Commit ee83b755 authored by Tim Mattox's avatar Tim Mattox
Browse files

USER-DPD: Split the SSA stencil and neighbor list into subphases. 

NOTE: pair evaluation order changes, causing numerical differences!
This enables processing neighbors in subphase groups that enforce
a geometrical seperation of pairs, allowing greater parallelism
once fix_shardlow (SSA) is converted to Kokkos.
parent ce2da506

src/USER-DPD/npair_half_bin_newton_ssa.cpp

+31 −27
Original line number Diff line number Diff line
@@ -74,7 +74,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) 


  NStencilSSA *ns_ssa = dynamic_cast<NStencilSSA*>(ns);

  if (!ns_ssa) error->one(FLERR, "NStencil wasn't a NStencilSSA object");

  int nstencil_half = ns_ssa->nstencil_half;

  int *nstencil_ssa = &(ns_ssa->nstencil_ssa[0]);

  int nstencil_full = ns_ssa->nstencil;



  NBinSSA *nb_ssa = dynamic_cast<NBinSSA*>(nb);
@@ -150,7 +150,9 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) 


    // loop over all local atoms in other bins in "half" stencil



    for (k = 0; k < nstencil_half; k++) {

    k = 0;

    for (int subphase = 0; subphase < 4; subphase++) {

      for (; k < nstencil_ssa[subphase]; k++) {

        for (j = binhead[ibin+stencil[k]]; j >= 0;

             j = bins[j]) {
@@ -179,6 +181,8 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) 
          }

        }

      }

      list->ndxAIR_ssa[i][subphase] = n; // record end of this subphase

    }



    if (n > 0) {

      ilist[inum++] = i;

src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp

+46 −8
Original line number Diff line number Diff line
@@ -42,31 +42,69 @@ NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) : 
void NStencilHalfBin2dNewtonSSA::create()

{

  int i,j,pos = 0;



  // Subphase 0: upper right front bins (red)

  for (j = 0; j <= sy; j++)

    for (i = -sx; i <= sx; i++)

      if (j > 0 || (j == 0 && i > 0))

    for (i = 0; i <= sx; i++)

      if (j > 0 || i > 0) // skip the centroid

        if (bin_distance(i,j,0) < cutneighmaxsq) {

          stencilxyz[pos][0] = i;

          stencilxyz[pos][1] = j;

          stencilxyz[pos][2] = 0;

          stencil[pos++] = j*mbinx + i;

        }

  nstencil_ssa[0] = pos;



  // Subphase 1: upper left front bins (light blue)

  for (j = 1; j <= sy; j++)

    for (i = -sx; i < 0; i++)

      if (bin_distance(i,j,0) < cutneighmaxsq) {

        stencilxyz[pos][0] = i;

        stencilxyz[pos][1] = j;

        stencilxyz[pos][2] = 0;

        stencil[pos++] = j*mbinx + i;

      }

  nstencil_ssa[1] = pos;



  // Subphase 2: lower left front bins (blue)

  nstencil_ssa[2] = pos;



  nstencil_half = pos; // record where normal half stencil ends

  // Subphase 3: lower right front bins (yellow)

  nstencil_ssa[3] = pos;



  // include additional bins for AIR ghosts only

  // Now include additional bins for AIR ghosts, and impure-to-pure locals

  // Subphase 4: upper right back bins (pink)

  nstencil_ssa[4] = pos;



  // Subphase 5: upper left back bins (light green)

  nstencil_ssa[5] = pos;



  // Subphase 6: lower left back bins (purple)

  for (j = -sy; j <= 0; j++)

    for (i = -sx; i <= sx; i++) {

      if (j == 0 && i > 0) continue;

    for (i = -sx; i < 0; i++)

      if (bin_distance(i,j,0) < cutneighmaxsq) {

        stencilxyz[pos][0] = i;

        stencilxyz[pos][1] = j;

        stencilxyz[pos][2] = 0;

        stencil[pos++] = j*mbinx + i;

      }

  nstencil_ssa[6] = pos;



  // Subphase 7: lower right back bins (white)

  for (j = -sy; j < 0; j++)

    for (i = 0; i <= sx; i++)

      if (bin_distance(i,j,0) < cutneighmaxsq) {

        stencilxyz[pos][0] = i;

        stencilxyz[pos][1] = j;

        stencilxyz[pos][2] = 0;

        stencil[pos++] = j*mbinx + i;

      }

  nstencil_ssa[7] = pos;



  // Also, include the centroid for the AIR ghosts.

  stencilxyz[pos][0] = 0;

  stencilxyz[pos][1] = 0;

  stencilxyz[pos][2] = 0;

  stencil[pos++] = 0;



  nstencil = pos; // record where full stencil ends

}

src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp

+85 −21
Original line number Diff line number Diff line
@@ -42,45 +42,109 @@ NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) : 
void NStencilHalfBin3dNewtonSSA::create()

{

  int i,j,k,pos = 0;

  // Subphase 0: upper right front bins (red)

  for (k = 0; k <= sz; k++)

    for (j = 0; j <= sy; j++)

      for (i = 0; i <= sx; i++)

        if (k > 0 || j > 0 || i > 0) // skip the centroid

          if (bin_distance(i,j,k) < cutneighmaxsq) {

            stencilxyz[pos][0] = i;

            stencilxyz[pos][1] = j;

            stencilxyz[pos][2] = k;

            stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;

          }

  nstencil_ssa[0] = pos;



  // Subphase 1: upper left front bins (light blue)

  for (k = 0; k <= sz; k++)

    for (j = -sy; j <= sy; j++)

      for (i = -sx; i <= sx; i++)

        if (k > 0 || j > 0 || (j == 0 && i > 0))

    for (j = 1; j <= sy; j++)

      for (i = -sx; i < 0; i++)

        if (bin_distance(i,j,k) < cutneighmaxsq) {

          stencilxyz[pos][0] = i;

          stencilxyz[pos][1] = j;

          stencilxyz[pos][2] = k;

          stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;

        }

  nstencil_ssa[1] = pos;



  nstencil_half = pos; // record where normal half stencil ends

  // Subphase 2: lower left front bins (blue)

  for (k = 1; k <= sz; k++)

    for (j = -sy; j <= 0; j++)

      for (i = -sx; i < 0; i++)

        if (bin_distance(i,j,k) < cutneighmaxsq) {

          stencilxyz[pos][0] = i;

          stencilxyz[pos][1] = j;

          stencilxyz[pos][2] = k;

          stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;

        }

  nstencil_ssa[2] = pos;



  // include additional bins for AIR ghosts only

  // Subphase 3: lower right front bins (yellow)

  for (k = 1; k <= sz; k++)

    for (j = -sy; j < 0; j++)

      for (i = 0; i <= sx; i++)

        if (bin_distance(i,j,k) < cutneighmaxsq) {

          stencilxyz[pos][0] = i;

          stencilxyz[pos][1] = j;

          stencilxyz[pos][2] = k;

          stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;

        }

  nstencil_ssa[3] = pos;



  // Now include additional bins for AIR ghosts, and impure-to-pure locals

  // Subphase 4: upper right back bins (pink)

  for (k = -sz; k < 0; k++)

    for (j = -sy; j <= sy; j++)

      for (i = -sx; i <= sx; i++)

    for (j = 0; j <= sy; j++)

      for (i = 0; i <= sx; i++)

        if (bin_distance(i,j,k) < cutneighmaxsq) {

          stencilxyz[pos][0] = i;

          stencilxyz[pos][1] = j;

          stencilxyz[pos][2] = k;

          stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;

        }

  nstencil_ssa[4] = pos;



  // For k==0, make sure to skip already included bins

  // Subphase 5: upper left back bins (light green)

  for (k = -sz; k < 0; k++)

    for (j = 1; j <= sy; j++)

      for (i = -sx; i < 0; i++)

        if (bin_distance(i,j,k) < cutneighmaxsq) {

          stencilxyz[pos][0] = i;

          stencilxyz[pos][1] = j;

          stencilxyz[pos][2] = k;

          stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;

        }

  nstencil_ssa[5] = pos;



  k = 0;

  // Subphase 6: lower left back bins (purple)

  for (k = -sz; k <= 0; k++)

    for (j = -sy; j <= 0; j++)

    for (i = -sx; i <= sx; i++) {

      if (j == 0 && i > 0) continue;

      for (i = -sx; i < 0; i++)

        if (bin_distance(i,j,k) < cutneighmaxsq) {

          stencilxyz[pos][0] = i;

          stencilxyz[pos][1] = j;

          stencilxyz[pos][2] = k;

          stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;

        }

  nstencil_ssa[6] = pos;



  // Subphase 7: lower right back bins (white)

  for (k = -sz; k <= 0; k++)

    for (j = -sy; j < 0; j++)

      for (i = 0; i <= sx; i++)

        if (bin_distance(i,j,k) < cutneighmaxsq) {

          stencilxyz[pos][0] = i;

          stencilxyz[pos][1] = j;

          stencilxyz[pos][2] = k;

          stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;

        }

  nstencil_ssa[7] = pos;



  // Also, include the centroid for the AIR ghosts.

  stencilxyz[pos][0] = 0;

  stencilxyz[pos][1] = 0;

  stencilxyz[pos][2] = 0;

  stencil[pos++] = 0;



  nstencil = pos; // record where full stencil ends

}

src/USER-DPD/nstencil_ssa.h

+1 −1
Original line number Diff line number Diff line
@@ -24,7 +24,7 @@ class NStencilSSA : public NStencil { 
  ~NStencilSSA() {}

  virtual void create() = 0;



  int nstencil_half;   // where the half stencil ends

  int nstencil_ssa[8];  // last stencil index for each subphase

};



}

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