Commit 227489b1 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@80 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent afce2f00

src/delete_atoms.cpp

+11 −18
Original line number Diff line number Diff line
@@ -43,7 +43,6 @@ void DeleteAtoms::command(int narg, char **arg) 
    error->all("Cannot use delete_atoms unless atoms have IDs");



  int natoms_previous = static_cast<int> (atom->natoms);

  int tag_lowest = natoms_previous + 1;



  // allocate and initialize deletion list
@@ -53,7 +52,6 @@ void DeleteAtoms::command(int narg, char **arg) 
  for (int i = 0; i < nlocal; i++) list[i] = 0;



  // delete the atoms

  // return tag_lowest = min tag of each proc's deleted atoms



  if (strcmp(arg[0],"group") == 0) delete_group(narg,arg,list);

  else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg,list);
@@ -62,14 +60,12 @@ void DeleteAtoms::command(int narg, char **arg) 


  // delete local atoms in list

  // reset nlocal

  // tag_lowest_all = smallest deleted atom tag on any proc



  int *tag = atom->tag;



  int i = 0;

  while (i < nlocal) {

    if (list[i]) {

      tag_lowest = MIN(tag_lowest,tag[i]);

      atom->copy(nlocal-1,i);

      list[i] = list[nlocal-1];

      nlocal--;
@@ -78,19 +74,14 @@ void DeleteAtoms::command(int narg, char **arg) 
  atom->nlocal = nlocal;

  delete [] list;



  int tag_lowest_all;

  MPI_Allreduce(&tag_lowest,&tag_lowest_all,1,MPI_INT,MPI_MIN,world);



  // if non-molecular system, reset atom tags to be contiguous

  // set all atom IDs >= tag_lowest_all to 0

  // tag_extend() will reset tags for those atoms

  // set all atom IDs to 0, call tag_extend()



  if (atom->molecular == 0) {

    int *tag = atom->tag;

    int nlocal = atom->nlocal;

 

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

      if (tag[i] >= tag_lowest_all) tag[i] = 0;

    for (i = 0; i < nlocal; i++) tag[i] = 0;

    atom->tag_extend();

  }
@@ -188,14 +179,17 @@ void DeleteAtoms::delete_overlap(int narg, char **arg, int *list) 


  // init entire system since comm->borders and neighbor->build is done

  // comm::init needs neighbor::init needs pair::init needs kspace::init, etc

  // set half_command since will require half neigh list even if

  //   neighbor would otherwise not create one, then unset it



  if (comm->me == 0 && screen)

    fprintf(screen,"System init for delete_atoms ...\n");

  neighbor->half_command = 1;

  sys->init();

  neighbor->half_command = 0;



  // setup domain, communication and neighboring

  // acquire ghosts

  // build half neighbor list via explicit call

    

  domain->pbc();

  domain->reset_box();
@@ -204,8 +198,11 @@ void DeleteAtoms::delete_overlap(int narg, char **arg, int *list) 
  comm->exchange();

  comm->borders();



  if (!neighbor->half) neighbor->build_half_setup();

  neighbor->build_half();

  // call to build() forces memory allocation for neighbor lists

  // build half list explicitly if build() doesn't do it



  neighbor->build();

  if (!neighbor->half_every) neighbor->build_half();



  // error check on cutoff
@@ -289,10 +286,6 @@ void DeleteAtoms::delete_overlap(int narg, char **arg, int *list) 
    }

  }



  // cleanup after neighbor list



  if (!neighbor->half) neighbor->build_half_cleanup();



  // delete temporary atom map



  if (mapflag) {

src/neighbor.cpp

+5 −41
Original line number Diff line number Diff line
@@ -87,7 +87,7 @@ Neighbor::Neighbor() 


  // half neighbor list info



  half = 0;

  half = half_command = 0;

  maxpage = 0;

  numneigh = NULL;

  firstneigh = NULL;
@@ -385,8 +385,9 @@ void Neighbor::init() 
  }



  half = full = 0;

  if (half_every || half_once) half = 1;

  if (half_every || half_once || half_command) half = 1;

  if (full_every || full_once) full = 1;

  half = 1;



  // setup/delete memory for half and full lists
@@ -720,7 +721,7 @@ void Neighbor::build() 


  // extend atom arrays if necessary

  // check half/full instead of half_every/full_every so memory will be

  //   allocated correctly when build_half() and build_full() are called

  //   allocated correctly whenever build_half() and build_full() are called



  if (atom->nlocal > maxlocal) {

    maxlocal = atom->nmax;
@@ -792,27 +793,6 @@ void Neighbor::build() 
  }

}



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

   prepare for one-time call to build a half neighbor list

   only needs to be called if Neighbor::init() set half = 0

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



void Neighbor::build_half_setup()

{

  numneigh = (int *) memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh");

  firstneigh =

    (int **) memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh");

  add_pages(0);



  if (style == 0) {

    if (force->newton_pair == 0) half_build = &Neighbor::half_nsq_no_newton;

    else half_build = &Neighbor::half_nsq_newton;

  } else if (style == 1) {

    if (force->newton_pair == 0) half_build = &Neighbor::half_bin_no_newton;

    else half_build = &Neighbor::half_bin_newton;

  }

}



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

   one-time call to build a half neighbor list made by other classes

------------------------------------------------------------------------- */
@@ -823,23 +803,7 @@ void Neighbor::build_half() 
}



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

   clean-up from one-time call to build a half neighbor list

   only needs to be called if Neighbor::init() set half = 0

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



void Neighbor::build_half_cleanup()

{

  memory->sfree(numneigh);

  memory->sfree(firstneigh);

  for (int i = 0; i < maxpage; i++) memory->sfree(pages[i]);

  memory->sfree(pages);

  pages = NULL;

  maxpage = 0;

  half_build = NULL;

}



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

   build a full neighbor list, called occasionally by a fix

   one-time call to build a full neighbor list made by other classes

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



void Neighbor::build_full()

src/neighbor.h

+1 −2
Original line number Diff line number Diff line
@@ -39,6 +39,7 @@ class Neighbor : public LAMMPS { 
  int full_every;                  // 0/1 if full list built every step

  int half_once;                   // 0/1 if half pair list built occasionally

  int full_once;                   // 0/1 if full pair list built occasionally

  int half_command;                // 0/1 if command requires half list



  int *numneigh;                   // # of half neighbors for each atom

  int **firstneigh;                // ptr to 1st half neighbor of each atom
@@ -74,9 +75,7 @@ class Neighbor : public LAMMPS { 
  int check_distance();       // check max distance moved since last build

  void setup_bins();          // setup bins based on box and cutoff

  void build();               // create all neighbor lists (half,full,bond)

  void build_half_setup();    // setup for one-time creation of half list

  void build_half();          // one-time creation of half neighbor list

  void build_half_cleanup();  // cleanup of one-time creation of half list

  void build_full();          // one-time creation of full neighbor list

  void modify_params(int, char**);  // modify parameters of neighbor build

  int memory_usage();         // tally memory usage

src/pressure.cpp

+1 −1
Original line number Diff line number Diff line
@@ -150,7 +150,7 @@ void Pressure::compute(Temperature *temperature) 


  double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);



  if (force->pair->tail_flag)

  if (force->pair && force->pair->tail_flag)

    for (i = 0; i < n; i++) virial[i] += force->pair->ptail * inv_volume;



  // compute just total average pressure or entire pressure tensor

src/thermo.cpp

+4 −4
Original line number Diff line number Diff line
@@ -837,7 +837,7 @@ void Thermo::compute_pe() 
  MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);



  if (force->kspace) dvalue += force->kspace->energy;

  if (force->pair->tail_flag) {

  if (force->pair && force->pair->tail_flag) {

    double volume = domain->xprd * domain->yprd * domain->zprd;

    dvalue += force->pair->etail / volume;

  }
@@ -881,7 +881,7 @@ void Thermo::compute_evdwl() 


  MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);



  if (force->pair->tail_flag) {

  if (force->pair && force->pair->tail_flag) {

    double volume = domain->xprd * domain->yprd * domain->zprd;

    dvalue += force->pair->etail / volume;

  }
@@ -912,7 +912,7 @@ void Thermo::compute_epair() 
  MPI_Allreduce(&tmp,&dvalue,1,MPI_DOUBLE,MPI_SUM,world);



  if (force->kspace) dvalue += force->kspace->energy;

  if (force->pair->tail_flag) {

  if (force->pair && force->pair->tail_flag) {

    double volume = domain->xprd * domain->yprd * domain->zprd;

    dvalue += force->pair->etail / volume;

  }
@@ -993,7 +993,7 @@ void Thermo::compute_elong() 


void Thermo::compute_etail()

{

  if (force->pair->tail_flag) {

  if (force->pair && force->pair->tail_flag) {

    double volume = domain->xprd * domain->yprd * domain->zprd;

    dvalue = force->pair->etail / volume;

    if (normflag) dvalue /= natoms;

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