ATOMS Output Files

The main purpose of ATOMS is to write input files for FEFF. However the input files for FEFF6 and FEFF8 are slightly different. Fortunately ATOMS comes with several predefined output file types, including FEFF6, FEFF8, and several others. Even better, ATOMS uses flexible template files mechanism to structure its output files. Thus you can modify the existing output files types and even create entirely new ones. Complete details for doing so are given in Appendix .

The output file types that come with the ATOMS distribution are:

feff6

This produces an input file the is suitable for running any of versions 5, 6, or 7 of FEFF.

feff8

This produces an input file the is suitable for running FEFF8.

alchemy

This produces a file of atomic coordinates in the alchemy format, and so can be used by many ball-and-stick viewers as input data.

xyz

This produces a file of atomic coordinates in the xyz format, and so can be used by many ball-and-stick viewers as input data.

pdb

This produces a file of atomic coordinates using the Brookhaven Protein Data Bank format.

p1

This produces an input file suitable for running ATOMS but with a description of the unit cell using the P 1 space group and the entire contents of the unit cell. This means that all of the unique coordinates have been expanded and all lattice constants and angles are explicitly specified. This list reflects the stoichiometry of the crystal.

unit

This produces a description of the unit cell which I refer to as ``overfilled''. This means that atoms which are located near the walls, edges, and corners of the unit cell are copied to the other side of the cell. For example, an overfilled cell for perovskite EuTiO₃ would would have an Eu atom at each of the eight corners, an oxygen atom on each of the six walls, and a Ti atom in the center of the cube. This list does not reflect the stoichiometry of the crystal.

symmetry

This file type displays a list of the symmetry operations of the chosen space group. An example is shown in Figure .

geom

This file produces a 'geom.dat' file suitable for use with FEFF's pathfinder. Note that this output file is only correctly made for orthogonal space groups. Unless you know exactly what this file is used for by FEFF, it is unlikely that you actually need it.

gnxas_cry

This writes a file containing input data for the GNXAS CRYMOL program using the ``CRY'' format.

gnxas_sym

This writes a file containing input data for the GNXAS CRYMOL program using the ``SYM'' format.

formulas

This file produces a fie containing formulas for the positions of every atom in the cluster. This is a test bed for a future interface between ATOMS and IFEFFIT.

atoms

This rewrites the input data in the form of a proper ATOMS input file. This is primarily used by TkATOMS and WebATOMS for saving input data.

absorption

This writes a report of the results from the Absorption notecard in TkATOMS.

dafs

This produces the output from the DAFS calculation made by 'dafs.pl' or the DAFS notecard in TkATOMS.

powder

This produces the output from the powder different calculation made by 'powder.pl' or the Powder notecard in TkATOMS.

molecule6

This writes a FEFF6 input file for a molecule. It is used by the Molecule notecard in TkATOMS.

molecule8

This writes a FEFF8 input file for a molecule. It is used by the Molecule notecard in TkATOMS.

template6

This writes an empty template for a FEFF6 input file.

template8

This writes an empty template for a FEFF8 input file.

test

This file produces a diagnostic file useful for testing ATOMS and for submitting bug reports.

The way of selecting output file types is discussed in detail for the command line, Tk, and Web versions of ATOMS in Chapters , , and . In brief, the output file type can be selected in an ATOMS input file using the output keyword. In the command-line version of ATOMS, there are command-line switches for selecting the output type. In the Tk and web versions there are menus for selecting the file type.

Although the output file types described above are the only ones distributed with ATOMS, there actually are no hardwired output types in the ATOMS source code. All output files are generated from external files called ATOMS template files, or atp files. ATOMS reads the appropriate atp file and using the encoding information contained in it to generate the appropriate output file.

Because all output files are generated from external files, the user can easily modify the existing output files types or even create entirely new ones. On a multi-user system, you may keep a library of modified or newly created atp files in your personal ATOMS directory.^4.1 This directory is searched before the system-wide directory, so when a personal atp file has the same name as a system-wide atp file, the personal one will be used by ATOMS.

The best way to modify one of the standard output file types is to copy the atp file from the 'atp/' directory in the ATOMS installation location to your personal ATOMS directory. On systems like the Macintosh and Windows 9x which do not have personal disk space, just edit the atp files in the ATOMS installation.

The format of the template files is described in detail in Appendix , and Section  answers some common questions about using atp files and controlling the output of ATOMS.