122 lines
4.0 KiB
Plaintext
122 lines
4.0 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute ptm/atom command :h3
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[Syntax:]
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compute ID group-ID ptm/atom structures threshold :pre
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ID, group-ID are documented in "compute"_compute.html command
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ptm/atom = style name of this compute command
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structures = structure types to search for
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threshold = lattice distortion threshold (RMSD) :ul
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[Examples:]
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compute 1 all ptm/atom default 0.1
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compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15
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compute 1 all ptm/atom all 0 :pre
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[Description:]
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Define a computation that determines the local lattice structure
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around an atom using the PTM (Polyhedral Template Matching) method.
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The PTM method is described in "(Larsen)"_#Larsen.
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Currently, there are seven lattice structures PTM recognizes:
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fcc = 1
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hcp = 2
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bcc = 3
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ico (icosahedral) = 4
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sc (simple cubic) = 5
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dcub (diamond cubic) = 6
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dhex (diamond hexagonal) = 7
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graphene = 8 :ul
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The value of the PTM structure will be 0 for unknown types and -1 for atoms not in the specified
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compute group. The choice of structures to search for can be specified using the "structures"
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argument, which is a hyphen-separated list of structure keywords.
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Two convenient pre-set options are provided:
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default: fcc-hcp-bcc-ico
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all: fcc-hcp-bcc-ico-sc-dcub-dhex-graphene :ul
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The 'default' setting detects the same structures as the Common Neighbor Analysis method.
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The 'all' setting searches for all structure types. A performance penalty is
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incurred for the diamond and graphene structures, so it is not recommended to use this option if
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it is known that the simulation does not contain these structures.
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PTM identifies structures using two steps. First, a graph isomorphism test is used
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to identify potential structure matches. Next, the deviation is computed between the
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local structure (in the simulation) and a template of the ideal lattice structure.
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The deviation is calculated as:
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:c,image(Eqs/ptm_rmsd.jpg)
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Here, u and v contain the coordinates of the local and ideal structures respectively,
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s is a scale factor, and Q is a rotation. The best match is identified by the
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lowest RMSD value, using the optimal scaling, rotation, and correspondence between the
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points.
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The 'threshold' keyword sets an upper limit on the maximum permitted deviation before
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a local structure is identified as disordered. Typical values are in the range 0.1-0.15,
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but larger values may be desirable at higher temperatures.
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A value of 0 is equivalent to infinity and can be used if no threshold is desired.
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The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (e.g. each time a snapshot of atoms
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is dumped). Thus it can be inefficient to compute/dump this quantity
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too frequently or to have multiple compute/dump commands, each with a
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{ptm/atom} style.
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[Output info:]
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This compute calculates a per-atom array, which can be accessed by
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any command that uses per-atom values from a compute as input. See
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the "Howto output"_Howto_output.html doc page for an overview of
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LAMMPS output options.
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Results are stored in the per-atom array in the following order:
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type
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rmsd
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interatomic distance
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qw
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qx
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qy
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qz :ul
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The type is a number from -1 to 8. The rmsd is a positive real number.
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The interatomic distance is computed from the scale factor in the RMSD equation.
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The (qw,qx,qy,qz) parameters represent the orientation of the local structure
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in quaternion form. The reference coordinates for each template (from which the
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orientation is determined) can be found in the {ptm_constants.h} file in the PTM source directory.
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[Restrictions:]
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This fix is part of the USER-PTM package. It is only enabled if
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LAMMPS was built with that package. See the "Build
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package"_Build_package.html doc page for more info.
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[Related commands:]
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"compute centro/atom"_compute_centro_atom.html
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"compute cna/atom"_compute_cna_atom.html
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[Default:] none
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:line
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:link(Larsen)
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[(Larsen)] Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
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