# WebAtoms Help

This page provides quick, on-line help for using WebATOMS. For complete documentation of ATOMS and its algorithms, please check out the ATOMS documentation page.

This page is basically just a big long list of the keywords in ATOMS with a few words of explanation. Just enough to get you going.

- Overview
- A, B, and C
- Alpha
- Beta
- Central Atom
- Edge
- Element
- Gamma
- Output Types
- Rmax
- Shift
- Space Groups
- Site Tag
- Titles
- X, Y, and Z coordinates

### Overview

Run Atoms button

  Click this button to submit your crystallographic data.

Clear button

  Click this button to start over with a fresh page.

Reset button

  Click this button to reset everything to its starting values. This is most useful when modifying an input file read in from the Atoms Database.

Adding more atom positions

  At the bottom of the form is a space to indicate how many atom positions you need. Simply fill in the number and press the button marked "Do it!".

A, B, and C

  Fill in these text fields with the lengths of the unit cell axes. These should be numbers in Ångstroms. For many space groups, it is ok to leave some of these blank. For example, for the cubic groups, you only need to specify A. For hexagonal and trigonal groups, you need to specify A and C, but you can leave B blank. For low symmetry groups, you will, of course, need to specify all three.

Alpha

  Use this text field to specify the angle between the B and C axes. This is needed for rhombohedral groups in the rhombohedral setting, triclinic groups, and some settings of some monoclinic groups.

Beta

  Use this text field to specify the angle between the A and C axes. This is needed for triclinic groups, and the standard settings of monoclinic groups.

Central Atom

  Choose a site from the list of unique sites to be the central atom of your cluster by selecting the radio button in the row containing that site.

Edge

  Select a symbol from the popup menu. This is the symbol of the absorption edge to use when ATOMS writes a FEFF input file. If you leave the popup widget blank, then ATOMS will choose an edge for you. If your central atom is lighter than Cerium (Ce, number 58), the K edge will be used. Otherwise the L3 edge is used.

Element

  Specify the atomic species occupying a site by entering its one- or two letter symbol in this column.

Gamma

  Use this text field to specify the angle between the A and B axes. This is needed for triclinic groups, and the certain settings of some monoclinic groups. For hexagonal, trigonal, and rhombohedral groups in the trigonal setting, ATOMS will set this to 120 for you.

Output Types

  Use this popup menu to select the type of calculation you would like ATOMS to make. You choices include input files for FEFF6 and FEFF8, a couple of common file formats for ball-and-stick viewers (alchemy and xyz), a list of the entire contents of of the unit cell (p1.inp), a non-stoichiometric description of the unit cell (unit.dat), some calculations involving tables of absorption coefficients (absorption), and two input formats for the GNXAS' CRYMOL program.

Rmax

  This defines the size of the cluster to be calculated by ATOMS. It should be a positive number in Ångstroms. It can also be left blank in which case ATOMS will choose a sensible default.

Shift

  Some space groups are commonly referenced to a choice of symmetry positions. If your source of crystal data references the structure to a symmetry position other than the one that ATOMS uses, you will need to specify the vector by which all the unique sites ill need to be shifted so that the calculation will be made correctly. In most situations it will be clear that you will need to use a shift vector because the atom list in the FEFF input file will be wrong and WebATOMS will print a little note to you browser.

Site Tag

  Specify a unique label for a site in this column. These can be up to 10 characters long. These tags are used to differentiate between different sites which contain the same atomic species.

Space Group

  Use this text field to enter the symbol for the space group of your crystal. ATOMS is capable of interpreting lots of different things as a space group symbols, including Hermann-Maguin symbols, Schoenflies symbols, numeric indeces from the International Tables, and some special words like "fcc" and "diamond". You have a lot of latitude as to how you write the symbols. With only a few obscure exceptions, spaces can be used in writing the space group group symbols or they can be omited. "pm3m" means the same thing as "P m 3 m".

Titles

  Use this text field to enter any user-defined title lines that you would like to have printed in the output of the ATOMS calculation.

X, Y, and Z coordinates

  Specify the fractional coordinate of a site in one of the cell axis directions. You may use simple fractions such as "1/2".

### Features of ATOMS

Although WebATOMS is pretty handy at generating input files for FEFF and other interesting kinds of files, there are many features of ATOMS which are only available in the version that you download and run on your own computer. Here is an incomplete list of features. Perhaps this will entice you to try it out!

1. Fine grained control over the appearence and content of the output files and the ability to make entirely new kinds of output files.

2. Dopants can be used.

3. Other functionality, such as calculations using tables of absorption coefficients, DAFS simulations, powder diffraction simulations (coming soon), and conversion of molecule files into FEFF input files.

4. The ability to have ATOMS communicate with you in languages other than English. Currently supported are French, Spanish, and German.

5. Object oriented perl libraries which you can use in your own programs.

Modified: 3-Feb-2006