From abb48f4b1019ed20ba5540398c1db3cdacc38204 Mon Sep 17 00:00:00 2001 From: cvs Date: Thu, 22 Jan 2004 13:39:18 +0000 Subject: [PATCH] - Added missing issing doc files --- doc/manager/rs232.htm | 76 ++++++++ doc/user/autocloud.htm | 151 ++++++++++++++++ doc/user/peaksearch.htm | 98 ++++++++++ doc/user/psddata.htm | 16 ++ doc/user/tascommands.html | 1 + doc/user/tasvariables.html | 1 + doc/user/trscan.htm | 34 ++++ doc/user/xds.htm | 359 +++++++++++++++++++++++++++++++++++++ 8 files changed, 736 insertions(+) create mode 100644 doc/manager/rs232.htm create mode 100644 doc/user/autocloud.htm create mode 100644 doc/user/peaksearch.htm create mode 100644 doc/user/psddata.htm create mode 100644 doc/user/tascommands.html create mode 100644 doc/user/tasvariables.html create mode 100644 doc/user/trscan.htm create mode 100644 doc/user/xds.htm diff --git a/doc/manager/rs232.htm b/doc/manager/rs232.htm new file mode 100644 index 00000000..febf668e --- /dev/null +++ b/doc/manager/rs232.htm @@ -0,0 +1,76 @@ + + +Direct Access to RS232 Controllers + + +

Direct Access to RS232 Controllers

+

+Usually serial ports are accessed by SICS through David Maden's +SerPortServer program which then communicates with a terminal server +box through the TCP/IP network. This limits the amount of control over +the controller. If more control is required, the RS232 controllers can +be accessed directly from SICS through the terminal server, thereby +bypassing the SerPortServer program. Please note, that these two modes +of operation are mutually exclusive: a given port can either be +accessed through the mechanism described here OR through +SerPortServer. +

+Before being able to use this system, the RS232 controller has to be +configured into SICS as described in the hardware initialization +section through the following command in the initialization file: +
+MakeRS232Controller name terminalserver port
+
+For example: +
+MakeRS232Controller hugo psts213 3004
+
+name is the SICS name for the controller, terminalserver is the name +of the terminal server the device is connected to and port is the port +number at which the terminal server publishes the RS232 channel to +which the device is connected. This is usally the port number plus 3000. +

+

+Now various commands are available for interfacing with the RS232 +controller. In the following description the SICS name of the +controller is replaced by the symbol rs232name. +

+
rs232name sendterminator +
prints the current terminator used when sending data to the device +as hexadecimal numbers. +
rs232name sendterminator h1h2..hn +
sets the current terminator used when sending data to the device +to the characters described by the hexadecimal numbers h1 to hn. The +numbers are in the format 0xval, where val is the hex number. +
rs232name replyterminator +
prints the current terminator expected to terminate a response +from the device as a hexadecimal number. +
rs232name replyterminator h1h2..hn +
sets the current terminator expected to terminate a response from +the device to the characters described by the hexadecimal numbers h1 +to hn. +The numbers are in the format 0xval, where val is the hex number. +
rs232name timeout +
prints the current timeout when waiting for a reponse from the +device. +
rs232name timeout val +
sets the timeout for waiting for responses from the device. The +value is in microseconds. +
rs232name send data data data +
sends the remainder of the line to the RS232 device and waits for +a response terminated with the proper reply terminator specified. This +commands waits at maximum timeout microseconds for a response. If a +valid response is obtained it is printed, otherwise an error message +occurs. +
rs232name write data data data +
writes the remainder of the line after write to the device without +waiting for a response. +
rs232 available +
checks if data is pending to be read from the device. +
rs232 read +
reads data from the device. +
+

+ + + diff --git a/doc/user/autocloud.htm b/doc/user/autocloud.htm new file mode 100644 index 00000000..b4050c0c --- /dev/null +++ b/doc/user/autocloud.htm @@ -0,0 +1,151 @@ + + +Autocloud + + +

Autocloud

+

+With the advent of position sensitive detectors in X-ray and neutron +diffraction the problem arises how integrated reflection intensities +may be extratcted from the collected volumes of data. Typically a +series of frames is measured while rotating the crystal under +investigation in omega. Autocloud implements a novel approach for the +extraction of reflection intensities from such data. Other currently +used integration packages use a UB-matrix to predict the position of a + reflection on the detector and then integrate the intensity in a box + around the predicted position. In contrast autocloud tries to + determine reflection +positions and intensities directly from the data. In order to do so a +template matching algorithm is used. One advantage of this approach is +that crystals with magnetic or incommensurate structures can be easily +analysed. Typically packages for intensity integration do not have +facilities for predicting such reflections. The other advantage is ease +of use. Data analysis with autocloud requires only two steps: +Integration followed by indexing. +

+ +

Running Autocloud

+

+The syntax is: +

autocloud options datafile
+
+The following options are known: +
+
-a val +
Selects the algorithm to use. The following algorithms are +currently supported: +
+
max +
perform only a local maximum search +
template +
Perform template matching. This is the default. +
cross +
Perform template matching using the cross correlation function. +
+
-b AAxBBxCC +
For the evaluation of the initial template a preliminary box size +is needed. This can be specified through this option. Three values +separated by the character 'x' are required, one for each dimension in +the order x, y, z. +
-d val +
After the correlation of the data volume with the template another +maximum search is started in order to locate the reflections. In order +to suppress spurious peaks, a minimum steepness of the candidate peak +can be set with the -d option. +
-e val +
Some systems store frames a single files. With the -e option the +end file number of the frame files can be set. +
-m val +
When the maximum search only option is set a, a threshold is +required for suppressing spurious peaks. This threshold can be set +with the -m option. +
-o file +
Redirects output to the file name specified. By default all output +is written to stdout. +
-s val +
Some systems store frames a single files. With the -s option the +start file number of the frame files can be set. +
-t type +
This option sets the type of the data file. Currently understood +are: +
+
sxd +
For NeXus data from SXD at ISIS. +
trics +
For NeXus data files from TRICS, SINQ +
debug +
An internal format used during software testing. +
+
-v val +
Increases the verbosity of the output. +
+

+ +

The Autocloud Algorithm

+

+The autocloud algorithm has the following steps: +

    +
  1. Location of strong peaks for template evaluation. +
  2. Background Subtraction. +
  3. Evaluation of a template for volume matching. +
  4. Correlation of the template with the data volume. +
  5. Location of maxima in the correlated data. +
  6. Integration of the reflections found. +
+

+

Location of Strong Peaks for Template Evaluation

+

+This is basically a local maximum detection scheme. A local maxima +must be the strongest intensity within a 7 by 7 by 7 volume. All +maxima smaller then 10% of the largest maximum found are discarded. +

+ +

Background Subtraction

+

+Background subtraction is done with essentially the same algorithm XDS +uses. For each x, y coordinate in the frame values are summed along +the third dimension. Points belonging to a local maimum are +excluded. The background +for this x,y coordinate is then the average of the values +summed. The data volume is then corrected for the background with +these values. This works well as long as the assumption holds that the +background varies mostly across the detector and not much with the +third dimension. +

+ +

Template Evaluation

+

+The template to be used for template matching later on is calculated +by summing all local maxima first. Then the limits of the reflection +are calculated for each scanline using the Lehmann-Larsen +algorithm. The reflection thus found is scaled to a value of 1 and +used as the template. +

+ +

Template Matching

+

+For the actual correlation of the template with the data two variantes +can be used: Normal simple correlation or cross correlation. +

+ +

Peak Detection

+

+This is again a local maximum detection within a 7 by 7 by 7 +box. Another criterium for the supression of wrong identifications is +a minimum steepness. This means that the candidate local maximum must +at least be higher by a certain amount (the steepness) then the points +at the border of its 7 by 7 by 7 box. +

+ +

Peak Integration

+

+A scale factor is calculated for each candidate reflection between the +data and the template. The intensity is derived from this scale factor +and the standard deviation is calculated as the squared difference +between the scaled template and the data. This scheme is the same as +learnt profile fitting as described by Ford for the 1- and 2d cases. +

+ + + + diff --git a/doc/user/peaksearch.htm b/doc/user/peaksearch.htm new file mode 100644 index 00000000..99c789fe --- /dev/null +++ b/doc/user/peaksearch.htm @@ -0,0 +1,98 @@ + + +TRICS PSD Peak Search + + +

TRICS PSD Peak Search

+

+For almost any measurement at TRICS a UB matrix has to be determined +beforehand. In order to do this a couple of peak must be located by +some means. This section describes how the computer can help in +finding an initial set of peaks. +

+

+The algorithm is quite simple: It consists of a big loop over ranges + of the four circle angles two theta, omega, chi and phi. At each + position a counting operation is performed. Then peaks are located on + all three detectors through a local maximum search. For this, the +local maximum search module is used. +If a candidate + peak is found, it is refined in omega and written to a file. The + tricky bit is the adjustement of the local maximum search parameters + in order to minimize false maxima caused by a spicky background or + powder lines. +

+

+The peak search facility need a lot of parameters in order to +operate. This includes angle ranges, count parameters and the maximum +search parameters. Commands are provided for adjusting these +parameters. The general operation of these commands follow a pattern: +typing the command alone prints the current values of the +parameters. In order to set new values the command name must be typed +plus new values for all the parameters listed by this command. An +Example: +

+ps.sttrange
+
+prints the range in two theta for the peaksearch. +
+ps.sttrange startval endval step
+
+sets new values for the two theta range and prints them afterwards. +The following commands are provided: +
+
ps.sttrange +
adjustment of the two theta range for the peak search. +
ps.omrange +
adjustment of the omega range for the peak search. +
ps.chirange +
adjustment of the chi range for the peak search. +
ps.phirange +
adjustment of the phi range for the peak search. +
ps.countpar +
adjustment of the counting parameters for the peak search. +
ps.scanpar +
adjustment of the parameters used by ps.scanlist for scanning +located peaks. See below. +
ps.maxpar +
Adjusts the maximum finding parameters for the peak search. These +parameters need some explanation: +
+
window +
window is the size of the quadratic area which will be searched + around each point in order to determine if it is a local maximum. +
threshold +
This is a minimum intensity a candidate local maximum must have + before it is accepted as a peak. The value given is multiplied + with the average counst on the data frame before use. This threshold + is the strongest selection parameter. +
steepness +
A candidate peak should drop of towards the sides. This is + tested for by checking if the pixels on the borders of the local + maximum detection window are below maximum value - steepness. +
cogwindow +
In order to refine the peaks position a center of gravity + calculation is perfomed. For this calculation pixels within the + cogwindow around the candidate peak position are considered. +
cogcontour +
In order not to base the COG calculation on background pixels, + only pixels above cogcontour * maxvalue are used for the + calculation. With the spicky background at TRICS .5 seems a good value. +
+
ps.list +
lists all parameters for the peak search. +
ps.listpeaks +
lists all the peaks already found. +
ps.run filename +
starts the peak search and stores peaks identified in file + filename. +
ps.continue +
continues a peak search which was interrupted for one reason or + another. +
ps.scanlist +
performs an omega scan for each reflection found in the current + peak list. +
+

+ + diff --git a/doc/user/psddata.htm b/doc/user/psddata.htm new file mode 100644 index 00000000..98b4e7e8 --- /dev/null +++ b/doc/user/psddata.htm @@ -0,0 +1,16 @@ + + +TRICS PSD Data Analysis + + +

TRICS PSD Data Analysis

+

+As of now two packages are provided: +

+

+ + diff --git a/doc/user/tascommands.html b/doc/user/tascommands.html new file mode 100644 index 00000000..4fcc5a58 --- /dev/null +++ b/doc/user/tascommands.html @@ -0,0 +1 @@ +

TASMAD Commands


AU  AUto          : Put motors in auto mode, positions are updated.
AS  ASsign        : Assign Power Supplies.
CK  ChecK         : Checks syntax of jobfile.
CL  CLear         : Unfixes one or more motors or power supplies.
CO  COunt         : Counts for given preset TIme or MoNitor.
DO  DO            : Runs a jobfile without testing the syntax first.
DR  DRive         : Changes a variable and drives spectrometer to
			its new position.
EX  EXit          : Exit.
FI  FIx           : Fixes a given motor or power supply, FIx without
			argument will give a list of fixed motors and
			power supplies.
FM  FindMax       : As FindZero but SetZero is not performed, the 
			spectrometer is only driven to the maximum.
FZ  FindZero      : Scans a simple variable, finds maximum, drives to 
			maximum and performs a SetZero with the given
			value.
HE  HElp          : The MAD help facility in started up.
LI  LIst          : Listing of variables and parameters.
			LE ListEnergies    Energies, k and Q values.
			LL ListLimits      Limits and zeros.
			LZ ListZero        Limits and zeros.
			LM ListMach        Machine parameters.
			LS ListSample      Sample parameters.
			LT ListTargets     Targets and positions.
			LD ListDiaphragms  Diaphragms.
			LP ListPower       Power supply values.
LO  LOg           : Controls terminal logging.
MT  MTe           : Move temperature to new value.
OF  OFf           : Turns flipper off.
ON  ON            : Turns flipper on.
OU  OUtput        : Defines output variables.
PA  Pol.An.       : Defines a polarization analysis file (default
			file ext'n is .PAL).
PL  PLot          : Plot a spectrum on the terminal.
PR  PRint         : Prints one ore more variables or parameters.
PT  PTe           : Set temperature and Pause.
RT  RTe           : Read temperature from ILLPTC.
RU  RUn           : Runs a jobfile.
SA  SAve          : Makes a TMP**.SCN file permanent as next SV****.SCN.
SC  SCan          : Scans a variable with given or previously
			defined increment, number of points and
			time interval or monitor count.
SE  SEt           : Sets a parameter value.
SF  ScanFast      : Scans a variable quickly.
ST  STatus        : Gives status of one or more motors.
SW  SWitch        : Sets some switches.
SZ  SetZero       : Set zero in such a way that value as given
			is defined as actual position of variable
			(works only for simple variables, i.e.
			variables that have a zero).
WA  WAit          : Wait for temperature to be within range
			(target_temp-DTL) to (target_temp+DTU)
			or time-out of TO minutes.

Special commands

MAD recognises the following special commands:
set title ...
Sets the title string (up to 72 characters) to be written to the data file header.
set user ...
Sets the experiment user's name (6 characters).
set local ...
Sets the local contact's name (6 characters).
set xou 0
Turns off the log file.
set xou 1
Turns on the log file.
! ...
Any command line beginning with ! will be ignored (comment).
Comment by DM: From looking at the code, I think that the "set xou" commands should not be used any more. They seem to have been superseded by the log command. \ No newline at end of file diff --git a/doc/user/tasvariables.html b/doc/user/tasvariables.html new file mode 100644 index 00000000..4ec52914 --- /dev/null +++ b/doc/user/tasvariables.html @@ -0,0 +1 @@ +

TASMAD Variables


	Variables are divided into five groups:  

	(i) parameters which define some aspect of the instrument configuration
	but are not directly related to a motor angle or power supply value. 
	These variables are changed by the SET command.

	(ii) parameters which relate to the sample.These are also changed by 
	SET.

	(iii) limits and zeroes for motors and power supplies, also changed by 
	SET.

	(iv) Variables which are explicitly or implicitly related to a motor 
	position or power supply value. These variables are changed by the 
	DRive command.

	(v) Increments (steps) for the variables of type (iv); these are changed
	 by SET.

	The following list gives the variable identifiers and definitions, 
	where the order is as the variables are stored in THE Program.


	 P.A Variables : Variables marked with an asterisk are not recognized 
	unless THE  Program is run in polarization analysis mode(see SWitch).

Instrument variables


DM 	Monochromator d-spacing 		[].
DA 	Analyzer d-spacing 			[].
SM	Scattering sense at Mono 		(+ve to the left)
SS	Scattering sense at Sample 		(+ve to the left)
SA 	Scattering sense at Analyzer 		(+ve to the left)
ALF1	Horizontal collimation before mono 	[minutes FwHm]
ALF2	Horizontal collimation mono to sample	[minutes FwHm]
ALF3	Horizontal collimation sample to anal. 	[minutes FwHm]
ALF4	Horizontal collimation before detector 	[minutes FwHm]
BET1	Vertical collimation before mono   	[minutes FwHm]
BET2	Vertical collimation mono to sample 	[minutes FwHm]
BET3	Vertical collimation sample to analyzer [minutes FwHm]
BET4	Vertical collimation before detector 	[minutes FwHm]
ETAM	Monochromator mosaic 			[minutes FwHm]
ETAA	Analyzer mosaic 			[minutes FwHm]
FX 	=1 for constant Ki;	=2 for constant Kf
NP 	Number of points in a scan
TI 	Preset time [seconds] for a COunt or SCan
MN 	Preset monitor for a COunt or SCan
TO 	Time-out in for WAit command 		[minutes]
DTL	lower temperature error allowed  	[Kelvin]
DTU	upper temperature error allowed 	[Kelvin]

*IF1V	IF1V and IF2V are currents [Amps] in the vertical-field
*IF2V	coils for Flipper 1 and Flipper 2.
*IF1H	Horizontal-field currents are KI*IF1H for Flipper1 and
*IF2H	KF*IF2H for F2.
*HELM  Angle between axis of Helmholtz pair one and KI.

remark:  ALF1 to ETAA are not used by MAD Program but stored for your own 
	convenience.
	Please DO NOT FORGET to update ALF1-ALF4 variable after collimator 
	change to avoid confusion when you analyse your data after one or 
	two years!

Sample variables


AS  -\
BS    +--  Sample unit-cell edges	[]
CS  -/

AA  -\
BB    +--  Sample unit-cell angles 	[degrees]
CC  -/

ETAS	Sample mosaic			[minutes FwHm]

AX  -\
AY    +--  Components of a recip. lattice vector in scattering plane
AZ  -/       of the sample. A3 is the angle between KI and (AX,AY,AZ).

BX  -\
BY    +--  Components of a second distinct recip. lattice vector in
BZ  -/       the sample's scattering plane.

Limits and Zeros


	Lower and upper limits and zeros for all variables given in (iv) 
	below. L, U and Z are appended as a prefix to the variable names to 
	indicate Lower limit, Upper limit and Zero.
	Storage order is the same as for the corresponding variables, i.e. : 
	LA1, UA1, ZA1, LA2, UA2, ZA2, LA3 ... 
	(see (iv) below).

Targets and Positions


A1	Monochromator angle 		(Bragg angle in degrees)
A2 	Scattering angle at mono.	(twice Bragg angle in degrees)
A3	Sample angle (degs) 		(A3=0 when (AX,AY,AZ) is along KI)
A4	Scattering angle at sample 	[degrees]
A5	Analyzer angle 			(Bragg angle in deg, TOPSI: not used)
A6	Scattering angle at analyzer	(twice A5 in deg.,   TOPSI: not used)

	SINQ Instruments:
MCV	Mono curvature vertical
SRS	Sample table second ring
ACH	Anal curvature horizontal
MTL	Mono   lower translation
MTU	Mono   upper translation
STL	Sample lower translation
STU	Sample upper translation
ATL	Anal   lower translation
ATU	Anal   upper translation
MGL	Mono   lower goniometer		(Reserved)
MGU	Mono   upper goniometer
SGL	Sample lower goniometer
SGU	Sample upper goniometer
AGL	Anal   lower goniometer		(Reserved)
AGU	Anal   upper goniometer
MSC	Mono   "sample" changer		(TASP only)
ASC	Anal   "sample" changer		(TASP only)
CSC	Collimator "sample" changer	(TASP only)

D1T D1B D1R D1L Diaphragm 1 (top/bottom/right/left)
D2T D2B D2R D2L Diaphragm 2 (top/bottom/right/left)
D3T D3B D3R D3L Diaphragm 3 (top/bottom/right/left)

	ILL Instruments:
	CH 	Monochromator changer position 	[degrees or mm]
	TM (LM)	Monochromator translation 	[(IN20 : 5mm)]
	GM	Monochromator goniometer angle 	[1 unit = 4]
	RM	Monochromator curvature
	GL	Sample goniometer angle; lower arc 	[1 unit = 4]
	GU 	Sample goniometer angle; upper arc 	[1 unit = 4]
	TA 	Analyzer translation 		[ ? mm]
	GA 	Analyzer goniometer angle 	[ .4degrees]
	RA	Analyzer curvature

EI 	Incident neutron energy 	[THz or meV]
KI 	Incident neutron wavevector 	[ -1]
EF 	Final neutron energy 		[THz or meV]
KF 	Final neutron wavevector 	[ -1]

QH  -\
QK    +--  Components of Q in Reciprocal Lattice Units [R.L.U.]
QL  -/

EN	Energy transfer; +ve neutron energy loss 	[THz or meV]
QM	Length of Q 				[ -1]
TT (T)	Temperature of sample thermometer 	[K]
TRT(RT)	Temperature of regulation thermometer 	[K]
	   (can only be printed out)
*I1   -\
*I2     \
*I3   	 +--  power supply current values [A]
 .      /
*I11  -/

*HX   -\     Components of Helmholtz fields at sample in Oersteds.
*HY   	+--  HX is parallel to Q and HY is perpendicular to Q in
*HZ   -/     the scattering plane.

*F1   -\     Status of flippers one and two; these variables take the 
*F2   -/     values ON or OFF.

Increments Variables

	For all variables A1 through T in the  list of type (iv) variables 
	above, the identifier for the step used with a SCan command is obtained
	by prefixing the variable name with the letter D.
	Storage order is DA1, DA2, DA3....etc as for type (iv) variables above.
\ No newline at end of file diff --git a/doc/user/trscan.htm b/doc/user/trscan.htm new file mode 100644 index 00000000..5c3e22de --- /dev/null +++ b/doc/user/trscan.htm @@ -0,0 +1,34 @@ + + +TRICS specific Count and Scan Command + + +

PSD-TRICS Count and Tricsscan Command

+

+Two special commands have been defined for TRICS with a PSD: +

+
count mode preset +
counts with all three detectors. The parameter mode defines which + counting mode is used, supported are preset for counting up to a + preset monitor or timer for counting for a specified time intervall. + The second prameter preset is either the preset monitor or the preset + counting time, depending on the mode choosen. Both parameters are + optional, if they are notc specified values from the last run will be used. + count does not store any data. +
tricsscan start step np mode preset +
This command creates a new data file and then performs a scan in omega, + storing meausured data after each step. start step np define the + scan range in omega. Start is the start position, step the step width to + use and np is the number of steps to do. The optional parameters mode and + preset have the same meaning as in the count command described above. + Mode and preset how data is collected at each step in omega. +
psdrefscan filename step np mode preset +
reads reflection HKL values from file filename and performs +tricsscans for each reflection. These will be done eith step width +step, the number of steps np with counting mode mode and a preset of +preset. These parameters have the same meaning as described above. +
+

+ + + diff --git a/doc/user/xds.htm b/doc/user/xds.htm new file mode 100644 index 00000000..12cf97d8 --- /dev/null +++ b/doc/user/xds.htm @@ -0,0 +1,359 @@ + + +TRICS Data Analysis with XDS + + +

TRICS Data Analysis with XDS

+

+A set of programs exist for TRICS data analysis which have been derived from +the XDS package designed and written by Wolfgang Kabsch. Due to the different + diffraction geometry at TRICS the program had to be subdivided. Data Analysis +with this system requires four steps: +

    +
  1. Location of strong diffraction spots with the program spots. +
  2. Indexing of diffraction spots and refining of a UB matrix with programs of + your choice. +
  3. Integration of the diffraction spots with the program reflex. +
  4. Optionally, reflections collected in various runs can be merged +with the program xscale. +
+The main limitation of this software is that only reflections at normal +lattice positions can be analysed. Magnetic or superstructure reflections +will not be integrated due to the fact that XDS uses predicted reflection +positions for integration and has no facilities to predict either magnetic +or superstructure reflections. +

+

LEGAL STUFF

+

+The programs spots, reflexand xscale are no +official versions of XDS. The responsability for these programs lies +with PSI and not with Wolfang + Kabsch. Binaries of the above mentioned programs may be distributed, but + according to an agreement with Wolgang Kabsch the source code may not be + redistributed. If you are interested in an official version of XDS, please + contact Wolgang Kabsch directly. +

+ +

Spots and reflex Control File

+

+The programs spots and reflex both require a control file + to be specified as a command line parameter. The format of this control + file resembles a Windows .ini file and is common for both programs. The syntax +is: keyword = value. +

+ +

Running spots

+

+The purpose of spots is to search for strong diffraction spots +in the data and write them out in a format suitable for +indexing. spots can be started by typing: +

+spots controlfile
+
+at the unix command prompt. All necessary parameters live in the +control file. spots recognizes the following keywords in the control +file: +
+
numfiles +
The number of files to process. +
fileXX +
Replace XX by the number of the file. For instance file00 is the +first file to process. The value for this keyword is the filename to +process. +
numdetectors +
The number of detectors to process. TRICS can have up to three +detector banks, if the electronics group finally makes them available +by an act of grace. +
det1dist, det2dist, det3dist +
The respective distances of the detectors from the sample +positions. +
det1x, det2x, det3x +
The number of pixels each detector supports in the x-direction. +
det1y, det2y, det3y +
The number of pixels each detector supports in the y-direction. +
+
det1pixx, det2pixx,det3pixx +
The size of a detector pixel in x-direction in mm for each detector. +
det1pixy, det2pixy,det3pixy +
The size of a detector pixel in y-direction in mm for each +detector. +
wavelength +
The neutron wavelength. +
bifile +
Switches on the writing of reflection positions converted to +bissecting positions as from a normal four circle diffractometer. The +value is the name of the file to which to write the list. +
nbfile +
Switches on the writing of reflection positions converted to +normal beam positions as from a normal beamdiffractometer. The +value is the name of the file to which to write the list. +
xyzfile +
Switches on the writing of reflection positions in XYZ format. The +value is the name of the file to which to write the list. +
+bifile, nbfile or xyzfile are choices. Chhose the one which fits best +with your preferred indexing program. +

+

Indexing and UB Matrix Refinement

+

+For indexing a variety of programs are available: +

+

+

Running orient

+

+In order to start orient, type orient at the unix prompt. A +selection dialog for the file type will show up. Select 2, then give +the path to the file created with the spots option bifile. You will +also be asked for the neutron wavelength. The following dialogs are +self explaining. When orient finishes, the new UB matrix can be found +in either the LPT1 or printer.out file. +

+ +

Running reflex

+

+reflex is controlled through the same style control.ini file as +used by spots. The options specified for spots have to be +present in the control file for reflex as well. Additionally the +following options are required: +

+
ub1, ub2, ub3 +
The three rows of the UB-matrix as determined by one of the +indexing programs. +
axis=0 0 -1 +
These are the coordinates of the rotation axis in XDS's own +coordinate system. Leave this at the values stated, +everything else is shit if you are using TRICS. +
beam=0 1 0 +
These are the coordinates of the incoming neutron beam in XDS's own +coordinate system. Leave this at the values stated, +everything else is shit if you are using TRICS. +
polarisation=.5 1 0 0 +
Some values for handling X-ray polarisation. Leave at the values +given. +
spacegroup +
Set this to the space group selected. Expected is the number of +the space group as given in the international tables. +
divergence +
The beam divergence. See below for a comment. +
mosaic +
The crystal mosaic. mosaic and divergence together determine the +size of the box in reciprocal space which will be integrated for each +reflection. reflex writes a representation of the integration box and + of the reflection to its output file (PROFIT.LP). Inspect this + carefully. If reflections are cut of in the reflection box or the + reflection box is to large, modify these values in order to achieve a + good fit. As more experience is gathered, the instrument scientist + will be able to provide you with reasonable defaults for these values. +
+reflex is run by typing reflex control.ini at the unix +prompt. control.ini is the name of the control file. PROFIT.LP is the +main log file which shows what has been done. PROFIT.HKL is a binary +file holding the reflections integrated. +

+ +

Running xscale

+

+xscale has not been modified since it has been received from +W. Kabsch. Therefore the original documentation, reproduced below is +still valid. +

+C***********************************************************************
+C********************** DESCRIPTION OF FILES ***************************
+C***********************************************************************
+C                                                                      *
+C                     XSCALE.INP     (formatted sequential)            *
+C                     ==========                                       *
+C                                                                      *
+C This file contains the input parameters you have to provide to run   *
+C the XSCALE program.(free format)                                     *
+C                                                                      *
+C line #            DESCRIPTION OF INPUT PARAMETERS                    *
+C                                                                      *
+C   1      Resolution shell limits (Angstrom). Only the high resolution*
+C          limit of each shell is given. Up to NRES (20) resolution    *
+C          shells will be accepted. The shell limits must be specified *
+C          in decreasing order. The resolution shells are used to      *
+C          report statistical properties of the data sets as a function*
+C          of resolution.                                              *
+C   2      Space group number and unit cell parameters                 *
+C          (Angstrom and degrees)                                      *
+C   3...   Each line describes a reflection file used for scaling      *
+C          and contains the following items:                           *
+C          >Optional control character - or * of the following meaning *
+C            -: ignore this data set (this line will be skipped)       *
+C            *: put all data sets to the same scale as this one;       *
+C               default is the first data set.                         *
+C          >File name of data set used for scaling.                    *
+C            The name must not be longer than 50 characters and        *
+C            intervening blanks are not allowed.                       *
+C          >File type must be one of the three following keywords      *
+C            DIRECT: the file is of type XDS.HKL as generated by XDS.  *
+C            UNIQUE: the file is of type UNIQUE.HKL as produced by XDS.*
+C            OLDHKL: the ASCII file consists of free format records    *
+C                    H,K,L,INTENSITY,SIGMA                             *
+C                    The standard deviation SIGMA may be omitted and   *
+C                    is estimated then as SIGMA=0.1*INTENSITY          *
+C                    Reflection data files of type UNIQUE or OLDHKL    *
+C                    may be unsorted and the reflection indices need   *
+C                    not be the asymmetric indices. This simplifies    *
+C                    the scaling of data sets generated by other       *
+C                    programs than XDS.                                *
+C          >Resolution window for accepting reflections from this file *
+C            low  resolution limit (Angstrom)                          *
+C            high resolution limit (Angstrom)                          *
+C          >Frame separation (mandatory for data sets of type DIRECT)  *
+C            specifying the maximum number of frames between FRIEDEL-  *
+C            pairs to be included in the estimated anomalous intensity *
+C            difference.                                               *
+C          >Number of batches (optional for data sets of type DIRECT)  *
+C            This number gives the number of subdivisions of the       *
+C            rotation range covering the data set. Typically, it is    *
+C            the total rotation range divided by 2.5...5 degrees, but  *
+C            should not exceed a value of 36. This leads to at most    *
+C            9*36=324 scaling factors for a single data set. The total *
+C            number of scaling factors from all data sets together     *
+C            must not exceed the value given by "MAXFAC" (1000).       *
+C          >SAVE=file-name (optional); default file-name is XSCALE.HKL *
+C            The type of the SAVE-file produced is UNIQUE. Symmetry    *
+C            related reflections from input data sets sharing the same *
+C            SAVE-file are used after scaling to estimate a mean       *
+C            intensity, an anomalous intensity difference, and their   *
+C            standard deviations. Scaling factors for each data set    *
+C            are determined from all symmetry related reflections      *
+C            regardless whether they go to different SAVE-files.       *
+C                                                                      *
+C***********************************************************************
+C                                                                      *
+C                     XSCALE.LP      (formatted sequential)            *
+C                     =========                                        *
+C                                                                      *
+C This file contains the printed messages and results from running the *
+C XSCALE-program.                                                      *
+C                                                                      *
+C***********************************************************************
+C                                                                      *
+C Description of XSCALE input file format of type DIRECT as produced   *
+C by XDS.                                                              *
+C                                                                      *
+C                       XDS.HKL  (unformatted direct access)           *
+C                       =======                                        *
+C                                                                      *
+C The corrected reflection intensities are saved on this unformatted   *
+C direct access file of record length 68 bytes for each reflection.    *
+C The file is sorted with respect to the unique reflection indices.    *
+C This means:                                                          *
+C  For each reflection with the original indices H,K,L all symmetry    *
+C  equivalent indices are generated including Friedel related ones.    *
+C  Among all these indices we choose the unique reflection indices     *
+C  HA,KA,LA in the following order: HA is the largest H-index, among   *
+C  those with the same HA-value select those with the largest K-index  *
+C  which is KA, and finally the largest L-index which is called LA.    *
+C  The unique indices HA,KA,LA thus found are packed into a 32-bit     *
+C  word  KEY=(LA+511)+(KA+511)*1024+(HA+511)*1048576  .                *
+C  The reflections are then sorted in growing values of KEY.           *
+C                                                                      *
+C                     Record structure                                 *
+C                                                                      *
+C  16bit-WORD #                     CONTENTS                           *
+C       1         HA    (The last record is indicated by HA=10000)     *
+C       2         KA     HA,KA,LA are the unique reflection indices.   *
+C       3         LA     Any two reflections have the same unique      *
+C                        indices if and only if they are related by    *
+C                        symmetry. (HA,KA,LA are integer*2)            *
+C       4          H     Original reflection indices H,K,L.            *
+C       5          K     H,K,L are integer*2.                          *
+C       6          L                                                   *
+C       7          S     Identifying number of symmetry operator used  *
+C                        to go from original to unique indices.        *
+C                        (integer*2). A negative sign indicates that   *
+C                        a mirror operation has been applied. This     *
+C                        information may be useful if a special        *
+C                        treatment for anomalous differences is        *
+C                        required which goes beyond the method of      *
+C                        the XDS-program.                              *
+C       8        IPEAK   Percentage of observed reflection intensity.  *
+C                        A value less than 100 indicates either a      *
+C                        reflection overlap or bad spots in the profile*
+C       9        ICORR   Percentage of correlation (integer*2) between *
+C                        observed and expected reflection profile.     *
+C     10,11      FFADD   LP-corrected intensity of this reflection     *
+C                        obtained by straight summation of counts      *
+C                        within spot region ( background subtracted).  *
+C                        The intensity is also corrected for radiation *
+C                        damage and absorption.      (real*4)          *
+C     12,13      SDADD   Standard deviation of FFADD.(real*4)          *
+C     14,15      RLP     Reciprocal LP-correction factor (real*4)      *
+C       16      ABSCAY   Combined absorption and decay correction      *
+C                        factor*1000 (integer*2).                      *
+C                        In case you want to remove this calculated    *
+C                        correction, divide intensities and standard   *
+C                        deviations by ABSCAY/1000.0  .                *
+C       17       IALFA   IALFA and IBETA (both integer*2) are polar-   *
+C       18       IBETA   coordinates of the spindle axis in units of a *
+C                        hundreth of a degree. The lab coordinates of  *
+C                        the spindle axis are:                         *
+C                        Ux=sin(BETA)*cos(ALPHA)                       *
+C                        Uy=sin(BETA)*sin(ALPHA)                       *
+C                        Uz=cos(BETA)                                  *
+C                        where ALPHA=IALFA/5729.578,                   *
+C                              BETA =IBETA/5729.578.                   *
+C       19       IFRM    Frame number at diffraction of this reflection*
+C                        (integer*2)                                   *
+C       20       PHI     Calculated spindle position for this          *
+C                        reflection at diffraction in units of a       *
+C                        hundreth of a degree. (integer*2)             *
+C       21        IX,    Calculated detector x- and y-coordinates for  *
+C       22        IY     this reflection at diffraction in units of a  *
+C                        tenth of a pixel times 512.0/NX and 512.0/NY, *
+C                        respectively. NX, NY are the numbers of pixels*
+C                        along the detector X- and Y-axis.             *
+C                        IX,IY are integer*2.                          *
+C     23-28       S0     Laboratory coordinates of direct beam wave-   *
+C                        vector ( rec. Angstroem). S0 points from the  *
+C                        x-ray source towards the crystal.             *
+C     29-34       S1     Laboratory coordinates of scattered beam wave-*
+C                        vector. Length is 1.0/lambda (rec. Angstroem) *
+C                        S0 and S1 are real*4 arrays of length 3. S1   *
+C                        points from the crystal towards the detector. *
+C                        At diffraction, laboratory coordinates of the *
+C                        reflection H,K,L are: S1(.)-S0(.)             *
+C                                                                      *
+C***********************************************************************
+C                                                                      *
+C Description of XSCALE input file format of type UNIQUE as produced   *
+C by XDS.                                                              *
+C                                                                      *
+C                       UNIQUE.HKL (formatted sequential)              *
+C                       ==========                                     *
+C                                                                      *
+C              DESCRIPTION OF SHORT OUTPUT FILE                        *
+C                                                                      *
+C Symmetry related reflections are averaged and written with           *
+C FORMAT(3I5,4E12.4). Each record consists of                          *
+C                                                                      *
+C   HA,KA,LA,INTENSITY,STANDARD DEVIATION OF INTENSITY,                *
+C   ANOMALOUS INTENSITY DIFFERENCE,STANDARD DEVIATION OF DIFFERENCE    *
+C                                                                      *
+C where HA,KA,LA are the unique reflection indices. The file is sorted *
+C with respect to these unique reflection indices. The last record     *
+C is indicated by HA=10000.                                            *
+C Unobserved ANOMALOUS INTENSITY DIFFERENCE and its STANDARD DEVIATION *
+C are both set to zero.                                                *
+C                                                                      *
+C***********************************************************************
+
+xscale can be started by typing xscale at the unix +prompt. Please note that xscale expects an input file named XSCALE.INP +in the current directory. +

+ +