The constructor of the derived class sets values for several variables -that you must set when defining a new atom style. The atom arrays -themselves are defined in atom.cpp. Search for the word "customize" -and you will find locations you will need to modify. +that you must set when defining a new atom style, which are documented +in atom_vec.h. New atom arrays are defined in atom.cpp. Search for +the word "customize" and you will find locations you will need to +modify.
atom_style style args-
args = none for any style except hybrid hybrid args = list of one or more sub-styles @@ -59,7 +59,6 @@charge charge atomic system with charges colloid angular velocity extended spherical particles - dipole charge and dipole moment atomic system with dipoles dpd default values, also communicates velocities DPD models ellipsoid quaternion for particle orientation, angular momentum extended aspherical particles full molecular + charge bio-molecules @@ -68,7 +67,7 @@ granular diameter, density, angular velocity granular models All of the styles define point particles, except the colloid, -dipole, ellipsoid, granular, and peri styles. These define +dipole, ellipsoid, granular, and peri styles, which define finite-size particles. For colloid, dipole, and ellipsoid systems, the shape command is used to specify the size and shape of particles on a per-type basis, which is spherical for @@ -85,13 +84,6 @@ particle's mass. For peri systems, the speficied volume and density are used to calculate each particle's mass.
-Only the colloid, dpd, and granular styles communicate -velocities and angular velocities (if defined) with ghost atoms; the -others do not. This is because the pairwise interactions calculated -by the pair styles that typically use these atom styles -(e.g. pair_style dpd and pair_style -granular) require velocities of both particles. -
Typically, simulations require only a single (non-hybrid) atom style. @@ -103,10 +95,10 @@
The only scenario where the hybrid style is needed is if there is no single style which defines all needed properties of all atoms. For -example, if you want charged DPD particles, you would need to use -"atom_style hybrid dpd charge". When a hybrid style is used, atoms -store and communicate the union of all quantities implied by the -individual styles. +example, if you want colloidal particles with charge, you would need +to use "atom_style hybrid colloid charge". When a hybrid style is +used, atoms store and communicate the union of all quantities implied +by the individual styles.
LAMMPS can be extended with new atom styles; see this section. @@ -118,13 +110,12 @@
The angle, bond, full, and molecular styles are part of the "molecular" package. The granular style is part of the "granular" -package. The dpd style is part of the "dpd" package. The colloid -style is part of the "colloid" package. The dipole style is part of -the "dipole" package. The ellipsoid style is part of the "asphere" -package. The peri style is part of the "peri" package for -Peridynamics. They are only enabled if LAMMPS was built with that -package. See the Making LAMMPS section for -more info. +package. The colloid style is part of the "colloid" package. The +dipole style is part of the "dipole" package. The ellipsoid style +is part of the "asphere" package. The peri style is part of the +"peri" package for Peridynamics. They are only enabled if LAMMPS was +built with that package. See the Making +LAMMPS section for more info.
Related commands:
diff -Naur lammps-11Nov09/doc/atom_style.txt lammps-12Nov09/doc/atom_style.txt --- lammps-11Nov09/doc/atom_style.txt 2009-11-06 14:01:28.000000000 -0700 +++ lammps-12Nov09/doc/atom_style.txt 2009-11-09 11:30:55.000000000 -0700 @@ -13,7 +13,7 @@ atom_style style args :pre style = {angle} or {atomic} or {bond} or {charge} or {colloid} or {dipole} or \ - {dpd} or {ellipsoid} or {full} or {granular} or {molecular} or \ + {ellipsoid} or {full} or {granular} or {molecular} or \ {peri} or {hybrid} :ul args = none for any style except {hybrid} {hybrid} args = list of one or more sub-styles :pre @@ -56,7 +56,6 @@ {charge} | charge | atomic system with charges | {colloid} | angular velocity | extended spherical particles | {dipole} | charge and dipole moment | atomic system with dipoles | -{dpd} | default values, also communicates velocities | DPD models | {ellipsoid} | quaternion for particle orientation, angular momentum | extended aspherical particles | {full} | molecular + charge | bio-molecules | {granular} | diameter, density, angular velocity | granular models | @@ -64,7 +63,7 @@ {peri} | density, volume | mesocopic Peridynamic models :tb(c=3,s=|) All of the styles define point particles, except the {colloid}, -{dipole}, {ellipsoid}, {granular}, and {peri} styles. These define +{dipole}, {ellipsoid}, {granular}, and {peri} styles, which define finite-size particles. For {colloid}, {dipole}, and {ellipsoid} systems, the "shape"_shape.html command is used to specify the size and shape of particles on a per-type basis, which is spherical for @@ -81,13 +80,6 @@ particle's mass. For {peri} systems, the speficied volume and density are used to calculate each particle's mass. -Only the {colloid}, {dpd}, and {granular} styles communicate -velocities and angular velocities (if defined) with ghost atoms; the -others do not. This is because the pairwise interactions calculated -by the pair styles that typically use these atom styles -(e.g. "pair_style dpd"_pair_dpd.html and "pair_style -granular"_pair_gran.html) require velocities of both particles. - :line Typically, simulations require only a single (non-hybrid) atom style. @@ -99,10 +91,10 @@ The only scenario where the {hybrid} style is needed is if there is no single style which defines all needed properties of all atoms. For -example, if you want charged DPD particles, you would need to use -"atom_style hybrid dpd charge". When a hybrid style is used, atoms -store and communicate the union of all quantities implied by the -individual styles. +example, if you want colloidal particles with charge, you would need +to use "atom_style hybrid colloid charge". When a hybrid style is +used, atoms store and communicate the union of all quantities implied +by the individual styles. LAMMPS can be extended with new atom styles; see "this section"_Section_modify.html. @@ -114,13 +106,12 @@ The {angle}, {bond}, {full}, and {molecular} styles are part of the "molecular" package. The {granular} style is part of the "granular" -package. The {dpd} style is part of the "dpd" package. The {colloid} -style is part of the "colloid" package. The {dipole} style is part of -the "dipole" package. The {ellipsoid} style is part of the "asphere" -package. The {peri} style is part of the "peri" package for -Peridynamics. They are only enabled if LAMMPS was built with that -package. See the "Making LAMMPS"_Section_start.html#2_3 section for -more info. +package. The {colloid} style is part of the "colloid" package. The +{dipole} style is part of the "dipole" package. The {ellipsoid} style +is part of the "asphere" package. The {peri} style is part of the +"peri" package for Peridynamics. They are only enabled if LAMMPS was +built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff -Naur lammps-11Nov09/doc/communicate.html lammps-12Nov09/doc/communicate.html --- lammps-11Nov09/doc/communicate.html 2008-08-21 08:03:21.000000000 -0600 +++ lammps-12Nov09/doc/communicate.html 2009-11-09 11:30:55.000000000 -0700 @@ -19,10 +19,11 @@
group value = group-ID = only communicate atoms in the group - cutoff value = Rcut (distance units) = communicate atoms from this far away +cutoff value = Rcut (distance units) = communicate atoms from this far away + group value = group-ID = only communicate atoms in the group + vel value = yes or no = do or do not communicate velocity info with ghost atoms
communicate multi communicate multi group solvent -communicate single cutoff 5.0 +communicate single ghost yes +communicate single cutoff 5.0 ghost yes
Description:
@@ -52,13 +54,6 @@ neighbor list construction option that may also be beneficial for simulations of this kind. -The group option will limit communication to atoms in the specified -group. This can be useful for models where no ghost atoms are needed -for some kinds of particles. All atoms (not just those in the -specified group) will still migrate to new processors as they move. -The group specified with this option must also be specified via the -atom_modify first command. -
The cutoff option allows you to set a ghost cutoff distance, which is the distance from the borders of a processor's sub-domain at which ghost atoms are acquired from other processors. By default the ghost @@ -98,6 +93,22 @@ potential). Setting the ghost cutoff appropriately can insure it will find the needed atoms.
+The group option will limit communication to atoms in the specified +group. This can be useful for models where no ghost atoms are needed +for some kinds of particles. All atoms (not just those in the +specified group) will still migrate to new processors as they move. +The group specified with this option must also be specified via the +atom_modify first command. +
+The vel option enables velocity information to be communicated with +ghost particles. Depending on the atom_style, +velocity info includes the translational velocity, angular velocity, +and angular momentum of a particle. If the vel option is set to +yes, then ghost atoms store these quantities; if no then they do +not. The yes setting is needed by some pair styles which require +the velocity state of both the I and J particles to compute a pairwise +I,J interaction. +
Restrictions: none
Related commands: @@ -106,8 +117,8 @@
Default:
-The default settings are style = single, group = all, cutoff = 0.0. -The cutoff default of 0.0 means that effectively ghost cutoff = +
The default settings are style = single, group = all, cutoff = 0.0, +ghost = no. The cutoff default of 0.0 means that ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin.