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koennecke
2005-03-03 13:54:07 +00:00
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commit 164682c028
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113
doc/user/mesure.htm
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@ -5,65 +5,72 @@
<BODY>
<H1>Reflection List Processor</H1>
<P>
This section describes the means for doing a standard single counter four
circle diffractometer measurement with SICS. A prerequisite for that is a
file with a list of reflections to measure. This is a simple file with
three floating point values per line giving the HKL of the reflection to
measure. Do not forget to put standard reflections into that file any now
and then. Another prerequisite is, that the UB-matrix had been determined
beforehand and that SICS has the updated values. Also check the value of
lambda in the hkl-object.
</P>
<p>
The measurement procedure is rather simple: If a reflection is accessible
the diffractometer is positioned on that reflection. Then a scan is done for
the reflection and data written to file. The scans all run with a fixed scan
widths, counter preset and countmode. There is a choice of omega scan or
omega two theta scan. It is known that there are more sophisticated
measurement schemes for four circle diffraction, but as TRICS is only
temporarily operated with a single counter not much optimisation seemed
necessary.
This module performs four circle diffractometer measurements with a single
counter . In a first view this
module takes a list of reflections as input, drive to each reflection in the list
and performs a scan for each reflection. Some more feautures are supported:
<ul>
<li>Two different input file formats are supported: the simplest contains a three
values for H,K,L per line. Some users prefer to perform the angle calculations
themselves; for such cases the input list can contain four values: two theta, omega, chi
and phi per line.
<li>This module supports phi scans: the reflection list must then contain H,K,L and phi
per line.
<li>Both measurements in normal bisecting mode and normal beam mode are supported.
<li>Optionally weak reflections can be remeasured with the preset multiplied by 5.
<li>Optionally scans are performed in fastscan mode: Between steps, the motor and the
counter are started at the same time. The step is finished when both operations terminate.
<li>The module maintains a table of two theta ranges and scan step widths and scan
variables. This allows to perform scans with varying step widths with two theta and to
switch between omega and omega - two theta scan mode.
</ul>
</p>
<p>
Three files will be written starting from a root such as tricsnumberyear.
For instance trics05601998 means file number 560 in 1998. The file ending in
Three files will be written starting from a root such as tricsyearnnumber.
For instance trics1998n000560 means file number 560 in 1998. The file ending in
.log will contain the console log. This is extremely verbose. Another file
ending with .col will contain the reflection, diffractometer settings and
the measured profile. The third file, ending with .rfl will contain for each
refelction, the HKL, the diffractometer settings and the intensity and sigma
intensity as calculated by the SICS internal integration routine. It does
a Grant Gabe integration (see J.Appl. Cryst (1978), 11, 114-120).
intensity as calculated by the SICS internal integration routine. A
Grant Gabe integration (see J.Appl. Cryst (1978), 11, 114-120) is performed.
</p>
<p>
For the purpose of the command description it is assumed, that this facility
is accessible as object mess within SICS.
is accessible as object dataset within SICS.
Interaction with this object happens through the following commands:
<dl>
<DT>mess start
<DT>dataset start
<DD>Creates a new set of files and writes some header info.
<DT>mess measure filename iSkip
<DT>dataset measure filename iSkip
<DD>Starts a measurement. Reads reflections from the file filename. iSkip is
an optional parameter which allows to skip iSkip lines in the file. This
is for recovery in cases of accidental or purposeful interruption
of the measurement.
<DT>mess genlist filename iSkip
<DT>dataset genlist filename iSkip
<DD>Mesures reflection from filename. The file is expected to have been
created by hklgen and to include all the angle settings. The optional
parameter iSkip determines the number of lines to skip in the file. This
feature allows to continue measurement on not fully processed files.
<DT>mess reopen filename
<DT>dataset reopen filename
<DD>Reopens an already existing file set for appending. Only the file root
without directory info or endings needs to be given.
<DT>mess close
<DT>dataset close
<DD>Closes the current data file set.
<DT>mess file
<DT>dataset file
<DD>Prints the current data file name.
<dt>dataset list
<dd>prints the current parameters.
<dt>dataset calc file
<dd>Tries to calculate all the reflections listen in file and prints an estimate how
many reflections are within limits. As file format only a H,K,L type file is
supported.
</dl>
Then there are a few parameter commands. They follow the general scheme:
<dl>
<DT>mess parameter
<DT>dataset parameter
<DD>Prints the current value of the parameter
<DT>mess parameter value
<DT>dataset parameter value
<DD>Sets the parameter to the new value.
</dl>
This object knows about the following parameters:
@ -72,9 +79,6 @@ This object knows about the following parameters:
<DD>The counting mode to use. Possible values are timer or monitor.
<DT>preset
<DD>The preset to use for counting
<DT>mode
<DD>The measurement mode. Posssible values are omega for omega scans and
omega2theta for omega two theta scans.
<DT>np
<DD>number of points to collect for each profile.
<DT>step
@ -82,16 +86,41 @@ omega2theta for omega two theta scans.
<DT>compact
<DD>Determines if the scan data output to the SICS is in normal
(compact = 0) or condensed (compact = 1) form. The default is 1.
<DT>weak
<DD>0 or 1: switches on special processing of weak reflections.
<DT>weakthreshold
<dd>The threshold used to decide what constitues a weak reflection. The test is:
max count in scan - 2* min count in scan.
<dt>fastscan
<dd>0 or 1: switches fastscan mode.
</dl>
</p>
<p>
mess supports two geometries: the first is the usual bisecting geometry. The
Then there are command which allow to configure the table of two theta ranges and
scan parameters. All table rleated commands start with: dataset table. The following
commands are supported:
<dl>
<dt>dataset table list
<dd>prints the content of the table.
<dt>dataset table add start end scanmode step
<dd>configures two theta range. start and end define the two theta range. scanmode can either
be om for omega scans or o2t for omega 2 theta scans. step is the step width to use.
<dt>dataset table del num
<dd>deletes the entry num from the table. Counting starts with 0!
<dt>dataset table clear
<dd>clears the whole table.
</dl>
When there is no two theta range configured for a given two theta value, the omega scan
mode applies with the step width given as a parameter to dataset.
</p>
<p>
dataset supports two geometries: the first is the usual bisecting geometry. The
second is the normal beam geometry where the detector is moved out of plane.
This si accounted for by two switches:
<dl>
<dt>mess bi
<dt>dataset bi
<dd>switches into bissectiong mode. This is the default.
<dt>mess nb
<dt>dataset nb
<dd>switches into normal beam mode.
</dl>
</p>
@ -102,19 +131,19 @@ files and continuation of reflection processing at a point way down the
reflection file is supported. Consequently the start of a new experiment
requires the following steps:
<ul>
<li>Create a new set of files with <b>mess start</b>.
<li>Create a new set of files with <b>dataset start</b>.
<li>Configure the scans with the parameter commands.
<li>Start processing a reflection file with either the <b>mess genlist</b>
or <b>mess measure</b> commands.
<li>Start processing a reflection file with either the <b>dataset genlist</b>
or <b>dataset measure</b> commands.
</ul>
If you need to continue reflection file processing after an abort or after
solving a problem the following steps are required:
<ul>
<li>Determine the file number you were working at and the line number in the
reflection file where you wish to continue processing.
<li>Set the file root with the <b>mess reopen</b> command.
<li>Set the file root with the <b>dataset reopen</b> command.
<li>Configure the scan parameters again.
<li>Restart the measurement with either <b> mess genlist</b> or <b> mess
<li>Restart the measurement with either <b> dataset genlist</b> or <b> dataset
measure</b> but specify the iSkip parameter according to the position in
the reflection file where processing should continue.
</ul>