 |
Most
Xtal calculations are initiated, and
controlled, from a input line file usually known as the
Xtal employs two basic file types: line (character) and binary.
Line
files are composed of ascii text which may be
manipulated with a normal text editor. The two principal
line files are the line
input file (
compid.dat) and
print file (
compid.lst). The former contains data
that determines which and how calculations are performed,
and the latter is the printed results of these
calculations.
Xtal uses other line files for certain
calculations. These include a
punch file,
formatted sequential files,
formatted direct-access files, various
ancillary database files (e.g.
Binary files are used extensively as working files (ie. intermediate files for exchanging within, and between, calculations), and to archive certain types of data. Binary files are more efficient than line files for certain operations because of their compactness and because they do not require decoding or encoding when data is extracted from or transferred to computer memory. A binary file is often referred to in Xtal documentation as a ' bdf ' (binary data file).
Xtal binary files are divided into two
categories:
archive and
auxilliary.
Archive bdf's are used as
an archive record of accumulated crystal structure data.
These files are updated as the analysis progresses. For
example,
Auxilliary bdf's are used to transfer data from one calculation to another. They are created by a calculation for a specific data exchange purpose. Electron density maps are typical of data stored in an auxiliary file. The actual format of these files is similar to the archival files, but their contents are only known to the programs that write or read them. These are dicussed in detail later. The convention for filename construction for all
Xtal files is normally
<compid>.
<ext> where
compid is the compound identification
code (maximum of six characters), and
ext is the extension code (three
characters). The compid code is defined by the user at the
start of the input commands with the line "
The concept of an
archive bdf has been introduced
above. Most
Xtal programs employ two archive
binary files; one for input and one for output. These
have filename extensions
Xtal provides a procedure for
automatically saving the latest archive bdf. This is
referred to as the
master file option. When this is
switched
on the most recent archive binary
file (
The master file option is set during installation
via the definition of the the macro
masterfile:. This option may also be
set at run time using the
master line (described
in 2. below). If this option is switched off, the user is
responsible for ensuring that at the start of a
calculation the latest archive binary file is labelled
The need for master archive files will depend on
local applications and on the local computing
environment. If you are an expert user, or there is a
shortage of disc space, or there are very large files,
the extra time and space needed for master file
operations may be unacceptable. Where
Xtal is being applied to many
analyses simultaneously this option should be useful to
ensure that the latest archive file is retained after
each run. It is recommended that master file be made the
default condition (i.e. set
masterfile: to
yes: on installation) and users
switch it off with a
Unlike the archive files, auxiliary files are only
used for the storage of intermediate data. Programs which
write auxiliary files assign filename extensions to files
according to their contents. Files with the extensions
Xtal line files may be free format or fixed format. Character data is case insensitive (i.e. upper- or lower-case alphabetical characters are treated identically except for atom site labels). A field is a string of contiguous characters delimited by a blank. Every input line must start (in column 1) with a line identification code. This requirement may be overridden with the setid system command (see the setid description in System). The identification code constitutes field 0 of the input line and must terminate with a blank. In free format input mode subsequent fields are numbered from left to right, 1, 2, 3, etc. If the system lines field and/or order are entered, the widths and/or the numbering of the input fields may be specified by the user (the field and order descriptions are in 2. below). Note that the sequential numbering of fields should not be confused with the order that data is entered in a given program. For many calculations data may be entered in any order. This is clearly indicated in the User's Guide when no field numbers are attached. This is usually the case when numerical data follows control codes (e.g. see the reset line described in System). There are three distinct types of input field; the numerical field, the alphanumerical field, and the void field. They are defined as follows:
Numerical field: a set of contiguous
characters composed of the integers
Alphanumerical field: a set of
contiguous characters containing at least one alphabetic
character (
Void field: a field that contains only a blank. Internally this type of field is identified as a floating-point word with a value defined by the macro voidflg:. The default value for voidflg: is -4.0+20 -- this value must not be used for any other purpose. The digraph
param 5 $5 9
The digraph
map 2.6 *6 C $5 1 .31
will result in the number
map *6 C *1 2.6 *12 1 .31
The character colon (:) is used to signal the end of input fields. Note that a colon in column 1 of a line implies that the line is to be ignored. The colon allows additional unprocessed information to be placed on the input image. For example, the image containing the following line is processed only through to the field containing .035.
atom C12 .5 .6 .9 .035
:pig
|
|
