Merge pull request #797 from peastman/triclinic

C++ libraries support triclinic boxes

platforms/opencl/src/kernels/monteCarloBarostat.cl

@@ -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

@@ -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/reference/include/GBVIParameters.h

@@ -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();
 
       /**---------------------------------------------------------------------------------------