Merge pull request #1581 from akohlmey/comm-cutoff-with-bond

Self-explanatory. :dd

{Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost} :dt

The communication cutoff defaults to the maximum of what is inferred from

pair and bond styles (will be zero, if none are defined) and what is specified

via "comm_modify cutoff"_comm_modify.html (defaults to 0.0).  If this results

to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use

incorrect periodic images of atoms in interaction lists.  To avoid, either use

"pair style zero"_pair_zero.html with a suitable cutoff or use "comm_modify

cutoff"_comm_modify.html. :dd

{Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt

Self-explanatory. :dd

force cutoff + neighbor skin.  See the "neighbor"_neighbor.html command

for more information about the skin distance.  If the specified Rcut is

greater than the neighbor cutoff, then extra ghost atoms will be acquired.

If the provided cutoff is smaller, the provided value will be ignored

and the ghost cutoff is set to the neighbor cutoff. Specifying a

cutoff value of 0.0 will reset any previous value to the default.

If the provided cutoff is smaller, the provided value will be ignored,

the ghost cutoff is set to the neighbor cutoff and a warning will be

printed. Specifying a cutoff value of 0.0 will reset any previous value

to the default. If bonded interactions exist and equilibrium bond length

information is available, then also a heuristic based on that bond length

is computed. It is used as communication cutoff, if there is no pair

style present and no {comm_modify cutoff} command used. Otherwise a

warning is printed, if this bond based estimate is larger than the

communication cutoff used. A

The {cutoff/multi} option is equivalent to {cutoff}, but applies to

communication mode {multi} instead. Since in this case the communication

#include "atom_vec.h"

#include "force.h"

#include "pair.h"

#include "bond.h"

#include "modify.h"

#include "fix.h"

#include "compute.h"

  }

}

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

   determine suitable communication cutoff.

   this uses three inputs: 1) maximum neighborlist cutoff, 2) an estimate

   based on bond lengths and bonded interaction styles present, and 3) a

   user supplied communication cutoff.

   the neighbor list cutoff (1) is *always* used, since it is a requirement

   for neighborlists working correctly. the bond length based cutoff is

   *only* used, if no pair style is defined and no user cutoff is provided.

   otherwise, a warning is printed. if the bond length based estimate is

   larger than what is used.

   print a warning, if a user specified communication cutoff is overridden.

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

double Comm::get_comm_cutoff()

{

  double maxcommcutoff, maxbondcutoff = 0.0;

  if (force->bond) {

    int n = atom->nbondtypes;

    for (int i = 1; i <= n; ++i)

      maxbondcutoff = MAX(maxbondcutoff,force->bond->equilibrium_distance(i));

    // apply bond length based heuristics.

    if (force->newton_bond) {

      if (force->dihedral || force->improper) {

        maxbondcutoff *= 2.25;

      } else {

        maxbondcutoff *=1.5;

      }

    } else {

      if (force->dihedral || force->improper) {

        maxbondcutoff *= 3.125;

      } else if (force->angle) {

        maxbondcutoff *= 2.25;

      } else {

        maxbondcutoff *=1.5;

      }

    }

    maxbondcutoff += neighbor->skin;

  }

  // always take the larger of max neighbor list and user specified cutoff

  maxcommcutoff = MAX(cutghostuser,neighbor->cutneighmax);

  // use cutoff estimate from bond length only if no user specified

  // cutoff was given and no pair style present. Otherwise print a

  // warning, if the estimated bond based cutoff is larger than what

  // is currently used.

  if (!force->pair && (cutghostuser == 0.0)) {

    maxcommcutoff = MAX(maxcommcutoff,maxbondcutoff);

  } else {

    if ((me == 0) && (maxbondcutoff > maxcommcutoff)) {

      char mesg[256];

      snprintf(mesg,256,"Communication cutoff %g is shorter than a bond "

               "length based estimate of %g. This may lead to errors.",

               maxcommcutoff,maxbondcutoff);

      error->warning(FLERR,mesg);

    }

  }

  // print warning if neighborlist cutoff overrides user cutoff

  if (me == 0) {

    if ((cutghostuser > 0.0) && (maxcommcutoff > cutghostuser)) {

      char mesg[128];

      snprintf(mesg,128,"Communication cutoff adjusted to %g",maxcommcutoff);

      error->warning(FLERR,mesg);

    }

  }

  return maxcommcutoff;

}

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

   determine which proc owns atom with coord x[3] based on current decomp

   x will be in box (orthogonal) or lamda coords (triclinic)

    return 0;    // all nout_rvous are 0, no 2nd irregular

  }

  // create procs and outbuf for All2all if necesary

  if (!outorder) {

  void set_processors(int, char **);      // set 3d processor grid attributes

  virtual void set_proc_grid(int outflag = 1); // setup 3d grid of procs

  double get_comm_cutoff();     // determine communication cutoff

  virtual void setup() = 0;                      // setup 3d comm pattern

  virtual void forward_comm(int dummy = 0) = 0;  // forward comm of atom coords

  virtual void reverse_comm() = 0;               // reverse comm of forces

E: Cannot put data on ring from NULL pointer

W: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost.

The communication cutoff defaults to the maximum of what is inferred from pair and

bond styles (will be zero, if none are defined) and what is specified via

"comm_modify cutoff" (defaults to 0.0).  If this results to 0.0, no ghost atoms will

be generated and LAMMPS may lose atoms or use incorrect periodic images of atoms in

interaction lists.  To avoid, either define pair style zero with a suitable cutoff

or use comm_modify cutoff.

UNDOCUMENTED

U: OMP_NUM_THREADS environment is not set.

  int ntypes = atom->ntypes;

  double *prd,*sublo,*subhi;

  double cut = MAX(neighbor->cutneighmax,cutghostuser);

  double cut = get_comm_cutoff();

  if ((cut == 0.0) && (me == 0))

    error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms "

                   "will be generated. Atoms may get lost.");

  if (triclinic == 0) {

    prd = domain->prd;