VIBRATZ uses many types of files for data storage, input and output. With the exception of the.mds atomic-motion file, these are all text or ASCII files. Where file extensions are given, this is only a preference - it is always possible to specify "all files (*.*)" when opening a file, or to override the extension when writing.
Main data storage files (.VBR, .VIB). The data for each VIBRATZ problem or structure are contained in a text file with extension .VBR. After changing any parameters (mostly in the Input and Forces dialogs), it is necessary to save these files with the Save or Save As commands in the File menu or the buttons in the Control Window, although if a file has not been saved before you read in a new one or quit the program you will be asked if you want to save it.
Input files for the old Fortran version (called VIBRAT) should have extension .VIB. These are read with the same Open command (File menu) as the currect .VBR files. However, you cannot save a file of type .VIB - once such a file has been read in the extension is changed to .VBR.
Setup files. VIBRATZ uses a setup or preferences file called SCRPTR, which is in the same folder as the VIBRATZ application. This contains operating parameters which are not specific to individual structures. Parameters which are specific to individual structures and which are saved in the main data (.vbr) file, but which are not absolutely intrinsic to the structures, i.e. pertain to the way the structure is displayed or calculated, are also saved in the file DEFAULTS. This file is read whenever VIBRATZ is started up, and it is saved with the Save Defaults command in the Settings menu. It may be re-read at any time, with the Read Defaults command in the Settings menu, to replace the current values. The SCRPTR and DEFAULTS files are actually replaced after the first startup by a single user- and platform-specific file.
ELEMENTS.DAT file. This file is used by VIBRATZ for two functions: it is read on startup to supply the default Atom Type List, which gives standard atomic numbers, weights and charges. It is also read when a data file from other software is imported, to assign atomic numbers (type numbers) to input atoms based on standard elemental symbols. Each line of this file refers to one element or atom type and contains the following fields: the atomic number or type number; the one- or two-letter symbol; the red, green and blue components, as numbers from 0 to 255, of the atom color (for the Atoms graphics window or output when in color), the gray shade as a number from 0 (white) to 15 (black) (for the Atoms graphics window or output when in black-and-white); the atomic weight; and the formal charge. There must be 102 lines or atom types, but otherwise the values may be edited as desired. Following are the first four lines from the standard file:
1 H 0.32 148 148 148 8 1.00797 1.000
2 HE 1.50 0 0 255 6 4.0026 0.000
3 LI 1.52 255 0 255 6 6.939 1.000
4 BE 1.11 255 0 255 6 9.0122 2.000
Output files. Files with extension .VBD, when opened by VIBRATZ, are displayed in a Text window, which has its own menu bar with standard commands for text editing, printing, etc. VIBRATZ itself generates some files of this type, including the main output file in which are printed the results of the calculation. This file is given the name infile.VBD, if infile.vbr is the name of the main data file for this problem. The Coordination option in the Input Atoms dialog (Input menu) also writes a text file called BONDS.VBD. Both of these files are displayed in a text window as soon as they are written.
Special input files. VIBRATZ may need to read several types of files to get certain special types of data. Cartesian symmetry files, with extension.SYM provide symmetry for non-crystallographic point groups. Instead of using valence forces, a matrix of Cartesian atomic forces may be read in, and conversely, transformed valence forces may be written as a matrix of Cartesian atomic forces - files of this type are given the extension.CAR. Lists of atomic coordinates, with labels, may be read in with.INP files. A complete set of valence force specifications may be written and reread; this type of file has extension.FRC. The observed wavenumbers may be read in in a text file with extension.FRQ.
Structure import files. VIBRATZ can import structure data from many different program systems. The file extensions are too numerous to mention and are sometimes not exclusive.
Special output files. Two special types of output file are written by VIBRATZ. The spectrum data file, with extension.SPC, contains data on the calculated intensity and polarization components of the frequencies, primarily for use in plotting spectra. VIBRATZ itself will produce plots of spectra, so these files are not needed unless a specialized plotting program is written. The atomic-motion data file, with extension.MOT, contains the basic data on location of atoms in the molecule or unit cell, plus the displacements of atoms in each mode. This is intended specifically for the program ATOMS, which can give a more sophisticated representation of the structure.
Binary atomic-motion files. When atomic-motion plotting is selected in VIBRATZ, the atomic motions are saved in a binary file named infile.MDS, if infile. VBR is the name of the main data file. This allows quick recovery of the data for each mode. Also, when atomic-motion data are transmitted to ATOMS using a.MOT file, ATOMS constructs an identical.MDS file. ATOMS can read.MDS files written by VIBRATZ, which allows updating of the atomic motions without disturbing the display characteristics for the structure which are set up in ATOMS.
Standard graphics output files. VIBRATZ can write graphics output files for the spectrum and atomic-motion plots in several standard formats, including both.WMF and.EMF metafiles, and .BMP, .PCX and .TIF raster files (Windows) or Pict files and .PNG raster files (Macintosh)
Alphabetical list of file extensions used by VIBRATZ
.CAR Input or output file containing a force field in terms of the Cartesian coordinates of the atoms. Specified in the Cartesian forces option in the Control Window, when Cartesian input forces are to be used instead of valence forces; or in the Write Cartesian File option in the Forces menu, when writing a file.
.DAT The ELEMENTS.DAT file, containing standard data on the elements. This file is read automatically by VIBRATZ when needed.
.FRC File containing valence force specifications, which can be written and read with commands in the Settings menu.
.FRQ File containing observed wavenumbers. Read through the Observed Wavenumbers dialog in the Input menu.
.MDS Binary file containing the atomic motions for each mode. This may used by the program ATOMS as well as the Atoms window in VIBRATZ.
.MOT Text output file containing atom locations and motions in each mode, for export to the structure-display program ATOMS.
.VBD Text output files. These are displayed in text windows on screen. Infile.out is written during every calculation and contains the printed results. BONDS.OUT contains the result of the Coordination option (Input Atoms dialog, Input menu). These files had the extension .OUT in earlier versions of VIBRATZ.
.SPC Output file containing intensities and polarization data for each mode
.SYM Input file containing symmetry information for non-crystallographic point groups
.VBR Main data file, containing complete information on the current problem.
.VIB Old data file from VIBRAT (Fortran precursor to VIBRATZ)
------Macintosh only --------------------
All macintosh files have two identifying 4-character strings, the file type and the creator signature. The file type for all files listed above, with the exception of binary .MDS files is "TEXT". The creator for main data files (.VBR) and for text output files (.VBD) is "VIBR". The assignment of creator "VIBR" to the .VBR and .VBD files allows startup of VIBRATZ by double-clicking on these files. The creator for other types of text files is "ttxt"; double-clicking on these files will start up the standard Macintosh word-processing program TeachText or SimpleText.