+Syntax: +
+pair_style list listfile cutoff keyword ++
Examples: +
+pair_style list restraints.txt 200.0 +pair_coeff * * ++
pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0 +pair_coeff * * lj/cut 1.0 1.0 +pair_coeff 3* 3* list ++
Description: +
+Style list computes interactions between explicitly listed pairs of +atoms with the option to select functional form and parameters for +each individual pair. Because the parameters are set in the list +file, the pair_coeff command has no parameters (but still needs to be +provided). The check and nocheck keywords enable/disable a test +that checks whether all listed bonds were present and computed. +
+This pair style can be thought of as a hybrid between bonded, +non-bonded, and restraint interactions. It will typically be used as +an additional interaction within the hybrid/overlay pair style. It +currently supports three interaction styles: a 12-6 Lennard-Jones, a +Morse and a harmonic potential. +
+The format of the list file is as follows: +
+ID1 = atom ID of first atom + ID2 = atom ID of second atom + style = style of interaction + coeffs = list of coeffs + cutoff = cutoff for interaction (optional) ++ +
The cutoff parameter is optional. If not specified, the global cutoff +is used. +
+Here is an example file: +
+# this is a comment ++
15 259 lj126 1.0 1.0 50.0 +15 603 morse 10.0 1.2 2.0 10.0 # and another comment +18 470 harmonic 50.0 1.2 5.0 ++
The style lj126 computes pairwise interactions with the formula +
+
+and the coefficients: +
+The style morse computes pairwise interactions with the formula +
+
+and the coefficients: +
+The style harmonic computes pairwise interactions with the formula +
+
+and the coefficients: +
+Note that the usual 1/2 factor is included in K. +
+Mixing, shift, table, tail correction, restart, rRESPA info: +
+This pair style does not support mixing since all parameters are +explicit for each pair. +
+The pair_modify shift option is supported by this +pair style. +
+The pair_modify table and tail options are not +relevant for this pair style. +
+This pair style does not write its information to binary restart +files, so pair_style and pair_coeff commands need +to be specified in an input script that reads a restart file. +
+This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords. +
+Restrictions: +
+This pair style does not use a neighbor list and instead identifies +atoms by their IDs. This has two consequences: 1) The cutoff has to be +chosen sufficiently large, so that the second atom of a pair has to be +a ghost atom on the same node on which the first atom is local; +otherwise the interaction will be skipped. You can use the check +option to detect, if interactions are missing. 2) Unlike for the rest +of LAMMPS, minimum image conventions apply. +
+This style is part of the USER-MISC package. It is only enabled if +LAMMPS is build with that package. See the Making of +LAMMPS section for more info. +
+Related commands: +
+pair_coeff, +pair_style hybrid/overlay, +pair_style lj/cut, +pair_style morse, +bond_style harmonic +
+Default: none +
+ diff --git a/doc/pair_list.txt b/doc/pair_list.txt new file mode 100644 index 0000000000..aa541b9a6c --- /dev/null +++ b/doc/pair_list.txt @@ -0,0 +1,142 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style list command :h3 + +[Syntax:] + +pair_style list listfile cutoff keyword :pre + +listfile = name of file with list of pairwise interactions +cutoff = global cutoff (distance units) +keyword = optional flag {nocheck} or {check} (default is {check}) :ul + +[Examples:] + +pair_style list restraints.txt 200.0 +pair_coeff * * :pre + +pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0 +pair_coeff * * lj/cut 1.0 1.0 +pair_coeff 3* 3* list :pre + +[Description:] + +Style {list} computes interactions between explicitly listed pairs of +atoms with the option to select functional form and parameters for +each individual pair. Because the parameters are set in the list +file, the pair_coeff command has no parameters (but still needs to be +provided). The {check} and {nocheck} keywords enable/disable a test +that checks whether all listed bonds were present and computed. + +This pair style can be thought of as a hybrid between bonded, +non-bonded, and restraint interactions. It will typically be used as +an additional interaction within the {hybrid/overlay} pair style. It +currently supports three interaction styles: a 12-6 Lennard-Jones, a +Morse and a harmonic potential. + +The format of the list file is as follows: + +one line per pair of atoms :ulb,l +empty lines will be ignored :l +comment text starts with a '#' character +line syntax: ID1 ID2 style coeffs cutoff :l + ID1 = atom ID of first atom + ID2 = atom ID of second atom + style = style of interaction + coeffs = list of coeffs + cutoff = cutoff for interaction (optional) :pre +:ule + +The cutoff parameter is optional. If not specified, the global cutoff +is used. + +Here is an example file: + +# this is a comment :pre + +15 259 lj126 1.0 1.0 50.0 +15 603 morse 10.0 1.2 2.0 10.0 # and another comment +18 470 harmonic 50.0 1.2 5.0 :pre + +The style {lj126} computes pairwise interactions with the formula + +:c,image(Eqs/pair_lj.jpg) + +and the coefficients: + +epsilon (energy units) +sigma (distance units) :ul + +The style {morse} computes pairwise interactions with the formula + +:c,image(Eqs/pair_morse.jpg) + +and the coefficients: + +D0 (energy units) +alpha (1/distance units) +r0 (distance units) :ul + +The style {harmonic} computes pairwise interactions with the formula + +:c,image(Eqs/bond_harmonic.jpg) + +and the coefficients: + +K (energy units) +r0 (distance units) :ul + +Note that the usual 1/2 factor is included in K. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support mixing since all parameters are +explicit for each pair. + +The "pair_modify"_pair_modify.html shift option is supported by this +pair style. + +The "pair_modify"_pair_modify.html table and tail options are not +relevant for this pair style. + +This pair style does not write its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands need +to be specified in an input script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +This pair style does not use a neighbor list and instead identifies +atoms by their IDs. This has two consequences: 1) The cutoff has to be +chosen sufficiently large, so that the second atom of a pair has to be +a ghost atom on the same node on which the first atom is local; +otherwise the interaction will be skipped. You can use the {check} +option to detect, if interactions are missing. 2) Unlike for the rest +of LAMMPS, minimum image conventions apply. + +This style is part of the USER-MISC package. It is only enabled if +LAMMPS is build with that package. See the "Making of +LAMMPS"_Section_start.html#3 section for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, +"pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style lj/cut"_pair_lj.html, +"pair_style morse"_pair_morse.html, +"bond_style harmonic"_bond_harmonic.html + +[Default:] none