forked from lijiext/lammps
207 lines
8.8 KiB
Plaintext
207 lines
8.8 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_modify command :h3
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[Syntax:]
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pair_modify keyword values ... :pre
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one or more keyword/value pairs may be listed :ulb,l
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keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or {tabinner/disp} or {tail} or {compute} :l
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{pair} values = sub-style N
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sub-style = sub-style of "pair hybrid"_pair_hybrid.html
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N = which instance of sub-style (only if sub-style is used multiple times)
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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} :pre
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:ule
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[Examples:]
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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 :pre
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[Description:]
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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 "hybrid and
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hybrid/overlay"_pair_hybrid.html pair styles. It means that the
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following parameters will only be modified for the specified
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sub-style, which must be a sub-style defined by the "pair_style
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hybrid"_pair_hybrid.html command. If the sub-style is defined
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multiple times, then an additional numeric argument {N} must also be
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specified which is a number from 1 to M where M is the number of times
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the sub-style was listed in the "pair_style hybrid"_pair_hybrid.html
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command. The extra number indicates which instance of the sub-style
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these modifications apply to. Note that if the {pair} keyword is not
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used, and the pair style is {hybrid} or {hybrid/overlay}, the
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pair_modify keywords will be applied to all sub-styles.
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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 "data
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file"_read_data.html. 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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"pair_coeff"_pair_coeff.html 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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epsilon_ij = sqrt(epsilon_i * epsilon_j)
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sigma_ij = sqrt(sigma_i * sigma_j) :pre
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mix {arithmetic}
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epsilon_ij = sqrt(epsilon_i * epsilon_j)
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sigma_ij = (sigma_i + sigma_j) / 2 :pre
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mix {sixthpower}
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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) :pre
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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 "(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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See the doc page for individual styles to see which support this
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option. These corrections are included in the calculation and
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printing of thermodynamic quantities (see the
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"thermo_style"_thermo_style.html command). Their effect will also be
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included in constant NPT or NPH simulations where the pressure
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influences the simulation box dimensions (e.g. the "fix
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npt"_fix_nh.html and "fix nph"_fix_nh.html commands). The formulas
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used for the long-range corrections come from equation 5 of
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"(Sun)"_#Sun.
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Several assumptions are inherent in using tail corrections, including
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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. :ulb,l
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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. :l
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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. :l,ule
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The {compute} keyword allows pairwise computations to be turned off,
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even though a "pair_style"_pair_style.html 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 "rerun"_rerun.html 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 "pair_style hybrid"_pair_hybrid.html 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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"kspace_style"_kspace_style.html command requires a Kspace-compatible
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pair style be defined.
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[Restrictions:] 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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"pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html,
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"thermo_style"_thermo_style.html
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[Default:]
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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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:line
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:link(Wolff)
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[(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
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:link(Sun)
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[(Sun)] Sun, J Phys Chem B, 102, 7338-7364 (1998).
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