diff --git a/doc/src/fix_reaxff_species.rst b/doc/src/fix_reaxff_species.rst index a6da15b161..fba7fcaa93 100644 --- a/doc/src/fix_reaxff_species.rst +++ b/doc/src/fix_reaxff_species.rst @@ -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 `. 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) `. 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 `. 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).