forked from lijiext/lammps
258 lines
10 KiB
Plaintext
258 lines
10 KiB
Plaintext
.. index:: pair_style table/rx
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pair_style table/rx command
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===========================
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Syntax
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""""""
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.. parsed-literal::
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pair_style table style N
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style = *lookup* or *linear* or *spline* or *bitmap* = method of interpolation
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N = use N values in *lookup*\ , *linear*\ , *spline* tables
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N = use 2^N values in *bitmap* tables
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Examples
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""""""""
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.. parsed-literal::
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pair_style table/rx linear 1000
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pair_style table/rx bitmap 12
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pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0
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pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0
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pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0
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Description
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"""""""""""
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Style *table/rx* is used in reaction DPD simulations,where the
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coarse-grained (CG) particles are composed of *m* species whose
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reaction rate kinetics are determined from a set of *n* reaction rate
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equations through the :doc:`fix rx <fix_rx>` command. The species of
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one CG particle can interact with a species in a neighboring CG
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particle through a site-site interaction potential model. Style
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*table/rx* creates interpolation tables of length *N* from pair
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potential and force values listed in a file(s) as a function of
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distance. The files are read by the :doc:`pair_coeff <pair_coeff>`
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command.
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The interpolation tables are created by fitting cubic splines to the
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file values and interpolating energy and force values at each of *N*
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distances. During a simulation, these tables are used to interpolate
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energy and force values as needed. The interpolation is done in one
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of 4 styles: *lookup*\ , *linear*\ , *spline*\ , or *bitmap*\ .
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For the *lookup* style, the distance between 2 atoms is used to find
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the nearest table entry, which is the energy or force.
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For the *linear* style, the pair distance is used to find 2
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surrounding table values from which an energy or force is computed by
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linear interpolation.
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For the *spline* style, a cubic spline coefficients are computed and
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stored at each of the *N* values in the table. The pair distance is
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used to find the appropriate set of coefficients which are used to
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evaluate a cubic polynomial which computes the energy or force.
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For the *bitmap* style, the N means to create interpolation tables
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that are 2^N in length. The pair distance is used to index into the
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table via a fast bit-mapping technique :ref:`(Wolff) <Wolff>` and a linear
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interpolation is performed between adjacent table values.
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The following coefficients must be defined for each pair of atoms
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types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
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above.
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* filename
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* keyword
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* species1
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* species2
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* cutoff (distance units)
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The filename specifies a file containing tabulated energy and force
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values. The keyword specifies a section of the file. The cutoff is
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an optional coefficient. If not specified, the outer cutoff in the
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table itself (see below) will be used to build an interpolation table
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that extend to the largest tabulated distance. If specified, only
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file values up to the cutoff are used to create the interpolation
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table. The format of this file is described below.
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The species tags define the site-site interaction potential between
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two species contained within two different particles. The species
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tags must either correspond to the species defined in the reaction
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kinetics files specified with the :doc:`fix rx <fix_rx>` command or they
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must correspond to the tag "1fluid", signifying interaction with a
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product species mixture determined through a one-fluid approximation.
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The interaction potential is weighted by the geometric average of the
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concentrations of the two species. The coarse-grained potential is
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stored before and after the reaction kinetics solver is applied, where
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the difference is defined to be the internal chemical energy (uChem).
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----------
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Here are some guidelines for using the pair_style table/rx command to
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best effect:
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* Vary the number of table points; you may need to use more than you think
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to get good resolution.
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* Always use the :doc:`pair_write <pair_write>` command to produce a plot
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of what the final interpolated potential looks like. This can show up
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interpolation "features" you may not like.
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* Start with the linear style; it's the style least likely to have problems.
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* Use *N* in the pair_style command equal to the "N" in the tabulation
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file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation
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is not needed. See discussion below.
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* Make sure that your tabulated forces and tabulated energies are consistent
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(dE/dr = -F) along the entire range of r values.
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* Use as large an inner cutoff as possible. This avoids fitting splines
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to very steep parts of the potential.
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----------
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The format of a tabulated file is a series of one or more sections,
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defined as follows (without the parenthesized comments):
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.. parsed-literal::
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# Morse potential for Fe (one or more comment or blank lines)
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.. parsed-literal::
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MORSE_FE (keyword is first text on line)
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N 500 R 1.0 10.0 (N, R, RSQ, BITMAP, FPRIME parameters)
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(blank)
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1 1.0 25.5 102.34 (index, r, energy, force)
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2 1.02 23.4 98.5
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...
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500 10.0 0.001 0.003
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A section begins with a non-blank line whose 1st character is not a
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"#"; blank lines or lines starting with "#" can be used as comments
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between sections. The first line begins with a keyword which
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identifies the section. The line can contain additional text, but the
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initial text must match the argument specified in the pair_coeff
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command. The next line lists (in any order) one or more parameters
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for the table. Each parameter is a keyword followed by one or more
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numeric values.
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The parameter "N" is required and its value is the number of table
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entries that follow. Note that this may be different than the *N*
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specified in the :doc:`pair_style table/rx <pair_style>` command. Let
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Ntable = *N* in the pair_style command, and Nfile = "N" in the
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tabulated file. What LAMMPS does is a preliminary interpolation by
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creating splines using the Nfile tabulated values as nodal points. It
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uses these to interpolate as needed to generate energy and force
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values at Ntable different points. The resulting tables of length
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Ntable are then used as described above, when computing energy and
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force for individual pair distances. This means that if you want the
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interpolation tables of length Ntable to match exactly what is in the
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tabulated file (with effectively no preliminary interpolation), you
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should set Ntable = Nfile, and use the "RSQ" or "BITMAP" parameter.
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The internal table abscissa is RSQ (separation distance squared).
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All other parameters are optional. If "R" or "RSQ" or "BITMAP" does
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not appear, then the distances in each line of the table are used
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as-is to perform spline interpolation. In this case, the table values
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can be spaced in *r* uniformly or however you wish to position table
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values in regions of large gradients.
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If used, the parameters "R" or "RSQ" are followed by 2 values *rlo*
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and *rhi*\ . If specified, the distance associated with each energy and
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force value is computed from these 2 values (at high accuracy), rather
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than using the (low-accuracy) value listed in each line of the table.
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The distance values in the table file are ignored in this case.
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For "R", distances uniformly spaced between *rlo* and *rhi* are
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computed; for "RSQ", squared distances uniformly spaced between
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*rlo*rlo* and *rhi*rhi* are computed.
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If used, the parameter "BITMAP" is also followed by 2 values *rlo* and
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*rhi*\ . These values, along with the "N" value determine the ordering
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of the N lines that follow and what distance is associated with each.
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This ordering is complex, so it is not documented here, since this
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file is typically produced by the :doc:`pair_write <pair_write>` command
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with its *bitmap* option. When the table is in BITMAP format, the "N"
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parameter in the file must be equal to 2^M where M is the value
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specified in the pair_style command. Also, a cutoff parameter cannot
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be used as an optional 3rd argument in the pair_coeff command; the
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entire table extent as specified in the file must be used.
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If used, the parameter "FPRIME" is followed by 2 values *fplo* and
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*fphi* which are the derivative of the force at the innermost and
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outermost distances listed in the table. These values are needed by
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the spline construction routines. If not specified by the "FPRIME"
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parameter, they are estimated (less accurately) by the first 2 and
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last 2 force values in the table. This parameter is not used by
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BITMAP tables.
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Following a blank line, the next N lines list the tabulated values.
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On each line, the 1st value is the index from 1 to N, the 2nd value is
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r (in distance units), the 3rd value is the energy (in energy units),
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and the 4th is the force (in force units). The r values must increase
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from one line to the next (unless the BITMAP parameter is specified).
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Note that one file can contain many sections, each with a tabulated
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potential. LAMMPS reads the file section by section until it finds
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one that matches the specified keyword.
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----------
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**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
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This pair style does not support mixing. Thus, coefficients for all
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I,J pairs must be specified explicitly.
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The :doc:`pair_modify <pair_modify>` shift, table, and tail options are
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not relevant for this pair style.
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This pair style writes the settings for the "pair_style table/rx" command
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to :doc:`binary restart files <restart>`, so a pair_style command does
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not need to specified in an input script that reads a restart file.
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However, the coefficient information is not stored in the restart
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file, since it is tabulated in the potential files. Thus, pair_coeff
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commands do need to be specified in the restart input script.
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This pair style can only be used via the *pair* keyword of the
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:doc:`run_style respa <run_style>` command. It does not support the
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*inner*\ , *middle*\ , *outer* keywords.
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----------
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Restrictions
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""""""""""""
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This command is part of the USER-DPD package. It is only enabled if
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LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`
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**Default:** none
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----------
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.. _Wolff:
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**(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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