File Types

ATOMS uses several different types of auxiliary files, with different extensions.

Structure data files (.str). These hold the information on individual structures. The Open, Save and Save As commands in the File menu of the Graphics window pertain to these files.

Internal files. These are for ATOMS internal use and should not normally be modified by the user (but see section IV-8 of instructions for special cases). SCRPTR is the main start-up file which saves current settings. DEFAULTS saves default display variables for use with the New command. PPLOT contains data on pen plotters. CPATOMS.HLP [Windows] or ATOMS HELP [Macintosh] is the help file, which is in condensed format and not modifiable by the user. CIFDIC.SHT is the (shortened) dictionary file used when importing CIF files.

Space-group file. The file HALL.DAT contains space-group information.

Scattering factor file. The file SCATFAC.DAT contains the X-ray scattering factor data for neutral atoms in the exponential form as given in the International Tables, Vol. 4, for use in the Powder and Precession diffraction options (Display menu). This file may be modified to use other scattering factors (e.g. for ionized atoms). The scattering factors are keyed by sequence number as read from this file to the atom type. There is a maximum of 100 scattering factors.

Cartesian symmetry files (.sym). These contain Cartesian point-symmetry matrices generated by the auxiliary program SYMGRP.

Palette files (.pal). These contain RGB values for two 16-color palettes which (a) form the basis for 8-bit (256-color) palettes; and (b) are used to convert PC-DOS color numbers to RGB values. They can be modified, read and written with the Palettes commands in the Settings menu.

Atom parameter input files (.inp). These are files supplied by the user, containing at least the atom labels and coordinates, and optionally other parameters. They are read in through the Input Atoms dialog in the Input1 menu, not the Open command in the

File menu (Startup) or File menu (Graphics).

Atom parameter default file (ELEMENTS.ION or ELEMENTS.COV). This contains default atom types, radii and colors for use when reading in atom parameters from.inp files. It can be modified by the user to give the desired parameters. By default,

ELEMENTS.ION contains standard ionic radii and ELEMENTS.COV contains standard covalent radii.

Radius values for bonds. The RADII file supplies values for generating input bonds. It

also has index values for each element, which optionally may be used avoid superfluous or impossible bonds. The values currently used are 1 for cations, -1 for anions, 0 for

"non-metals", and 3 for inert (rare gases). At the time of generating input bonds, the values for the two candidates (input atoms) are added together, and pairs with absolute values greater than 1 are rejected.

Imported data files. These include the following. These files types are sometimes given arbitrary extensions, but any filename can be opened. (1) CCDC FDAT files (.fdt). (2) SHELX refinement input files (.ins). (3) CIF - Crystallographic Information Files (.cif).

(4) DBWS/LHPM Rietveld refinement files (.dbw and.lhp). (5)

Inorganic Crystal Structure Database (ICSD) files (.ret and.cry). (6) ORTEP data files (.ort). (7) XTLVIEW structure display files (.xtl). (8) VIBRAT motion files (.mot). (9)

Protein Data Bank files (.pdb). (10) RIETAN Rietveld files (.xyz). (11) GSAS Los Alamos program system files (.exp). (12) American Mineralogist structure database files (.amc). (13) FULLPROF refinement files (.pcr). (13) Free-form (.inp) files.

Text output files (.atd). These contain the input to and/or results of the ATOMS calculations. The file infile.ATD contains output of the atom-locating calculation on the structure file infile.STR, such as atom locations, atoms in bonds and polyhedra, bond length and angles. INPUT.ATD lists the input data. GENATOMS.ATD lists the Cartesian coordinates of all the generated atoms in their current orientations.

FACES.ATD lists attributes of the current boundary and/or display crystal faces.

TOTALS.ATD gives totals of various types and the current maxima for these values.

BONDS.ATD gives bonds and angles around each or all input atoms. These files may all appear in a Text window, and are saved independently of the ATOMS structure data files.

Graphics output files. ATOMS can write graphics output files of various types:

encapsulated PostScript files (.eps); HPGL vector files (.pgl), 3D VRML files and Windows only

----raster files (.bmp,.pcx,.tif,.png); and Windows metafiles (.wmf or.emf).

Macintosh only

----PICT files (.pic) in either Picture (metafile) or bitmap format and.png raster files.

End Windows/Mac only

----File Locations

ATOMS expects to find certain files in the "home" directory, which is the directory containing the ATOMS program file (CPATOMS.EXE for Windows). These files are

SCRPTR, DEFAULTS, PPLOT, SPCGRP.DAT, CPATOMS.HLP, ELEMENTS, HALL.DAT, CIFDIC.SHT, RADII, SCATFAC.DAT and palette (.PAL) files.

If you are using Cartesian symmetry files (.sym), they should be in the same directory ("data" directory) as the structure file. The data directory is reset whenever you read or write a structure file (.str). Most output files, including EPS, raster, HPGL, metafiles and calculation output files (infile.atd), will be written to the data directory. However, the data files (.atd) from the List... options in the File menu are written to the home

directory, to avoid cluttering the disks. To save these files permanently, use Save As to give them new names in the directory of your choice.

When reading files, the extensions are not mandatory, and you can always use a different extension when saving a file, or specify "all files" when browsing or searching for a file.

Macintosh only

----File and Creator Types

Most output and data text files have file creator 'ATOM' and file type 'TEXT'. The main ATOMS data files (.STR) have file type 'ATDT', to prevent accidental damage by editing with a word processor. However, you can can change the file type to 'TEXT' with a utility program if necessary. Only files with creator 'ATOM' and extension.STR will be opened as data files by ATOMS when they are double-clicked.

Files from previous versions of ATOMS may have different creator and file types.

End Macintosh only ----4.12 Frames

With printed and pen-plot output, you have a choice of using the full page, or confining the output to a frame. For Raster Files and Metafiles or PICT files (File menu) output always goes to a frame.

If you are using the Universal or Maximize Each View scale modes (Scaling dialog in the Input2 menu), the image is scaled to fit in the frame. If you are using the Fixed scale mode, the image is clipped to the frame.

In printed and pen-plot output, the frame can be positioned on the page; the offset gives the displacement of the upper left corner of the frame from the upper left corner of the page.

In some cases, you can choose the units for the size and offset of the window; either inches, centimeters or dots (pixels), and you may also be able to specify the nominal dots

per inch or centimeter. The units setting is independent of the overall choice of inches or centimeters in the Preferences dialog in the Settings menu.