forked from lijiext/lammps
293 lines
12 KiB
Plaintext
293 lines
12 KiB
Plaintext
.. index:: pair_modify
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pair_modify 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_modify keyword values ...
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* one or more keyword/value pairs may be listed
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* keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner* or *tabinner/disp* or *tail* or *compute*
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.. parsed-literal::
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*pair* values = sub-style N *special* which wt1 wt2 wt3
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sub-style = sub-style of :doc:`pair hybrid <pair_hybrid>`
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N = which instance of sub-style (only if sub-style is used multiple times)
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*special* which wt1 wt2 wt3 = override *special_bonds* settings (optional)
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which = *lj/coul* or *lj* or *coul*
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w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
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*mix* value = *geometric* or *arithmetic* or *sixthpower*
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*shift* value = *yes* or *no*
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*table* value = N
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2^N = # of values in table
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*table/disp* value = N
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2^N = # of values in table
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*tabinner* value = cutoff
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cutoff = inner cutoff at which to begin table (distance units)
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*tabinner/disp* value = cutoff
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cutoff = inner cutoff at which to begin table (distance units)
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*tail* value = *yes* or *no*
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*compute* value = *yes* or *no*
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Examples
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""""""""
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.. parsed-literal::
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pair_modify shift yes mix geometric
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pair_modify tail yes
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pair_modify table 12
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pair_modify pair lj/cut compute no
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pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
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Description
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"""""""""""
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Modify the parameters of the currently defined pair style. Not all
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parameters are relevant to all pair styles.
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If used, the *pair* keyword must appear first in the list of keywords.
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It can only be used with the :doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles. It means that all the
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following parameters will only be modified for the specified
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sub-style. If the sub-style is defined multiple times, then an
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additional numeric argument *N* must also be specified, which is a
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number from 1 to M where M is the number of times the sub-style was
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listed in the :doc:`pair_style hybrid <pair_hybrid>` command. The extra
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number indicates which instance of the sub-style the remaining
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keywords will be applied to. Note that if the *pair* keyword is not
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used, and the pair style is *hybrid* or *hybrid/overlay*\ , then all the
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specified keywords will be applied to all sub-styles.
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The *special* keyword can only be used in conjunction with the *pair*
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keyword and must directly follow it. It allows to override the
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:doc:`special_bonds <special_bonds>` settings for the specified sub-style.
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More details are given below.
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The *mix* keyword affects pair coefficients for interactions between
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atoms of type I and J, when I != J and the coefficients are not
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explicitly set in the input script. Note that coefficients for I = J
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must be set explicitly, either in the input script via the
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"pair_coeff" command or in the "Pair Coeffs" section of the :doc:`data file <read_data>`. For some pair styles it is not necessary to
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specify coefficients when I != J, since a "mixing" rule will create
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them from the I,I and J,J settings. The pair_modify *mix* value
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determines what formulas are used to compute the mixed coefficients.
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In each case, the cutoff distance is mixed the same way as sigma.
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Note that not all pair styles support mixing. Also, some mix options
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are not available for certain pair styles. See the doc page for
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individual pair styles for those restrictions. Note also that the
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:doc:`pair_coeff <pair_coeff>` command also can be to directly set
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coefficients for a specific I != J pairing, in which case no mixing is
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performed.
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mix *geometric*
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.. parsed-literal::
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epsilon_ij = sqrt(epsilon_i * epsilon_j)
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sigma_ij = sqrt(sigma_i * sigma_j)
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mix *arithmetic*
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.. parsed-literal::
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epsilon_ij = sqrt(epsilon_i * epsilon_j)
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sigma_ij = (sigma_i + sigma_j) / 2
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mix *sixthpower*
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.. parsed-literal::
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epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
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(sigma_i^6 + sigma_j^6)
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sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
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The *shift* keyword determines whether a Lennard-Jones potential is
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shifted at its cutoff to 0.0. If so, this adds an energy term to each
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pairwise interaction which will be included in the thermodynamic
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output, but does not affect pair forces or atom trajectories. See the
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doc page for individual pair styles to see which ones support this
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option.
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The *table* and *table/disp* keywords apply to pair styles with a
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long-range Coulombic term or long-range dispersion term respectively;
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see the doc page for individual styles to see which potentials support
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these options. If N is non-zero, a table of length 2^N is
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pre-computed for forces and energies, which can shrink their
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computational cost by up to a factor of 2. The table is indexed via a
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bit-mapping technique :ref:`(Wolff) <Wolff>` and a linear interpolation is
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performed between adjacent table values. In our experiments with
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different table styles (lookup, linear, spline), this method typically
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gave the best performance in terms of speed and accuracy.
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The choice of table length is a tradeoff in accuracy versus speed. A
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larger N yields more accurate force computations, but requires more
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memory which can slow down the computation due to cache misses. A
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reasonable value of N is between 8 and 16. The default value of 12
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(table of length 4096) gives approximately the same accuracy as the
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no-table (N = 0) option. For N = 0, forces and energies are computed
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directly, using a polynomial fit for the needed erfc() function
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evaluation, which is what earlier versions of LAMMPS did. Values
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greater than 16 typically slow down the simulation and will not
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improve accuracy; values from 1 to 8 give unreliable results.
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The *tabinner* and *tabinner/disp* keywords set an inner cutoff above
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which the pairwise computation is done by table lookup (if tables are
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invoked), for the corresponding Coulombic and dispersion tables
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discussed with the *table* and *table/disp* keywords. The smaller the
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cutoff is set, the less accurate the table becomes (for a given number
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of table values), which can require use of larger tables. The default
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cutoff value is sqrt(2.0) distance units which means nearly all
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pairwise interactions are computed via table lookup for simulations
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with "real" units, but some close pairs may be computed directly
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(non-table) for simulations with "lj" units.
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When the *tail* keyword is set to *yes*\ , certain pair styles will add
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a long-range VanderWaals tail "correction" to the energy and pressure.
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These corrections are bookkeeping terms which do not affect dynamics,
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unless a constant-pressure simulation is being performed. See the doc
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page for individual styles to see which support this option. These
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corrections are included in the calculation and printing of
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thermodynamic quantities (see the :doc:`thermo_style <thermo_style>`
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command). Their effect will also be included in constant NPT or NPH
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simulations where the pressure influences the simulation box
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dimensions (e.g. the :doc:`fix npt <fix_nh>` and :doc:`fix nph <fix_nh>`
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commands). The formulas used for the long-range corrections come from
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equation 5 of :ref:`(Sun) <Sun>`.
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.. note::
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The tail correction terms are computed at the beginning of each
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run, using the current atom counts of each atom type. If atoms are
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deleted (or lost) or created during a simulation, e.g. via the :doc:`fix gcmc <fix_gcmc>` command, the correction factors are not
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re-computed. If you expect the counts to change dramatically, you can
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break a run into a series of shorter runs so that the correction
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factors are re-computed more frequently.
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Several additional assumptions are inherent in using tail corrections,
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including the following:
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* The simulated system is a 3d bulk homogeneous liquid. This option
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should not be used for systems that are non-liquid, 2d, have a slab
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geometry (only 2d periodic), or inhomogeneous.
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* G(r), the radial distribution function (rdf), is unity beyond the
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cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
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LJ fluid), and it is probably a good idea to verify this assumption by
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checking the rdf. The rdf is not exactly unity beyond the cutoff for
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each pair of interaction types, so the tail correction is necessarily
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an approximation.
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The tail corrections are computed at the beginning of each simulation
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run. If the number of atoms changes during the run, e.g. due to atoms
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leaving the simulation domain, or use of the :doc:`fix gcmc <fix_gcmc>`
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command, then the corrections are not updates to relect the changed
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atom count. If this is a large effect in your simulation, you should
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break the long run into several short runs, so that the correction
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factors are re-computed multiple times.
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* Thermophysical properties obtained from calculations with this option
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enabled will not be thermodynamically consistent with the truncated
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force-field that was used. In other words, atoms do not feel any LJ
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pair interactions beyond the cutoff, but the energy and pressure
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reported by the simulation include an estimated contribution from
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those interactions.
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The *compute* keyword allows pairwise computations to be turned off,
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even though a :doc:`pair_style <pair_style>` is defined. This is not
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useful for running a real simulation, but can be useful for debugging
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purposes or for performing a :doc:`rerun <rerun>` simulation, when you
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only wish to compute partial forces that do not include the pairwise
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contribution.
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Two examples are as follows. First, this option allows you to perform
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a simulation with :doc:`pair_style hybrid <pair_hybrid>` with only a
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subset of the hybrid sub-styles enabled. Second, this option allows
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you to perform a simulation with only long-range interactions but no
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short-range pairwise interactions. Doing this by simply not defining
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a pair style will not work, because the
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:doc:`kspace_style <kspace_style>` command requires a Kspace-compatible
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pair style be defined.
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----------
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Use of *special* keyword
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^^^^^^^^^^^^^^^^^^^^^^^^
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The *special* keyword allows to override the 1-2, 1-3, and 1-4
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exclusion settings for individual sub-styles of a
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:doc:`hybrid pair style <pair_hybrid>`. It requires 4 arguments similar
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to the :doc:`special_bonds <special_bonds>` command, *which* and
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wt1,wt2,wt3. The *which* argument can be *lj* to change the
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Lennard-Jones settings, *coul* to change the Coulombic settings,
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or *lj/coul* to change both to the same set of 3 values. The wt1,wt2,wt3
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values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
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1-3, and 1-4 bond topology neighbors, respectively. The *special*
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keyword can only be used in conjunction with the *pair* keyword
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and has to directly follow it.
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.. note::
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The global settings specified by the
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:doc:`special_bonds <special_bonds>` command affect the construction of
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neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
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exclude those pairs from the neighbor list entirely. Weights of 1.0
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store the neighbor with no weighting applied. Thus only global values
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different from exactly 0.0 or 1.0 can be overridden and an error is
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generated if the requested setting is not compatible with the global
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setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
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usually a sufficient workaround in this case without causing a
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significant error.
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----------
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Restrictions
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""""""""""""
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none
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You cannot use *shift* yes with *tail* yes, since those are
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conflicting options. You cannot use *tail* yes with 2d simulations.
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Related commands
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""""""""""""""""
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:doc:`pair_style <pair_style>`, :doc:`pair_coeff <pair_coeff>`,
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:doc:`thermo_style <thermo_style>`
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Default
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"""""""
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The option defaults are mix = geometric, shift = no, table = 12,
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tabinner = sqrt(2.0), tail = no, and compute = yes.
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Note that some pair styles perform mixing, but only a certain style of
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mixing. See the doc pages for individual pair styles for details.
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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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.. _Sun:
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**(Sun)** Sun, J Phys Chem B, 102, 7338-7364 (1998).
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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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