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atoms writes a list of atomic coordinates for any crystal given
its crystallographic information. The list will be sorted by radial
distance from an atom chosen as the central atom. atoms also
estimates the bulk absorption and density of the material and various
corrections to XAFS data due to experimental effects.
atoms runs from an input file, which uses keywords to specify the
input parameters. The code requires a file called atoms.inp
.
Because some operating systems are case sensitive the code will search
for ATOMS.INP
if atoms.inp
is not found. The output is a
text file that can serve as the input file for feff. This file
will run feff5 or feff6 but not feff3 or feff4.
atoms.inp
must contain all the data necessary to uniquely specify
the crystal. The information that the program requires is:
- The Hermann-Maguin or Schoenflies notation for the crystal space
group. The notation conventions are slightly modified to work with a
keyboard. This document lists all 230 groups as recognized by the
program.
- The non-redundant, non-default cell axis lengths and angles
between the axes.
- The two letter symbol and cell coordinates of each unique
atom. The definition of unique atom is an atom occupying a unique
crystallographic site. Sodium chloride (NaCl) has two unique atoms
that must be specified. In Lead Titanate (PbTiO3), for example,
there are two unique oxygen sites, so four unique atoms must be
specified. One of the atoms must be chosen as the central atom.
Usually this data can be taken directly from the crystallography
literature. When confusion arises, consult The International
Tables of X-Ray Crystallography. This is the standard by which
the program was written.
Chapter 3 should be read carefully. That chapter explains all of the
conventions necessary to specify crystallographic information in
atoms. This is a wonderful program in that it quickly generates
a list of atomic coordinates for an arbitrarily complicated crystal.
It is an awful program in that it requires you, the user, to speak its
language. There are numerous quirks and limitations to the algorithms
that interpret unit cell structure. Much error checking is included
in the code. If atoms finds something in the input file that it
does not like, it should give a useful run-time message.
The output is a file that can be used to run feff, the ab
initio multiple scattering XAFS code written by Rehr and
Zabinsky. The atom positions are organized into a list in the format
read by feff. atoms makes reasonable guesses for several
other inputs to feff. The feff.inp
file generated by
atoms will run feff to completion.
atoms has been extensively tested, but is not guaranteed to be
free of bugs. If you are displeased with the result of a run and you
have followed all of the instructions and hints in this document, then
you may have found a bug. To report your bug, first capture to a file
all screen messages from the run with the suspect input file. Send
the screen messages, the input file, and any output files to the
author. Also tell what kind of computer you are using and which
Fortran compiler you used to make the executable. You will find the
author's e-mail address on the title page of this document. His
postal address, phone number and fax number are:
Bruce Ravel
University of Washington
Department of Physics
Box 351560
Seattle WA, USA, 98195
phone: (206) 543-0435
fax: (206) 685-0635
Please note that the author greatly prefers to receive bug reports by
e-mail. Electronic communication allows for the quickest and most
convenient respose to a problem. Call or fax only in an unusual
situation or if electronic communication is impossible.
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