• NAME
• VERSION
• SYNOPSIS
• DESCRIPTION
• COMMAND LINE SWITCHES
• CIF FILES
• CONFIGURATION AND ENVIRONMENT
• DEPENDENCIES
• BUGS AND LIMITATIONS
• AUTHOR
• LICENCE AND COPYRIGHT

NAME

atoms - Convert crystallography data to a feff.inp file

VERSION

This documentation refers to Demeter version 0.9.26.

SYNOPSIS

  datoms [--output format] [--rmax #] [--cif --rec=#] [--wx] mydata.inp

If no input or CIF file is specified at the command line, atoms.inp in the current working directory will be used, if available.

If the --wx flag for running the GUI is given, all other command line arguments are ignored.

DESCRIPTION

This reads an atoms input file or a CIF file (CIF is not working at this time) and writes the results of a calculation using that crystallography data to standard output. Typically the output is a feff.inp file, but it may also be a summary of the space group, calculation using tables of X-ray absorption coefficients, etc.

COMMAND LINE SWITCHES

By default, an input file for Feff6 is written. This and some aspects of the feff.inp file can be overridden from the command line.

--wx

Run the wxWidgets-based GUI (ignoring all other command-line flags).

--output=format or -o format

Specify the output type. Must be (case-insensitive) one of

feff6, 6

Write a feff.inp file for feff6.

feff8, 8

Write a feff.inp file for feff8.

feff85test, 85

Write a feff.inp file for use with the feff85exafs testing framework.

spacegroup

Write a file with information about the space group.

p1

Write the crystal structure as an atoms input file using the P1 space group, i.e. the fully decorated unit cell.

absorption

Write a file with the results of calculations based on the crystal structure and tables of X-ray absorption coefficients.

atoms

Write the input data as an atoms input file (mostly useful for CIF to atoms.inp conversion)

xyz

Write the cluster in the simple XYZ molecule format.

alchemy

Write the cluster in the alchemy molecule format.

overfull

Write the contents of the unit cell in Cartesian coordinates with all atoms near a cell wall replicated near the opposite cell wall. This is written in the form of an XYZ molecule format file. The purpose of this output type is generate nice figures of unit cells with decorations on all the corners, sides, and edges.

--rmax=# or -r #

Specify a cluster size from the command line.

  datoms -r 5.2 mydata.inp

CIF FILES

Reding CIF files requires the use of one or two additional command line switches:

--cif or -c

This flag indicates that the file given on the command line is a CIF file rather than an Atoms input file. No effort is made to figure out whether your file is CIF or Atoms input -- it is up to you to correctly identify it using this command line flag.

  datoms --cif --rec=2 my_cif_file.cif

--rec=#

If your CIF file is a multi-record file, use this switch to indicate which record to import. The default is to read the first record, so this switch does not need to be used for a single-record file.

Note that a CIF file does not identify a central atom. Demeter's CIF importer assuems that the heaviest atom in the material is the absorber. As a command line utility, there is no convenient way to unambiguously identify the central atom. Probably the best solution is to use this script to convert the CIF file to an atoms input file, edit that, then rerun this script to generate the Feff input file.

CONFIGURATION AND ENVIRONMENT

See Demeter::Config for a description of Demeter's configuration system. Atoms uses the atoms configuration group.

DEPENDENCIES

The dependencies of the Demeter system are in the Build.PL file.

BUGS AND LIMITATIONS

See Demeter::Atoms for bugs and limitations of the underlying libraries.

Missing command line switches:

• -v and -h

• ipot style

• feff7, overfull

• OpenBabel integration

• snarf atoms.inp files from Matt's database or CIF files from the web

Please report problems to the Ifeffit Mailing List (http://cars9.uchicago.edu/mailman/listinfo/ifeffit/)

Patches are welcome.

AUTHOR

Bruce Ravel (http://bruceravel.github.io/home)

http://bruceravel.github.io/demeter/

LICENCE AND COPYRIGHT

Copyright (c) 2008-2018 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.