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.

• How to use this archive
• Output formats
• Format of the atoms.inp files
• Advanced searching
• How to donate data or submit bug reports
• How to get your own copy of ATOMS and FEFF

• search the Atoms.inp Archive
• ATOMS home page
• FEFF home page
• UWXAFS home page
• Other Useful Tools from the UWXAFS project

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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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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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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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.

[ top of document | table of contents | other useful links | search the Atoms.inp Archive ]

[ top of document | table of contents | other useful links | search the Atoms.inp Archive ]

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