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fix_gcmc: direct type label support

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apparently changed text in doc description is just reflowing
This commit is contained in:
Jacob Gissinger
2024-05-11 15:20:53 -04:00
parent c19db76eae
commit 9d7e449767
2 changed files with 48 additions and 53 deletions
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71
doc/src/fix_gcmc.rst
View File

@ -15,7 +15,7 @@ Syntax
* N = invoke this fix every N steps
* X = average number of GCMC exchanges to attempt every N steps
* M = average number of MC moves to attempt every N steps
* type = atom type for inserted atoms (must be 0 if mol keyword used)
* type = atom type (1-Ntypes or type label) for inserted atoms (must be 0 if mol keyword used)
* seed = random # seed (positive integer)
* T = temperature of the ideal gas reservoir (temperature units)
* mu = chemical potential of the ideal gas reservoir (energy units)
@ -45,7 +45,7 @@ Syntax
*group* value = group-ID
group-ID = group-ID for inserted atoms (string)
*grouptype* values = type group-ID
type = atom type (int)
type = atom type (1-Ntypes or type label)
group-ID = group-ID for inserted atoms (string)
*intra_energy* value = intramolecular energy (energy units)
*tfac_insert* value = scale up/down temperature of inserted atoms (unitless)
@ -62,52 +62,47 @@ Examples
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
labelmap atom 1 Li
fix 2 ion gcmc 10 1000 1000 Li 29494 298.0 -0.5 0.01
Description
"""""""""""
This fix performs grand canonical Monte Carlo (GCMC) exchanges of
atoms or molecules with an imaginary ideal gas
reservoir at the specified T and chemical potential (mu) as discussed
in :ref:`(Frenkel) <Frenkel2>`. It also
attempts Monte Carlo (MC) moves (translations and molecule
rotations) within the simulation cell or
region. If used with the :doc:`fix nvt <fix_nh>`
This fix performs grand canonical Monte Carlo (GCMC) exchanges of atoms or
molecules with an imaginary ideal gas reservoir at the specified T and
chemical potential (mu) as discussed in :ref:`(Frenkel) <Frenkel2>`. It
also attempts Monte Carlo (MC) moves (translations and molecule rotations)
within the simulation cell or region. If used with the :doc:`fix nvt <fix_nh>`
command, simulations in the grand canonical ensemble (muVT, constant
chemical potential, constant volume, and constant temperature) can be
performed. Specific uses include computing isotherms in microporous
materials, or computing vapor-liquid coexistence curves.
Every N timesteps the fix attempts both GCMC exchanges
(insertions or deletions) and MC moves of gas atoms or molecules.
On those timesteps, the average number of attempted GCMC exchanges is X,
while the average number of attempted MC moves is M.
For GCMC exchanges of either molecular or atomic gasses,
these exchanges can be either deletions or insertions,
with equal probability.
Every N timesteps the fix attempts both GCMC exchanges (insertions or
deletions) and MC moves of gas atoms or molecules. On those timesteps, the
average number of attempted GCMC exchanges is X, while the average number
of attempted MC moves is M. For GCMC exchanges of either molecular or
atomic gasses, these exchanges can be either deletions or insertions, with
equal probability.
The possible choices for MC moves are translation of an atom,
translation of a molecule, and rotation of a molecule.
The relative amounts of each are determined by the optional
*mcmoves* keyword (see below).
The default behavior is as follows.
If the *mol* keyword is used, only molecule translations
and molecule rotations are performed with equal probability.
Conversely, if the *mol* keyword is not used, only atom
translations are performed.
M should typically be
chosen to be approximately equal to the expected number of gas atoms
or molecules of the given type within the simulation cell or region,
which will result in roughly one MC move per atom or molecule
per MC cycle.
The possible choices for MC moves are translation of an atom, translation
of a molecule, and rotation of a molecule. The relative amounts of each are
determined by the optional *mcmoves* keyword (see below). The default
behavior is as follows. If the *mol* keyword is used, only molecule
translations and molecule rotations are performed with equal probability.
Conversely, if the *mol* keyword is not used, only atom translations are
performed. M should typically be chosen to be approximately equal to the
expected number of gas atoms or molecules of the given type within the
simulation cell or region, which will result in roughly one MC move per
atom or molecule per MC cycle.
All inserted particles are always added to two groups: the default
group "all" and the fix group specified in the fix command.
In addition, particles are also added to any groups
specified by the *group* and *grouptype* keywords. If inserted
particles are individual atoms, they are assigned the atom type given
by the type argument. If they are molecules, the type argument has no
effect and must be set to zero. Instead, the type of each atom in the
inserted molecule is specified in the file read by the
All inserted particles are always added to two groups: the default group
"all" and the fix group specified in the fix command. In addition,
particles are also added to any groups specified by the *group* and
*grouptype* keywords. If inserted particles are individual atoms, they are
assigned the atom type given by the type argument. If they are molecules,
the type argument has no effect and must be set to zero. Instead, the type
of each atom in the inserted molecule is specified in the file read by the
:doc:`molecule <molecule>` command.
.. note::

30
src/MC/fix_gcmc.cpp
View File

@ -94,22 +94,22 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
// required args
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
nexchanges = utils::inumeric(FLERR,arg[4],false,lmp);
nmcmoves = utils::inumeric(FLERR,arg[5],false,lmp);
ngcmc_type = utils::inumeric(FLERR,arg[6],false,lmp);
seed = utils::inumeric(FLERR,arg[7],false,lmp);
reservoir_temperature = utils::numeric(FLERR,arg[8],false,lmp);
chemical_potential = utils::numeric(FLERR,arg[9],false,lmp);
displace = utils::numeric(FLERR,arg[10],false,lmp);
nevery = utils::inumeric(FLERR, arg[3], false, lmp);
nexchanges = utils::inumeric(FLERR, arg[4], false, lmp);
nmcmoves = utils::inumeric(FLERR, arg[5], false, lmp);
ngcmc_type = utils::expand_type_int(FLERR, arg[6], Atom::ATOM, lmp);
seed = utils::inumeric(FLERR, arg[7], false, lmp);
reservoir_temperature = utils::numeric(FLERR, arg[8], false, lmp);
chemical_potential = utils::numeric(FLERR, arg[9], false, lmp);
displace = utils::numeric(FLERR, arg[10], false, lmp);
if (nevery <= 0) error->all(FLERR,"Illegal fix gcmc command");
if (nexchanges < 0) error->all(FLERR,"Illegal fix gcmc command");
if (nmcmoves < 0) error->all(FLERR,"Illegal fix gcmc command");
if (seed <= 0) error->all(FLERR,"Illegal fix gcmc command");
if (nevery <= 0) error->all(FLERR, "Illegal fix gcmc command");
if (nexchanges < 0) error->all(FLERR, "Illegal fix gcmc command");
if (nmcmoves < 0) error->all(FLERR, "Illegal fix gcmc command");
if (seed <= 0) error->all(FLERR, "Illegal fix gcmc command");
if (reservoir_temperature < 0.0)
error->all(FLERR,"Illegal fix gcmc command");
if (displace < 0.0) error->all(FLERR,"Illegal fix gcmc command");
error->all(FLERR, "Illegal fix gcmc command");
if (displace < 0.0) error->all(FLERR, "Illegal fix gcmc command");
// read options from end of input line
@ -359,7 +359,7 @@ void FixGCMC::options(int narg, char **arg)
ngrouptypesmax*sizeof(char *),
"fix_gcmc:grouptypestrings");
}
grouptypes[ngrouptypes] = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
grouptypes[ngrouptypes] = utils::expand_type_int(FLERR, arg[iarg+1], Atom::ATOM, lmp);
grouptypestrings[ngrouptypes] = utils::strdup(arg[iarg+2]);
ngrouptypes++;
iarg += 3;