ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

create_atoms: direct type label support

Browse Source
This commit is contained in:
Jacob Gissinger
2024-04-16 19:56:37 -04:00
parent de8b1b49a6
commit e590e27faa
2 changed files with 15 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
doc/src/create_atoms.rst
View File

@ -10,7 +10,7 @@ Syntax
create_atoms type style args keyword values ... create_atoms type style args keyword values ...
* type = atom type (1-Ntypes) of atoms to create (offset for molecule creation) * type = atom type (1-Ntypes or type label) of atoms to create (offset for molecule creation)
* style = *box* or *region* or *single* or *mesh* or *random* * style = *box* or *region* or *single* or *mesh* or *random*
.. parsed-literal:: .. parsed-literal::
@ -37,7 +37,7 @@ Syntax
seed = random # seed (positive integer) seed = random # seed (positive integer)
*basis* values = M itype *basis* values = M itype
M = which basis atom M = which basis atom
itype = atom type (1-N) to assign to this basis atom itype = atom type (1-Ntypes or type label) to assign to this basis atom
*ratio* values = frac seed *ratio* values = frac seed
frac = fraction of lattice sites (0 to 1) to populate randomly frac = fraction of lattice sites (0 to 1) to populate randomly
seed = random # seed (positive integer) seed = random # seed (positive integer)
@ -74,7 +74,13 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
create_atoms 1 box create_atoms 1 box
create_atoms 3 region regsphere basis 2 3
labelmap atom 1 Pt
create_atoms Pt box
labelmap atom 1 C 2 Si
create_atoms C region regsphere basis Si C
create_atoms 3 region regsphere basis 2 3 ratio 0.5 74637 create_atoms 3 region regsphere basis 2 3 ratio 0.5 74637
create_atoms 3 single 0 0 5 create_atoms 3 single 0 0 5
create_atoms 1 box var v set x xpos set y ypos create_atoms 1 box var v set x xpos set y ypos

8
src/create_atoms.cpp
View File

@ -89,7 +89,9 @@ void CreateAtoms::command(int narg, char **arg)
// parse arguments // parse arguments
if (narg < 2) utils::missing_cmd_args(FLERR, "create_atoms", error); if (narg < 2) utils::missing_cmd_args(FLERR, "create_atoms", error);
ntype = utils::inumeric(FLERR, arg[0], false, lmp); char *typestr = utils::expand_type(FLERR, arg[0], Atom::ATOM, lmp);
ntype = utils::inumeric(FLERR, typestr?typestr:arg[0], false, lmp);
delete[] typestr;
const char *meshfile; const char *meshfile;
int iarg; int iarg;
@ -163,7 +165,9 @@ void CreateAtoms::command(int narg, char **arg)
if (strcmp(arg[iarg], "basis") == 0) { if (strcmp(arg[iarg], "basis") == 0) {
if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "create_atoms basis", error); if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "create_atoms basis", error);
int ibasis = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); int ibasis = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
int itype = utils::inumeric(FLERR, arg[iarg + 2], false, lmp); char *typestr = utils::expand_type(FLERR, arg[iarg + 2], Atom::ATOM, lmp);
int itype = utils::inumeric(FLERR, typestr?typestr:arg[iarg + 2], false, lmp);
delete[] typestr;
if (ibasis <= 0 || ibasis > nbasis || itype <= 0 || itype > atom->ntypes) if (ibasis <= 0 || ibasis > nbasis || itype <= 0 || itype > atom->ntypes)
error->all(FLERR, "Out of range basis setting '{} {}' in create_atoms command", ibasis, error->all(FLERR, "Out of range basis setting '{} {}' in create_atoms command", ibasis,
itype); itype);