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|
NONIUSCAD4/MACH3 User manual |
 |
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Introduction
Commandsin relation
with the automatic run
The standard automatic run
Changing the automatic run
Descriptionof
the stand alone programs used during the automatic run
In principal it is possible to measure a crystal only using the commands NEWCMP, GO and DISTRB.
The purpose of the automatic procedure is to make things easier forthe
user. The procedure developed in Utrecht is based on a lot of experience.
Of course it is possible to deviate from the standard procedure. If youwant
to do so, you can make the changes you want in the cad4_jobs directory.In
fact 'c4code'in the jobnnnn.cat files stands for the compound identification
code, which will be transposed in NEWCMP to
get jobnnnn.cat files in the ca'n'_data directory with the given name(in
the text marked as xxxxxx).
Commandsin relation with the automatic run
NEWCMP
With NEWCMP xxxxxx a new compound is started; xxxxxx is the code ofthe new compound (6 characters). All files have names starting with thiscode. The NEWCMP command generates a sequence of jobnnnn.cat files in theca"n"_data directory (nnnn is a sequence number).
GO
After mounting and centering the crystal the automatic procedure canbe started by typing GO. The job files will be executed sequentially. Thejobnnnn.cat file with the lowest sequence number will be executed first.When completed each jobnnnn.cat file is deleted and the next jobnnnn.catfile is executed. Apart from standard CAD4 commands, the jobnnnn.cat filesalso 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 subdirectoryxxxxxx of ca"n"_data.
RUN
With RUN an image is started as a subprocess. Optional parameters arepassed through to the subprocess. The image will create a file jobxxxx.catin 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:
| Input: | |||||
| 'image'.inp | input file for image, created by cad4 process and deleted after terminationof the subprocess. | ||||
| holy.data | ascii file containing constants for all programs. First this file isfirst looked for in the directory ca"n"_config. If not found then cad4_global is tried. If not found at all an error is generated. | ||||
| Output | |||||
| 'image'.out | output file of image, displayed and deleted by cad4 process after subprocesstermination. | ||||
| jobxxxx.cat | indirect command file created by subprocess. The subprocess terminates with an status number.
|
!! Text
This is a comment which has no effect on the cad4 run, but which willcome in the log file so that the master proces (for the ARGUS display)knows the status of the CAD4 proces (status in main menu of ARGUS display)
!HIS Text
This is a comment which has no effect on the cad4 run, but which willcome in the log file so that the master proces (for the ARGUS display)knows the step of the CAD4 proces (history in main menu of ARGUS display).
!ARGUS Text
This is a comment which has no effect on the cad4 run, but which willcome in the log file so that during the master proces a report file, named:
ca"n"_master/master.log
can be made.
ECHO filename
This is a command to log a part of the output. Used as input for thestand alone programs, invoked with the command RUN.
NOECHO
This stops the (extra) logging.
NEWCRY, NEWDAT, NEWHKL file_name
Connection to resp. new .cry, .dat and .hkl file. (see also Changingfile assignments)
OLDCRY, OLDDAT and OLDHKL file_name
Connection to resp. old .cry, .dat and .hkl file (see also Changingfile assignments)
& file_name
This resembles the @ command (see Indirectcommand files), with the following differences:
For a complete default automatic run all that is needed is to centera crystal, type NEWCMP, enter the crystal identification code and typeGO.
The standard run consists of the following steps:
| 1) Search | 2) Setang | 3) Set4 | 4) Index | 5) Check_Index |
| 6) Trans | 7) SelDom | 8) SelSap | 9) OmThplot | 10) Sphere |
| 11) SelOcr | 12) SelIcr | 13) Prelim | 14) HKLlimits | 15) Shells |
| 16) Psi_Scan | 17) HKLlimits2 | 18) Shells2 |
If all data are measured type DISTRB with the crystal identificationcode. All data will come in a subdirectory of ca'n'_data with the nameof the crystal identification code.
Description of all steps during the automatic procedure for sample 'xxxxxx'
is given below.
job0100.cat Initializing before search.
!!Search:Find 25 reflections
NOECHO
LOG
xxxxxx_auto.log
!ARGUS Search
!HIS 1 Search
!oldcry CODE
OLDCRY xxxxxx.cry
GONCON
Quit
SETPAR
2.00 / 4.00 ////
!ARGUS Swoma 2.00 before SEARCH
LK
1 25
LH
0 0 0 0 25 times
.
0 0 0 0
LCH
1 25
NNNNNNNNNNNNNNNNNNNNNNNNN
Yes
&JOB*
job0200.cat Search for reflections 1-8.
!!Search:reflections 1-8
!ARGUS Search
!HIS 1 Search
LK
1 8
!ARGUS Speed 12.0 Disfac 2.0
!ARGUS Theta 12.0 Chi 35.0
!ARGUS Phi 115.0 Phi_Offset -120.0
bp
12.0 -120.0 35.0 0
sap
6
scan
o
2 1
SEARCH
12.0 35.0 115.0
-120.0
12.0 2.0
GONCON
Quit
&JOB*
job0300.cat Search for reflections 9-16.
!!Search:reflections 9-16
LK
9 16
!ARGUS Phi 115.0 Phi_Offset 0.0
SEARCH
12.0 35.0 115.0
0.0
12.0 2.0
&JOB*
job0400.cat Search for reflections 17-25 and findorientation (INDEX).
!!Search:reflections 17-25
GONCON
Quit
LK
17 25
!ARGUS Phi 115.0 Phi_Offset +120.0
SEARCH
12.0 35.0 115.0
+120.0
B12.0 2.0
GONCON
Quit
@index.cat
LS
RO
run show_cell
&JOB*
job0500.cat Show index flag of list reflections andstore results in xxxxxx_search.cry.
!!Search:continue after show_cell
LCH
1 25
HHHHHHHHHHHHHHHHHHHHHHHHH
Yes
RO
!newcry CODE_SEARCH
NEWCRY xxxxxx_search.cry
!oldcry CODE
OLDCRY xxxxxx.cry
&JOB*
| 2) Setang | Determine the best scan angle; adapt, if necessary, the psi angle; optimize angles by centering twice and index to find the orientation. |
job0600.cat RUN set_swoma to calculate the best SWOMA value.
!!Setang:Optimize angles for all reflections
NOECHO
LOG
!ARGUS Setang
!HIS 2 Setang
!oldcry CODE
OLDCRY xxxxxx.cry
run set_swoma
&JOB*
job0700.cat RUN set_psi to see if list reflectionsshould be measured at other psi value.
!!Setang:continue with new Swoma
run set_psi
&JOB*
job0800.cat Set flags for SETANG by LCA.
!!Setang:continue with new psi values
LCA
1 25
AAAAAAAAAAAAAAAAAAAAAAAAA
Yes
&JOB*
job0900.cat Optimize angles by SETANG (twice), INDEX again and RUN show_cell.
!!Setang:setang after LCA
SETANG
LCH
1 25
HHHHHHHHHHHHHHHHHHHHHHHHH
Yes
SETANG try to catch lost refls.
@index.cat
LS
RO
run show_cell
&JOB*
job1000.cat Store Setang results in xxxxxx_setang.cry.
!!Setang:continue after show_cell
LCH
1 25
HHHHHHHHHHHHHHHHHHHHHHHHH
Yes
RO
!newcry CODE_SETANG
NEWCRY xxxxxx_setang.cry
!oldcry CODE
OLDCRY xxxxxx.cry
&JOB*
| 3) Set4 | Determine best scan angle again and center reflections and Friedel reflections at positive and negative theta and calculate systematic error free reflection vectors. |
job1100.cat RUN set_swoma to calculate new SWOMA value.
!!Set4:Determine SET4 angles for all reflections
NOECHO
LOG
!ARGUS Set4
!HIS 3 Set4
!oldcry CODE
OLDCRY xxxxxx.cry
run set_swoma
&JOB*
job1200.cat Do SET4, store results in xxxxxx_set4.cry and RUN set_swoma again.
!!Set4:continue with new Swoma
SET4
!newcry CODE_SET4
NEWCRY xxxxxx_set4.cry
!oldcry CODE
OLDCRY xxxxxx.cry
run set_swoma
&JOB*
4) Index Determine the orientation matrix.
job1300.cat INDEX, Least Squares and RUN show_cell.
!!Index:25 reflections => cell parameters??
NOECHO
LOG
!ARGUS Index
!HIS 4 Index
!oldcry CODE
OLDCRY xxxxxx.cry
@index.cat
!INDEX second time
LS
RO
run show_cell
&JOB*
| 5) Check_index | Halt if not more than 3 reflections can be indexed. (This number canbe changed in ca'n'_config/holy.data) |
!!Check_index:Continue if enough reflections have status H
NOECHO
LOG
!ARGUS Check_index
!HIS 5 Check_index
!oldcry CODE
OLDCRY xxxxxx.cry
LS
RO
RUN check_index
&JOB*
| 6) Trans | Determine Bravais symmetry based upon geometrical properties of theprimitive cell. If a non-primitive lattice is chosen the absent conditions are set accordingly. |
| job1500.cat | Switch to new file xxxxxx_trans.cry, do TRANS, calculate withTH number of reflections and calculate bisecting positions of axis reflections. Store this and other information in xxxxxx_trans.lis and RUN show_cell. |
!!Trans:Transform into code_TRANS.CRY and handle absents
NOECHO
LOG
!ARGUS Trans
!HIS 6 Trans
!oldcry CODE
OLDCRY xxxxxx.cry
!newcry CODE_TRANS
NEWCRY xxxxxx_trans.cry
ECHO xxxxxx_trans.lis
!Trans Output for xxxxxx
!ARGUS number 0
LS
TRANS
/
/
Save
Yes
DATCIN
Modify
TEXT
/
Quit
Quit
LO
1 25
TH
0 27.50 ! for Mo radiation !!
TH
27.50 28.47 ! one shell
TH
0 30.26 ! for extreme HKL (Mo radiation)
HB
1 0 0
HB
0 1 0
HB
0 0 1
BH
90 0 90
NOECHO
run show_cell
&JOB*
job1600.cat RUN absents to set absent conditions.
!!Trans:continue after show_cell
run absents
&JOB*
7) Chk_abs Check absents if present.
job1700.cat RUN check_absents (if absents are present) to check the absents in a small data-collection.
!!Chk_abs:Collect 3 wafers (absent check)
NOECHO
LOG
!ARGUS Chk_abs
!HIS 7 Chk_abs
!oldcry CODE_TRANS
OLDCRY xxxxxx_trans.cry
RUN check_absent
&JOB*
| 8) Seldom | Select a appropriate reflection from the list of 25 and determine thebest scan angle by analyzing a succession of scans using a wide aperture and a logarithmically increasing scan angle. |
job1800.cat RUN seldom to generate scans with different scan angles for a selected reflection.
!!Seldom:Get best scan angle and set DOMA
NOECHO
LOG
!ARGUS Seldom
!HIS 8 Seldom
!oldcry CODE_TRANS
OLDCRY xxxxxx_trans.cry
RUN seldom
&JOB*
job1900.cat RUN a_seldom to analyze seldom resultsand setting optimal DOMA.
!!Seldom:analyse seldom and set Doma
RUN a_seldom
&JOB*
| 9) Selsap | Determine the best aperture in a similar way, applying the scan anglefound by seldom. |
job2000.cat RUN selsap to generate scans with different apertures for a selected reflection.
!!Selsap:Get best aperture and set APTA
NOECHO
LOG
!ARGUS Selsap
!HIS 9 Selsap
!oldcry CODE_TRANS
OLDCRY xxxxxx_trans.cry
RUN selsap
&JOB*
job2100.cat RUN a_selsap to analyze selsap resultsand setting optimal APTA.
!!Selsap:analyse selsap and set APTA
RUN a_selsap
&JOB*
| 10) Omthplot | Select a suitable reflection from the list and execute a series ofvertical slit scans over the reflection range, with omega and scan angle center offset varying as in an omega/2theta scan. |
job2200.cat RUN omthplot to generate omage/theta scans for a selected reflection.
!!Omthplot:Collect omega/theta scans
NOECHO
LOG
!ARGUS Omthplot
!HIS 10 Omthplot
!oldcry CODE_TRANS
OLDCRY xxxxxx_trans.cry
RUN omthplot
&JOB*
| 11) Sphere | Measure three sets of reflections (about 35 per set) from type 2kl,h2l, hk2, forming three more or less mutually perpendicular half-circular segments (signs of hkl chosen such as to measure as much as possible above the horizon). From each set an intensity control reflection will be selected by Selicr below. |
| job2300.cat | Switch to new files xxxxxx_sphere.cry and xxxxxx_sphere.dat, RUN sphereand store the information from sphere in xxxxxx_sphere.lis. |
!!Sphere:datacolection on 3 wafers (sphere)
NOECHO
LOG
!ARGUS Sphere
!HIS 11 Sphere
!oldcry CODE_TRANS
OLDCRY xxxxxx_trans.cry
!newcry CODE_SPHERE
NEWCRY xxxxxx_sphere.cry
!newdat CODE_SPHERE
NEWDAT xxxxxx_sphere.dat
DATCIN
Modify
INT
1.5 0.02 1 1 1
FLAG
/ / 1 set non-equal on
Quit
Output
Save
GONCON
Quit
ro
ECHO xxxxxx_sphere.lis
RUN sphere
&JOB*
job2400.cat RUN nonequal.
!!Sphere:check non_equal
NOECHO
RUN NonEqual
&JOB*
job2500.cat Switch to old cry and dat file.
!!Sphere:reset cryst and dat files after sphere
!oldcry CODE
OLDCRY xxxxxx.cry
!olddat CODE
OLDDAT xxxxxx.dat
&JOB*
| 12) Selocr | Select from the list 3 reflections that are most perpendicular mutuallyas orientation control reflections, together with their Friedel opponents.These 6 reflections and the 3 intensity control reflections are kept in a separate cryst file, active during data collection only. |
job2600.cat Switch to xxxxxx_trans.cry and RUN selocr.
!!SelOcr:Select Orient Control Reflections
NOECHO
LOG
!ARGUS SelOcr
!HIS 12 SelOcr
!oldcry CODE_TRANS
OLDCRY xxxxxx_trans.cry
RUN selocr
&JOB*
13) Selicr Select 3 intensity control reflections from the Sphere data.
job2700.cat Switch to xxxxxx_meas.cry (created injob2600 by selocr) and RUN selicr.
!!SelIcr:Select Intensity Control Reflections
NOECHO
LOG
!ARGUS SelIcr
!HIS 13 SelIcr
!oldcry CODE_MEAS
OLDCRY xxxxxx_meas.cry
RUN SelIcr
&JOB*
| 14) Prelim | A preliminary Datcol to center and to inspect the 6 orientation andthe 3 intensity controls and to calculate a datcol matrix. There is a clearand intentional distinction between cell dimensions for structure refinement (for that the matrix found after SET4 is normaly the best) and the orientation matrix for data collection. The datcol matrix is used only to predict reflection positions, automatically taking care of minor mis-settings. |
job2800.cat Switch to file xxxxxx_prelim.cry and RUN prelim.
!!Prelim:Preliminary data collection
NOECHO
LOG
!ARGUS Prelim
!HIS 14 Prelim
!oldcry CODE_MEAS
OLDCRY xxxxxx_meas.cry
!newcry CODE_PRELIM
NEWCRY xxxxxx_prelim.cry
RUN prelim
&JOB*
job2900.cat Switch to file xxxxxx_datcol.cry.
!!Prelim:Copy crystfile after prelim to code_DATCOL.cry
!newcry CODE_DATCOL
NEWCRY xxxxxx_datcol.cry
&JOB*
| 15) HklLimits | Calculate the hkl limits for the most faqvourably oriented ('upward') unique part of the Ewald sphere, taking into account the Bravais symmetry, and set the fastest sequence for hkl incrementing. Tetragonal and cubicspace groups are measured as orthorhombic. |
job3000.cat RUN show_cell.
!!HklLimits:Set HKL limits
NOECHO
LOG
!ARGUS HklLimits
!HIS 15 HklLimits
!oldcry CODE_DATCOL
OLDCRY xxxxxx_datcol.cry
run show_cell
&JOB*
job3100.cat RUN hkl_limits (auto).
!!HklLimits:continue after show_cell
RUN hkl_limits auto
&JOB*
| 16) Shells_file | Datcol for 10 spherical theta layers ("shells") up to 27.5 degr., eachcontaining an equal number of reflections. Start with the 3rd theta shell (for Mo radiation 15.67 - 18.01); if this shell is weak continuation ofdatacollection almost certainly will not make sense. For Mo radiation thetheta shell limits are: 0.1 - 12.38 -15.67 - 18.01 - 19.89 - 21.50 - 22.92 - 24.20 - 25.38 - 26.48 - 27.50 (theta = 27.5 for Mo radiation isequivalent to theta = 90 for Cu radiation). Datcol is executed in HKL filemode: hkl's are generated for all shells with the same matrix to ensurethat a reflections figures precisely once. |
job3200.cat RUN shells_file.
!!Shells_file:data collection first pass
NOECHO
LOG
!ARGUS Shells_file
!HIS 16 Shells_file
!oldcry CODE_DATCOL
OLDCRY xxxxxx_datcol.cry
RUN shells_file 3 1 2 4 5 6 7 8 9 10
&JOB*
job3300.cat Finish data collection by measuring theICR's
Datcin
M
Mode
Zigzag
0 0 0 0 0 0
0 0 0
hkl
q
s
datcon
| 17) Psi_scan | 36 scans at psi = 0,10,...,350 for 3 reasonably strong reflections more or less along the Z-axis. Actually the 36 scans are not measured inthis psi sequence but at (n*50 modulo 360). |
job3400.cat Switch to xxxxxx_psi.cry and RUN check_h.
!!Psi_scan:Measure PSI scans (based on final data collection)
NOECHO
LOG
!ARGUS Psi_scan
!HIS 17 Psi_scan
!oldcry CODE_DATCOL
OLDCRY xxxxxx_datcol.cry
!newcry CODE_PSI
NEWCRY xxxxxx_psi.cry
!newdat CODE_PSI
NEWDAT xxxxxx_psi.dat
RUN check_h
&JOB*
job3500.cat RUN psi_scan.
!!Psi_scan:continue psi_scan after check_h
RUN psi_scan
&JOB*
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 for the collectionon
redundant data.
So from here the measurement can be interrupted at any time, withoutinfluencing
the
data completeness.
| 18) HklLimits2 | Calculate hkl limits for next best accessible unique part of the Ewaldsphere. |
job3600.cat RUN show_cell.
!!HklLimits2:Set HKL limits second best part
NOECHO
LOG
!ARGUS HklLimits2
!HIS 18 HklLimits2
!oldcry CODE_DATCOL
OLDCRY xxxxxx_datcol.cry
run show_cell
&JOB*
job3700.cat RUN hkl_limits (auto2).
!!HklLimits2:continue after show_cell
RUN hkl_limits auto2
&JOB*
| 19) Shells2_file | Data collection for hkllimits2, starting with the high theta shell |
job3800.cat RUN shells_file.
!!Shells2_file:data collection second pass
NOECHO
LOG
!ARGUS Shells2_file
!HIS 19 Shells2_file
!oldcry CODE_DATCOL
OLDCRY xxxxxx_datcol.cry
RUN shells_file 10 9 8 7 6 5 4 3 2 1
&JOB*
20) Finish
job9000.cat Finish and go to view position.
!!Finish:end of job
!ARGUS jobs finished
@viewx.cat
&JOB*
Of course it is possible to deviate from the standard procedure. Ifyou want to do so, you can make the changes you want in the cad4_jobs directory. Remember that 'c4code'in the jobnnnn.cat files stands for the compoundidentification code, which will be transposed in NEWCMP to get jobnnnn.catfiles in the ca'n'_data directory with the given name (xxxxxx). Beforemaking changes study carefully the default standard run in the previoussection, because the default standard run is based on a lot of experience.
Example of modifying the standard run
| No psi_scans | Suppose you never want to do psi scans. In that case rename the filesjob3400.cat and job3500.cat in the cad4_jobs directory to for instance job3400.tem and job3500.tem. |
If you only want to make changes for the current run, the procedureis different. First do NEWCMP, so that the .cat files for a standard runare in the directory ca'n'_data and then make the wanted changes on thejobnnnn.cat files in this directory.
Example of modifying the current run
| No shells | If you want to do a data collection following the ZIGZAG mode and
notin shells, delete job3300.cat and change job3200.cat in ca0_data as follows
(possibly some other datcin parameters should be changed):
NOECHO !oldcry CODE_DATCOL |
Descriptionof the stand alone programs used during the automatic run
The programs used during the automatic procedure are mentioned below(in
the order of occurence in the automatic run described in the previoussection).
All programs will produce a jobnnnn.cat file, mostly this isjob0010.cat.
If this file already exist it will be job0011.cat. If thisfile also exist
job0012.cat etc.
If some error occurs, the program will produce an abort_job: job0001.cat.
Of course all programs produce terminal output, which is also written inthe
log file. Some programs use values from the file ca'n'_config/holy.data.The
values delivered at distribution are given in parentheses.
| 1) show_cell | Show cell parameters. |
|
Input:
|
Current cryst file |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 2) set_swoma | Read current cryst file and determines maximum width forreflections with index status 'H'. If the maximum width is greater than the current SWOMA, which determines the scan angle, then increase SWOMAwith 0.5. |
|
Input:
|
Current cryst file |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 3) set_psi | Set Psi for Liquid Nitrogen Temperature or ANIVEC. If 'mode' is 'normal'and 'temperature' is 'lnt' then change psi for each reflection in currentcryst file until kappa is at least 30 degrees. If 'mode' is 'anivec' setpsi to 1000. |
|
Input:
|
Current cryst file Mode (extension of file mode.xxx in ca'n'_config) Temperature (extension of file temperature.xxx in ca'n'_config) |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 4) check_index | Continue if enough reflections have index status 'H', otherwisestop. |
|
Input:
|
Current cryst file ca'n'_config/holy.data: check_index_allowed: Maximum nr. of 'N' flagged reflections (3) |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 5) absents | Set absent conditions. Read current cryst file. If old absents ae present do nothing. Otherwise read file xxxxxx_trans.lis to get Bravais type. If Bravais = C : nabs = 1; H+KN2 If Bravais = I : nabs = 1; HKLN2 If Bravais = F : nabs = 2; H+KN2 L+HN2 If Bravais = H : nabs = 1; -HKLN3 If Bravais = P : do nothing |
|
Input:
|
Current cryst file xxxxxx_trans.lis |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 6) check_absent | Read current cryst file.If absents are defined (nabs > 0) a spherelike data-collection (see below) is started. The output can be examined. |
|
Input:
|
Current cryst file xxxxxx_trans.lis ca'n'_config/holy.data: 1) sphere_nrefls: Default nr. of refl.(33) 2) sphere_dmin: about 5 degrees Mo (4.0) 3) hkl_theta_mo: max. theta for Mo (30) 4) hkl_theta_cu: max. theta for Cu (75) |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 7) seldom | Select an appropriate reflection from the list and do some scans. Thelast encountered ICR from the list is used. If not present the reflection with the highest intensity < seldom_strongint is token. A wide aperture is used and a logarithmically increasing scan angle. Seldom is usuallyfollowed by the program a_seldom. |
|
Input:
|
Current cryst file ca'n'_config/holy.data: 1) seldom_strongint: Maximum allowed intensity (20000) 2) seldom_n_steps: Nr. of omega scans to be measured (20) 3) seldom_omega_start: Start value of scan angle for omega scans (0.5) 4) seldom_omega_stop: Last value of scan angle for omega scans (3.0) 5) seldom_sap: Aperture during scans (5.0) 6) seldom_npi: Speed during scans (1) 7) seldom_iscant: Scan type (0 , i.e. omega scan) |
|
Output:
|
ca'n'_data/xxxxxx_seldom.lis ca'n'_data/jobnnnn.cat |
| 8) a_seldom | Analyze data prepared by seldom and determine the best value for DOMA(which determines the the scan-angle, see Data collection). DOMA is set on this value. |
|
Input:
|
ca'n'_data/xxxxxx_seldom.lis ca'n'_config/holy.data: 1) a_seldom_default: Scan angle to use if no solution is found (0.80) 2) a_seldom_max_mis: Maximum allowed number of missing profiles (3) |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 9) selsap | Select an appropriate reflection from the list and do some scans. Thelast encountered ICR from the list is used. If not present the reflection with the highest intensity < selsap_strongint is taken. The currentscan width (DOMA, see 7 and 8) is used and a number of omega scans is donewith an increasing aperture. Selsap is usually followed by the programa_selsap. |
|
Input:
|
Current cryst file ca'n'_config/holy.data: 1) selsap_strongint: Maximum allowed intensity (20000) 2) selsap_n_steps: Nr. of omega scans to be measured (20) 3) selsap_aperture_start: Start value of slit for omega scans (1.30) 4) selsap_aperture_stop: Last value of slit for omega scans (5.90) 5) selsap_npi: Speed during scans (1) |
|
Output:
|
ca'n'_data/xxxxxx_selsap.lis ca'n'_data/jobnnnn.cat |
| 10) a_selsap | Analyze data prepared by selsap and determine the best value for APTA(which determines the the aperture, see Data collection).APTA is set to this value. |
|
Input:
|
ca'n'_data/xxxxxx_selsap.lis ca'n'_config/holy.data: 1) a_selsap_default: Aperture to use if no solution is found (3.0) 2) a_selsap_max_mis: Maximum allowed number of missing profiles (3) |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 11) omthplot | Select a strong reflection for omega/theta scans. The first encountered ICR from the list is used. If not present the reflection with the highest intensity < omthplot_strongint is taken. A series of vertical slit scans is executed over the reflection range, with omega and scan angle centeroffset varying as in an omega/2theta scan. The scan profiles are presentedas an omega/theta plot. |
|
Input:
|
Current cryst file ca'n'_config/holy.data: 1) omthplot_strongint: Maximum allowed intensity (18000) 2) omthplot_whole_delta_omega: Omega range (1.5) 3) omthplot_imin: Number of scans negative (15) 4) omthplot_imax: Number of scans positive (15) 5) omthplot_max_apt: Aperture range (4) 6) omthplot_scan_npi: Scan speed (3) 7) omthplot_scan_type: Scan type (6 i.e. omega/2theta) 8) omthplot_radius: Radius (173) |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 12)sphere: | Do data-collection on three wafers with one reflection fixed. Measure three sets of reflections from type 2kl, h2l and hk2, formingthree more or less mutually perpendicular half-cicular segments (signsof hkl chosen such as to measure as much as possible above the horizontal).From each set an intensity control reflection will be selected by selicrbelow. If Bravais = C : nrefls = nrefls * 2 If Bravais = I : nrefls = nrefls * 2 If Bravais = F : nrefls = nrefls * 4 If Bravais = H : nrefls = nrefls * 3 |
|
Input:
|
Current cryst file ca'n'_data/xxxxxx_trans.lis ca'n'_config/holy.data: 1) sphere_nrefls: Default nr. of refl.(33) 2) sphere_dmin: about 5 degrees Mo (4.0) 3) hkl_theta_mo: max. theta for Mo (30) 4) hkl_theta_cu: max. theta for Cu (75) |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 13)nonequal | Analyze if there are non-equal reflections (see example below). |
| 14)selocr | Select 3 reflections from current cryst file with approximately
the same theta and mutually perpendicular; create new cryst file (xxxxxx_meas.cry) with these reflections and their Friedel pairs as orientation control (OOORRR). Setang these reflections. |
|
Input:
|
Current cryst file |
|
Output:
|
New crystfile (xxxxxx_meas.cry) ca'n'_data/jobnnnn.cat |
| 15)check_o | Check 'H' status of orient reflection |
|
Input:
|
Current cryst file |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 16)selicr | Select 3 intensity control reflections from sphere data. |
|
Input:
|
Current cryst file ca'n'_data/xxxxxx_sphere.dat ca'n'_config/holy.data: 1) selicr_strong (25000) |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 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 |
|
Input:
|
Current cryst file |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 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. Index status should be HHHHHHHHH, otherwise an abortjob is created. |
|
Input:
|
Current cryst file |
|
Output:
|
New datfile (xxxxxx_prelim.dat) ca'n'_data/jobnnnn.cat |
| 19) hkl_limits | Set appropriate hkl limits. |
|
Input:
|
Current cryst file ca'n'_config/holy.data: 1) hkl_almost_zero: Allowed difference for determination of angles.eq. 90 (0.10) 2) hkl_almost_equal: Allowed difference for equal axes (0.005) 3) hkl_theta_mo: max. theta for Mo (30) 4) hkl_theta_cu: max. theta for Cu (75) |
|
Output:
|
ca'n'_data/jobnnnn.cat |
| 20) shells_file | Do data-collection on one or more theta-shells in FILE mode. |
|
Input:
|
Current cryst file ca'n'_data/xxxxxx_trans.lis datcol.done |
|
Output:
|
his.his shellnn.hkl for each shell 3 ca'n'_data/jobnnnn.cat files for every shell |
| 21) psi_scan | Do a Psi scan on suitable reflections. |
|
Input:
|
Current cryst file ca'n'_config/holy.data: 1) psi_scan_nref: (2) 2) psi_scan_maxsig: (10.0) |
|
Output:
|
ca'n'_data/jobnnnn.cat |
Example of using the one of the programs stand alone
CD0> files<CR>
CRY: ca0_data/a00000.cry
DAT: ca0_data/a00000_sphere.dat
HKL: ca0_data/a00000.hkl
LOG: ca0_data/a00000.log
CD0> run nonequal<CR>
full image =[cad4_system/nonequal]
Created:ca0_data/nonequal.inp
cad4_system/nonequal version 1.0
Read_Para cad4: 0 field: 2 ok.
Data from ca0_data/a00000_sphere.dat
111 Reflections
100 NonEqual0
6 NonEqual1
5 NonEqual2
CD0> go<CR>
& Opened ca0_data/job0010.cat
CD0> !! nonequal:NonEqual
CD0> !ARGUS 111 Reflections
CD0> !ARGUS 100 NonEqual0
CD0> !ARGUS 6 NonEqual1
CD0> !ARGUS 5 NonEqual2
CD0> !! nonequal finished
CD0> &JOB*
& Deleted ca0_data/job0010.cat
& No more files
CD0>
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