diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index 664937ef61..b45a50573a 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -247,7 +247,9 @@ or *lj/coul* to change both to the same set of 3 values. The wt1,wt2,wt3 values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2, 1-3, and 1-4 bond topology neighbors, respectively. The *special* keyword can only be used in conjunction with the *pair* keyword -and has to directly follow it. +and has to directly follow it. This option is not compatible with +pair styles from the GPU or the USER-INTEL package and attempting +it will cause an error. .. note:: @@ -278,10 +280,11 @@ and allows to selectively disable or enable processing of the various Restrictions """""""""""" - none You cannot use *shift* yes with *tail* yes, since those are conflicting options. You cannot use *tail* yes with 2d simulations. +You cannot use *special* with pair styles from the GPU or +USER-INTEL package. Related commands """""""""""""""" diff --git a/doc/txt/pair_modify.txt b/doc/txt/pair_modify.txt deleted file mode 100644 index c446aa29d0..0000000000 --- a/doc/txt/pair_modify.txt +++ /dev/null @@ -1,281 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_modify command :h3 - -[Syntax:] - -pair_modify keyword values ... :pre - -one or more keyword/value pairs may be listed :ulb,l -keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} -or {tabinner/disp} or {tail} or {compute} or {nofdotr} :l - {pair} values = sub-style N {special} which wt1 wt2 wt3 - or sub-style N {compute/tally} flag - sub-style = sub-style of "pair hybrid"_pair_hybrid.html - N = which instance of sub-style (only if sub-style is used multiple times) - {special} which wt1 wt2 wt3 = override {special_bonds} settings (optional) - which = {lj/coul} or {lj} or {coul} - w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive - {compute/tally} flag = {yes} or {no} - {mix} value = {geometric} or {arithmetic} or {sixthpower} - {shift} value = {yes} or {no} - {table} value = N - 2^N = # of values in table - {table/disp} value = N - 2^N = # of values in table - {tabinner} value = cutoff - cutoff = inner cutoff at which to begin table (distance units) - {tabinner/disp} value = cutoff - cutoff = inner cutoff at which to begin table (distance units) - {tail} value = {yes} or {no} - {compute} value = {yes} or {no} - {nofdotr} :pre -:ule - -[Examples:] - -pair_modify shift yes mix geometric -pair_modify tail yes -pair_modify table 12 -pair_modify pair lj/cut compute no -pair_modify pair tersoff compute/tally no -pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0 :pre - -[Description:] - -Modify the parameters of the currently defined pair style. Not all -parameters are relevant to all pair styles. - -If used, the {pair} keyword must appear first in the list of keywords. -It can only be used with the "hybrid and -hybrid/overlay"_pair_hybrid.html pair styles. It means that all the -following parameters will only be modified for the specified -sub-style. If the sub-style is defined multiple times, then an -additional numeric argument {N} must also be specified, which is a -number from 1 to M where M is the number of times the sub-style was -listed in the "pair_style hybrid"_pair_hybrid.html command. The extra -number indicates which instance of the sub-style the remaining -keywords will be applied to. Note that if the {pair} keyword is not -used, and the pair style is {hybrid} or {hybrid/overlay}, then all the -specified keywords will be applied to all sub-styles. - -The {special} and {compute/tally} keywords can [only] be used in -conjunction with the {pair} keyword and must directly follow it. -{special} allows to override the -"special_bonds"_special_bonds.html settings for the specified sub-style. -{compute/tally} allows to disable or enable registering -"compute */tally"_compute_tally.html computes for a given sub-style. -More details are given below. - -The {mix} keyword affects pair coefficients for interactions between -atoms of type I and J, when I != J and the coefficients are not -explicitly set in the input script. Note that coefficients for I = J -must be set explicitly, either in the input script via the -"pair_coeff" command or in the "Pair Coeffs" section of the "data -file"_read_data.html. For some pair styles it is not necessary to -specify coefficients when I != J, since a "mixing" rule will create -them from the I,I and J,J settings. The pair_modify {mix} value -determines what formulas are used to compute the mixed coefficients. -In each case, the cutoff distance is mixed the same way as sigma. - -Note that not all pair styles support mixing. Also, some mix options -are not available for certain pair styles. See the doc page for -individual pair styles for those restrictions. Note also that the -"pair_coeff"_pair_coeff.html command also can be to directly set -coefficients for a specific I != J pairing, in which case no mixing is -performed. - -mix {geometric} - -epsilon_ij = sqrt(epsilon_i * epsilon_j) -sigma_ij = sqrt(sigma_i * sigma_j) :pre - -mix {arithmetic} - -epsilon_ij = sqrt(epsilon_i * epsilon_j) -sigma_ij = (sigma_i + sigma_j) / 2 :pre - -mix {sixthpower} - -epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) / - (sigma_i^6 + sigma_j^6) -sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre - -The {shift} keyword determines whether a Lennard-Jones potential is -shifted at its cutoff to 0.0. If so, this adds an energy term to each -pairwise interaction which will be included in the thermodynamic -output, but does not affect pair forces or atom trajectories. See the -doc page for individual pair styles to see which ones support this -option. - -The {table} and {table/disp} keywords apply to pair styles with a -long-range Coulombic term or long-range dispersion term respectively; -see the doc page for individual styles to see which potentials support -these options. If N is non-zero, a table of length 2^N is -pre-computed for forces and energies, which can shrink their -computational cost by up to a factor of 2. The table is indexed via a -bit-mapping technique "(Wolff)"_#Wolff1 and a linear interpolation is -performed between adjacent table values. In our experiments with -different table styles (lookup, linear, spline), this method typically -gave the best performance in terms of speed and accuracy. - -The choice of table length is a tradeoff in accuracy versus speed. A -larger N yields more accurate force computations, but requires more -memory which can slow down the computation due to cache misses. A -reasonable value of N is between 8 and 16. The default value of 12 -(table of length 4096) gives approximately the same accuracy as the -no-table (N = 0) option. For N = 0, forces and energies are computed -directly, using a polynomial fit for the needed erfc() function -evaluation, which is what earlier versions of LAMMPS did. Values -greater than 16 typically slow down the simulation and will not -improve accuracy; values from 1 to 8 give unreliable results. - -The {tabinner} and {tabinner/disp} keywords set an inner cutoff above -which the pairwise computation is done by table lookup (if tables are -invoked), for the corresponding Coulombic and dispersion tables -discussed with the {table} and {table/disp} keywords. The smaller the -cutoff is set, the less accurate the table becomes (for a given number -of table values), which can require use of larger tables. The default -cutoff value is sqrt(2.0) distance units which means nearly all -pairwise interactions are computed via table lookup for simulations -with "real" units, but some close pairs may be computed directly -(non-table) for simulations with "lj" units. - -When the {tail} keyword is set to {yes}, certain pair styles will add -a long-range VanderWaals tail "correction" to the energy and pressure. -These corrections are bookkeeping terms which do not affect dynamics, -unless a constant-pressure simulation is being performed. See the doc -page for individual styles to see which support this option. These -corrections are included in the calculation and printing of -thermodynamic quantities (see the "thermo_style"_thermo_style.html -command). Their effect will also be included in constant NPT or NPH -simulations where the pressure influences the simulation box -dimensions (e.g. the "fix npt"_fix_nh.html and "fix nph"_fix_nh.html -commands). The formulas used for the long-range corrections come from -equation 5 of "(Sun)"_#Sun. - -NOTE: The tail correction terms are computed at the beginning of each -run, using the current atom counts of each atom type. If atoms are -deleted (or lost) or created during a simulation, e.g. via the "fix -gcmc"_fix_gcmc.html command, the correction factors are not -re-computed. If you expect the counts to change dramatically, you can -break a run into a series of shorter runs so that the correction -factors are re-computed more frequently. - -Several additional assumptions are inherent in using tail corrections, -including the following: - -The simulated system is a 3d bulk homogeneous liquid. This option -should not be used for systems that are non-liquid, 2d, have a slab -geometry (only 2d periodic), or inhomogeneous. :ulb,l - -G(r), the radial distribution function (rdf), is unity beyond the -cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an -LJ fluid), and it is probably a good idea to verify this assumption by -checking the rdf. The rdf is not exactly unity beyond the cutoff for -each pair of interaction types, so the tail correction is necessarily -an approximation. :l - -The tail corrections are computed at the beginning of each simulation -run. If the number of atoms changes during the run, e.g. due to atoms -leaving the simulation domain, or use of the "fix gcmc"_fix_gcmc.html -command, then the corrections are not updated to reflect the changed -atom count. If this is a large effect in your simulation, you should -break the long run into several short runs, so that the correction -factors are re-computed multiple times. - -Thermophysical properties obtained from calculations with this option -enabled will not be thermodynamically consistent with the truncated -force-field that was used. In other words, atoms do not feel any LJ -pair interactions beyond the cutoff, but the energy and pressure -reported by the simulation include an estimated contribution from -those interactions. :l -:ule - -The {compute} keyword allows pairwise computations to be turned off, -even though a "pair_style"_pair_style.html is defined. This is not -useful for running a real simulation, but can be useful for debugging -purposes or for performing a "rerun"_rerun.html simulation, when you -only wish to compute partial forces that do not include the pairwise -contribution. - -Two examples are as follows. First, this option allows you to perform -a simulation with "pair_style hybrid"_pair_hybrid.html with only a -subset of the hybrid sub-styles enabled. Second, this option allows -you to perform a simulation with only long-range interactions but no -short-range pairwise interactions. Doing this by simply not defining -a pair style will not work, because the -"kspace_style"_kspace_style.html command requires a Kspace-compatible -pair style be defined. - -The {nofdotr} keyword allows to disable an optimization that computes -the global stress tensor from the total forces and atom positions rather -than from summing forces between individual pairs of atoms. - -:line - -The {special} keyword allows to override the 1-2, 1-3, and 1-4 -exclusion settings for individual sub-styles of a -"hybrid pair style"_pair_hybrid.html. It requires 4 arguments similar -to the "special_bonds"_special_bonds.html command, {which} and -wt1,wt2,wt3. The {which} argument can be {lj} to change the -Lennard-Jones settings, {coul} to change the Coulombic settings, -or {lj/coul} to change both to the same set of 3 values. The wt1,wt2,wt3 -values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2, -1-3, and 1-4 bond topology neighbors, respectively. The {special} -keyword can only be used in conjunction with the {pair} keyword -and has to directly follow it. - -NOTE: The global settings specified by the -"special_bonds"_special_bonds.html command affect the construction of -neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors) -exclude those pairs from the neighbor list entirely. Weights of 1.0 -store the neighbor with no weighting applied. Thus only global values -different from exactly 0.0 or 1.0 can be overridden and an error is -generated if the requested setting is not compatible with the global -setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is -usually a sufficient workaround in this case without causing a -significant error. - -The {compute/tally} keyword takes exactly 1 argument ({no} or {yes}), -and allows to selectively disable or enable processing of the various -"compute */tally"_compute_tally.html styles for a given -"pair hybrid or hybrid/overlay"_pair_hybrid.html sub-style. - -NOTE: Any "pair_modify pair compute/tally" command must be issued -[before] the corresponding compute style is defined. - -:line - -[Restrictions:] none - -You cannot use {shift} yes with {tail} yes, since those are -conflicting options. You cannot use {tail} yes with 2d simulations. - -[Related commands:] - -"pair_style"_pair_style.html, "pair_style hybrid"_pair_hybrid.html, -pair_coeff"_pair_coeff.html, "thermo_style"_thermo_style.html, -"compute */tally"_compute_tally.html - -[Default:] - -The option defaults are mix = geometric, shift = no, table = 12, -tabinner = sqrt(2.0), tail = no, and compute = yes. - -Note that some pair styles perform mixing, but only a certain style of -mixing. See the doc pages for individual pair styles for details. - -:line - -:link(Wolff1) -[(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). - -:link(Sun) -[(Sun)] Sun, J Phys Chem B, 102, 7338-7364 (1998).