243 lines
11 KiB
ReStructuredText
243 lines
11 KiB
ReStructuredText
.. index:: fix reaxff/species
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.. index:: fix reaxff/species/kk
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fix reaxff/species command
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==========================
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Accelerator Variants: *reaxff/species/kk*
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Syntax
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""""""
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.. code-block:: LAMMPS
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fix ID group-ID reaxff/species Nevery Nrepeat Nfreq filename keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* reaxff/species = style name of this command
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* Nevery = sample bond-order every this many timesteps
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* Nrepeat = # of bond-order samples used for calculating averages
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* Nfreq = calculate average bond-order every this many timesteps
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* filename = name of output file
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* zero or more keyword/value pairs may be appended
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* keyword = *cutoff* or *element* or *position* or *delete* or *delete_rate_limit*
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.. parsed-literal::
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*cutoff* value = I J Cutoff
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I, J = atom types (see asterisk form below)
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Cutoff = Bond-order cutoff value for this pair of atom types
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*element* value = Element1, Element2, ...
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*position* value = posfreq filepos
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posfreq = write position files every this many timestep
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filepos = name of position output file
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*delete* value = filedel keyword value
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filedel = name of delete species output file
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keyword = *specieslist* or *masslimit*
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*specieslist* value = Nspecies Species1 Species2 ...
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Nspecies = number of species in list
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*masslimit* value = massmin massmax
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massmin = minimum molecular weight of species to delete
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massmax = maximum molecular weight of species to delete
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*delete_rate_limit* value = Nlimit Nsteps
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Nlimit = maximum number of deletions allowed to occur within interval
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Nsteps = the interval (number of timesteps) over which to count deletions
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all reaxff/species 10 10 100 species.out
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fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2*3 0.55
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fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
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fix 1 all reaxff/species 1 100 100 species.out delete species.del masslimit 0 50
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Description
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"""""""""""
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Write out the chemical species information computed by the ReaxFF
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potential specified by :doc:`pair_style reaxff <pair_reaxff>`.
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Bond-order values (either averaged or instantaneous, depending on
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value of *Nrepeat*\ ) are used to determine chemical bonds. Every
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*Nfreq* timesteps, chemical species information is written to
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*filename* as a two line output. The first line is a header
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containing labels. The second line consists of the following:
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timestep, total number of molecules, total number of distinct species,
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number of molecules of each species. In this context, "species" means
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a unique molecule. The chemical formula of each species is given in
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the first line.
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.. warning::
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In order to compute averaged data, it is required that there are no
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neighbor list rebuilds for at least Nrepeat\*Nevery steps preceding
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each *Nfreq* step. For that reason, fix *reaxff/species* may
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change your neighbor list settings. Reneighboring will occur no
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more frequently than every Nrepeat\*Nevery timesteps, and will
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occur less frequently if *Nfreq* is not a multiple of
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Nrepeat\*Nevery. There will be a warning message showing the new
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settings. Having a *Nfreq* setting that is larger than what is
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required for correct computation of the ReaxFF force field
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interactions, in combination with certain *Nrepeat* and *Nevery*
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settings, can thus lead to incorrect results. For typical ReaxFF
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calculations, reneighboring only every 100 steps is already quite a
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low frequency.
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If the filename ends with ".gz", the output file is written in gzipped
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format. A gzipped dump file will be about 3x smaller than the text version,
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but will also take longer to write.
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.. versionadded:: 15Jun2023
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Support for wildcards added
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Optional keyword *cutoff* can be assigned to change the minimum
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bond-order values used in identifying chemical bonds between pairs of
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atoms. Bond-order cutoffs should be carefully chosen, as bond-order
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cutoffs that are too small may include too many bonds (which will result
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in an error), while cutoffs that are too large will result in fragmented
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molecules. The default cutoff of 0.3 usually gives good results. A
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wildcard asterisk can be used in place of or in conjunction with the I,J
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arguments to set the bond-order cutoff for multiple pairs of atom types.
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This takes the form "\*" or "\*n" or "n\*" or "m\*n". If :math:`N` is
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the number of atom types, then an asterisk with no numeric values means
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all types from 1 to :math:`N`. A leading asterisk means all types from
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1 to n (inclusive). A trailing asterisk means all types from n to
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:math:`N` (inclusive). A middle asterisk means all types from m to n
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(inclusive).
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The optional keyword *element* can be used to specify the chemical
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symbol printed for each LAMMPS atom type. The number of symbols must
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match the number of LAMMPS atom types and each symbol must consist of
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1 or 2 alphanumeric characters. By default, these symbols are the same
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as the chemical identity of each LAMMPS atom type, as specified by the
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:doc:`ReaxFF pair_coeff <pair_reaxff>` command and the ReaxFF force
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field file.
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The optional keyword *position* writes center-of-mass positions of
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each identified molecules to file *filepos* every *posfreq* timesteps.
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The first line contains information on timestep, total number of
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molecules, total number of distinct species, and box dimensions. The
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second line is a header containing labels. From the third line
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downward, each molecule writes a line of output containing the
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following information: molecule ID, number of atoms in this molecule,
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chemical formula, total charge, and center-of-mass xyz positions of
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this molecule. The xyz positions are in fractional coordinates
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relative to the box dimensions.
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For the keyword *position*, the *filepos* is the name of the output
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file. It can contain the wildcard character "\*". If the "\*"
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character appears in *filepos*, then one file per snapshot is written
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at *posfreq* and the "\*" character is replaced with the timestep
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value. For example, AuO.pos.\* becomes AuO.pos.0, AuO.pos.1000, etc.
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.. versionadded:: 3Aug2022
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The optional keyword *delete* enables the periodic removal of molecules
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from the system :ref:`(Gissinger) <Delete>`. Criteria for deletion can
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be either a list of specific chemical formulae or a range of molecular
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weights. Molecules are deleted every *Nfreq* timesteps, and bond
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connectivity is determined using the *Nevery* and *Nrepeat* keywords. The
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*filedel* argument is the name of the output file that records the species
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that are removed from the system. The *specieslist* keyword permits
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specific chemical species to be deleted. The *Nspecies* argument specifies
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how many species are eligible for deletion and is followed by a list of
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chemical formulae, whose strings are compared to species identified by this
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fix. For example, "specieslist 2 CO CO2" deletes molecules that are
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identified as "CO" and "CO2" in the species output file. When using the
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*specieslist* keyword, the *filedel* file has the following format: the
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first line lists the chemical formulae eligible for deletion, and each
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additional line contains the timestep on which a molecule deletion occurs
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and the number of each species deleted on that timestep. The *masslimit*
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keyword permits deletion of molecules with molecular weights between
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*massmin* and *massmax*. When using the *masslimit* keyword, each line of
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the *filedel* file contains the timestep on which deletions occurs,
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followed by how many of each species are deleted (with quantities preceding
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chemical formulae). The *specieslist* and *masslimit* keywords cannot both
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be used in the same *reaxff/species* fix. The *delete_rate_limit* keyword
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can enforce an upper limit on the overall rate of molecule deletion. The
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number of deletion occurrences is limited to Nlimit within an interval of
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Nsteps timesteps. Nlimit can be specified with an equal-style
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:doc:`variable <variable>`. When using the *delete_rate_limit* keyword, no
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deletions are permitted to occur within the first Nsteps timesteps of the
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first run (after reading a either a data or restart file).
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----------
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The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
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timesteps the bond-order values are sampled to get the average bond
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order. The species analysis is performed using the average bond-order
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on timesteps that are a multiple of *Nfreq*\ . The average is over
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*Nrepeat* bond-order samples, computed in the preceding portion of the
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simulation every *Nevery* timesteps. *Nfreq* must be a multiple of
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*Nevery* and *Nevery* must be non-zero even if *Nrepeat* is 1.
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Also, the timesteps
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contributing to the average bond-order cannot overlap,
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i.e. Nrepeat\*Nevery can not exceed Nfreq.
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For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
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values on timesteps 90,92,94,96,98,100 will be used to compute the
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average bond-order for the species analysis output on timestep 100.
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`.
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None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
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This fix computes both a global vector of length 2 and a per-atom vector,
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either of which can be accessed by various :doc:`output commands <Howto_output>`.
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The values in the global vector are "intensive".
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The 2 values in the global vector are as follows:
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#. total number of molecules
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#. total number of distinct species
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The per-atom vector stores the molecule ID for each atom as identified
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by the fix. If an atom is not in a molecule, its ID will be 0.
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For atoms in the same molecule, the molecule ID for all of them
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will be the same, and molecule IDs will range from 1 to the number
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of molecules.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command.
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This fix is not invoked during :doc:`energy minimization <minimize>`.
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This fix supports dynamic groups only if the *Nrepeat* setting is 1,
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i.e. there is no averaging.
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----------
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.. include:: accel_styles.rst
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----------
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Restrictions
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""""""""""""
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The "fix reaxff/species" requires that :doc:`pair_style reaxff <pair_reaxff>` is used.
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This fix is part of the REAXFF package. It is only enabled if LAMMPS was built with that
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package. See the :doc:`Build package <Build_package>` page for more info.
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To write gzipped species files, you must compile LAMMPS with the -DLAMMPS_GZIP option.
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Related commands
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""""""""""""""""
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:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`
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Default
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"""""""
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The default values for bond-order cutoffs are 0.3 for all I-J pairs.
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The default element symbols are taken from the ReaxFF pair_coeff command.
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Position files are not written by default.
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.. _Delete:
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**(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).
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