Commit 01051e4c authored by Steve Plimpton's avatar Steve Plimpton
Browse files

refactoring of neighbor history

parent 93c9a927

src/GRANULAR/pair_gran_hertz_history.cpp

+4 −3
Original line number Diff line number Diff line
@@ -24,6 +24,7 @@ 
#include "update.h"

#include "force.h"

#include "fix.h"

#include "fix_neigh_history.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "comm.h"
@@ -95,8 +96,8 @@ void PairGranHertzHistory::compute(int eflag, int vflag) 
  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;

  firsttouch = list->listhistory->firstneigh;

  firstshear = list->listhistory->firstdouble;

  firsttouch = fix_history->firstflag;

  firstshear = fix_history->firstvalue;



  // loop over neighbors of my atoms
@@ -407,7 +408,7 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype, 


  int jnum = list->numneigh[i];

  int *jlist = list->firstneigh[i];

  double *allshear = list->listhistory->firstdouble[i];

  double *allshear = fix_history->firstvalue[i];



  for (int jj = 0; jj < jnum; jj++) {

    neighprev++;

src/GRANULAR/pair_gran_hooke_history.cpp

+14 −43
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ 
#include "update.h"

#include "modify.h"

#include "fix.h"

#include "fix_shear_history.h"

#include "fix_neigh_history.h"

#include "comm.h"

#include "neighbor.h"

#include "neigh_list.h"
@@ -64,7 +64,7 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp) 
PairGranHookeHistory::~PairGranHookeHistory()

{

  delete [] svector;

  if (fix_history) modify->delete_fix("SHEAR_HISTORY");

  if (fix_history) modify->delete_fix("NEIGH_HISTORY");



  if (allocated) {

    memory->destroy(setflag);
@@ -137,8 +137,8 @@ void PairGranHookeHistory::compute(int eflag, int vflag) 
  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;

  firsttouch = listhistory->firstneigh;

  firstshear = listhistory->firstdouble;

  firsttouch = fix_history->firstflag;

  firstshear = fix_history->firstvalue;



  // loop over neighbors of my atoms
@@ -400,35 +400,28 @@ void PairGranHookeHistory::init_style() 
  if (comm->ghost_velocity == 0)

    error->all(FLERR,"Pair granular requires ghost atoms store velocity");



  // need a granular neigh list and optionally a granular history neigh list

  // need a granular neigh list



  int irequest = neighbor->request(this,instance_me);

  neighbor->requests[irequest]->size = 1;

  if (history) {

    irequest = neighbor->request(this,instance_me);

    neighbor->requests[irequest]->id = 1;

    neighbor->requests[irequest]->history = 1;

    neighbor->requests[irequest]->dnum = 3;

  }

  if (history) neighbor->requests[irequest]->history = 1;



  dt = update->dt;



  // if shear history is stored:

  // if first init, create Fix needed for storing shear history



  if (history && fix_history == NULL) {

    char dnumstr[16];

    sprintf(dnumstr,"%d",3);

    char **fixarg = new char*[4];

    fixarg[0] = (char *) "SHEAR_HISTORY";

    fixarg[0] = (char *) "NEIGH_HISTORY";

    fixarg[1] = (char *) "all";

    fixarg[2] = (char *) "SHEAR_HISTORY";

    fixarg[2] = (char *) "NEIGH_HISTORY";

    fixarg[3] = dnumstr;

    modify->add_fix(4,fixarg);

    modify->add_fix(4,fixarg,1);

    delete [] fixarg;

    fix_history = (FixShearHistory *) modify->fix[modify->nfix-1];

    fix_history = (FixNeighHistory *) modify->fix[modify->nfix-1];

    fix_history->pair = this;

    neighbor->requests[irequest]->fix_history = fix_history;

  }



  // check for FixFreeze and set freeze_group_bit
@@ -494,23 +487,12 @@ void PairGranHookeHistory::init_style() 
  // set fix which stores history info



  if (history) {

    int ifix = modify->find_fix("SHEAR_HISTORY");

    if (ifix < 0) error->all(FLERR,"Could not find pair fix ID");

    fix_history = (FixShearHistory *) modify->fix[ifix];

    int ifix = modify->find_fix("NEIGH_HISTORY");

    if (ifix < 0) error->all(FLERR,"Could not find pair fix neigh history ID");

    fix_history = (FixNeighHistory *) modify->fix[ifix];

  }

}



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

   neighbor callback to inform pair style of neighbor list to use

   optional granular history list

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



void PairGranHookeHistory::init_list(int id, NeighList *ptr)

{

  if (id == 0) list = ptr;

  else if (id == 1) listhistory = ptr;

}



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

   init for one type pair i,j and corresponding j,i

------------------------------------------------------------------------- */
@@ -704,7 +686,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype, 


  int jnum = list->numneigh[i];

  int *jlist = list->firstneigh[i];

  double *allshear = list->listhistory->firstdouble[i];

  double *allshear = fix_history->firstvalue[i];



  for (int jj = 0; jj < jnum; jj++) {

    neighprev++;
@@ -797,14 +779,3 @@ double PairGranHookeHistory::memory_usage() 
  double bytes = nmax * sizeof(double);

  return bytes;

}
 


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

   return ptr to FixShearHistory class

   called by Neighbor when setting up neighbor lists

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



void *PairGranHookeHistory::extract(const char *str, int &dim)

{

  if (strcmp(str,"history") == 0) return (void *) fix_history;

  return NULL;

}

src/GRANULAR/pair_gran_hooke_history.h

+1 −3
Original line number Diff line number Diff line
@@ -32,7 +32,6 @@ class PairGranHookeHistory : public Pair { 
  virtual void settings(int, char **);

  void coeff(int, char **);

  void init_style();

  void init_list(int, class NeighList *);

  double init_one(int, int);

  void write_restart(FILE *);

  void read_restart(FILE *);
@@ -43,7 +42,6 @@ class PairGranHookeHistory : public Pair { 
  int pack_forward_comm(int, int *, double *, int, int *);

  void unpack_forward_comm(int, int, double *);

  double memory_usage();

  void *extract(const char *, int &);



 protected:

  double kn,kt,gamman,gammat,xmu;
@@ -56,7 +54,7 @@ class PairGranHookeHistory : public Pair { 
  double *onerad_dynamic,*onerad_frozen;

  double *maxrad_dynamic,*maxrad_frozen;



  class FixShearHistory *fix_history;

  class FixNeighHistory *fix_history;



  // storage of rigid body masses for use in granular interactions

src/fix.h

+24 −19
Original line number Diff line number Diff line
@@ -113,6 +113,7 @@ class Fix : protected Pointers { 
  virtual void setup(int) {}

  virtual void setup_pre_exchange() {}

  virtual void setup_pre_neighbor() {}

  virtual void setup_post_neighbor() {}

  virtual void setup_pre_force(int) {}

  virtual void setup_pre_reverse(int, int) {}

  virtual void min_setup(int) {}
@@ -120,6 +121,7 @@ class Fix : protected Pointers { 
  virtual void post_integrate() {}

  virtual void pre_exchange() {}

  virtual void pre_neighbor() {}

  virtual void post_neighbor() {}

  virtual void pre_force(int) {}

  virtual void pre_reverse(int,int) {}

  virtual void post_force(int) {}
@@ -155,6 +157,7 @@ class Fix : protected Pointers { 


  virtual void min_pre_exchange() {}

  virtual void min_pre_neighbor() {}

  virtual void min_post_neighbor() {}

  virtual void min_pre_force(int) {}

  virtual void min_pre_reverse(int,int) {}

  virtual void min_post_force(int) {}
@@ -244,25 +247,27 @@ namespace FixConst { 
  static const int POST_INTEGRATE =          1<<1;

  static const int PRE_EXCHANGE =            1<<2;

  static const int PRE_NEIGHBOR =            1<<3;

  static const int PRE_FORCE =               1<<4;

  static const int PRE_REVERSE =             1<<5;

  static const int POST_FORCE =              1<<6;

  static const int FINAL_INTEGRATE =         1<<7;

  static const int END_OF_STEP =             1<<8;

  static const int POST_RUN =                1<<9;

  static const int THERMO_ENERGY =           1<<10;

  static const int INITIAL_INTEGRATE_RESPA = 1<<11;

  static const int POST_INTEGRATE_RESPA =    1<<12;

  static const int PRE_FORCE_RESPA =         1<<13;

  static const int POST_FORCE_RESPA =        1<<14;

  static const int FINAL_INTEGRATE_RESPA =   1<<15;

  static const int MIN_PRE_EXCHANGE =        1<<16;

  static const int MIN_PRE_NEIGHBOR =        1<<17;

  static const int MIN_PRE_FORCE =           1<<18;

  static const int MIN_PRE_REVERSE =         1<<19;

  static const int MIN_POST_FORCE =          1<<20;

  static const int MIN_ENERGY =              1<<21;

  static const int FIX_CONST_LAST =          1<<22;

  static const int POST_NEIGHBOR =           1<<4;

  static const int PRE_FORCE =               1<<5;

  static const int PRE_REVERSE =             1<<6;

  static const int POST_FORCE =              1<<7;

  static const int FINAL_INTEGRATE =         1<<8;

  static const int END_OF_STEP =             1<<9;

  static const int POST_RUN =                1<<10;

  static const int THERMO_ENERGY =           1<<11;

  static const int INITIAL_INTEGRATE_RESPA = 1<<12;

  static const int POST_INTEGRATE_RESPA =    1<<13;

  static const int PRE_FORCE_RESPA =         1<<14;

  static const int POST_FORCE_RESPA =        1<<15;

  static const int FINAL_INTEGRATE_RESPA =   1<<16;

  static const int MIN_PRE_EXCHANGE =        1<<17;

  static const int MIN_PRE_NEIGHBOR =        1<<18;

  static const int MIN_POST_NEIGHBOR =       1<<19;

  static const int MIN_PRE_FORCE =           1<<20;

  static const int MIN_PRE_REVERSE =         1<<21;

  static const int MIN_POST_FORCE =          1<<22;

  static const int MIN_ENERGY =              1<<23;

  static const int FIX_CONST_LAST =          1<<24;

}



}

src/fix_shear_history.cpp→src/fix_neigh_history.cpp

+315 −183

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