Crystals Manual

Chapter 2: Definitions And Conventions

2.1: Syntax of Commands

2.2: Types of Commands:

2.3: Immediate Instructions

2.4: Errors and Warnings

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 preceeded 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.

example:

      \DISTANCE
      SELECT RANGE=LIMITS
      LIM 0.0 1.9 0.0 0
      END

Those parts of the manual describing data and instruction input will generally be in the following format:

      1. A summary of the complete command, with all directives and
         keywords. Ellipis (....) 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.

These contain related data items, grouped together so that CRYSTALS can check that the data is complete. These lists are stored in the CRYSTALS data-base. 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
 

 
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.
 

 

 
Instructions

These cause CRYSTALS to 'do' something, for example, compute a Fourier map. There are two type of syntax for Instructions, similar to those used for LISTS:
 

 
Keyed Instructions
 
Lexical Insructions
 

 

 
Immediate Instructions

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 an INSTRUCTION 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.
 

This is the last instruction card in each set of instructions. This card has no parameters.
 
\ ..... COMMENTS ....

This is a comment card. 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 card may appear at any point in the input.
 
\TITLE ..... A title to be printed .....

This instruction 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 card contains the title.
 
\SET EXPORT state

If 'state' is 'on' then LISTS 5,12 and 16 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

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 instructions. 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 instruction 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.
 
\COMMANDS instruction

This instruction, which takes as parameter other instruction-names (without the \ ), produces a listing of the available parameters, keywords and defaults for those instructions. The listing is derived directly from the 'command file', and is thus completely up to date for the program being run. This instruction will not operate correctly if the preceeding instruction ended in error. Clear the error flag by performing some succesfull operation. The facility is an aide-memoire, and not intended to replace the manual. The full significance of the output is detailed in the section DATABASE.
 
? text

This facility allows the user to make brief inquiries from the command file on the instructions, directives, and parameters available at the current point in the job. If an instruction is not being processed, and '?' is enterd alone, a list of the instructions is displayed. If '? instruction' is entered, a list of the directives available with that instruction is dirplayed. If '? instruction directive' is entered, a list of parameters for the given instruction and directive is displayed, and so on.

If an instruction is currently being processed, the behaviour is similar, but no instruction name is allowed. Then '?' gives a list of directives, '? directive' a list of parameters, and so on. In this case care should be taken if a previous directive is CONTINUEd after using '?', as the parameter index is reset, and as the system assumes the next parameter to be input will be number 1, its name should be given explicitly.
 
\SPAWN JCL command

A JCL command can be issued from inside CRYSTALS with this instruction. \SPAWN without a command spawns a sub-process and passes control of the sub-process to the terminal. Return to CRYSTALS by LOGGING out of the sub-process. ONLY available under VAX/VMS and UNIX.
 
\$ JCL command

A JCL command can be issued from inside CRYSTALS with this instruction. A typical example is $ DIR.
 
$ JCLcommand

This facility works in exactly the same way as \SPAWN or \$, described above.
 
\SET LIST state

This instruction allows the user to control the monitoring level of transfer of lists to and from the database in conjunction with the SET WATCH instruction. 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, so that only operations creating or modifying list 5 will be monitored.
 
\SET WATCH number

This instruction 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 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.
 
\PAUSE interval

This instruction causes the program to wait for 'interval' seconds before proceding. The maximum value of 'interval' is 200 seconds.
 
\TYPE 'filename'

The file 'filename' is typed on the users terminal without its contents being interpreted by CRYSTALS. Thus \ instructions in this file are NOT acted on, giving the user a method of previewing a USE file.
 
\SET LOG state

If STATE = ON then all user input commands are written to a log file. If STATE = OFF then subsequent commands are not written to the log. Any change made to the log state applies only to the current level of USE file and any USE file called by it. Because the log file is a direct copy of the users commands, it may subsequently be used (probably after modification) as a control 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 instruction 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 instruction 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

This instruction 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 instruction 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 instruction is used to control output to the 'printer' file. The state OFF suppresses printer output.
 
\SET OPENMESSAGE state

This instruction is used to enable or disable file handling messages. OFF suppresses messages.
 
\SET GENERATE state

This instruction is used to control the generation of output file names and pseudo-generation numbers on non- VMS systems. OFF suppresses automatic name generation.
 
\SET MESSAGE state

This instruction 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 instruction is used to control mirroring of CRYSTALS internal commands. The normal state OFF suppresses the mirroring.
 

 
\SET FILE type

This instruction 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.

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 instruction. 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.
 
\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 instruction 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 instructions 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.
 

CRYSTALS 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.