int2* restrict pmeAtomGridIndex, real4 periodicBoxSize, real4 invPeriodicBoxSize) {
__global int2* restrict pmeAtomGridIndex, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
const real4 scale = 1/(real) (PME_ORDER-1);
for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
__local real4* data = &bsplinesCache[get_local_id(0)*PME_ORDER];
real4 pos = posq[i];
pos.x -= floor(pos.x*invPeriodicBoxSize.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*invPeriodicBoxSize.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*invPeriodicBoxSize.z)*periodicBoxSize.z;
real4 t = (real4) ((pos.x*invPeriodicBoxSize.x)*GRID_SIZE_X,
(pos.y*invPeriodicBoxSize.y)*GRID_SIZE_Y,
(pos.z*invPeriodicBoxSize.z)*GRID_SIZE_Z, 0.0f);
real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
pos.z*recipBoxVecZ.z);
t.x = (t.x-floor(t.x))*GRID_SIZE_X;
t.y = (t.y-floor(t.y))*GRID_SIZE_Y;
t.z = (t.z-floor(t.z))*GRID_SIZE_Z;
real4 dr = (real4) (t.x-(int) t.x, t.y-(int) t.y, t.z-(int) t.z, 0.0f);
int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
((int) t.y) % GRID_SIZE_Y,
......@@ -41,7 +41,7 @@ __kernel void updateBsplines(__global const real4* restrict posq, __global real4
/**
* For each grid point, find the range of sorted atoms associated with that point.
*/
__kernel void findAtomRangeForGrid(__global int2* restrict pmeAtomGridIndex, __global int* restrict pmeAtomRange, __global const real4* restrict posq, real4 periodicBoxSize, real4 invPeriodicBoxSize) {
__kernel void findAtomRangeForGrid(__global int2* restrict pmeAtomGridIndex, __global int* restrict pmeAtomRange, __global const real4* restrict posq) {
int start = (NUM_ATOMS*get_global_id(0))/get_global_size(0);
int end = (NUM_ATOMS*(get_global_id(0)+1))/get_global_size(0);
int last = (start == 0 ? -1 : pmeAtomGridIndex[start-1].y);
......@@ -68,13 +68,13 @@ __kernel void findAtomRangeForGrid(__global int2* restrict pmeAtomGridIndex, __g
* The grid index won't be needed again. Reuse that component to hold the z index, thus saving
* some work in the charge spreading kernel.
*/
__kernel void recordZIndex(__global int2* restrict pmeAtomGridIndex, __global const real4* restrict posq, real4 periodicBoxSize, real4 invPeriodicBoxSize) {
__kernel void recordZIndex(__global int2* restrict pmeAtomGridIndex, __global const real4* restrict posq, real4 periodicBoxSize, real4 recipBoxVecZ) {
int start = (NUM_ATOMS*get_global_id(0))/get_global_size(0);
int end = (NUM_ATOMS*(get_global_id(0)+1))/get_global_size(0);
for (int i = start; i < end; ++i) {
real posz = posq[pmeAtomGridIndex[i].x].z;
posz -= floor(posz*invPeriodicBoxSize.z)*periodicBoxSize.z;
int z = ((int) ((posz*invPeriodicBoxSize.z)*GRID_SIZE_Z)) % GRID_SIZE_Z;
posz -= floor(posz*recipBoxVecZ.z)*periodicBoxSize.z;
int z = ((int) ((posz*recipBoxVecZ.z)*GRID_SIZE_Z)) % GRID_SIZE_Z;
pmeAtomGridIndex[i].y = z;
}
}
......@@ -83,7 +83,7 @@ __kernel void recordZIndex(__global int2* restrict pmeAtomGridIndex, __global co
#pragma OPENCL EXTENSION cl_khr_int64_base_atomics : enable
__kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
__global long* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 invPeriodicBoxSize) {
__global long* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
const real4 scale = 1/(real) (PME_ORDER-1);
real4 data[PME_ORDER];
......@@ -93,12 +93,15 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
int atom = pmeAtomGridIndex[i].x;
real4 pos = posq[atom];
pos.x -= floor(pos.x*invPeriodicBoxSize.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*invPeriodicBoxSize.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*invPeriodicBoxSize.z)*periodicBoxSize.z;
real4 t = (real4) ((pos.x*invPeriodicBoxSize.x)*GRID_SIZE_X,
(pos.y*invPeriodicBoxSize.y)*GRID_SIZE_Y,
(pos.z*invPeriodicBoxSize.z)*GRID_SIZE_Z, 0.0f);
pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
pos.z*recipBoxVecZ.z);
t.x = (t.x-floor(t.x))*GRID_SIZE_X;
t.y = (t.y-floor(t.y))*GRID_SIZE_Y;
t.z = (t.z-floor(t.z))*GRID_SIZE_Z;
int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
((int) t.y) % GRID_SIZE_Y,
((int) t.z) % GRID_SIZE_Z, 0);
......@@ -163,7 +166,7 @@ __kernel void finishSpreadCharge(__global long* restrict pmeGrid) {
}
#elif defined(DEVICE_IS_CPU)
__kernel void gridSpreadCharge(__global const real4* restrict posq, __global const int2* restrict pmeAtomGridIndex, __global const int* restrict pmeAtomRange,
__global real2* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 invPeriodicBoxSize) {
__global real2* restrict pmeGrid, __global const real4* restrict pmeBsplineTheta, real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ) {
const int firstx = get_global_id(0)*GRID_SIZE_X/get_global_size(0);
const int lastx = (get_global_id(0)+1)*GRID_SIZE_X/get_global_size(0);
if (firstx == lastx)
......@@ -177,12 +180,15 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
for (int i = 0; i < NUM_ATOMS; i++) {
int atom = i;//pmeAtomGridIndex[i].x;
real4 pos = posq[atom];
pos.x -= floor(pos.x*invPeriodicBoxSize.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*invPeriodicBoxSize.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*invPeriodicBoxSize.z)*periodicBoxSize.z;
real4 t = (real4) ((pos.x*invPeriodicBoxSize.x)*GRID_SIZE_X,
(pos.y*invPeriodicBoxSize.y)*GRID_SIZE_Y,
(pos.z*invPeriodicBoxSize.z)*GRID_SIZE_Z, 0.0f);
pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
pos.z*recipBoxVecZ.z);
t.x = (t.x-floor(t.x))*GRID_SIZE_X;
t.y = (t.y-floor(t.y))*GRID_SIZE_Y;
t.z = (t.z-floor(t.z))*GRID_SIZE_Z;
int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
((int) t.y) % GRID_SIZE_Y,
((int) t.z) % GRID_SIZE_Z, 0);
......@@ -290,7 +296,7 @@ __kernel void gridSpreadCharge(__global const real4* restrict posq, __global con
#endif
__kernel void reciprocalConvolution(__global real2* restrict pmeGrid, __global real* restrict energyBuffer, __global const real* restrict pmeBsplineModuliX,
__global const real* restrict pmeBsplineModuliY, __global const real* restrict pmeBsplineModuliZ, real4 invPeriodicBoxSize, real recipScaleFactor) {
__global const real* restrict pmeBsplineModuliY, __global const real* restrict pmeBsplineModuliZ, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, real recipScaleFactor) {
const unsigned int gridSize = GRID_SIZE_X*GRID_SIZE_Y*GRID_SIZE_Z;
real energy = 0.0f;
for (int index = get_global_id(0); index < gridSize; index += get_global_size(0)) {
......@@ -303,9 +309,9 @@ __kernel void reciprocalConvolution(__global real2* restrict pmeGrid, __global r
int mx = (kx < (GRID_SIZE_X+1)/2) ? kx : (kx-GRID_SIZE_X);
int my = (ky < (GRID_SIZE_Y+1)/2) ? ky : (ky-GRID_SIZE_Y);
int mz = (kz < (GRID_SIZE_Z+1)/2) ? kz : (kz-GRID_SIZE_Z);
real mhx = mx*invPeriodicBoxSize.x;
real mhy = my*invPeriodicBoxSize.y;
real mhz = mz*invPeriodicBoxSize.z;
real mhx = mx*recipBoxVecX.x;
real mhy = mx*recipBoxVecY.x+my*recipBoxVecY.y;
real mhz = mx*recipBoxVecZ.x+my*recipBoxVecZ.y+mz*recipBoxVecZ.z;
real bx = pmeBsplineModuliX[kx];
real by = pmeBsplineModuliY[ky];
real bz = pmeBsplineModuliZ[kz];
......@@ -320,7 +326,7 @@ __kernel void reciprocalConvolution(__global real2* restrict pmeGrid, __global r
}
__kernel void gridInterpolateForce(__global const real4* restrict posq, __global real4* restrict forceBuffers, __global const real2* restrict pmeGrid,
real4 periodicBoxSize, real4 invPeriodicBoxSize, __global int2* restrict pmeAtomGridIndex) {
real4 periodicBoxSize, real4 recipBoxVecX, real4 recipBoxVecY, real4 recipBoxVecZ, __global int2* restrict pmeAtomGridIndex) {
const real4 scale = 1/(real) (PME_ORDER-1);
real4 data[PME_ORDER];
real4 ddata[PME_ORDER];
......@@ -332,12 +338,15 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
int atom = pmeAtomGridIndex[i].x;
real4 force = 0.0f;
real4 pos = posq[atom];
pos.x -= floor(pos.x*invPeriodicBoxSize.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*invPeriodicBoxSize.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*invPeriodicBoxSize.z)*periodicBoxSize.z;
real4 t = (real4) ((pos.x*invPeriodicBoxSize.x)*GRID_SIZE_X,
(pos.y*invPeriodicBoxSize.y)*GRID_SIZE_Y,
(pos.z*invPeriodicBoxSize.z)*GRID_SIZE_Z, 0.0f);
pos.x -= floor(pos.x*recipBoxVecX.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*recipBoxVecY.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*recipBoxVecZ.z)*periodicBoxSize.z;
real3 t = (real3) (pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x,
pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y,
pos.z*recipBoxVecZ.z);
t.x = (t.x-floor(t.x))*GRID_SIZE_X;
t.y = (t.y-floor(t.y))*GRID_SIZE_Y;
t.z = (t.z-floor(t.z))*GRID_SIZE_Z;
int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
((int) t.y) % GRID_SIZE_Y,
((int) t.z) % GRID_SIZE_Z, 0);
......@@ -385,9 +394,9 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
}
real4 totalForce = forceBuffers[atom];
real q = pos.w*EPSILON_FACTOR;
totalForce.x -= q*force.x*GRID_SIZE_X*invPeriodicBoxSize.x;
totalForce.y -= q*force.y*GRID_SIZE_Y*invPeriodicBoxSize.y;
totalForce.z -= q*force.z*GRID_SIZE_Z*invPeriodicBoxSize.z;
totalForce.x -= q*(force.x*GRID_SIZE_X*recipBoxVecX.x);
totalForce.y -= q*(force.x*GRID_SIZE_X*recipBoxVecY.x+force.y*GRID_SIZE_Y*recipBoxVecY.y);
totalForce.z -= q*(force.x*GRID_SIZE_X*recipBoxVecZ.x+force.y*GRID_SIZE_Y*recipBoxVecZ.y+force.z*GRID_SIZE_Z*recipBoxVecZ.z);
forceBuffers[atom] = totalForce;
}
}
......
platforms/opencl/tests/TestOpenCLCustomManyParticleForce.cpp
View file @ 83ed602e
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2014 Stanford University and the Authors. *
* Portions copyright (c) 2014-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -55,7 +55,17 @@ const double TOL = 1e-5;
OpenCLPlatform platform;
void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize) {
Vec3 computeDelta(const Vec3& pos1, const Vec3& pos2, bool periodic, const Vec3* periodicBoxVectors) {
Vec3 diff = pos1-pos2;
if (periodic) {
diff -= periodicBoxVectors[2]*floor(diff[2]/periodicBoxVectors[2][2]+0.5);
diff -= periodicBoxVectors[1]*floor(diff[1]/periodicBoxVectors[1][1]+0.5);
diff -= periodicBoxVectors[0]*floor(diff[0]/periodicBoxVectors[0][0]+0.5);
}
return diff;
}
void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize, bool triclinic) {
// Create a System and Context.
int numParticles = force->getNumParticles();
......@@ -63,7 +73,18 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
Vec3 boxVectors[3];
if (triclinic) {
boxVectors[0] = Vec3(boxSize, 0, 0);
boxVectors[1] = Vec3(0.2*boxSize, boxSize, 0);
boxVectors[2] = Vec3(-0.3*boxSize, -0.1*boxSize, boxSize);
}
else {
boxVectors[0] = Vec3(boxSize, 0, 0);
boxVectors[1] = Vec3(0, boxSize, 0);
boxVectors[2] = Vec3(0, 0, boxSize);
}
system.setDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
system.addForce(force);
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
......@@ -74,20 +95,14 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p
// See if the energy matches the expected value.
double expectedEnergy = 0;
bool periodic = (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic);
for (int i = 0; i < (int) expectedSets.size(); i++) {
int p1 = expectedSets[i][0];
int p2 = expectedSets[i][1];
int p3 = expectedSets[i][2];
Vec3 d12 = positions[p2]-positions[p1];
Vec3 d13 = positions[p3]-positions[p1];
Vec3 d23 = positions[p3]-positions[p2];
if (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic) {
for (int j = 0; j < 3; j++) {
d12[j] -= floor(d12[j]/boxSize+0.5f)*boxSize;
d13[j] -= floor(d13[j]/boxSize+0.5f)*boxSize;
d23[j] -= floor(d23[j]/boxSize+0.5f)*boxSize;
}
}
Vec3 d12 = computeDelta(positions[p2], positions[p1], periodic, boxVectors);
Vec3 d13 = computeDelta(positions[p3], positions[p1], periodic, boxVectors);
Vec3 d23 = computeDelta(positions[p3], positions[p2], periodic, boxVectors);
double r12 = sqrt(d12.dot(d12));
double r13 = sqrt(d13.dot(d13));
double r23 = sqrt(d23.dot(d23));
......@@ -210,7 +225,7 @@ void testNoCutoff() {
positions.push_back(Vec3(0.4, 0, -0.8));
int sets[4][3] = {{0,1,2}, {1,2,3}, {2,3,0}, {3,0,1}};
vector<const int*> expectedSets(&sets[0], &sets[4]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testCutoff() {
......@@ -235,7 +250,7 @@ void testCutoff() {
positions.push_back(Vec3(0.2, 0.5, -0.1));
int sets[7][3] = {{0,1,2}, {0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,2,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[7]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testPeriodic() {
......@@ -261,7 +276,33 @@ void testPeriodic() {
double boxSize = 2.1;
int sets[5][3] = {{0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[5]);
validateAxilrodTeller(force, positions, expectedSets, boxSize);
validateAxilrodTeller(force, positions, expectedSets, boxSize, false);
}
void testTriclinic() {
CustomManyParticleForce* force = new CustomManyParticleForce(3,
"C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
"theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
"r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
force->addGlobalParameter("C", 1.5);
force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
force->setCutoffDistance(1.05);
vector<double> params;
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
force->addParticle(params);
vector<Vec3> positions;
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(1, 0, 0));
positions.push_back(Vec3(0, 1.1, 0.3));
positions.push_back(Vec3(0.4, 0, -0.8));
positions.push_back(Vec3(0.2, 0.5, -0.1));
double boxSize = 2.1;
int sets[4][3] = {{0,1,3}, {0,1,4}, {0,3,4}, {1,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[4]);
validateAxilrodTeller(force, positions, expectedSets, boxSize, true);
}
void testExclusions() {
......@@ -286,7 +327,7 @@ void testExclusions() {
force->addExclusion(0, 3);
int sets[5][3] = {{0,1,4}, {1,2,3}, {1,2,4}, {1,3,4}, {2,3,4}};
vector<const int*> expectedSets(&sets[0], &sets[5]);
validateAxilrodTeller(force, positions, expectedSets, 2.0);
validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
}
void testAllTerms() {
......@@ -672,6 +713,7 @@ int main(int argc, char* argv[]) {
testNoCutoff();
testCutoff();
testPeriodic();
testTriclinic();
testExclusions();
testAllTerms();
testParameters();
......
platforms/opencl/tests/TestOpenCLCustomNonbondedForce.cpp
View file @ 83ed602e
......@@ -7,7 +7,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -261,6 +261,65 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(1.9+1+0.9, state.getPotentialEnergy(), TOL);
}
void testTriclinic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
Vec3 a(3.1, 0, 0);
Vec3 b(0.4, 3.5, 0);
Vec3 c(-0.1, -0.5, 4.0);
system.setDefaultPeriodicBoxVectors(a, b, c);
VerletIntegrator integrator(0.01);
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("r");
nonbonded->addParticle(vector<double>());
nonbonded->addParticle(vector<double>());
nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
const double cutoff = 1.5;
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int iteration = 0; iteration < 50; iteration++) {
// Generate random positions for the two particles.
positions[0] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
positions[1] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
context.setPositions(positions);
// Loop over all possible periodic copies and find the nearest one.
Vec3 delta;
double distance2 = 100.0;
for (int i = -1; i < 2; i++)
for (int j = -1; j < 2; j++)
for (int k = -1; k < 2; k++) {
Vec3 d = positions[1]-positions[0]+a*i+b*j+c*k;
if (d.dot(d) < distance2) {
delta = d;
distance2 = d.dot(d);
}
}
double distance = sqrt(distance2);
// See if the force and energy are correct.
State state = context.getState(State::Forces | State::Energy);
if (distance >= cutoff) {
ASSERT_EQUAL(0.0, state.getPotentialEnergy());
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[0], 0);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[1], 0);
}
else {
const Vec3 force = delta/sqrt(delta.dot(delta));
ASSERT_EQUAL_TOL(distance, state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(force, state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(-force, state.getForces()[1], TOL);
}
}
}
void testContinuous1DFunction() {
System system;
system.addParticle(1.0);
......@@ -924,6 +983,7 @@ int main(int argc, char* argv[]) {
testExclusions();
testCutoff();
testPeriodic();
testTriclinic();
testContinuous1DFunction();
testContinuous2DFunction();
testContinuous3DFunction();
......
platforms/opencl/tests/TestOpenCLEwald.cpp
View file @ 83ed602e
......@@ -201,6 +201,57 @@ void testEwald2Ions() {
ASSERT_EQUAL_TOL(-217.276, state.getPotentialEnergy(), 0.01/*10*TOL*/);
}
void testTriclinic() {
// Create a triclinic box containing eight particles.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(2.5, 0, 0), Vec3(0.5, 3.0, 0), Vec3(0.7, 0.9, 3.5));
for (int i = 0; i < 8; i++)
system.addParticle(1.0);
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
force->setNonbondedMethod(NonbondedForce::PME);
force->setCutoffDistance(1.0);
force->setPMEParameters(3.45891, 32, 40, 48);
for (int i = 0; i < 4; i++)
force->addParticle(-1, 0.440104, 0.4184); // Cl parameters
for (int i = 0; i < 4; i++)
force->addParticle(1, 0.332840, 0.0115897); // Na parameters
vector<Vec3> positions(8);
positions[0] = Vec3(1.744, 2.788, 3.162);
positions[1] = Vec3(1.048, 0.762, 2.340);
positions[2] = Vec3(2.489, 1.570, 2.817);
positions[3] = Vec3(1.027, 1.893, 3.271);
positions[4] = Vec3(0.937, 0.825, 0.009);
positions[5] = Vec3(2.290, 1.887, 3.352);
positions[6] = Vec3(1.266, 1.111, 2.894);
positions[7] = Vec3(0.933, 1.862, 3.490);
// Compute the forces and energy.
VerletIntegrator integ(0.001);
Context context(system, integ, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// Compare them to values computed by Gromacs.
double expectedEnergy = -963.370;
vector<Vec3> expectedForce(8);
expectedForce[0] = Vec3(4.25253e+01, -1.23503e+02, 1.22139e+02);
expectedForce[1] = Vec3(9.74752e+01, 1.68213e+02, 1.93169e+02);
expectedForce[2] = Vec3(-1.50348e+02, 1.29165e+02, 3.70435e+02);
expectedForce[3] = Vec3(9.18644e+02, -3.52571e+00, -1.34772e+03);
expectedForce[4] = Vec3(-1.61193e+02, 9.01528e+01, -7.12904e+01);
expectedForce[5] = Vec3(2.82630e+02, 2.78029e+01, -3.72864e+02);
expectedForce[6] = Vec3(-1.47454e+02, -2.14448e+02, -3.55789e+02);
expectedForce[7] = Vec3(-8.82195e+02, -7.39132e+01, 1.46202e+03);
for (int i = 0; i < 8; i++) {
ASSERT_EQUAL_VEC(expectedForce[i], state.getForces()[i], 1e-4);
}
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-4);
}
void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
// Create a cloud of random point charges.
......@@ -307,6 +358,7 @@ int main(int argc, char* argv[]) {
testEwaldPME(false);
testEwaldPME(true);
// testEwald2Ions();
testTriclinic();
testErrorTolerance(NonbondedForce::Ewald);
testErrorTolerance(NonbondedForce::PME);
testPMEParameters();
......
platforms/opencl/tests/TestOpenCLMonteCarloAnisotropicBarostat.cpp
View file @ 83ed602e
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman, Lee-Ping Wang *
* Contributors: *
* *
......@@ -236,6 +236,82 @@ void testRandomSeed() {
}
}
void testTriclinic() {
const int numParticles = 64;
const int frequency = 10;
const int steps = 1000;
const double pressure = 1.5;
const double pressureInMD = pressure*(AVOGADRO*1e-25); // pressure in kJ/mol/nm^3
const double temperature = 300.0;
const double initialVolume = numParticles*BOLTZ*temperature/pressureInMD;
const double initialLength = std::pow(initialVolume, 1.0/3.0);
// Create a gas of noninteracting particles.
System system;
Vec3 initialBox[3];
initialBox[0] = Vec3(initialLength, 0, 0);
initialBox[1] = Vec3(0.2*initialLength, initialLength, 0);
initialBox[2] = Vec3(0.1*initialLength, 0.3*initialLength, initialLength);
system.setDefaultPeriodicBoxVectors(initialBox[0], initialBox[1], initialBox[2]);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
system.addParticle(1.0);
positions[i] = Vec3(initialLength*genrand_real2(sfmt), initialLength*genrand_real2(sfmt), initialLength*genrand_real2(sfmt));
}
MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temperature, true, true, true, frequency);
system.addForce(barostat);
// Run a simulation
LangevinIntegrator integrator(temperature, 0.1, 0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the volume is correct.
double volume = 0.0;
for (int j = 0; j < steps; ++j) {
Vec3 box[3];
context.getState(0).getPeriodicBoxVectors(box[0], box[1], box[2]);
volume += box[0][0]*box[1][1]*box[2][2];
integrator.step(frequency);
}
volume /= steps;
double expected = (numParticles+1)*BOLTZ*temperature/pressureInMD;
ASSERT_USUALLY_EQUAL_TOL(expected, volume, 3/std::sqrt((double) steps));
// Make sure the box vectors have been scaled consistently.
State state = context.getState(State::Positions);
Vec3 box[3];
state.getPeriodicBoxVectors(box[0], box[1], box[2]);
double xscale = box[2][0]/(0.1*initialLength);
double yscale = box[2][1]/(0.3*initialLength);
double zscale = box[2][2]/(1.0*initialLength);
for (int i = 0; i < 3; i++) {
ASSERT_EQUAL_VEC(Vec3(xscale*initialBox[i][0], yscale*initialBox[i][1], zscale*initialBox[i][2]), box[i], 1e-5);
}
// The barostat should have put all particles inside the first periodic box. One integration step
// has happened since then, so they may have moved slightly outside it.
for (int i = 0; i < numParticles; i++) {
Vec3 pos = state.getPositions()[i];
ASSERT(pos[2]/box[2][2] > -1 && pos[2]/box[2][2] < 2);
pos -= box[2]*floor(pos[2]/box[2][2]);
ASSERT(pos[1]/box[1][1] > -1 && pos[1]/box[1][1] < 2);
pos -= box[1]*floor(pos[1]/box[1][1]);
ASSERT(pos[0]/box[0][0] > -1 && pos[0]/box[0][0] < 2);
}
}
/**
* Run a constant pressure simulation on an anisotropic Einstein crystal
* using isotropic and anisotropic barostats. There are a total of 15 simulations:
......@@ -389,6 +465,7 @@ int main(int argc, char* argv[]) {
testIdealGasAxis(1);
testIdealGasAxis(2);
testRandomSeed();
testTriclinic();
//testEinsteinCrystal();
}
catch(const exception& e) {
......
platforms/opencl/tests/TestOpenCLNonbondedForce.cpp
View file @ 83ed602e
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -355,6 +355,67 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(2*ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf), state.getPotentialEnergy(), TOL);
}
void testTriclinic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
Vec3 a(3.1, 0, 0);
Vec3 b(0.4, 3.5, 0);
Vec3 c(-0.1, -0.5, 4.0);
system.setDefaultPeriodicBoxVectors(a, b, c);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(1.0, 1, 0);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
const double cutoff = 1.5;
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
const double eps = 78.3;
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
for (int iteration = 0; iteration < 50; iteration++) {
// Generate random positions for the two particles.
positions[0] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
positions[1] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
context.setPositions(positions);
// Loop over all possible periodic copies and find the nearest one.
Vec3 delta;
double distance2 = 100.0;
for (int i = -1; i < 2; i++)
for (int j = -1; j < 2; j++)
for (int k = -1; k < 2; k++) {
Vec3 d = positions[1]-positions[0]+a*i+b*j+c*k;
if (d.dot(d) < distance2) {
delta = d;
distance2 = d.dot(d);
}
}
double distance = sqrt(distance2);
// See if the force and energy are correct.
State state = context.getState(State::Forces | State::Energy);
if (distance >= cutoff) {
ASSERT_EQUAL(0.0, state.getPotentialEnergy());
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[0], 0);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[1], 0);
}
else {
const Vec3 force = delta*ONE_4PI_EPS0*(-1.0/(distance*distance*distance)+2.0*krf);
ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(1.0/distance+krf*distance*distance-crf), state.getPotentialEnergy(), TOL);
ASSERT_EQUAL_VEC(force, state.getForces()[0], TOL);
ASSERT_EQUAL_VEC(-force, state.getForces()[1], TOL);
}
}
}
void testLargeSystem() {
const int numMolecules = 600;
......@@ -865,6 +926,33 @@ void testSwitchingFunction(NonbondedForce::NonbondedMethod method) {
}
}
void testReordering() {
// Check that reordering of atoms doesn't alter their positions.
const int numParticles = 200;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(2.1, 6, 0), Vec3(-1.5, -0.5, 6));
NonbondedForce *nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::PME);
system.addForce(nonbonded);
vector<Vec3> positions;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
nonbonded->addParticle(0.0, 0.0, 0.0);
positions.push_back(Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5)*20);
}
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
integrator.step(1);
State state = context.getState(State::Positions | State::Velocities);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(positions[i], state.getPositions()[i], 1e-6);
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
......@@ -875,6 +963,7 @@ int main(int argc, char* argv[]) {
testCutoff();
testCutoff14();
testPeriodic();
testTriclinic();
testLargeSystem();
// testBlockInteractions(false);
// testBlockInteractions(true);
......@@ -885,6 +974,7 @@ int main(int argc, char* argv[]) {
testParallelComputation(NonbondedForce::PME);
testSwitchingFunction(NonbondedForce::CutoffNonPeriodic);
testSwitchingFunction(NonbondedForce::PME);
testReordering();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/reference/include/GBVIParameters.h
View file @ 83ed602e
......@@ -65,7 +65,7 @@ class GBVIParameters {
bool _cutoff;
bool _periodic;
RealOpenMM _periodicBoxSize[3];
OpenMM::RealVec _periodicBoxVectors[3];
RealOpenMM _cutoffDistance;
int _bornRadiusScalingMethod;
......@@ -244,11 +244,11 @@ class GBVIParameters {
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic( OpenMM::RealVec& boxSize );
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
......@@ -264,7 +264,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMM* getPeriodicBox();
const OpenMM::RealVec* getPeriodicBox();
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ObcParameters.h
View file @ 83ed602e
......@@ -64,7 +64,7 @@ class ObcParameters {
bool _cutoff;
bool _periodic;
RealOpenMM _periodicBoxSize[3];
OpenMM::RealVec _periodicBoxVectors[3];
RealOpenMM _cutoffDistance;
/**---------------------------------------------------------------------------------------
......@@ -329,11 +329,11 @@ class ObcParameters {
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic( const OpenMM::RealVec& boxSize );
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
......@@ -345,11 +345,11 @@ class ObcParameters {
/**---------------------------------------------------------------------------------------
Get the periodic box dimension
Get the periodic box vectors
--------------------------------------------------------------------------------------- */
const RealOpenMM* getPeriodicBox();
const OpenMM::RealVec* getPeriodicBox();
};
......
platforms/reference/include/ReferenceCustomGBIxn.h
View file @ 83ed602e
......@@ -41,7 +41,7 @@ class ReferenceCustomGBIxn {
bool cutoff;
bool periodic;
const OpenMM::NeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
OpenMM::RealVec periodicBoxVectors[3];
RealOpenMM cutoffDistance;
std::vector<Lepton::ExpressionProgram> valueExpressions;
std::vector<std::vector<Lepton::ExpressionProgram> > valueDerivExpressions;
......@@ -263,11 +263,11 @@ class ReferenceCustomGBIxn {
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic( OpenMM::RealVec& boxSize );
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomHbondIxn.h
View file @ 83ed602e
......@@ -43,7 +43,7 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn {
class DihedralTermInfo;
bool cutoff;
bool periodic;
RealOpenMM periodicBoxSize[3];
OpenMM::RealVec periodicBoxVectors[3];
RealOpenMM cutoffDistance;
std::vector<std::vector<int> > donorAtoms, acceptorAtoms;
Lepton::ExpressionProgram energyExpression;
......@@ -111,11 +111,11 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn {
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec& boxSize);
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomManyParticleIxn.h
View file @ 83ed602e
......@@ -46,7 +46,7 @@ class ReferenceCustomManyParticleIxn {
int numParticlesPerSet, numPerParticleParameters, numTypes;
bool useCutoff, usePeriodic, centralParticleMode;
RealOpenMM cutoffDistance;
RealOpenMM periodicBoxSize[3];
OpenMM::RealVec periodicBoxVectors[3];
Lepton::ExpressionProgram energyExpression;
std::vector<std::vector<std::string> > particleParamNames;
std::vector<std::set<int> > exclusions;
......@@ -118,11 +118,11 @@ class ReferenceCustomManyParticleIxn {
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec& boxSize);
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceCustomNonbondedIxn.h
View file @ 83ed602e
......@@ -43,7 +43,7 @@ class ReferenceCustomNonbondedIxn {
bool useSwitch;
bool periodic;
const OpenMM::NeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
OpenMM::RealVec periodicBoxVectors[3];
RealOpenMM cutoffDistance, switchingDistance;
Lepton::CompiledExpression energyExpression;
Lepton::CompiledExpression forceExpression;
......@@ -129,11 +129,11 @@ class ReferenceCustomNonbondedIxn {
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic( OpenMM::RealVec& boxSize );
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceForce.h
View file @ 83ed602e
......@@ -24,6 +24,7 @@
#ifndef __ReferenceForce_H__
#define __ReferenceForce_H__
#include "RealVec.h"
#include "lepton/CompiledExpression.h"
#include "openmm/internal/windowsExport.h"
......@@ -97,18 +98,20 @@ class OPENMM_EXPORT ReferenceForce {
static void getDeltaRPeriodic( const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
const RealOpenMM* boxSize, RealOpenMM* deltaR );
/**---------------------------------------------------------------------------------------
Get deltaR between atomI and atomJ (static method): deltaR: j - i
/**---------------------------------------------------------------------------------------
Get deltaR and distance and distance**2 between atomI and atomJ, assuming periodic
boundary conditions (static method); deltaR: j - i
@param atomCoordinatesI atom i coordinates
@param atomCoordinatesI atom j coordinates
@param deltaR deltaX, deltaY, deltaZ upon return
@param boxVectors the vectors defining the periodic box
@param deltaR deltaX, deltaY, deltaZ, R2, R upon return
--------------------------------------------------------------------------------------- */
static void getDeltaROnly( const RealOpenMM* atomCoordinatesI, const RealOpenMM* atomCoordinatesJ,
RealOpenMM* deltaR );
static void getDeltaRPeriodic( const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
const OpenMM::RealVec* boxVectors, RealOpenMM* deltaR );
/**
* Get a pointer to the memory for setting a variable in a CompiledExpression. If the expression
......
platforms/reference/include/ReferenceLJCoulombIxn.h
View file @ 83ed602e
......@@ -40,7 +40,7 @@ class ReferenceLJCoulombIxn {
bool ewald;
bool pme;
const OpenMM::NeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
OpenMM::RealVec periodicBoxVectors[3];
RealOpenMM cutoffDistance, switchingDistance;
RealOpenMM krf, crf;
RealOpenMM alphaEwald;
......@@ -118,11 +118,11 @@ class ReferenceLJCoulombIxn {
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
@param vectors the vectors defining the periodic box
--------------------------------------------------------------------------------------- */
void setPeriodic( OpenMM::RealVec& boxSize );
void setPeriodic(OpenMM::RealVec* vectors);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceMonteCarloBarostat.h
View file @ 83ed602e
......@@ -61,14 +61,14 @@ class ReferenceMonteCarloBarostat {
Apply the barostat at the start of a time step, scaling x, y, and z coordinates independently.
@param atomPositions atom positions
@param boxSize the periodic box dimensions
@param boxVectors the periodic box vectors
@param scaleX the factor by which to scale atomic x coordinates
@param scaleY the factor by which to scale atomic y coordinates
@param scaleZ the factor by which to scale atomic z coordinates
--------------------------------------------------------------------------------------- */
void applyBarostat(std::vector<OpenMM::RealVec>& atomPositions, const OpenMM::RealVec& boxSize, RealOpenMM scaleX, RealOpenMM scaleY, RealOpenMM scaleZ);
void applyBarostat(std::vector<OpenMM::RealVec>& atomPositions, const OpenMM::RealVec* boxVectors, RealOpenMM scaleX, RealOpenMM scaleY, RealOpenMM scaleZ);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceNeighborList.h
View file @ 83ed602e
......@@ -22,7 +22,7 @@ void OPENMM_EXPORT computeNeighborListNaive(
int nAtoms,
const AtomLocationList& atomLocations,
const std::vector<std::set<int> >& exclusions,
const RealVec& periodicBoxSize,
const RealVec* periodicBoxVectors,
bool usePeriodic,
double maxDistance,
double minDistance = 0.0,
......@@ -35,9 +35,9 @@ void OPENMM_EXPORT computeNeighborListNaive(
void OPENMM_EXPORT computeNeighborListVoxelHash(
NeighborList& neighborList,
int nAtoms,
const AtomLocationList& atomLocations,
const AtomLocationList& atomLocations,
const std::vector<std::set<int> >& exclusions,
const RealVec& periodicBoxSize,
const RealVec* periodicBoxVectors,
bool usePeriodic,
double maxDistance,
double minDistance = 0.0,
......
platforms/reference/include/ReferencePME.h
View file @ 83ed602e
......@@ -72,16 +72,14 @@ pme_init(pme_t * ppme,
* charge Array of charges (units of e)
* box Simulation cell dimensions (nm)
* energy Total energy (will be written in units of kJ/mol)
* pme_virial Long-range part of the virial, output.
*/
int OPENMM_EXPORT
pme_exec(pme_t pme,
const std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& forces,
const std::vector<RealOpenMM>& charges,
const RealOpenMM periodicBoxSize[3],
RealOpenMM * energy,
RealOpenMM pme_virial[3][3]);
const OpenMM::RealVec periodicBoxVectors[3],
RealOpenMM * energy);
......
platforms/reference/include/ReferencePlatform.h
View file @ 83ed602e
......@@ -66,6 +66,7 @@ public:
void* velocities;
void* forces;
void* periodicBoxSize;
void* periodicBoxVectors;
void* constraints;
};
} // namespace OpenMM
......
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