compute ptm/atom command

Syntax

compute ID group-ID ptm/atom structures threshold
  • ID, group-ID are documented in compute command
  • ptm/atom = style name of this compute command
  • structures = structure types to search for
  • threshold = lattice distortion threshold (RMSD)

Examples

compute 1 all ptm/atom default 0.1
compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15
compute 1 all ptm/atom all 0

Description

Define a computation that determines the local lattice structure around an atom using the PTM (Polyhedral Template Matching) method. The PTM method is described in (Larsen).

Currently, there are seven lattice structures PTM recognizes:

  • fcc = 1
  • hcp = 2
  • bcc = 3
  • ico (icosahedral) = 4
  • sc (simple cubic) = 5
  • dcub (diamond cubic) = 6
  • dhex (diamond hexagonal) = 7
  • other = 8

The value of the PTM structure will be 0 for atoms not in the specified compute group. The choice of structures to search for can be specified using the “structures” argument, which is a hyphen-separated list of structure keywords. Two convenient pre-set options are provided:

  • default: fcc-hcp-bcc-ico
  • all: fcc-hcp-bcc-ico-sc-dcub-dhex

The ‘default’ setting detects the same structures as the Common Neighbor Analysis method. The ‘all’ setting searches for all structure types. A small performance penalty is incurred for the diamond structures, so it is not recommended to use this option if it is known that the simulation does not contain diamond structures.

PTM identifies structures using two steps. First, a graph isomorphism test is used to identify potential structure matches. Next, the deviation is computed between the local structure (in the simulation) and a template of the ideal lattice structure. The deviation is calculated as:

_images/ptm_rmsd.jpg

Here, u and v contain the coordinates of the local and ideal structures respectively, s is a scale factor, and Q is a rotation. The best match is identified by the lowest RMSD value, using the optimal scaling, rotation, and correspondence between the points.

The ‘threshold’ keyword sets an upper limit on the maximum permitted deviation before a local structure is identified as disordered. Typical values are in the range 0.1-0.15, but larger values may be desirable at higher temperatures. A value of 0 is equivalent to infinity and can be used if no threshold is desired.

The neighbor list needed to compute this quantity is constructed each time the calculation is performed (e.g. each time a snapshot of atoms is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each with a ptm/atom style.

Output info:

This compute calculates a per-atom array, which can be accessed by any command that uses per-atom values from a compute as input. See the Howto output doc page for an overview of LAMMPS output options.

Results are stored in the per-atom array in the following order:

  • type
  • rmsd
  • interatomic distance
  • qw
  • qx
  • qy
  • qw

The type is a number from 0 to 8. The rmsd is a positive real number. The interatomic distance is computed from the scale factor in the RMSD equation. The (qw,qx,qy,qz) parameters represent the orientation of the local structure in quaternion form. The reference coordinates for each template (from which the orientation is determined) can be found in the ptm_constants.h file in the PTM source directory.

Restrictions

This fix is part of the USER-PTM package. It is only enabled if LAMMPS was built with that package. See the Build package doc page for more info.