Commit 641bb4bb authored by Tim Mattox's avatar Tim Mattox
Browse files

USER-DPD: remove use of ssaAIR[], move coord2ssaAIR() to nbin_ssa.cpp 

Saves an int per atom and ghost, also simplifies and reduces code size.
parent f73c9a43

src/USER-DPD/fix_shardlow.cpp

+0 −116
Original line number Diff line number Diff line
@@ -109,26 +109,12 @@ FixShardlow::FixShardlow(LAMMPS *lmp, int narg, char **arg) : 
  if(pairDPD == NULL && pairDPDE == NULL)

    error->all(FLERR,"Must use pair_style dpd/fdt or dpd/fdt/energy with fix shardlow");



  // Setup the ssaAIR array

  atom->ssaAIR = NULL;

  grow_arrays(atom->nmax);

  memset(atom->ssaAIR, 0, sizeof(int)*atom->nlocal);



  // Setup callbacks for maintaining atom->ssaAIR[]

  atom->add_callback(0); // grow (aka exchange)

  atom->add_callback(1); // restart

  atom->add_callback(2); // border

}



/* ---------------------------------------------------------------------- */



FixShardlow::~FixShardlow()

{

  atom->delete_callback(id, 0);

  atom->delete_callback(id, 1);

  atom->delete_callback(id, 2);



  memory->destroy(atom->ssaAIR);

}



/* ---------------------------------------------------------------------- */
@@ -137,7 +123,6 @@ int FixShardlow::setmask() 
{

  int mask = 0;

  mask |= INITIAL_INTEGRATE;

  mask |= PRE_EXCHANGE | MIN_PRE_EXCHANGE;

  return mask;

}
@@ -161,27 +146,6 @@ void FixShardlow::init_list(int id, NeighList *ptr) 


/* ---------------------------------------------------------------------- */



void FixShardlow::pre_exchange()

{

  memset(atom->ssaAIR, 0, sizeof(int)*atom->nlocal);

}



/* ---------------------------------------------------------------------- */



void FixShardlow::setup_pre_exchange()

{

  memset(atom->ssaAIR, 0, sizeof(int)*atom->nlocal);

}



/* ---------------------------------------------------------------------- */



void FixShardlow::min_pre_exchange()

{

  memset(atom->ssaAIR, 0, sizeof(int)*atom->nlocal);

}



/* ---------------------------------------------------------------------- */



void FixShardlow::setup(int vflag)

{

  bool fixShardlow = false;
@@ -659,91 +623,11 @@ void FixShardlow::unpack_reverse_comm(int n, int *list, double *buf) 
  }

}



/* ----------------------------------------------------------------------

   convert atom coords into the ssa active interaction region number

------------------------------------------------------------------------- */



int FixShardlow::coord2ssaAIR(double *x)

{

  int ix, iy, iz;



  ix = iy = iz = 0;

  if (x[2] < domain->sublo[2]) iz = -1;

  if (x[2] >= domain->subhi[2]) iz = 1;

  if (x[1] < domain->sublo[1]) iy = -1;

  if (x[1] >= domain->subhi[1]) iy = 1;

  if (x[0] < domain->sublo[0]) ix = -1;

  if (x[0] >= domain->subhi[0]) ix = 1;



  if(iz < 0){

    return -1;

  } else if(iz == 0){

    if( iy<0 ) return -1; // bottom left/middle/right

    if( (iy==0) && (ix<0)  ) return -1; // left atoms

    if( (iy==0) && (ix==0) ) return 0; // Locally owned atoms

    if( (iy==0) && (ix>0)  ) return 3; // Right atoms

    if( (iy>0)  && (ix==0) ) return 2; // Top-middle atoms

    if( (iy>0)  && (ix!=0) ) return 4; // Top-right and top-left atoms

  } else { // iz > 0

    if((ix==0) && (iy==0)) return 5; // Back atoms

    if((ix==0) && (iy!=0)) return 6; // Top-back and bottom-back atoms

    if((ix!=0) && (iy==0)) return 7; // Left-back and right-back atoms

    if((ix!=0) && (iy!=0)) return 8; // Back corner atoms

  }



  return -2;

}



/* ---------------------------------------------------------------------- */



void FixShardlow::grow_arrays(int nmax)

{

  memory->grow(atom->ssaAIR,nmax,"fix_shardlow:ssaAIR");

}



void FixShardlow::copy_arrays(int i, int j, int delflag)

{

  atom->ssaAIR[j] = atom->ssaAIR[i];

}



void FixShardlow::set_arrays(int i)

{

  atom->ssaAIR[i] = 0; /* coord2ssaAIR(x[i]) */

}



int FixShardlow::pack_border(int n, int *list, double *buf)

{

  for (int i = 0; i < n; i++) {

    int j = list[i];

    if (atom->ssaAIR[j] == 0) atom->ssaAIR[j] = 1; // not purely local anymore

  }

  return 0;

}



int FixShardlow::unpack_border(int n, int first, double *buf)

{

  int i,last = first + n;

  for (i = first; i < last; i++) {

    atom->ssaAIR[i] = coord2ssaAIR(atom->x[i]);

  }

  return 0;

}



int FixShardlow::unpack_exchange(int i, double *buf)

{

  atom->ssaAIR[i] = 0; /* coord2ssaAIR(x[i]) */

  return 0;

}



void FixShardlow::unpack_restart(int i, int nth)

{

  atom->ssaAIR[i] = 0; /* coord2ssaAIR(x[i]) */

}



double FixShardlow::memory_usage()

{

  double bytes = 0.0;

  bytes += memory->usage(atom->ssaAIR,atom->nmax);

  bytes += sizeof(double)*3*atom->nghost; // v_t0[]

  return bytes;

}

src/USER-DPD/fix_shardlow.h

+0 −13
Original line number Diff line number Diff line
@@ -35,18 +35,6 @@ class FixShardlow : public Fix { 
  virtual void init_list(int, class NeighList *);

  virtual void setup(int);

  virtual void initial_integrate(int);

  void setup_pre_exchange();

  void pre_exchange();

  void min_pre_exchange();



  void grow_arrays(int);

  void copy_arrays(int, int, int);

  void set_arrays(int);



  int pack_border(int, int *, double *);

  int unpack_border(int, int, double *);

  int unpack_exchange(int, double *);

  void unpack_restart(int, int);



  double memory_usage();
@@ -63,7 +51,6 @@ class FixShardlow : public Fix { 
 private:

  double dtsqrt; // = sqrt(update->dt);



  int coord2ssaAIR(double *);  // map atom coord to an AIR number

  void ssa_update_dpd(int, int *, int);  // Constant Temperature

  void ssa_update_dpde(int, int *, int); // Constant Energy

src/USER-DPD/nbin_ssa.cpp

+37 −3
Original line number Diff line number Diff line
@@ -20,6 +20,7 @@ 
#include "atom.h"

#include "update.h"

#include "group.h"

#include "domain.h"

#include "memory.h"

#include "error.h"
@@ -58,7 +59,6 @@ void NBinSSA::bin_atoms() 
  if (includegroup) nlocal = atom->nfirst;

  double **x = atom->x;

  int *mask = atom->mask;

  int *ssaAIR = atom->ssaAIR;

  int xbin,ybin,zbin;



  last_bin = update->ntimestep;
@@ -82,7 +82,7 @@ void NBinSSA::bin_atoms() 
    int bitmask = group->bitmask[includegroup];

    int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above

    for (i = nall-1; i >= nowned; i--) {

      ibin = ssaAIR[i];

      ibin = coord2ssaAIR(x[i]);

      if (ibin < 2) continue; // skip ghost atoms not in AIR

      if (mask[i] & bitmask) {

        bins[i] = gairhead_ssa[ibin];
@@ -91,7 +91,7 @@ void NBinSSA::bin_atoms() 
    }

  } else {

    for (i = nall-1; i >= nlocal; i--) {

      ibin = ssaAIR[i];

      ibin = coord2ssaAIR(x[i]);

      if (ibin < 2) continue; // skip ghost atoms not in AIR

      bins[i] = gairhead_ssa[ibin];

      gairhead_ssa[ibin] = i;
@@ -148,3 +148,37 @@ bigint NBinSSA::memory_usage() 
  }

  return bytes;

}



/* ----------------------------------------------------------------------

   convert atom coords into the ssa active interaction region number

------------------------------------------------------------------------- */

int NBinSSA::coord2ssaAIR(const double *x)

{

  int ix, iy, iz;



  ix = iy = iz = 0;

  if (x[2] < domain->sublo[2]) iz = -1;

  if (x[2] >= domain->subhi[2]) iz = 1;

  if (x[1] < domain->sublo[1]) iy = -1;

  if (x[1] >= domain->subhi[1]) iy = 1;

  if (x[0] < domain->sublo[0]) ix = -1;

  if (x[0] >= domain->subhi[0]) ix = 1;



  if(iz < 0){

    return -1;

  } else if(iz == 0){

    if( iy<0 ) return -1; // bottom left/middle/right

    if( (iy==0) && (ix<0)  ) return -1; // left atoms

    if( (iy==0) && (ix==0) ) return 0; // Locally owned atoms

    if( (iy==0) && (ix>0)  ) return 3; // Right atoms

    if( (iy>0)  && (ix==0) ) return 2; // Top-middle atoms

    if( (iy>0)  && (ix!=0) ) return 4; // Top-right and top-left atoms

  } else { // iz > 0

    if((ix==0) && (iy==0)) return 5; // Back atoms

    if((ix==0) && (iy!=0)) return 6; // Top-back and bottom-back atoms

    if((ix!=0) && (iy==0)) return 7; // Left-back and right-back atoms

    if((ix!=0) && (iy!=0)) return 8; // Back corner atoms

  }



  return -2;

}

src/USER-DPD/nbin_ssa.h

+1 −0
Original line number Diff line number Diff line
@@ -155,6 +155,7 @@ class NBinSSA : public NBinStandard { 
  }



 private:

  int coord2ssaAIR(const double *);  // map atom coord to an AIR number

  double bboxlo_[3],bboxhi_[3];



};

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