The Atoms.inp Archive

This Archive is a collection of crystallographic data for use in XAFS analysis. The crystallographic data is stored as atoms.inp files, which contain all the information necessary to describe the crystal, and can be used by the program ATOMS to generate feff.inp files. These files can then be used by the FEFF program to calculate a theoretical XAFS spectrum for the crystal. Click here to search the Atoms.inp Archive.

This archive exists because it can take a considerable amount of time to locate a suitable reference for a model structure to use for making theoretical XAFS standards. Even then, references sometimes give non-standard or incomplete crystallographic notation that ATOMS has difficulty interpreting. All of this means that getting a reliable atoms.inp file can take quite a bit of effort. With enough people using ATOMS (it is distributed with FEFF), much of this work is being unnecessarily repeated. We hope that this collection of well-documented and well-tested atoms.inp files will eliminate much of the work in creating theoretical XAFS standards from FEFF.

The collection currently has more than 200 crystal structures, and we're planning on adding more. Submissions of any crystallographic data and suggestions for improvement of any of the existing data are welcome.


Table of Contents

More information is available on these topics:

Other Useful Links


How to use the archive

The archive contains many atoms.inp files, most of which you're probably not really interested in. You can get a list of all the files in the archive, or (better yet) a list of files that match some search pattern. You can then select one of these listed files, and retrieve the data in a few different formats. Searching the archive is pretty simple, and you can probably figure it out faster just by trying it, rather that reading all of this.

To do a search, type in a string in the space provided, pick one of the "search fields" to tell the program what to search for, and click on the List Matching Files button. You can perform searches for the string you type on the following parts of the files:
Atomic Sites This will match any of the atomic symbols in the unit cell, and is probably the most useful kind of search.
Example: typing "Pb" in the space provided will return a list of structures that contain lead.
Compound Name This will match any string in the "name" line of the atoms.inp files, which contains compound names, mineral names, and/or names of similar structures.
Example: typing "cassiterite" in the space provided will return a list of structures that are similar to the cassiterite structure of SnO2.
Space Group This will match any string in the "space" line of the atoms.inp file, containing the Hermann-Maguin notation for the space group.
Example: typing "i" in the space provided will return a list of body-centered structures.
All Title Lines This will match any string in the "title" lines of the atoms.inp files. In addition to the Atomic Sites and Compound Name information, these lines will include literature references, and other notes about the structure.
Example: typing "wyckoff" in the space provided will return a list of structures that were taken from the book Crystal Structures by Wyckoff.
To choose which of these kinds of searches to do, select which of the four search fields to search.

After clicking on List Matching Files, you will see a list of matching files. At this point you can pick one of the files (click on the little diamond-shaped button next to the file name). At this point you can also select the output format. Clicking on the Get File button will send to the screen the selected output format for of the selected structure.

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Output formats

Three formats that can be returned by the Archive, and can be chosen either before or after the search is done. The three formats are:
atoms.inp The atoms.inp file from the archive will be sent to the screen.
feff.inp This will run ATOMS (version 2.46b) on the selected atoms.inp from the archive, and send the resulting feff.inp to the screen. Since the ATOMS version is fairly recent, the feff.inp should work well. The main drawback to doing this is that you may want to alter the atoms.inp from the archive before running ATOMS. An interactive form for editing an atoms.inp from the archive and then running ATOMS would probably help.
xyz format This will also run ATOMS on the selected atoms.inp from the archive, and then pass the output through a filter (a perl script called at2xyz ) to make an "xyz" format file. This is a fairly simple format (listing Atomic Symbol, and x,y,z coordinates for each atoms) that can be used by many molecular drawing programs to make a three-dimensional picture of the structure. Free programs to do this, such as Xmol or Rasmol, are available. For a more complete list, see the SINCRIS list of crystallographic software.

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Format of the atoms.inp files

The atoms.inp stored in the archive follow a fairly rigid format, which makes searching and reading the files easier.

Here's an example file:

title name:     Cadmium Carbonate (otavite)
title formula:  CdCO_3
title sites:    Cd1,C1,O1
title refer1:   wyckoff, vol 1, ch VII, p 362
title refer2:
title schoen:   D_3d^6
title notes1:   calcite structure
title notes2:   wyckoff gives "u  = ca. 0.25 "
title notes3:   wyckoff gives "r -3 c" which gives 12 near neighbors?
space  r 3 c
a    = 6.1306
alpha= 47.31667
rmax = 6.00
core = Cd1
atom
Cd     0.25000   0.25000   0.25000  Cd1 (2b)
C      0.00000   0.00000   0.00000  C1 (2a)
O      0.25000  -0.25000   0.00000  O1 (6e)
------

The title lines list "Compound Name" (this first line is the only one looked at for a Compound Name search), chemical formula, atomic sites (listing all sites in the unit cell, and used for an Atomic Sites search), literature reference, Schoenflies version of the space group symbol, and then some extra notes, if needed. An All Title Lines search will look at all these lines.

After the title lines, the space group is listed (in the Hermann-Maguin notation) on its own line. This line is used for a Space Group search. The next line contains the unit cell parameters (in Angstroms) a, b, and c. If b, and c are the same as a, they do not need to be listed. The unit cell parameters alpha, beta, and gamma (in degrees) are listed on the next line. If they have the trivial default values of 90, they do not need to be listed.

The next line contains the value of rmax (in Angstroms) used by ATOMS and written to feff.inp. Currently this value is always 6.0, which is a reasonable default -- I like it more than ATOMS default of twice the near-neighbor distance.

The central atom site is listed on the next line with the keyword core. This must be one of the Site Tags listed in the file (not atomic symbol -- see below), and by default it is the first one listed. Like rmax, this is something you may very well want to change.

The atom line denotes that the rest of the lines will contain Atomic Symbol, x, y, z, and site tag. Note that x, y, and z are the positions in the unit cell of dimension a, b, and c. This means that the order of x, y, and z need to be the same as a, b, and c.

The Site Tag gives a unique string to each of the sites in the unit cell. All the Site Tag's in the archived files consist of the Atomic symbol and an integer, usually as indicated by the literature reference.

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Advanced searching

If you're familiar with the Unix pattern matching program grep, and want to try some more sophisticated searching, read on.

The patterns you type are passed as regular expressions to perl, which then uses its own pattern matching abilities. These abilities are very similar to egrep, an extension of the standard grep. For example, searching the All title lines with the string
" zinc[{ }+sulf] "
will return all the files with "zinc sulfide" in the title lines. So would searching for "zinc sulf", by the way (though the number of blank spaces between "zinc" and "sulf" is more restricted). What makes this particularly useful is if you search for
" zinc[^{ }+sulf] ".
This will returns files that contain "zinc" and not "zinc sulf", eliminating all the files with "zinc sulfide" in the title lines and returning a smaller set of file, including pure zinc and zincite.

If there are enough (any) complaints about the "simple" search approach, this whole business will probably be changed.

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How to donate data or submit bug reports

To donate data, send me e-mail at newville@cars.uchicago.edu. The more complete the information you give me, the faster it will make it into the archive. The literature reference is especially important, so that any other user can check it and cite it when the time to publish rolls around. Having an atoms.inp that is known to run to completion and give reasonable outputs (like the right number of near-neighbors at the right distances) is also important.

If you think data in any of the files in the archive has wrong or out-dated information in them, please let me know what is wrong, and (hopefully) how to fix the problem. A "fixed" atoms.inp file (with a reference, of course) would be great. For crystal structures still being debated in the literature, I am willing to let any and all of the suggested structures be listed in the archive until proven wrong.

For bug reports about ATOMS itself, send e-mail to Bruce Ravel at ravel@phys.washington.edu.

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How to get your own copy of ATOMS and FEFF

To find out more about getting source code and binaries for both ATOMS and FEFF, see the FEFF home page. ATOMS is also distributed as part of the UWXAFS Analysis Package. Both FEFF and the UWXAFS Analysis Package require a license (and a modest licensing fee) to use.

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Acknowledgments:

This archive has been constructed with help from Susan Carroll, Julie Cross, Margaret Ebert, Daniel Haskel, Peggy O'Day, Bruce Ravel, and Glenn Waychunas. and with support from the Earth and Environmental Sciences Directorate at Lawrence Livermore National Laboratory.


Matthew Newville
CARS, Bldg 434A, APS
Argonne National Lab, 9700 South CASS Ave
Argonne, IL 60439
email:
voice:
fax:

newville@cars.uchicago.edu
(630) 252-0431
(630) 252-0443

[ CARS | Advanced Photon Source | Argonne Natl Lab | Univ of Chicago | UWXAFS Project ]