| Description | Perl tools for X-ray Absorption Spectroscopy |
Demeter::Feff::MD::LAMMPS - Role supporting LAMPPS output files
This documentation refers to Demeter version 0.9.26.
From email with Mike Demkowicz
The model is periodic in the interface plane and terminates in free
surfaces in the direction normal to the interface plane. The file
contents are:
row 1: a series of 11 numbers, the last of which is the number of
atoms in the model. The first ten numbers are just
placeholders and don't denote anything.
rows 10-12: the 3x3 matrix that describes the shape and size of the
simulation cell. The vectors that describe the edges of the
cell are the rows of this matrix. As you can see, the matrix
is diagonal so the simulation cell edges are orthogonal. The
x and y directions (first 2 entries) are parallel to the
interface plane. The z direction (3rd entry) is normal to the
interface plane, but since the model is not periodic in that
direction this length is not of great importance (the actual
bilayer thickness is about 80A). All lengths in Angstroms.
- row 19 onwards: these are the four entries you requested. Every
row corresponds to one atom. The first number is the atom
type, where 1=Cu and 2=Nb. The remaining three entries in
every row are the x, y, and z coordinates of each atom, again
in Angstroms. I've shifted the model so that the interface is
at z=0. All the Cu atoms have z<0 and the Nb atoms have z>0._clusterFills clusters attribute with a list-of-lists, each inner list containing the cartesian coordinates and atomic species of each item in the cluster at that time step. The outer list is only 1 item long, as this file does not contain a time sequence.
Demeter's dependencies are in the Build.PL file.
Please report problems to the Ifeffit Mailing List (http://cars9.uchicago.edu/mailman/listinfo/ifeffit/)
Patches are welcome.
Bruce Ravel (http://bruceravel.github.io/home)
http://bruceravel.github.io/demeter/
Copyright (c) 2006-2018 Bruce Ravel (http://bruceravel.github.io/home). All rights reserved.
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See perlgpl.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.