NONIUS CAD4/MACH3 User manual

• Introduction
• Installation of the program
• Starting the program
• Using the CAD4
• Display CAD4 process
• Automatic measurement procedure
• Acknowledgements

Introduction

The CAD4-UNIX version was developed to run a CAD4 or MACH3 on a UNIX platform. Originally Nonius B.V. supported a VAX/VMS version (CAD4 express, CAD4 version 5.1) and a PC MSDOS version based on the CAD4 version 5.0 software. For the Unix version parts of both versions were used. The parts of the automatic measuring procedure, strategy and display are based on the VAX/VMS program system ARGUS developed at the University Utrecht.

At the moment the Unix version of the CAD4/MACH3 software is supported to run on PC's under Linux and on Silicon Graphics workstations.

Installation of the programs

LINUX (Intel based processors)

First a top directory has to be created, in which the .tar file should be extracted, e.g. /home/cad4.
Mount the floppy by:

mount -t msdos /dev/fd0 /mnt

Copy the two files, instal.lin and c4_lin.tgz to the top directory:

cp /mnt/* /home/cad4

Go to the home directory and run the script instal.lin:

cd /home/cad4
./instal.lin

The gzip compressed .tar.gz file is now uncompressed and the .tar file will
be extracted, so that the subdirectories and files will be created.

IRIX (Silicon Graphics computers)

First a top directory has to be created, e.g. /usr/people/cad4, in which the .tar file should be extracted. Then use the tar program to extract the two files, instal.sgi and c4_sgi.tar.Z from the tape into the top directory.

Go to the home directory and do instal.sgi:

cd /usr/people/cad4
./instal.sgi

The compressed .tar file is now uncompressed and the .tar file will be extracted, so that the subdirectories and files will be created.

The work_directory is the system subdirectory. In this directory the links are also made during the extraction of the .tar file. Optionally the file make_links in the top directory can be used.

In the work_directory are all programs used by the CAD4 system and the handlers (.tsk) files for the interfaces (Falcon, Falcon+ and LSI).

Data will come in subdirectories of the root, for example in data0/ for your first CAD4, in data1/ for your second CAD4. The other data directories (until data7) will not change or can be used
for simulation (see also the file start.doc). In the work_directory these data directories are linked to ca0_data, ca1_data etc.

Other directories of the root are jobs/ (linked in the work directory to cad4_jobs), used by the CAD4 command 'NEWCMP' to create the .cat files for the automatic procedure (see also start.doc) and global/ (linked to cad4_global in the work_directory), which contains files with general CAD4 values and parameters important for the automatic procedure.

Values and parameters important for a specific CAD4 are in files of the data subdirectories config/ (linked in the work_directory to ca0_config, ca1_config etc.).

Some files in ca"n"_config should be mentioned here:
 

rs232_port.xxxx	If xxxx = "simula" (in the distribution version for "n" = 1 to 7) the simulation version of the program will run. Otherwise the program assumes that xxxx is the device name of the serial(RS232) line. For instance cua1 for linux, ttyd2 for sgi.
lambda.xx	In the distribution xx is mo (Molybdenum radiation). For copper radiation rename this file to lambda.cu. This is important for the automatic measurement procedure (see also auto.doc).
temperature.xxx	In the distribution version xxx is lnt, which means that low (liquid nitrogen) temperature is assumed. In that case during the automatic procedure data collection is not always done at psi = 0. If you rename the file so that xxx is something else (max. 3 characters) room temperature is assumed and reflections are normally measured at psi = 0 in bisecting mode.
kv.xxx	In the distribution version xxx is 60, which means that for the generator 60 kV is assumed. This will come in text of the data-collection file, also if using the automatic procedure. If you use for instance 40 kV, rename this file to kv.40.
ma.xxx	In the distribution version xxx is 50, which means that for the generator 50 mA is assumed. This will come in the text of the data-collection file, also if using the automatic procedure. If you use for instance 40mA, rename this file to ma.40.
filter.xxx	In the distribution version xxx is mon, which means that a monochromator is assumed. This will come in the text of the data-collection file, also if using the automatic procedure. You can rename filter.mon so that xxx is something else.

Files necessary for the X-window version of the argus program are in the data subdirectories master/ (linked in the work_directory to ca0_master, ca1_master etc.). For a good working program system it is important that the files and links in all directories mentioned above are not changed, deleted or renamed (except for the files mentioned).

Starting and Finishing the CAD4 program.

Starting the programs

All programs are started from the work_directory cad4_system. To start the CAD4 program type:

"cad4" or "cad4 n"

in which "n" is the cad4 number. If "n" is not given the program will ask for the cad4 number.

The input and output of the cad4 process is piped to another process (canoper) and you can switch to another terminal channel by giving "quit", while the program is running. The connection later is done again by "cad4 n". It is also possible to run the cad4 program directly so that the cad4 process is all the time connected to your terminal channel. In that case it is not possible to give input to and observe output from the cad4 process on another terminal then you started the program. To start the direct version type:

"cad4_direct" or "cad4_direct n".

To display relevant information from the cad4 process the argus process can be started. This should be done in an X-window environment. So, in case you use linux, startx has been done before. If this is done another process (master) is started and will all the time update relevant information coming from the cad4 logfile. This information will be in constantly updated files in the ca"n"_master directory and will be displayed by the xargus program. One can also start this by typing: "argus" or "argus n".

Finishing the programs

The cad4 (and cad4_direct) process can be stopped by typing the command EXITXX. The cad4_run and canoper process will be finished then. The argus process can be stopped by the Quit button in the main menu of xargus. The master and xargus process will be finished then. All running processes can also be stopped by "abort_cad4 n" in case of emergency (see also Using the CAD4, Abortion).

Using the CAD4

After the startup of the program you can use the CAD4 as described in the Nonius CAD4 manual. The only difference is the way to abort a CAD4 movement and to give a value to the switch register, which mainly determines the way output will be given during the different procedures.

An overview of the standard CAD4 commands with a short description and with references to the CAD4 manual and some new commands, not described in the Nonius CAD4 manual, are listed at the end of this section. CAD4 commands can be entered lowercase or uppercase. In the documentation CAD4 commands are listed uppercase.

Aborting CAD4 actions

If you want to abort a CAD4 movement directly use Ctrl-\ (so type simultaneously on Control and Backslash) and <CR>. The computer will send a message to the interface to stop and will set the first bit of the switch register and a dialogue ,to continue or not, is started.

To abort the CAD4 process in the regular way enter the command EXITXX. If, by some reason no command can be given, all CAD4 processes can still be finished by abort_cad4 "n". In fact one should always do this if the cad4 process is not finished by EXITXX to be sure that no (hidden) processes are
runnning in the background and that configuration files are treated in the right way.

Switch register

The value of the switch register can be read on the command line by the command SHOWSW. An other value can be entered by the command SETSW xxxx (see below). During a procedure (i.e. SEARCH and DATCOL) it is possible to change the switch register by Ctrl-c (so type simultaneously on Control and c) and <CR>. The program will prompt for:

CA"n" Enter switch option:

You can give an octal value of four digits. For the meaning of each bit see the switch register codes below.

List of new CAD4 commands:
 

! text	for comment in log file
ECHO file_name	to log a part of the output
NOECHO	to stop the (extra) logging
FILES	overview of used files
NEWCRY file_name	connection to new .cry file
NEWDAT file_name	connection to new .dat file
NEWHKL file_name	connection to new .hkl file
OLDCRY file_name	connection to old .cry file
OLDDAT file_name	connection to old .dat file
OLDHKL file_name	connection to old .hkl file
SHOWSW	reading and explanation switch register
SETSW xxxx	setting new switch register
RUN file_name	to run one of the stand_alone programs in the directory cad4_system
DISTRB xxxxxx	save all data of compound xxxxxx in a subdirectory of ca"n"_data.
NEWCMP xxxxxx	start with a new compound xxxxxx
GO	start the automatic procedure
TIME	give day and time
VERSION	give version
EXITXX	to leave the program instead of exit.

Display of the CAD4 process by xargus

The display program xargus is started in an X-window environment by: argus n, in which "n" is the cad4 number. To display the information of the files in ca"n"_master. These files are created and updated during the cad4 run by the master process.
The main window contains information of the compound (cell, index status, logfile) and in case of the automatic measurement procedure the status of the process (which job is busy).

There are subwindows, which give information about the number of measu- rements (Counters), statistics during data collection (Theta), datcol input parameters (Crystal), division in shells (Shells), intensity control reflections (Icr), reflection rate (Rate) and the reflections in the .cry file (Refdump). In
the last case the angles (theta, phi etc.) can be displayed in four ways: bisecting, eulerian or kappa geometry or as c-vectors.

Automatic measurement procedure

The commands NEWCMP, GO and DISTRB are used in the automatic measurement procedure.

NEWCMP

With NEWCMP xxxxxx a new compound is started; xxxxxx is the code of the new compound (6 characters). All files have names starting with this code. The NEWCMP command generates a sequence of jobnnnn.cat files in the ca"n"_data directory (nnnn is a sequence number). These job files are
files containing the CAD4 script necessary to conduct an automatic measurement.

GO

After the mounting and centering the crystal the automatic procedure can be started by typing GO. The job files will be executed sequentially. The jobnnnn.cat file with the lowest sequence number will be executed first. When completed each jobnnnn.cat file is deleted and the next jobnnnn.cat file
is executed. Apart from standard CAD4 commands, the jobnnnn.cat files also contain
commands "RUN image", in which image is a stand-alone program (see below).

DISTRB

When GO has succesfully completed the data collection, the command DISTRB xxxxxx saves all the files related to compound xxxxxx in a subdirectory xxxxxx of ca"n"_data.

The command: RUN image

With RUN an image is started as a subprocess.
Optional parameters are passed through to the subprocess. The image will create a file jobxxxx.cat in the ca"n"_data directory. With the command &jobxxxx.cat (abbrev. &job* or simply &) that file is executed and deleted.

Files related to the RUN command:
 

'image'.inp	input file for image, created by cad4 process and deleted after termination of the subprocess
'image'.out	output file of image, displayed and deleted by cad4 process after subprocess termination
jobxxxx.cat	indirect command file created by subprocess
holy.data	ascii file containing constants for all programs. First this file is searched for in the directory ca"n"_config. If not found then cad4_global is tried. If not found at all an error is generated.

The subprocess terminates with an status number.
1: status ok.
2: some error occurred.

The programs used during the automatic procedure are:

1)	show_cell	Show cell parameters
2)	set_swoma	Increase SWOMA (which determines the scan angle, see Setang scan parameters) if necessary
3)	set_psi	Set Psi for Liquid Nitrogen Temperature or ANIVEC
4)	check_index	Continue if enough reflections have status H.
5)	absents	Set absent conditions
6)	check_absent	If absent a sphere like data-collection (see below) is started. The output can be examined.
7)	seldom	Select a reflection and do some scans to get a good value for DOMA (which determines the the scan angle, see "Data collection control parameters") . Usually followed by the program a_seldom.
8)	a_seldom	Read data prepared by seldom and set DOMA
9)	selsap	Select a reflection and do some scans to get a good value for APTA (which determines the horizontal width of the variable aperture, see Data collection control parameters). Usually followed by the program a_selsap.
10)	a_selsap	Read data prepared by selsap and set APTA.
11)	omthplot	Select a strong reflection fo omega/theta scans
12)	sphere	Do data-collection on three wafers with one reflection fixed. Used by selicr (see below)
13)	nonequal
14)	selocr	Select 3 reflections from current refl. list; create new cryst file with these reflections and their Friedel pairs as orient control (OOORRR).
15)	check_o	Check H status of orient reflection
16)	selicr	Select 3 ICR reflections from sphere data.
17)	check_h [string]	If H-status for all reflections which are flagged in the string are also H, a continuation job will be created. Otherwise an abortjob is created. Default string: HHHHHH
18)	prelim	Do a DATCOL on an empty HKLfile. Scan information for ICR refl. and a starting value for the orientation matrix will be obtained.
19)	hkl_limits	Set appropriate hkl limits.
20)	shells_file	Do data-collection on one or more theta-shells in FILE mode.
21)	psi_scan	Do a Psi scan on suitable reflections.

Description of all steps during the automatic procedure for sample xxxxxx.
 

1) Search
job0100.cat	Initializing before search.
job0200.cat	Search for reflections 1-8.
job0300.cat	Search for reflections 9-16.
job0400.cat	Search for reflections 17-25 and find orientation (INDEX).
job0500.cat	Show index flag of list reflections and store search results in xxxxxx_search.cry.
2) Setang
job0600.cat	RUN set_swoma to calculate the best SWOMA value.
job0700.cat	RUN set_psi to see if list reflections should be measured at other psi value.
job0800.cat	Set flags for SETANG by LCA.
job0900.cat	Optimize angles by SETANG (twice), INDEX again and RUN show_cell.
job1000.cat	Store Setang results in xxxxxx_setang.cry.
3) Set4
job1100.cat	RUN set_swoma to calculate new SWOMA value.
job1200.cat	Do SET4, store results in xxxxxx_set4.cry and RUN set_swoma again.
4) Index
job1300.cat	INDEX, Least Squares and RUN show_cell.
5) Check_index
job1400.cat	RUN check_index to see if there are enough reflections with index status H.
6) Trans
job1500.cat	Switch to new file xxxxxx_trans.cry, do TRANS, calculate with TH number of reflections and calculate bisecting positions of axis reflections. Store this and other information in xxxxxx_trans.lis and RUN show_cell.
job1600.cat	RUN absents to set absent conditions.
7) Chk_abs
job1700.cat	RUN check_absents (if absents are present) to check the absents in a small data-collection.
8) Seldom
job1800.cat	RUN seldom to generate scans with different scan angles for a selected reflection.
job1900.cat	RUN a_seldom to analyze seldom results and setting optimal DOMA
9) Selsap
job2000.cat	RUN selsap to generate scans with different apertures for a selected reflection.
job2100.cat	RUN a_selsap to analyze selsap results and setting optimal APTA.
10) Omthplot
job2200.cat	RUN omthplot to generate omage/theta scans for a selected reflection.
11) Sphere
job2300.cat	Switch to new files xxxxxx_sphere.cry and xxxxxx_sphere.dat, RUN sphere and store the information from sphere in xxxxxx_sphere.lis.
job2400.cat	RUN nonequal
job2500.cat	Switch to old cry and dat file.
12) Selocr
job2600.cat	Switch to xxxxxx_trans.cry and RUN selocr.
13) Selicr
job2700.cat	Switch to xxxxxx_meas.cry (created in job2600 by selocr) and RUN selicr.
14) Prelim
job2800.cat	Switch to file xxxxxx_prelim.cry and RUN prelim.
job2900.cat	Switch to file xxxxxx_datcol.cry.
15) HklLimits
job3000.cat	RUN show_cell.
job3100.cat	RUN hkl_limits (auto).
16) Shells_file
job3200.cat	RUN shells_file
17) Psi_scan
job3300.cat	Switch to xxxxxx_psi.cry and RUN check_h.
job3400.cat	RUN psi_scan.

Now the data collection on the unique part of the Ewald sphere is finished. Next jobs are there to prevent the CAD4 from being idle. They serve to conduct the collection on redundant data. So from here the measurement can be interrupted at any time, without influencing the data completeness.
 

18) HklLimits2
job3500.cat	RUN show_cell.
job3600.cat	RUN hkl_limits (auto2)
19) Shells2_file
job3700.cat	RUN shells_file.
20) Finish
job9000.cat	Finish and go to view position.

Acknowledgements

This work is based on the program system used at the Utrecht University and developed by Ab Duisenberg and Toine Schreurs. Further parts of the VAX/VMS version, developed by Nonius BV, Delft, were used as well as the MS-DOS version initaiated by Martin Kretchmar. For the communication with the CAD4-interface routines of John Skinner of Brookhaven National Laboratory were used.

The majority of this work was done by Conrad Kiers at the crystallography department of the Utrecht University. Anneke Sicherer Roetman and Toine Schreurs should be mentioned for their help and advice and especially Ton Spek, not only for the use of his CAD4 equipment, but also for his advice and interest.

We also thank Paul Boyle from North Carolina State University as one of the first users of this program. We are very grateful for his advice and the suggestions for improvements.