atom_style style args-
args = none for any style except body and hybrid
body args = bstyle bstyle-args
bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle
see the body doc page for details
+ template args = template-ID
+ template-ID = ID of molecule template specified in a separate molecule command
hybrid args = list of one or more sub-styles, each with their args
Examples: @@ -31,7 +33,8 @@ atom_style bond atom_style full atom_style body nparticle 2 10 atom_style hybrid charge bond -atom_style hybrid charge body nparticle 2 5 +atom_style hybrid charge body nparticle 2 5 +atom_style template myMols
Description:
@@ -73,6 +76,7 @@ quantities.All of the styles assign mass to particles on a per-type basis, using -the mass command, except for the finite-size particle -styles. They assign mass to individual particles on a per-particle +
All of the point-particle styles assign mass to particles on a +per-type basis, using the mass command, The finite-size +particle styles assign mass to individual particles on a per-particle basis.
For the sphere style, the particles are spheres and each stores a @@ -133,6 +137,30 @@ end points of the line segment). stores a per-particle mass and size and orientation (i.e. the corner points of the triangle).
+The template style allows molecular topolgy (bonds,angles,etc) to be +defined via a molecule template using the molecule +command. The template stores one or more molecules with a single copy +of the topology info (bonds,angles,etc) of each. Individual atoms +only store a template index and template atom to identify which +molecule and which atom-within-the-molecule they represent. Using the +template style instead of the bond, angle, molecular styles +can save memory for systems comprised of a large number of small +molecules, all of a single type (or small number of types). See the +paper by Grime and Voth, in (Grime), for examples of how this +can be advantageous for large-scale coarse-grained systems. +
+IMPORTANT NOTE: When using the template style with a molecule +template that contains multiple molecules, you should +insure the atom types, bond types, angle_types, etc in all the +molecules are consistent. E.g. if one molecule represents H2O and +another CO2, then you probably do not want each molecule file to +define 2 atom types and a single bond type, because they will conflict +with each other when a mixture system of H2O and CO2 molecules is +defined, e.g. by the read_data command. Rather the +H2O molecule should define atom types 1 and 2, and bond type 1. And +the CO2 molecule should define atom types 3 and 4 (or atom types 3 and +2 if a single oxygen type is desired), and bond type 2. +
For the body style, the particles are arbitrary bodies with internal attributes defined by the "style" of the bodies, which is specified by the bstyle argument. Body particles can represent complex entities, @@ -165,6 +193,10 @@ torque, you would need to use "atom_style hybrid sphere dipole". When a hybrid style is used, atoms store and communicate the union of all quantities implied by the individual styles.
+When using the hybrid style, you cannot combine the template style +with another molecular style that stores bond,angle,etc info on a +per-atom basis. +
LAMMPS can be extended with new atom styles as well as new body styles; see this section.
@@ -173,10 +205,10 @@ styles; see this section.This command cannot be used after the simulation box is defined by a read_data or create_box command.
-The angle, bond, full, and molecular styles are part of the -MOLECULAR package. The line and tri styles are part of the -ASPHERE pacakge. The body style is part of the BODY package. The -dipole style is part of the DIPOLE package. The peri style is +
The angle, bond, full, molecular, and template styles are +part of the MOLECULAR package. The line and tri styles are part +of the ASPHERE pacakge. The body style is part of the BODY package. +The dipole style is part of the DIPOLE package. The peri style is part of the PERI package for Peridynamics. The electron style is part of the USER-EFF package for electronic force fields. The meso style is part of the USER-SPH @@ -195,4 +227,11 @@ LAMMPS section for more info.
atom_style atomic
+(Grime) Grime and Voth, to appear in J Chem Theory & Computation +(2014). +