+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. +
+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. +
+ ++The syntax is: +
autocloud options datafile ++The following options are known: +
+The autocloud algorithm has the following steps: +
+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 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. +
+ ++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. +
+ ++For the actual correlation of the template with the data two variantes +can be used: Normal simple correlation or cross correlation. +
+ ++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. +
+ ++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 @@ + + ++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: +
+As of now two packages are provided: +
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.
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).
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!
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.
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).
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.
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 @@ + + +
+Two special commands have been defined for TRICS with a PSD: +
+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: +
+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. +
+ ++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. +
+ ++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: +
+For indexing a variety of programs are available: +
+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. +
+ ++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: +
+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. + + +