more changes to ATM source and doc file

Note that for the interaction between a triplet of atoms I,J,K, there

is no "central" atom.  The interaction is symmetric with respect to

permutation of the three atoms.  In fact, it is computed 3 times by

the code with each of I,J,K being atom 1.  Thus the nu value must be

the same for all those permutations of the atom types of I,J,K as

discussed below.

permutation of the three atoms. Thus the nu value is

the same for all those permutations of the atom types of I,J,K

and needs to be specified only once, as discussed below.

The {atm} potential is typically used in combination with a two-body

potential using the "pair_style hybrid/overlay"_pair_hybrid.html

command as in the example above.

The potential for a triplet of atom is calculated only if all 3

distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.

The potential is calculated if atoms J and K are in the

"neighbor list"_neighbor.html of atom I

and the distances between atoms satisfy rIJ rJK rKI > cutoff^3.

The following coefficients must be defined for each pair of atoms

types via the "pair_coeff"_pair_coeff.html command as in the examples

Note that for a simulation with a single atom type, only a single

entry is required, e.g.

pair_coeff 1 1 1 0.25 :per

pair_coeff 1 1 1 0.25 :pre

For a simulation with two atom types, four pair_coeff commands will

specify all possible nu values:

  double **f = atom->f;

  int *type = atom->type;

  double cutoffsq = cut_global*cut_global;

  double cutoff_sixth = cut_global*cut_global;

  cutoff_sixth = cutoff_sixth*cutoff_sixth*cutoff_sixth;

  inum = list->inum;

  ilist = list->ilist;

  numneigh = list->numneigh;

      j = jlist[jj];

      j &= NEIGHMASK;

      rij[0] = x[j][0] - xi;

      if (rij[0] < 0.0) continue;

      rij[1] = x[j][1] - yi;

      if (rij[0] == 0.0 and rij[1] < 0.0) continue;

      rij[2] = x[j][2] - zi;

      if (rij[0] == 0.0 and rij[1] == 0.0 and rij[2] < 0.0) continue;

      rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];

      for (kk = jj+1; kk < jnum; kk++) {

        k = jlist[kk];

        k &= NEIGHMASK;

        rik[0] = x[k][0] - xi;

        rik[1] = x[k][1] - yi;

        rik[2] = x[k][2] - zi;

        rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];

        rjk[0] = x[k][0] - x[j][0];

        if (rjk[0] < 0.0) continue;

        rjk[1] = x[k][1] - x[j][1];

        if (rjk[0] == 0.0 and rjk[1] < 0.0) continue;

        rjk[2] = x[k][2] - x[j][2];

        if (rjk[0] == 0.0 and rjk[1] == 0.0 and rjk[2] < 0.0) continue;

        rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];

        rik[0] = x[k][0] - xi;

        rik[1] = x[k][1] - yi;

        rik[2] = x[k][2] - zi;

        rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];

        r6 = rij2*rik2*rjk2;

        if (r6 > cutoffsq) continue;

        if (r6 > cutoff_sixth) continue;

        nu_local = nu[type[i]][type[j]][type[k]];

        if (nu_local == 0.0) continue;

void PairATM::init_style()

{

  if (force->newton_pair == 0)

    error->all(FLERR,"Pair style ATM requires newton pair on");

  // need a full neighbor list

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

   proc 0 writes to restart file

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

// 

// PLEASE HELP!

// 

// From the pair_hybrid documentation: 

// 

// "For the hybrid pair styles, the list of sub-styles and their respective

// settings are written to binary restart files, so a pair_style command

// does not need to specified in an input script that reads a restart file.

// However, the coefficient information is not stored in the restart file.

// Thus, pair_coeff commands need to be re-specified in the restart input

// script."

// 

// As a result, the function "PairATM::write_restart" is not called from

// "pair_hybrid.cpp". What is the best way to deal with this problem?

// 

void PairATM::write_restart(FILE *fp)

{

  write_restart_settings(fp);

Self-explanatory.  Check the input script or data file.

E: Pair style ATM requires newton pair on

See the newton command.  This is a restriction to use the ATM

potential.

E: All pair coeffs are not set

All pair coefficients must be set in the data file or by the