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

add reaxff/species delete citation

Browse Source
This commit is contained in:
Jacob Gissinger
2024-05-16 14:49:33 -04:00
parent 410cda27e0
commit febf7c38d3
1 changed files with 32 additions and 30 deletions
Download Patch File Download Diff File Expand all files Collapse all files

62
doc/src/fix_reaxff_species.rst
View File

@ -134,36 +134,34 @@ value. For example, AuO.pos.\* becomes AuO.pos.0, AuO.pos.1000, etc.
.. versionadded:: 3Aug2022
The optional keyword *delete* enables the periodic removal of
molecules from the system. Criteria for deletion can be either a list
of specific chemical formulae or a range of molecular weights.
Molecules are deleted every *Nfreq* timesteps, and bond connectivity
is determined using the *Nevery* and *Nrepeat* keywords. The
*filedel* argument is the name of the output file that records the
species that are removed from the system. The *specieslist* keyword
permits specific chemical species to be deleted. The *Nspecies*
argument specifies how many species are eligible for deletion and is
followed by a list of chemical formulae, whose strings are compared to
species identified by this fix. For example, "specieslist 2 CO CO2"
deletes molecules that are identified as "CO" and "CO2" in the species
output file. When using the *specieslist* keyword, the *filedel* file
has the following format: the first line lists the chemical formulae
eligible for deletion, and each additional line contains the timestep
on which a molecule deletion occurs and the number of each species
deleted on that timestep. The *masslimit* keyword permits deletion of
molecules with molecular weights between *massmin* and *massmax*.
When using the *masslimit* keyword, each line of the *filedel* file
contains the timestep on which deletions occurs, followed by how many
of each species are deleted (with quantities preceding chemical
formulae). The *specieslist* and *masslimit* keywords cannot both be
used in the same *reaxff/species* fix. The *delete_rate_limit*
keyword can enforce an upper limit on the overall rate of molecule
deletion. The number of deletion occurrences is limited to Nlimit
within an interval of Nsteps timesteps. Nlimit can be specified with
an equal-style :doc:`variable <variable>`. When using the
*delete_rate_limit* keyword, no deletions are permitted to occur
within the first Nsteps timesteps of the first run (after reading a
either a data or restart file).
The optional keyword *delete* enables the periodic removal of molecules
from the system :ref:`(Gissinger) <Delete>`. Criteria for deletion can
be either a list of specific chemical formulae or a range of molecular
weights. Molecules are deleted every *Nfreq* timesteps, and bond
connectivity is determined using the *Nevery* and *Nrepeat* keywords. The
*filedel* argument is the name of the output file that records the species
that are removed from the system. The *specieslist* keyword permits
specific chemical species to be deleted. The *Nspecies* argument specifies
how many species are eligible for deletion and is followed by a list of
chemical formulae, whose strings are compared to species identified by this
fix. For example, "specieslist 2 CO CO2" deletes molecules that are
identified as "CO" and "CO2" in the species output file. When using the
*specieslist* keyword, the *filedel* file has the following format: the
first line lists the chemical formulae eligible for deletion, and each
additional line contains the timestep on which a molecule deletion occurs
and the number of each species deleted on that timestep. The *masslimit*
keyword permits deletion of molecules with molecular weights between
*massmin* and *massmax*. When using the *masslimit* keyword, each line of
the *filedel* file contains the timestep on which deletions occurs,
followed by how many of each species are deleted (with quantities preceding
chemical formulae). The *specieslist* and *masslimit* keywords cannot both
be used in the same *reaxff/species* fix. The *delete_rate_limit* keyword
can enforce an upper limit on the overall rate of molecule deletion. The
number of deletion occurrences is limited to Nlimit within an interval of
Nsteps timesteps. Nlimit can be specified with an equal-style
:doc:`variable <variable>`. When using the *delete_rate_limit* keyword, no
deletions are permitted to occur within the first Nsteps timesteps of the
first run (after reading a either a data or restart file).
----------
@ -235,3 +233,7 @@ Default
The default values for bond-order cutoffs are 0.3 for all I-J pairs.
The default element symbols are taken from the ReaxFF pair_coeff command.
Position files are not written by default.
.. _Delete:
**(Gissinger)** Jacob R. Gissinger, Scott R. Zavada, Joseph G. Smith, Josh Kemppainen, Ivan Gallegos, Gregory M. Odegard, Emilie J. Siochi, and Kristopher E. Wise, Carbon, 202, 336-347 (2023).