forked from lijiext/lammps
167 lines
6.4 KiB
Plaintext
167 lines
6.4 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 value ... :pre
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one or more keyword/value pairs may be listed :ulb,l
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keyword = {shift} or {mix} or {table} or {tabinner} or {tail} :l
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{shift} value = {yes} or {no}
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{mix} value = {geometric} or {arithmetic} or {sixthpower}
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{table} 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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{tail} 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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The {shift} keyword determines whether the 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 printed in the thermodynamic
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output, but does not affect atom dynamics (forces). Pair styles that
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are already 0.0 at their cutoff such as {lj/charmm/coul/charmm} are
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not affected by this setting.
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The {mix} keyword affects how Lennard-Jones coefficients for epsilon,
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sigma, and the cutoff are generated for interactions between atoms of
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type I and J, when I != J. Coefficients for I = J are set explicitly
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in the data file or input script. The "pair_coeff"_pair_coeff.html
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command can be used in the input script to specify epilon/sigma for a
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specific I != J pairing, which overrides the setting of the {mix}
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keyword.
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These are the formulas used by the 3 {mix} options. In each case, the
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LJ cutoff is mixed the same way as sigma. Note that some of these
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options are not available for certain pair styles. See the doc page
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for individual pair styles for those restrictions.
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{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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{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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{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 {table} keyword applies to pair styles with a long-range Coulombic
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term (lj/cut/coul/long and lj/charmm/coul/long). If N is non-zero, a
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table of length 2^N is pre-computed for forces and energies, which can
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shrink their computational cost by up to a factor of 2. The table is
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indexed via a bit-mapping technique "(Wolff)"_#Wolff and a linear
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interpolation is performed between adjacent table values. In our
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experiments with different table styles (lookup, linear, spline), this
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method typically gave the best performance in terms of speed and
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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} keyword sets an inner cutoff above which the pairwise
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computation is done by table lookup (if tables are invoked). The
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smaller this value is set, the less accurate the table becomes (for a
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given number of table values), which can require use of larger tables.
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The default cutoff value is sqrt(2.0) distance units which means
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nearly all pairwise interactions are computed via table lookup for
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simulations with "real" units, but some close pairs may be computed
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directly (non-table) for simulations with "lj" units.
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When the {tail} keyword is set to {yes}, long-range VanderWaals tail
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"corrections" are added to the energy and pressure. These are
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included in the calculation and printing of thermodynamic quantities
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(see the "thermo_style"_thermo_style.html command). Their effect will
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also be included in constant NPT or NPH simulations where the pressure
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influences the simulation box dimensions (see the "fix
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npt"_fix_npt.html and "fix nph"_fix_nph.html commands).
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The {tail} keyword is only supported by "pair_style"_pair_style.html
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pairwise potentials which include Lennard-Jones interactions which are
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cutoff at a non-zero energy. This does not include the LJ CHARMM
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potentials or {lj/smooth} since they go to zero at the cutoff. The
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formulas 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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[Restrictions:] none
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Not all pair styles support mixing. See the doc page for individual
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pair styles for details.
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You cannot use {shift} yes with {tail} yes, since those are
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conflicting options.
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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 shift = no, mix = arithmetic (for lj/charmm
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pair styles), mix = geometric (for other pair styles), table = 12,
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and tabinner = sqrt(2.0), tail = no.
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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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