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Crystals ManualChapter 2: Definitions And Conventions
[Top] [Index] Manuals generated on Wednesday 8 November 2006 2.1: Syntax of CommandsFormat of Commands
All command packages follow the same general format. The command is introduced with a backslash (or alternatively, a hash symbol) and ends with the word 'END'. \COMMAND ([keyword=]value ) ... (DIRECTIVE ([keyword=]value ) ...) END
Actual data on a COMMAND or DIRECTIVE line is input in free format, with at least one space (or sometimes an optional comma) terminating an item. Data items may either be preceded with the keyword and its '=' sign, or if the order given in the definition is strictly followed, just by the data values. COMMANDS, DIRECTIVES and KEYWORDS can be abbreviated to the minimum string which resolves ambiguity. Both types of identification can be intermingled. The following examples are all identical to the program. They use the command \DISTANCES to compute all interatomic distances in the range 0.0-1.9 Angstrom, and all interatomic angles involving bonds in the range 1.6-2.1 Angstrom. \DISTANCE SELECT RANGE=LIMITS LIMITS DMIN=0.0 DMAX=1.9 AMIN=1.6 AMAX=2.1 END
\DIS SE RA=LI LI 0.0 1.9 1.6 2.1 EN
\DIST SEL RANGE=LIM LIMI DMAX=1.9 1.6 2.1 END
[Top] [Index] Manuals generated on Wednesday 8 November 2006 2.2: Syntax of the manualThose parts of the manual describing data and command input will generally be in the following format: 1. A summary of the complete command, with all directives and keywords. Ellipsis (...) may be printed to represent omitted but similar parameters. 2. An typical example. This may not demonstrate all the available options 3. A description of all the directives and keywords.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 2.3: Types of Commands:Lists
These contain related data items, grouped together so that CRYSTALS can check that the data is complete. These lists are stored in the CRYSTALS database. Usually, input of a new list of a given type over-writes an existing list of the same type. In general, LISTS do not 'do' anything. There are two types of syntax for LISTS: Keyed LISTS
In these, CRYSTALS can know in advance how much and what kind of input to expect. Each element of data is identified by an optional keyword. See, for example, LIST 1 (section 4.2). Lexical LISTS
In these, CRYSTALS cannot know in advance what kind of data the user may wish to input. Each line of input is processed by a lexical scanner, and parsed to determine the action needed. See, for example, LIST 12 (section 7.11). For a list of all the lists, see the Lists overview (section 3.3).
Commands
These cause CRYSTALS to 'do' something, for example, compute a Fourier map. There are two type of syntax for commands, similar to those used for LISTS: Keyed Commands
Immediate Commands
These are special commands which are acted upon immediately they are
issued. They are never more than one line long, and do not require an
'END'. They can be issued whenever the cursor is at the beginning of a
line, even inside a COMMAND or LIST. They are not usually involved with
the crystallographic calculation, but control some aspect of the way
CRYSTALS works, such as hooking in an external data file, or changing
the amount of output produced.
Comments
Any data line starting with a backslash or hash followed immediately with a space is ignored, and may thus be used as a comment, or to deactivate the line without deleting it from the file. Continuation Lines
The directive CONTINUE indicates that the data on the current line is a continuation of the previous line. [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.4: Immediate commands\FINISH
This command closes down CRYSTALS neatly. \ ..... COMMENTS ....
This is a comment line. Column 1 contains the \ character and column 2 must be left blank. The remaining columns (3-80) may be used for a descriptive comment. Such a comment line may appear at any point in the input. \TITLE ..... A title to be printed .....
This command changes the title that appears at the start of every operation. The characters \TITLE are terminated by a space in column 7 and the remainder of the line contains the title. \TYPE 'filename'
The file 'filename' is typed on the users terminal without its contents being interpreted by CRYSTALS. Thus \ commands in this file are NOT acted on, giving the user a method of previewing a USE file. \USE source
This command controls the source of commands for CRYSTALS. If 'source' is a filename then commands are read from that file. If 'source' is LAST ,the current USE file is closed and commands are read from the previous level USE file. If 'source' is CONTROL , all USE files open are closed and commands are read from the main control stream for the job , for example the terminal in an interactive job. One USE file may contain other USE commands. The maximum depth of USE files allowed will be installation dependent. Note that the USEd file need not be a complete list - it can be as little as only one line. An indirect file should end with '\USE LAST' , '\USE CONTROL' , or '\FINISH' . This command is only available in some implementations. \SCRIPT filename
This command is only available in interactive mode, and passes control to the 'script' file, which tries to assist the user by prompting him for data and information. A separate manual describes the writing of user define scripts. \SPAWN 'shell command'
A 'shell command' can be issued from inside CRYSTALS with this command. \SPAWN without a command spawns a sub-process and passes control of the sub-process to the terminal. Return to CRYSTALS by closing the sub-process. $ 'shell command'
A 'shell command' can be issued from inside CRYSTALS with this command.
Typical examples are: $dir, $notepad, $edit afile, $netscape something.html
\COMMANDS command
This command, which takes other command-names as a parameter (without the \ ), produces a listing of the available parameters, keywords and defaults for those commands. The listing is derived directly from the 'command file', and is thus completely up to date for the program being run. This command will not operate correctly if the preceding command ended in error. Clear the error flag by performing some successful operation. The facility is an aide-memoire, and not intended to replace the manual. The full significance of the output is detailed in section 3.0 on the CRYSTALS database. ? text
This facility allows the user to make brief inquiries from the command file on the commands, directives, and parameters available at the current point in the job. If a command is not being processed, and '?' is entered alone, a list of the commands is displayed. If '? command' is entered, a list of the directives available with that command is displayed. If '? command directive' is entered, a list of parameters for the given command and directive is displayed, and so on. If a command is currently being processed, the behaviour is similar, but no command name is allowed. Then '?' alone gives a list of directives, while '? directive' gives a list of parameters, and so on. In this case care should be taken: After a '?', CRYSTALS loses track of the last parameter that was input so using CONTINUE will have unpredictable results. To work around this, specify the parameter explicitly on the command line, for example: \EDIT \ Start entering a new atom to be added to the model: ATOM U 1.0 \ Refresh your memory as to the rest of the syntax: ?atom \ Carry on entering the atom, but give the \ parameter name, X, explicitly. CONTINUE X=0.2 0.4 0.5 END
\MANUAL 'name'
The 'name' parameter is the name of the volume whose index is required. The special name 'INDEX' gives a list of subjects for each volume. The special name 'LISTS' gives a list of the function of each LIST. \HELP 'topic'
The topic 'HELP' contains a list of topics for which help is given. This
is likely to be very site-specific.
\OPEN devicename filename
This command is similar to RELEASE, except that a wider range of device names may be specified, and different messages are produced. An important facility available with this command is to open a named HKLI file, for the reflection input commands HKLI and LIST 6, using the device name HKLI. Similarly permanent files may be used in data reduction work by using the device names M32 and M33 overriding the default scratch files. e.g. \OPEN HKLI reflection.hkl
\CLOSE devicename
Any file on specified device is closed. \RELEASE devicename filename
The file currently open on 'devicename' is closed, and a new file opened on that device if necessary. The file just closed can be examined using the \TYPE command. The filename parameter is optional. If it is specified, the new file will be opened with that name. Useful devices currently available include PRINTER, PUNCH, LOG and MONITOR.
\APPEND devicename filename
Output to the specified device is appended to any output already in
the specified file.
Device names
Devices are names used inside CRYSTALS to refer
to files that it has opened. Deviecs recognised by CRYSTALS are:
\PAUSE interval
This command causes the program to wait for 'interval' seconds before proceding. The maximum value of 'interval' is 200 seconds. It might be useful in a 'USE' file. \BENCH nparam nref
This simulates sfls (structure factor least squares, i.e. a cycle of refinement, see 7.42). to enable processor speeds to be compared. No real refinement is done, and the structure is not modified. nparam defaults to 500 nref defaults to 5000 Times for a Microvax 3800 (circa 1995) are printed for comparison.
\SET LIST state
This command allows the user to control the monitoring level of transfer of lists to and from the database in conjunction with the SET WATCH command. There are four states available. If state is OFF, no list logging information is produced. If state is READ or WRITE, list logging information is only produced when lists are read or written respectively. If state is BOTH, both reading and writing operations may be monitored. Note that the logging operation may be qualified by a list type specified by SET WATCH. The initial state is WRITE, with the specific watch set on list 5 (the model parameters), so that only operations creating or modifying list 5 will be monitored. \SET WATCH number
This command is used in conjunction with SET LIST to control monitoring of list operations. If number is 0, operations on all list types may be monitored, according to the state set with SET LIST. If number is a positive integer, representing a list type, only operations on that list type may be monitored. The initial value for the list watch is 5, which in conjunction with the initial monitoring state means that operations creating or modifying list 5 will be monitored. \SET FILE type
This command is used to control the case of file names generated by CRYSTALS. Possible values are: LOWER Filenames are converted to all lower case. UPPER Filenames are converted to all upper case. MIXED Filenames are left as input or defined.
\SET GENERATE state
This command is used to control the generation of output file names and pseudo-generation numbers on non-VMS systems. By default, CRYSTALS modifies the root of filenames for files which should not be overwritten (normally .LIS, .MON, .LOG). OFF suppresses automatic name generation. \SET EXPORT state
If 'state' is 'on' then LISTS 5 (atoms), 12 (constraints) and 16 (restraints) are copied to the PUNCH file when CRYSTALS closes down. These can be archived for safety, or exported to another computer. \SET UEQUIV state
This controls the calculation of Uequiv. Both definitions are acceptable to Acta. The arithmetic mean of the principle axes is often similar to the refined value of Uiso. The geometric mean is more sensitive to long or short axes, and so is more useful in publications. ARITH = (U1+U2+U3)/3 GEOM = (U1*U2*U3)**1/3
\SET PAUSE value
This command sets a time, in seconds, for which the program will pause at the end of each screen full of output. It is only effective on DOS machines, and enables the user to use the 'pause' key to hold a selected screen. The maximum value of 'interval' is 200 seconds. \SET LOG state
If state = ON then all user input commands are written
to a log file. \SET MONITOR state
If 'state' = ON, then all input is reflected in the monitor file. If 'state' = OFF, monitoring. is suppressed. Any change made to the monitoring state applies only to the current level of USE file and any USE file called by it. \SET PAGE length
This command is used to change the length of the assumed 'page' when displaying files on the monitor channel, using the commands 'HELP', 'MANUAL', and 'TYPE'. The initial length is 20 lines. After the number of lines specified have been typed, the listing stops and a message indicates the program is waiting. A blank line or carriage return at this point will cause the listing to continue. Any other input is executed normally. If the length is set to zero, or a negative number, the feature is disabled. \SET TERMINAL device
This command controls the display of SCRIPT menus on some terminals. Possible device types are UNKNOWN This is the default, and requires no special terminal. VT52 For use on terminals with limited screen management facilities. VT100 For use on advanced terminals. VGA For use on PC VGA terminals WIN For use under Win32 and X-windows.
\SET COMMUNICATION speed
This command is used to indicate to the program the speed of the communication line or terminal on which it is being run. This indication is used by some facilities to determine how much output to produce on the monitor channel. The possible values for the speed are "SLOW" and "FAST". These keywords are not associated with any particular terminal speed, and the appropriate value will depend on the user's patience. The initial value is "FAST" \SET TIME state
This command is used to indicate to the program whether the timing messages usually produced at the end of each facility are produced. If 'state' is "OFF" the messages are not displayed. If 'state' is "ON" the messages are displayed. \SET PRINTER state
This command is used to control output to the 'printer' file. The state OFF suppresses printer output. \SET OPENMESSAGE state
This command is used to enable or disable file handling messages. OFF suppresses messages. \SET MESSAGE state
This command is used to indicate to the program whether the command messages usually produced at the end of each facility are produced. If 'state' is "OFF" the messages are not displayed. If 'state' is "ON" the messages are displayed. Error messages are always displayed. \SET SRQ state
This command is used to control mirroring of CRYSTALS internal commands.
The normal state OFF suppresses the mirroring.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 2.5: FilesWhen CRYSTALS runs it stores all crystallographic data in a single file, by default named crfilev2.dsc. This is a binary file and should not be opened with any other program. CRYSTALS outputs results and analysis to several places: The listing file:
this will be called bfilenn.lis where nn is a number
from 00-99, incremented each time the program is run. When nn reaches 99
this file will be continuously overwritten every time CRYSTALS is run.
The listing file contains verbose output about all the calculations that take place. The punch file:
called bfile.pch by default. The idea of 'punching' data
is a throwback to the days of punched cards. This file is used to write out
specific bits of data as commands that can then be read back into the
program. For example, the parameters defining the crystallographic model
are stored in CRYSTALS as a 'List 5'. Then 'Punching List 5':
\PUNCH 5 END
\USE bfile.pch
The monitor file:
called bfilenn.mon this is obsolete. If there is any
output in it, it is from a bit of the program that hasn't been looked at
recently.
The log file:
called bfilenn.log, this contains everything that you typed into CRYSTALS,
and commands that were issued on your behalf by the menu system or script
processor.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 2.6: Errors and WarningsCRYSTALS recognises the following run time error categories, in addition to any detected by the operating system. Warnings
These will occur only for tasks which produce user-readable output, and do not write to the database. The current task is abandoned if necessary, and the next task fetched from the input stream. Errors
The error is such that the current task must be abandoned. In batch or online modes, the job will be terminated as well. In interactive mode the current task is abandoned , and control is returned to the user at terminal. The processing of any 'USE' file will be abandoned. Severe Errors
The error detected is such that it is not possible for the job to continue. These errors are usually caused by database management failures. Catastrophic Errors.
The job is completely terminated. This is usualy the consequence of errors in reading or writing to the database. Programming Errors
The program has detected an inconsistency either in the code, or in
the command file. A dump and error report will be generated if
possible. The error and the conditions that cause it should be reported
to Oxford.
Errors Detected During the Creation of a LIST
During all operations that create new versions of a list, either by input or internally, errors may be found that cause the new list not to be written to the database. To prevent the system using an old version of a list when the creation of the latest version has failed, the relevant list type is marked as an 'error list' in the 'list control table' (see below). This error flag is cleared when a new version of the list is created or by user action. If a list which is marked as an error list is accessed, a message will
be output, and the job terminated. However, for the printing of most lists,
the error flags are not checked.
[Introduction To The System | Definitions And Conventions | The Crystals Database | Initial Data Input | Reflection Data Input | Atomic And Structural Parameters | Structure Factors And Least Squares | Fourier Routines | Analysis Of Results | Twinned Crystals | Matrix Calculations | Obsolete Commands ] |
© Copyright Chemical Crystallography Laboratory, Oxford, 2006.
Comments or queries to David Watkin -
david.watkin@chem.ox.ac.uk Telephone +44 1865 285019.
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