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more changes and some debugging on a test script

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This commit is contained in:
Steve Plimpton
2022-05-04 15:28:50 -06:00
parent cc437c78a0
commit 6b47d6246b
3 changed files with 41 additions and 13 deletions
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31
doc/src/create_atoms.rst
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@ -345,10 +345,37 @@ new particles into a dense system using the *overlap* keyword),
setting the *maxtry* keyword to a large value may result in this
command running for a long time.
Here is an example for the *random* style using these commands
.. code-block:: LAMMPS
units lj
dimension 2
region box block 0 50 0 50 -0.5 0.5
create_box 1 box
create_atoms 1 random 2000 13487 NULL overlap 1.0 maxtry 50
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
to produce a system as shown in the image with 1520 particles (out of
2000 requested) that are moderately dense and which have no overlaps
sufficient to prevent the LJ pair_style from running properly (because
the overlap criterion = 1.0). The create_atoms command ran for 0.3 s
on a single CPU core.
.. image:: img/overlap.png
:scale: 50%
:align: center
.. raw:: html
Click on the image for a larger version.
The *units* keyword determines the meaning of the distance units used
to specify the coordinates of the one particle created by the *single*
style. A *box* value selects standard distance units as defined by
the :doc:`units <units>` command, e.g. Angstroms for units = real or
style, or the overlap distance *Doverlap* by the *overlap* keyword. A
*box* value selects standard distance units as defined by the
:doc:`units <units>` command, e.g. Angstroms for units = real or
metal. A *lattice* value means the distance units are in lattice
spacings.

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23
src/create_atoms.cpp
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@ -97,7 +97,6 @@ void CreateAtoms::command(int narg, char **arg)
region->init();
region->prematch();
iarg = 3;
;
} else if (strcmp(arg[1], "single") == 0) {
style = SINGLE;
if (narg < 5) error->all(FLERR, "Illegal create_atoms command");
@ -231,13 +230,6 @@ void CreateAtoms::command(int narg, char **arg)
subsetseed = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
if (nsubset <= 0 || subsetseed <= 0) error->all(FLERR, "Illegal create_atoms command");
iarg += 3;
} else if (strcmp(arg[iarg], "maxtrr") == 0) {
if (style != RANDOM)
error->all(FLERR, "Create_atoms maxtry can only be used with random style");
if (iarg + 2 > narg) error->all(FLERR, "Illegal create_atoms command");
maxtry = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (maxtry <= 0) error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg], "overlap") == 0) {
if (style != RANDOM)
error->all(FLERR, "Create_atoms overlap can only be used with random style");
@ -246,6 +238,13 @@ void CreateAtoms::command(int narg, char **arg)
if (overlap <= 0) error->all(FLERR, "Illegal create_atoms command");
overlapflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg], "maxtry") == 0) {
if (style != RANDOM)
error->all(FLERR, "Create_atoms maxtry can only be used with random style");
if (iarg + 2 > narg) error->all(FLERR, "Illegal create_atoms command");
maxtry = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (maxtry <= 0) error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else
error->all(FLERR, "Illegal create_atoms command");
}
@ -324,6 +323,7 @@ void CreateAtoms::command(int narg, char **arg)
xone[0] *= domain->lattice->xlattice;
xone[1] *= domain->lattice->ylattice;
xone[2] *= domain->lattice->zlattice;
overlap *= domain->lattice->xlattice;
}
// set bounds for my proc in sublo[3] & subhi[3]
@ -755,9 +755,9 @@ void CreateAtoms::add_random()
if (mode == MOLECULE) generate_molecule(xone);
// check for overlap of new atom with all others
// including prior insertions
// check for overlap of new atom with all others including prior insertions
// minimum_image() required to account for distances across PBC
if (overlapflag) {
double **x = atom->x;
int nlocal = atom->nlocal;
@ -768,6 +768,7 @@ void CreateAtoms::add_random()
delx = xone[0] - x[i][0];
dely = xone[1] - x[i][1];
delz = xone[2] - x[i][2];
domain->minimum_image(delx,dely,delz);
distsq = delx*delx + dely*dely + delz*delz;
if (distsq < odistsq) {
reject = 1;