Merge pull request #815 from akohlmey/collected-small-fixes

file = name of data file to read in :ulb,l

zero or more keyword/arg pairs may be appended :l

keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {extra/bond/per/atom} or {extra/angle/per/atom} or {extra/dihedral/per/atom} or {extra/improper/per/atom} or {group} or {nocoeff} or {fix} :l

  {add} arg = {append} or {Nstart} or {merge}

    append = add new atoms with IDs appended to current IDs

    Nstart = add new atoms with IDs starting with Nstart

    merge = add new atoms with their IDs unchanged

  {add} arg = {append} or {IDoffset} or {IDoffset MOLoffset} or {merge}

    append = add new atoms with atom IDs appended to current IDs

    IDoffset = add new atoms with atom IDs having IDoffset added

    MOLoffset = add new atoms with molecule IDs having MOLoffset added (only when molecule IDs are enabled)

    merge = add new atoms with their atom IDs (and molecule IDs) unchanged

  {offset} args = toff boff aoff doff ioff

    toff = offset to add to atom types

    boff = offset to add to bond types

This will separate the atoms in the bond, which can lead to "lost"

bond atoms or bad dynamics.

The three choices for the {add} argument affect how the IDs of atoms

in the data file are treated.  If {append} is specified, atoms in the

data file are added to the current system, with their atom IDs reset

so that an atomID = M in the data file becomes atomID = N+M, where N

is the largest atom ID in the current system.  This rule is applied to

all occurrences of atom IDs in the data file, e.g. in the Velocity or

Bonds section.  If {Nstart} is specified, then {Nstart} is a numeric

value is given, e.g. 1000, so that an atomID = M in the data file

becomes atomID = 1000+M.  If {merge} is specified, the data file atoms

The three choices for the {add} argument affect how the atom IDs and

molecule IDs of atoms in the data file are treated.  If {append} is

specified, atoms in the data file are added to the current system,

with their atom IDs reset so that an atomID = M in the data file

becomes atomID = N+M, where N is the largest atom ID in the current

system.  This rule is applied to all occurrences of atom IDs in the

data file, e.g. in the Velocity or Bonds section. This is also done

for molecule IDs, if the atom style does support molecule IDs or

they are enabled via fix property/atom. If {IDoffset} is specified,

then {IDoffset} is a numeric value is given, e.g. 1000, so that an

atomID = M in the data file becomes atomID = 1000+M. For systems

with enabled molecule IDs, another numerical argument {MOLoffset}

is required representing the equivalent offset for molecule IDs.

If {merge} is specified, the data file atoms

are added to the current system without changing their IDs.  They are

assumed to merge (without duplication) with the currently defined

atoms.  It is up to you to insure there are no multiply defined atom

IDs, as LAMMPS only performs an incomplete check that this is the case

by insuring the resulting max atomID >= the number of atoms.

by insuring the resulting max atomID >= the number of atoms. For

molecule IDs, there is no check done at all.

The {offset} and {shift} keywords can only be used if the {add}

keyword is also specified.

      memory->destroy(offset);

    }

  }

  if (ftable) free_tables();

}

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

  double c = param->cutoffC;

  double alpha = param->alpha;

  double x;

  double v1, v2, v3;

  double v1, v2;

  if(r < c + 1E-6)

  {

    jnum = numneigh[i];

    offseti = offset[itype];

    lj1i = lj1[itype]; lj2i = lj2[itype]; lj3i = lj3[itype]; lj4i = lj4[itype];

    fxtmp = fytmp = fztmp = 0.0;

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

      j = jlist[jj];

   call style-specific routine to parse line

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

void Atom::data_atoms(int n, char *buf, tagint id_offset, int type_offset,

                      int shiftflag, double *shift)

void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,

                      int type_offset, int shiftflag, double *shift)

{

  int m,xptr,iptr;

  imageint imagedata;

        coord[2] >= sublo[2] && coord[2] < subhi[2]) {

      avec->data_atom(xdata,imagedata,values);

      if (id_offset) tag[nlocal-1] += id_offset;

      if (mol_offset) molecule[nlocal-1] += mol_offset;

      if (type_offset) {

        type[nlocal-1] += type_offset;

        if (type[nlocal-1] > ntypes)