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koennecke
2006-05-08 02:00:00 +00:00
committed by Douglas Clowes
parent ae77364de2
commit 6e926b813f
388 changed files with 445529 additions and 14109 deletions
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77
doc/user/Conescan.html Normal file
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<html><head><title>Conescan.radi</title></head><body>
<h2>Conescan </h2>
<p>A conescan is a possibly useful procedure when setting up a single crystal
diffraction experiment. The first thing which needs to be done when
starting a single crystal experiment is the determination of the UB
matrix. In order to do that at least two reflections need to be
located through a search procedure. Now, consider the situation when
one reflection has been found and indexed. Then it is known that other
reflections can be found on a cone
with an opening angle determined by the lattice parameters and the
indices of the target reflection around the first (center)
reflection. The SICS conescan module allows to do just that, do a scan
around a given center reflection. The syntax is:
</p></p><dl><dt>conescan list
<dd> lists all the parameters of the conescan
<dt>conescan cell
<dd> prints the cell constants.
<dt>conescan cell a b c alpha beta gamma
<dd> sets new cell constants.
<dt>conescan center
<dd> prints the current values for the center reflection
<dt>conescan center h k l
<dd> uses h, k, l as the indices of the center
reflection. Motor positions are read from motors.
<dt>conescan center h k l stt om chi phi
<dd> defines a center position
complete with all angles.
<dt>conescan target
<dd> prints the current target for the conescan
<dt>conescan target h k l
<dd> defines the target indices for the conescan.
<dt>conescan qscale
<dd> prints the Q scale for the conescan. The conescan
module calculates the length of then scattering vector from the
lattice parameters and the indices. When the lattice constants are
only approximatly known it might be useful to vary the scattering
vector length for the conescan a little. This can be doen with the
qscale factor.
<dt>conescan qscale value
<dd> sets a new value for the qscale factor
<dt>conescan run step mode preset
<dd> starts a conescan with the nstep width
step, the couent mode mode and the preset preset.
<dt>conescan run
<dd> starts a conescan with defaults: step = .5,
mode = monitor, preset = 10000
<p></dl>This is the simple usage of the conescan. In fact cone is implemented
as a virtual motor. This means that arbitray scans can be performed on
cone as with any other motor. As with any other motor, cone can also
be driven to a cone angle.
</p></p><h3>Implementation Reference </h3>
<p>The conescan commands are just wrapper routines around the cone and
ubcalc module which actually work together to implement the
conescan. The ubcalc module, documented elsewhere, holds the cell
constants and the center reflection.
</p></p><p>The cone module does the actual cone calculation. Cone can be
configured with commands:
<dl></p><dt>cone center
<dd> prints the number of the reflection in ubcalc to use as
a center.
<dt>cone center num
<dd> sets the reflection in ubcalc to use a the center
for driving on the cone. Set to 0 to use the first reflection in
ubcalc.
<dt>cone target
<dd> prints the target reflection indices for the cone.
<dt>cone target h k l
<dd> sets the target reflection indices.
<dt>cone qscale
<dd> prints the current value of the scattering vector scale.
<dt>cone qscale val
<dd> sets a value for the scaling factor for the
scattering vector. Values should be close to 1.0;
</dl></body></html>

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@ -4,7 +4,7 @@
# Mark Koennecke, Juli 1998
#------------------------------------------------------------------------
all: topsi dmc sans focus poldi
all: topsi dmc sans focus poldi tricsman userrefman
topsi:
html2tex topman
@ -30,4 +30,20 @@ poldi:
html2tex poldiman
latex poldiman
latex poldiman
dvips -o poldiman.ps poldiman.dvi
dvips -o poldiman.ps poldiman.dvi
poldi:
html2tex poldiman
latex poldiman
latex poldiman
dvips -o poldiman.ps poldiman.dvi
tricsman:
html2tex tricsman
latex tricsman
latex tricsman
dvips -o tricsman.ps tricsman.dvi
userrefman:
html2tex userrefman
latex userrefman
latex userrefman
dvips -o userrefman.ps userrefman.dvi

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<HTML>
<HEAD>
<TITLE>AMOR Reference Manual</TITLE>
</HEAD>
<BODY>
<!latex-off>
<H1>AMOR Reference Manual</H1>
<!latex-on>
<P>
Welcome to the reflectometer AMOR at SINQ! This manual describes how
to operate AMOR through the SICS instrument control software.
SICS means: Sinq Instrument Control System. AMOR can be operated in
one out of two modes:
<ul>
<li>Single Counter Mode. In this mode normal scans are performed with
a single counter.
<li>Time-Of-Flight Mode. In this mode the position sensitive detector
is operated in time of flight mode with a chopper providing the time
structure of the neutron beam.
</ul>
</p>
<h1>SICS Introduction</h1>
<p>
SICS is a client server system. This means there is a magic server
program running on the instrument computer which does all the work.
The user interacts with SICS
only with client applications which communicate with the server
through the network. Most instrument hardware (motor controllers,
counter boxes etc.) is connected to the system through RS-232 serial
connections. These RS-232 ports are connected to a terminal server
which is accessed through another server program, the SerPortServer
program, which is also running on the instrument computer. Then there
is the position sensitive detector. Neutrons collected in the PSD are
formatted into a special message format by the elctronics and
forwarded through a fibre optic link to the histogram memory
computer. This is a VME Motorola on board computer which then is
responsible for summing the neutrons events appropriatetly. The on
board computer is connected to the TCP/IP network and acts as a
server as well which handles the configuration and readout of the
histogram memory.
The SICS server communicates with this terminal server and other
devices through the network.
</P>
<!latex-off>
<h1>Starting and Stopping</h1>
<ul>
<li><a href="sicsinvoc.htm">Logging</a> in to SICS.
<li>The <a href="amorcli.htm">AMOR client</a> program.
</ul>
<h1>General User Commands</h1>
<p>
<ul>
<li><a href="drive.htm">Driving</a> motors.
<li><a href="amomot.htm">List</a> of AMOR motors.
<li><a href="amor2t.htm">AMOR Two Theta</a> virtual motor.
<li><a href="logging.htm">Logging</a> actions.
<li><a href="batch.htm">Batch</a> processing.
<li><a href="token.htm">Grabbing control</a>.
<li><a href="amomisc.htm#shutter">Shutter</a> control.
</UL>
</p>
<h1>AMOR in Single Counter Mode</h1>
<p>
<ul>
<li>Some <a href="amorsingle.htm">general</a> remarks.
<li>Doing a <a href="topscan.htm">scan</a>.
</ul>
</p>
<h1>AMOR in Time-Of-Flight Mode</h1>
<p>
<ul>
<li>General <a href="amortof.htm">Remarks</a>.
<li>Configuring the <a href="amortof.htm#conf">histogram memory</a>.
<li>Configuring <a href="amortof.htm#chop"> chopper</a> related
parameters.
<li><a href="count.htm">Counting</a>.
<li><a href="amorstore.htm">Data Storage</a>
</ul>
</p>
<h1>Advanced Topics</h1>
<p>
<UL>
<li>Handling <a href="samenv.htm">sample environment</a> devices in SICS.
<li>Configuring <a href="histogram.htm">histogram memory</a>
<li><a href="motor.htm">Motor Parameters</a>.
<li>Dealing with the <a href="counter.htm">counter box</a>.
<li>Directly access a <a href="ctrl.htm">serial device.</a>
<li>SICS <a href="system.htm">system commands</a>.
<li>Configuring a <a href="config.htm">client connection</a> manually.
<li><a href="trouble.htm">Trouble</a> shooting.
</UL>
</p>
<h1>Download Manual</h1>
<ul>
<li><a href="amorman.ps">Postscript Format</a>,246KB
</ul>
<!latex-on>
</BODY>
</HTML>

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@ -46,6 +46,7 @@ Switzerland\\
%html commandlog.htm 3
%html batch.htm 2
%html macro.htm 3
%html exeman.htm 3
%html buffer.htm 3
%html token.htm 2
%html amomisc.htm 2

2
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@ -34,8 +34,6 @@ interrogated by typing the name of the variable, and set by typing the
name of the variable followed by the new value. The following
variables are relevant:
<dl>
<dt>chopperrotation
<dd>Chopper Rotation speed.
<dt>user
<dd>User name
<dt>email

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<HTML>
<HEAD>
<TITLE>TRICS Data Analysis with Autocloud</TITLE>
</HEAD>
<BODY>
<H1>TRICS Data Analysis with Autocloud</H1>
<P>
Autcloud is an experimental software which integrates reflections from a
3D data volume without any prior information. Reflections are located
through a template matching approach in 3D. Template Matching is a common
digital signal processing method for enhancing a signal against a
background. This program may still contain very major algorithmical
and programming errors as it could not yet be tested against real data.
Data Analysis with autocloud requires two steps:
<ul>
<li>Reflection <a href="autocloud.htm"> integration </a> with autocloud.
<li>Indexing of the reflections found. This can be done with the program
<b>orient</b>. Just select data type 3 and answer the questions asked.
</ul>
</P>
</BODY>
</HTML>

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<HTML>
<HEAD>
<TITLE>Automatic SMS Notification</TITLE>
</HEAD>
<BODY>
<H1>Automatic SMS Notification</H1>
<P>
On some instruments an automatic notification system is installed which
can be configured to send an SMS when the instrument is stopped. An
instrument is considered stopped when there has been no counting or driving
activity for a configurable amount of time and there is beam at SINQ. This
system can be controlled with the follwoing commands:
<dl>
<dt>autosms
<dd>Shows if the autosms system is enabled or disabled
<dt>autosms on | off
<dd>Switches automatic notfications on or off.
<dt>autosms number [val]
<dd>Without a parameter, displays the telphone number for the SMS, with a parameter
configures the telephone number. Telephone numbers must be all numbers without
hyphens or anything else.
<dt>autosms maxidle [val]
<dd>Without a parameter, queries the idle time before a SMS is sent. With a
parameter sets a new value for the inactivity period which triggers a message.
</dl>
Please use the configurable settle time with environment controllers such as
temperature controllers in order to avoid false messages while waiting for the
temperature to settle.
</P>
</BODY>
</HTML>

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@ -42,13 +42,16 @@ operation. The general syntax for handling such parameters is:
<pre>
objectname parametername
</pre>
prints the current value of the parameter
</p>
prints the current value of the parameter
<pre>
objectname parametername newvalue
</pre>
sets the parameter value to newvalue if you are properly authorized.
</p>
<h3>SICS variables</h3>
<p>
Most of the parameters SICS uses are hidden in the objects to which they belong. But some are separate objects of their own right and are accessible at top level. For instance things like Title or wavelength. They share a common syntax for changing and requesting their values. This is very simple: The command <i> objectname </i> will return the value, the command <i> objectname newvalue </i> will change the variable. But only if the authorisation codes match. </p>
<p>
<h3>Authorisation</h3>
<p>
A client server system is potentially open to unauthorised hackers
@ -60,25 +63,8 @@ sets the parameter value to newvalue if you are properly authorized.
<li> <b> Manager </b> has the permission to mess with almost everything. A very dangerous person.
<li> <b> Internal </b> is not accessible to the outside world and is used to circumvent protection for internal uses. However some parameters are considered to be so critical that they cannot be changed during the runtime of the SICS-server, not even by Managers.
</ul>
All this is stated here in order to explain the common error message: You are not authorised to do that and that or something along these lines.</p>
<h3>SICS variables</h3>
<p>
Most of the parameters SICS uses are hidden in the objects to which they belong. But some are separate objects of their own right and are accessible at top level. For instance things like Title or wavelength. They share a common syntax for changing and requesting their values. This is very simple: The command <i> objectname </i> will return the value, the command <i> objectname newvalue </i> will change the variable. But only if the authorisation codes match. </p>
<p>
<h3>The SICS Command Line Client</h3>
The most common client for controlling SICS is the <b>SICS command line
client</b>.
This application can be started by typing the command:
<pre>
sics &
</pre>
at the Unix prompt. Before this program is ready to collaborate with you you
have to connect it to an instrument using the options in the connect
pulldown menu. The screen is roughly divided in three areas: The top area
shows all input to and output from the server. The middle area shows the
command history. At the lower end is a text entry field which allows you to type
commands to be sent to the SICS server. For more information about this client consult
the online help of this application.
</p>
All this is stated here in order to explain the common error message:
You are not authorised to do that and that or something along these
lines.</p>
</body>
</html>

2
doc/user/batch.htm
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@ -13,6 +13,8 @@ sleep. SICS supports two different ways of doing this:
popular scripting language Tcl. The most primitive usage of this
facility is processing batch files.
<li>Second there is the <a href="buffer.htm">LNS R&#252;nbuffer</a> system.
<li>Third there is the new <a href="exeman.htm">Batch File</a> execution
system.
</ul>
</P>
</BODY>

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@ -5,8 +5,8 @@
<BODY>
<H1>Chopper Control</H1>
<P>
FOCUS is equipped with a Dornier Chopper system running two choppers:
a disk chopper and a fermi chopper. In most situations the diskchopper is
Some instruments are equipped with a Dornier Chopper system running one or more choppers:
a disk chopper and possibly a fermi chopper. In most situations the diskchopper is
in slave mode. This means his speed is a predefined ratio of the
speed of the fermichopper. Furthermore, there is a phase difference between
the two choppers in order to allow for the fligh time of neutrons
@ -41,7 +41,7 @@ The following virtual motor variables exist for the chopper system.
<dL>
<DT>fermispeed
<DD>fermi chopper speed
<DT>diskspeed
<DT>diskspeed or chopperspeed
<DD>disk chopper speed. Note, that driving this parameter while the
chopper system is in synchronous mode will throw an error condition.
<DT>phase

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@ -40,6 +40,12 @@ filename in unix.
<li><b> config close num</b> closes the log file denoted by num again.
<li><b>config list</b> lists the currently active values for outcode and user
rights.
<li><b>config myname</b> retruns the name of the connection.
<li><b>config myrights</b> prints the rights associated with your connection.
<li><b>config listen 0 or 1</b>switches listening to the commandlog on
or off for this conenction. If this on, all output to the commandlog,
i.e. all interesting things happening in SICS, is printed to your
connection as well.
</ul>
<p>
</body>

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@ -15,6 +15,6 @@
<DD> Calls count num times. num is a required parameter. The other two are
optional and are handled as described above for count.
</dl>
Both commands make sure, that measured data is written to files.
Both commands make sure that measured data is written to files.
</body>
</html>

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@ -51,6 +51,7 @@ adjusted to any value within its wavelength range.
%html system.htm 1
%html config.htm 1
%html macro.htm 1
%html exeman.htm 2
%html buffer.htm 1
%html drive.htm 1
%html logbook.htm 2

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@ -5,7 +5,7 @@
<body>
<h2>Drive commands</h2>
<p>
Many objects in SICS are <b> drivable </b>. This means they can run to a new value. Obvious examples are motors. Less obvious examples include composite adjustments such as setting a wavelength or an energy. This class of objects can be operated by the <b> drive, run, Success </b> family of commands. These commands cater for blocking and non-blocking modes of operation.</p>
Many objects in SICS are <b> drivable </b>. This means they can run to a new value. Obvious examples are motors. Less obvious examples include composite adjustments such as setting a wavelength or an energy. Such devices are alos called virtual motors. This class of objects can be operated by the <b> drive, run, Success </b> family of commands. These commands cater for blocking and non-blocking modes of operation.</p>
<p>
<b> run var newval var newval ... </b> can be called with one to n pairs of object new value pairs. This command will set the variables in motion and return to the command prompt without waiting for the requested operations to finish. This feature allows to operate other devices of the instrument while perhaps a slow device is still running into position.</p>
<p>

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<HTML>
<HEAD>
<TITLE>The Batch Buffer Manager</TITLE>
</HEAD>
<BODY>
<H1>The Batch Buffer Manager</H1>
<P>
The batch buffer manager handles the execution of batch files. It can
execute batch files directly. Additionally, batch files can be added
into a queue for later processing. The batch buffer manager supports
the following command described below. Please note, that the examples
assume that the batch manager has been configured into SICS under the
name of exe.
<dl>
<dt>exe buffername
<dd>directly load the buffer stored in the file buffername and execute
it. The file is searched in the batch buffer search path.
<dt>exe batchpath [newpath]
<dd>Without an argument, this command lists the directories which are
searched for batch files. With an argument, a new search path is
set. It is possible to specify multiple directories by separating them
with colons.
<dt>exe syspath [newpath]
<dd>Without an argument, this command lists the system directories which are
searched for batch files. With an argument, a new system search path is
set. It is possible to specify multiple directories by separating them
with colons.
<dt>exe info
<dd>prints the name of the currently executing batch buffer
<dt>exe info stack
<dd>prints the stack of nested batch files (i.e. batch files calling
each other).
<dt>exe info range [name]
<dd>Without an argument prints the range of code currently being
executed. With a parameter, prints the range of code executing in
named buffer within the stack of nested buffers. The reply looks like:
number of start character = number of end character = line number.
<dt>exe info text [name]
<dd>Without an argument prints the code text currently being
executed. With a parameter, prints the range of code text executing in the
named buffer within the stack of nested buffers.
<dt>exe enqueue buffername
<dd>Appends buffername to the queue of batch buffers to execute.
<dt>exe clear
<dt>Clears the queue of batch buffers
<dt>exe queue
<dd>Prints the content of the batch buffer queue.
<dt>exe run
<dd>Starts executing the batch buffers in the queue.
<dt>exe print buffername
<dd>Prints the content of the batch buffer buffername to the screen.
<dt>exe interest
<dd>Switches on automatic notification about starting batch files,
executing a new bit of code or for finishing a batch file. This is
most useful for SICS clients watching the progress of the experiment.
<dt>exe upload
<dd>Prepares the batch manager for uploading a buffer to SICS
<dt>exe append some text
<dd> Appends a line with everything after append to the upload buffer
<dt>exe save filename
<dd>saves the recently uploaded buffer under filename on the SICS server.
</dl>
</P>
</BODY>
</HTML>

1
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@ -43,6 +43,7 @@ Switzerland\\
%html commandlog.htm 3
%html batch.htm 2
%html macro.htm 3
%html exeman.htm 3
%html buffer.htm 3
%html token.htm 2
%html focussps.htm 2

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@ -12,14 +12,16 @@ handled automatically by the <a href="count.htm">count</a>
command. However, data file writing can be initiated and configured
manually from the command line through the following commands:
<dl>
<DT>storefocus start
<DT>focusstart
<DD>Write a new data file
<DT>storefocus update
<DT>focusupdatescript
<DD>Updates the current data file.
<DT>storefocus intervall
<DT>focuslink
<DD>Creates NeXus links in the data file.
<DT>focusupdate updateintervall
<DD>prints the current update intervall to use during counting. Units
is minutes.
<DT>storefocus intervall newval
<DT>focusupdate updateintervall newval
<DD>Sets the update intervall to newval minutes.
</DL>
FOCUS has three detector banks which may not all be active at all

3
doc/user/general.htm
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@ -17,6 +17,7 @@ the SICS server.
<li> A few commands <a href="config.htm">change</a> user rights, set output files and the like.
<li> SICS has a built in <a href="macro.htm">macro</a> facility which is accessible through a few commands.
<li> Then there is the <a href="buffer.htm">famous</a> LNS-R&#252;nbuffer system.
<li> The new <a href="exeman.htm">batch file</a> processing system.
<li> Motors and parameters need to be <a href="drive.htm">drive</a>n.
<li> SICS has a facility to <a href=optimise.htm>optimise</a> a peak with respect to several
parameters.
@ -26,7 +27,7 @@ parameters.
SICS has various ways (to many!) to log the I/O from and to an
instrument control server. This has devolped over time and may need a
cleanup.
<ol>
<ul>
<li>There exists a server log where all I/O and internal
messages is written to automatically. As this can get quite large the
files

6
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@ -3,7 +3,7 @@
<TITLE>Hklscan</TITLE>
</HEAD>
<BODY>
<H1>Hklscan and Hklscan2d</H1>
<H1>Hklscan and Hklscan2d (Obsolete)</H1>
<P>
Hklscan is a command which allows to scan in reciprocal space expressed as
Miller indizes on a four circle diffractometer. Hklscan operates with
@ -39,5 +39,9 @@ Data is written automatically into a slightly modified TOPSI data format
might be slightly erratic as it uses two theta as x-axis. Hklscan2d
writes data into NeXus files.
</P>
<p>
hklscan is obsolete. As of 2005, h, k, l are normal virtual motors and can be
used with the SICS built in scan commands.
</p>
</BODY>
</HTML>

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@ -0,0 +1,47 @@
<html>
<head>
<title>HRPT motor list</title>
</head>
<body>
<H2>HRPT motor list</H2>
<P>
<DL>
<DT>CEX1
<DD>inner collimator drum
<DT>CEX2
<DD>outer collimator drum
<DT>MOMU, A1
<DD>omega rotation of upper monochromator crystal.
<DT>MTVU, A12
<DD>translation vertical to the upper crystal.
<DT>MTPU, A13
<DD>translation paralell to the upper crystal
<DT>MGVU, A14
<DD>tilt goniometer vertical to upper crystal.
<DT>MGPU, A15
<DD>tilt goniometer paralell to upper crystal.
<DT>MCVU, A16
<dd>vertical curvature of upper crystal.
<DT>MOML, B1
<DD>omega rotation of lower monochromator crystal.
<DT>MTVL, A22
<DD>translation vertical to the lower crystal.
<DT>MTPL, A23
<DD>translation paralell to the lower crystal
<DT>MGVL, A24
<DD>tilt goniometer vertical to lower crystal.
<DT>MGPL, A25
<DD>tilt goniometer paralell to lower crystal.
<DT>MCVL, A26
<dd>vertical curvature of lower crystal.
<dT>MEXZ, A37
<DD>lift
<DT>Table, A3
<DD>Sample rotation.
<DT>TwoThetaD, A4
<DD>Two Theta detector.
</DL>
</p>
</body>
</html>

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@ -8,15 +8,6 @@
SICS offers not less then three different ways of logging your
commands and the SICS server's responses:
<ul>
<li>The SICS command line client allows to open a log file on your
local computer and on your account. This can be achieved through the
File/Open Logfile menu entry. Select a file name and hit save. From
then on, any output in the SICS clients terminal area will be written
into the selected file. There is a gotcha: ouptut may not be immediately
visible in the file. This is due to buffering of I/O by the operating
system. If you want to flush, either open a new file or exit the
client. Flushing I/O at each line written is possible, but would have
a massive and unacceptable performance impact.
<li>You may create a similar per client log file on the computer running
the SICS server through the <a href="logbook.htm">logbook</a> command.
<li>Then there is a way to log all activity registered from users with

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doc/user/macro.htm
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@ -16,7 +16,11 @@ configured in the variable batchroot and then executes that
batchfile. The usage scenerio is that you have a directory where you
keep batch files. Then the variable batcroot is set to contain the path
to that directory. Batchrun then allows to start scripts in that
directory without specifying the full path.
directory without specifying the full path. Please note that fileeval and batchrun are obsolete and
to be replaced by the new batch manager command, <a href="exeman.htm">exe</a>, as described below.
</p>
<p>
Then there are some special commands which can be used within macro-sripts:
<p>
<b> ClientPut sometext1 ... </b>Usally SICS suppresses any messages

24
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@ -0,0 +1,24 @@
<HTML>
<HEAD>
<TITLE>Simulation Mode</TITLE>
</HEAD>
<BODY>
<H1>Simulation Mode</H1>
<P>
For testing batch files or in order to check the movement of the
instrument it may be helpful to run SICS in simulation mode. You must
theb connect to a special simulation
SICS server which may have been setup for you. In the
simulation server, everything is like in the actual SICS server,
except that no hardware is moved, co counts collected and no data file
written. There is one speciality, however. The command:
<pre>
<em>sync</em>
</pre>
synchronizes the parameters and limits in the simulation server with
those in the instrument server.
</P>
</BODY>
</HTML>

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@ -5,65 +5,73 @@
<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 open
<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
<DT>dataset reopen 001/trics2005n000051
<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 +80,6 @@ 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 +87,51 @@ 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.
<dt>psimode
<dd>0 or 1: switches psi scanning mode. Please note that suitable HKL input files for this mode
must contain four numbers: H, K, L and psi.
<dt>psd
<dd>0 or 1: switches on PSD mode for measuring with the area detector. Currently this is mapped
to doing a tricsscan with the scan parameters as evaluted from the two theta range table. The
psi, compact and weak flags are ignored in PSD mode. Only a log file is openend, the rest of
the file management is done by tricsscan.
</dl>
</p>
<p>
mess 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:
Then there are command which allow to configure the table of two theta ranges and
scan parameters. All table related commands start with: dataset table. The following
commands are supported:
<dl>
<dt>mess bi
<dd>switches into bissectiong mode. This is the default.
<dt>mess nb
<dt>dataset table list
<dd>prints the content of the table.
<dt>dataset table add end scanvar step np
<dd>configures a two theta range. The end parameter describes the end of the two theta range to
which these parameters can be applied. Scanmode can either
be om for omega scans or o2t for omega 2 theta scans. step is the step width to use. np is the
number of points in the scan.
<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 is accounted for by two switches:
<dl>
<dt>dataset bi
<dd>switches into bissecting mode. This is the default.
<dt>dataset nb
<dd>switches into normal beam mode.
</dl>
</p>
@ -102,19 +142,19 @@ 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>

16
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@ -34,6 +34,7 @@ status display clients.
Please note that the actual driving of the motor is done via the <a href="drive.htm">drive</a> command.</p>
<hr size=4 width="66%">
<h2>The motor parameters</h2>
<p>
<ul>
<li> <b> HardLowerLim </b> is the hardware lower limit. This is read from the motor controller and is identical to the limit switch welded to the instrument. Can usually not be changed.
<li> <b> HardUpperLim </b> is the hardware upper limit. This is read from the motor controller and is identical to the limit switch welded to the instrument. Can usually not be changed.
@ -58,9 +59,12 @@ desired position was reached. If the position read back from the motor
is not within precision to the desired value, the motor is
restarted. This is done at max maxretry times. After maxretry retries,
the motor throws an error.
<li></b> ignorefault </b>If this is bigger then 0, positioning faults
<li><b> ignorefault </b>If this is bigger then 0, positioning faults
from the motor will be ignored.
</ul>
This list of parameters may be enhanced buy driver specific
parameters. motor list will show all parameters.
</p>
<p>
<h2>Motor Error Handling Concepts</h2>
<p>
@ -94,13 +98,13 @@ maxretries repositionings, a HWFault is assumed.
In any case lots of warnings and infos are printed.
</p>
<p>
If SICS tries to drive an axis which is for some reason broken to
often hardware damage may occur (and HAS occurred!). Now, SICS has no
If SICS tries to drive an axis which is broken hardware damage may
occur (and HAS occurred!). Now, SICS has no
means to detect if the mispositioning of a motor is due to a concrete
block in the path of the instrument or any other reason. What SICS can
do though is to count how often a motor mispositions in
sequence. This means SICS counts mispositionings if it cannot drive a
motor, if the motor is driven succesfully, the count is cleared. If
sequence. This means SICS increments a mispositioning counter if it cannot drive a
motor, if the motor is driven succesfully, the mispositioning counter is cleared. If
the count of mispositionings becomes higher then the parameter
failafter, SICS thinks that there is something really, really wrong
and aborts the measurement and prints an error message containing the
@ -116,7 +120,7 @@ check for the interrupt in upper level code.
<dt>SICS falsly reports mispositionings.
<dd>Solution: increase the precision parameter.
<dt>You know that a motor is broken, you cannot fix it, but you want
to measure anyway.
to measure anyway.
<dd>Solution: increase the precision parameter, if SICS finds the
positioning problem, increase maxretries, increase the failafter
parameter. In the worst case set the ignorefault parameter to greater

3
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@ -42,7 +42,8 @@ Switzerland\\
%html logbook.htm 3
%html commandlog.htm 3
%html batch.htm 2
%html macro.htm 3
%html macro.htm 3
%html exeman.htm 3
%html buffer.htm 3
%html token.htm 2

8
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@ -7,10 +7,12 @@
<p>
As of now two packages are provided:
<ul>
<li>A data analysis package based on <a href="xds.htm">XDS</a>.
<li>An experimental package based on a
novel <a href="auto.htm">volume matching </a> approach.
<li>A program called cami4pcd for visually inspecting TRICS data files and for performing
computer aided manual integration of TRICS data files.
<li>A program called anatric for extracting reflection positions for UB matrix refinement
and the extraction of integrated intensities for structure determination.
</ul>
Both programs are described in separate documents (or not as in the case of cami4psd).
</P>
</BODY>
</HTML>

6
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@ -88,6 +88,8 @@ implemented are:
<DT>Safe
<DD> Tries to run the environment device to a value considered safe by the
user.
<DT>Script
<DD>Run a user defined script to do any magic things you may want.
</DL>
</p>
@ -176,9 +178,13 @@ Possible values are:
<LI>1 for Pause.
<LI> 2 for Interrupt
<LI> 3 for Safe.
<LI> 4 for Script.
</UL> For an explanantion of these values see the section about <a
href="#error">error</a> handling
above.
<DT>errorscript
<DD>The user specified script to execute when the controlled value goes out of
tolerance. Will be used whne the ErrHandler 4, script, is used.
<DT> Interrupt
<DD> The interrupt to issue when an error is detected and Interrupt error
handling is set. Valid values are:

1
doc/user/sansman
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@ -42,6 +42,7 @@ programmers reference.
%html system.htm 1
%html config.htm 1
%html macro.htm 1
%html exeman.htm 2
%html buffer.htm 1
%html drive.htm 1
%html logbook.htm 3

83
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@ -29,7 +29,7 @@ Currently the following SICS clients are available:
<li> A command line control client for sending commands to the SICS
server and displaying its repsonses.
<li> A status display for the powder diffractometers DMC and HRPT.
<li> A status display for TOPSI.
<li> A status display for MORPHEUS and general scans.
<li> A status display for SANS and SANS2.
<li> A status display for FOCUS.
<li> A AMOR control and status program.
@ -53,7 +53,7 @@ privileged SICS user.
</p>
<h2>Starting SICS client applications </h2>
<p>
These programs can be started on a DigitalUnix system by issuing the
These programs can be started on a Linux system by issuing the
following commands at the command prompt:
<dl>
<DT>sics &
@ -61,7 +61,7 @@ following commands at the command prompt:
<DT>powderstatus &
<DD> for the DMC status display client.
<DT>topsistatus &
<DD>for the TOPSI status display.
<DD>for the MORPHEUS status display.
<DT>sansstatus &
<DD> for the SANS status display.
<DT>focustatus
@ -72,13 +72,9 @@ following commands at the command prompt:
<DD> for the triple axis status display and control application.
<DT>varwatch &
<DD> for the variable watcher.
<dt>trics-&
<dt>trics &
<dd>for the starting the TRICS graphical client.
</dl>
On a PC you may find icons for starting the different programs on the
desktop.
Each of these clients has usage instructions online which can be displayed
through the help/about menu entry.
</p>
<p>
Another option to start SICS clients is the Java Webstart mechanism
@ -102,41 +98,82 @@ active. A connection is established through the connect menu of the client.
SICS is a multi user instrument control system. In order to prevent
malicious manipulations of the instrument SICS supports a hierarchy of user
rights. In order to run an experiment you need at least user level privilege.
In order to achieve this privilege you have to invoke the User Parameter/Set
Rights dialog. There you have to enter the apropriate username and password
In order to achieve this privilege you have to invoke the Authorize
dialog. There you have to enter the apropriate username and password
kindly provided by your instrument scientist.
</p>
<h2>Restarting the Server</h2>
<p>
The SICS server should be running all the time. It is only down if something
went wrong. You can check for the presence of the SICS server by loging in
to the instrument computer and typing <b>CheckSICS</b> at the command
to the instrument computer and typing <b>monit status</b> at the command
prompt. The output will tell you what is happening. If you need to restart
the SICS server log in as the instrument user at the instrument computer and
invoke the appropriate command to start the server. These are:
<dl>
<DT>DMC
<DD>Computer = lnsa05, User = DMC
<DD>Computer = dmc, User = dmc
<DT>TOPSI
<DD>Computer = topsi, User = TOPSI
<DD>Computer = morpheus, User = morpheus
<DT>SANS
<DD>Computer = sans, User = SANS
<DD>Computer = sans, User = sans
<DT>SANSLI
<DD>Computer = sans2, User = sans2
<DT>TRICS
<DD>Computer = lnsa18, User = TRICS
<DD>Computer = trics, User = trics
<DT>HRPT
<DD>Computer = lnsa11, User = HRPT
<DD>Computer = hrpt, User = hrpt
<DT>FOCUS
<DD>Computer = lnsa16, User = FOCUS
<DD>Computer = focus, User = focus
<DT>AMOR
<DD>Computer = lnsa14, User = AMOR
<DD>Computer = amor, User = amor
<DT>TASP
<DD>Computer = tasp, User = TASP
<DD>Computer = tasp, User = tasp
<DT>POLDI
<DD>Computer = poldi, User = POLDI
<DD>Computer = poldi, User = poldi
</dl>
For starting the SICS server type <b>startsics</b>. This is a shell script
which will starts all necessary server programs. This script works only on
the instrument computer and in the appropriate instrument account.
The SICS server process are controlled through the monit program. Usually the monit
daemon is running. If not, for instance after a reboot, it can be
started by typing <b>monit</b> at the unix prompt logged in as the
instrument user. Further monit commands:
<dl>
<dt> monit start target
<dd>start the monit surveyed process target. For the choice of targets
see below.
<dt> monit stop target
<dd>stops the monit surveyed process target. For the choice of targets
see below.
<dt> monit restart target
<dd>restart the monit surveyed process target. Possible targets are:
<dl>
<dt>sicsserver
<dd>The SICServer
<dt>SerPortServer
<dd>The serial port control program
<dt>sync
<dd>The file synchronisation program. This is responsible for coyping
data files to the common AFS area.
<dt>simserver
<dd>Only on TASP: a simulation SICS server
<dt>all
<dd>Stop all processes
</dl>
<dt>monit status
<dd>prints a status listing of everything watched by monit
<dt>monit quit
<dd>Stops monit itself
</dl>
Stopping everything thus involves two commands:
<ul>
<li> monit stop all
<li> monit quit
</ul>
Restarting after this involves:
<ul>
<li>monit
</ul>
The older command startsics and killsics are still working and operate
on the monit daemon as of now.
</p>
<p>
If all this does not help look under <a href="trouble.htm">trouble shooting

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@ -0,0 +1,56 @@
<HTML>
<HEAD>
<TITLE>SICS Metadata</TITLE>
</HEAD>
<BODY>
<H1>SICS Metadata</H1>
<P>
This section describes the <b>list</b> command for retrieving and
setting information about a running SICS server and the objects living in it.
Each SICS object has metadata associated with it: some of it is generated by the system such
as the object type, the interface it implements etc. Some additional metadata can be set by the
user. Most commands print their data in the form of a Tcl-list. The list is terminated with the entry ENDLIST.
This entry can be searched for by clients interested to find the end of the transmission. The general form of the
metadata is a key value pair. The following commands are implemented:
<dl>
<dt>list
<dd>Prints a list of all SICS objects.
<dt>list server
<dd>Prints a list of all server options.
<dt>list sicsobject
<dd>Prints all the metadata associated with the SICS object sicsobject.
<dt>list sicsobject key
<dd>Prints the value of the key associated with the SICS object sicsobject.
<dt>list setatt sicsobject key value
<dd>Sets a user defined attribute with the name key and the value value for the SICS object sicsobject.
<dt>list metadatakey
<dd>List all unique entries for the specified metadata key. System supplied metadata keys are:
<dl>
<dt>type
<dd>The object class
<dt>interface
<dd>The object interfaces implemented by SICS
</dl>
This list may be augmented with user generated keys as defined through using the <b>list setatt obj key value</b> command.
An example:
<pre>
list type
</pre>
will print all the objects classes available in the SICS server.
<dt>list metadatakey value
<dd>List all the SICS objects which match the value for the metadatakey given as parameters. For example:
<pre>
list interface drivable
</pre>
will print all objects implementing the drivable interface in the SICS server.
<dt>list objstatus obj
<dd>Will query the current state of the SICS object obj. This makes sense for things like motors, counter etc. which
can be run asynchronously. The result can be idle, fault, busy etc.
<dt>list match mask
<dd>Will print the names of all SICS objects where the name
matches the wildcard given as mask.
</dl>
</P>
</BODY>
</HTML>

24
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@ -0,0 +1,24 @@
<HTML>
<HEAD>
<TITLE>The Sinq Module</TITLE>
</HEAD>
<BODY>
<H1>The SINQ Module</H1>
<P>
On some instruments a module is installed which listens to the broadcast messages
of the accelerator division. This gives information about the rinag and sinq status.
The following commands are recognized:
<dl>
<dt>sinq
<dd>Prints the last full text ring status message. Please note that this may be
empty for some minutes right after a restart of SICS.
<dT>sinq beam
<dd>Returns the current beam on SINQ
<dt>sinq beamavg
<dd>Returns the average beam on SINQ as measured the last 5 minutes.
<dt>sinq ring
<dd>Returns the acclerator ring current.
</dl>
</P>
</BODY>
</HTML>

4
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@ -72,5 +72,9 @@ when useless data files have been created during tests. As this is
critical command in normal user operations, this command requires
managers privilege.
</p>
<p>
<b>sicsidle</b> prints the number of seconds since the last invocation of a counting
or driving operation. Used in scripts.
</p>
</body>
</html>

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@ -0,0 +1,169 @@
<HTML>
<HEAD>
<TITLE>TASUB: The Triple Axis Calculation Module</TITLE>
</HEAD>
<BODY>
<H1>TASUB: The Triple Axis Calculation Module</H1>
<P>
On a triple axis instrument the parameters incoming energy, Q-position in 3D and
analyzed energy have to be changed frequently. These calculations are the task of
the TASUB module. This module uses the calculus described by M. Lumsden, J. L.
Roberston and M. Yethiraj in J. Appl. Cryst. (2005), 38, 405-411. The special feauture of
this algorithm is that the tilt cradles of the sample table are used to help during
alignment and in order to drive out of plane (within the limits of the tilt cradles).
For alignment, two reflections must be located and their angles and Q-E parameters
entered into the module. Then a UB matrix can be calculated. With a UB matrix, the
Q-E variables ei, ki, ef, kf, en, qh, qk and ql can be driven as virtual motors in
SICS.
</P>
<h2>Commands understood by Tasub</h2>
<p>
<h3>Monochromator and Analyzer Parameters
<p>
Incident and scattered energies are defined by monochromator crystals. In order for the
calculations to work, some parameters need to be configured. Monochromator and analyzer
parameters can be accessed with the prefixes:
<ul>
<li>tasub mono
<li>tasub ana
</ul>
The parameter syntax used is as usual: giving only the parameter name queries the value,
giving the parameter plus a value sets the parameter to the new value. The following
parameters are supported:
<dl>
<dt>dd
<dd>The d-spacing of the reflection used
<dt>ss
<dd>The scattering sense, 1 or -1 are possible.
<dt>hb1
<dd>First parameter for the calculation of the horizontal curvature
<dt>hb2
<dd>Second parameter for the calculation of the horizontal curvature
<dt>vb1
<dd>First parameter for the calculation of the vertical curvature
<dt>vb2
<dd>Second parameter for the calculation of the vertical curvature
</dl>
An example:
<dl>
<dt>tasub mono dd
<dd>will print the current d-spacing of the monochromator
<dt>tasub mono dd 4.3
<dd>Will set the d-spacing of the monochromator to 4.3
</dl>
</p>
<h3>Cell Parameters</h3>
<p>
In order for the UB matrix calculation to work, the cell constants must be known:
<dl>
<dt>tasub cell
<dd>This command prints the current cell parameters.
<dt>tasub cell a b c alpha beta gamma
<dd>This command sets the new cell parameters. All six values must be given.
</dl>
</p>
<h3>Reflection Management</h3>
<p>
In order to calculate a UB matrix a list of reflections must be maintained. This is done
with the commands in this section:
<dl>
<dt>tasub clear
<dd>Clears the reflection list
<dt>tasub listref
<dd>Prints a list of all known reflections.
<dt>tasub del num
<dd>Delete the reflection number num from the list
<dt>tasub addref qh qk ql
<dd>Adds a reflection to the list. The indices of the reflections are given. The angles
and energy values are read from the motors. Use this command only when the instrument is
positioned right on a reflection.
<dt>tasub addref qh qk ql a3 a4 sgu sgl ei ef
<dd>Add a new reflection to the list. Besides the indices all angles are given:
a3, the sample rotation, a4, sample two theta, sgu, upper tilt cradle, sgl, lower tilt
cradle and incoming energey ei and outgoing energy ef.
</dl>
</p>
<h3>Calculations</h3>
<p>
This section covers the parameters and commands to use to make the module do calculations
for you.
<dl>
<dt>tasbub const ki | kf
<dd>Sets a parameter to determine if KI or KF is fixed when the energy transfer en is
being driven. Allowed values: ki, kf
<dt>tasub const
<dd>Prints if ki or kf is fixed.
<dt>tasub ss
<dd>Prints the sample scattering sense.
<dt>tasub ss 1 | -1
<dd>Sets the sample scattering sense. Allowed values are either 1 or -1.
<dt>tasub makeub r1 r2
<dd>Calculate a new UB matrix from the current cell constants and the entries r1 and r2 in
the reflection list. r1 and r2 are integer numbers. This command will not only print the
new UB matrix but also the results of various back and forth calculations performed with
the new UB matrix. This can be inspected in order to check the new UB. WARNING: The calculation
will go wrong if the scattering sense at the sample has changed since the reflections used
for the UB matrix determination have been entered.
<dt>tasub listub
<dd>prints the current UB matrix.
<dt>tasub calcang qh qk ql ei ef
<dd>Will calculate new angles for the Q-E position specified. The angles will be
printed in the order: monochromator two theta, sample rotation, sample two theta,
lower tilt cradle, upper tilt cradle and analyzer two theta.
<dt>tasub calcqe a2 a3 a4 sgu sgl a6
<dd>Calculates and prints the Q-E position from the angles given: a2 = monochromator
two theta, a3 = sample rotation, a4 = sample tow theta, sgu = upper tilt cradle, sgl =
lower tilt cradle and a6 = analyzer two theta. The Q-E position is printed in the sequence:
qh, qk, ql, ei, ef.
</dl>
</p>
<h3>Virtual Motors</h3>
<p>
The tasub module also installs the following virtual motors into SICS: ei, ki, qh, qk, ql,
en, ef, kf and qm. All these motors can be used in SICS drive, run or scan commands like real
motors. Driving them triggers a recalculation of angles and the drives the real motors to
appropriate values. The virtual motors have a very limited command set
(shown at the example of qh):
<dl>
<dt>qh
<dd>The name of the motor alone will print its current position.
<dt>qh target
<dd>This will print the last requested target position for this virtual motor.
</dl>
</p>
<p>
The virtual motor qm implements <b>powder mode</b>. In this mode, only the sample two theta
and energy motors will be driven, sample rotation and tilt cradles will be left at their
respective positions. THis is commonly used to analyze the energy transfer of powder samples.
</p>
<p>
There is another important command:
<dl>
<dt>tasub update
<dd>This command will force a recalculation of the current Q-E position for the virtual
motors from angles. Normally tasub will take care of this. However, if any of the angle
motors are moved directly or manualy, this command might be required. The SICS dr
wrapper command, however, even takes care of this.
</dl>
</p>
<h3>Internal Commands</h3>
<p>
The tasub module supports some more commands which are used by SICS in order to restore
the tasub configuration between instantiations of SICS. These commands are documented here
for the sake of completeness:
<dl>
<dt>tasub setub ub11 ub12 ub13 ub21 ub22 ub23 ub31 ub32 ub33
<dd>Sets the UB matrix. Nine values are required.
<dt>tasub setnormal n1 n2 n3
<dd>This command sets the plane normal which is required in calculations. Normally this
plane normal is automatically generated during the calculation of the UB matrix.
<dt>tasub settarget qh qk ql qm ki kf
<dd>Sets the Q-E target.
<dt>tasub r1 qh qk ql a3 a4 sgu sgl ki kf
<dt>tasub r2 qh qkl ql a3 a4 sgu sgl ki kf
<dd>These commands set the values for the two reflections used for generating the UB
matrix.
</dl>
</p>
</BODY>
</HTML>

1
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@ -35,6 +35,7 @@ Switzerland\\
%html system.htm 1
%html config.htm 1
%html macro.htm 1
%html exeman.htm 2
%html buffer.htm 1
%html drive.htm 1
%html logbook.htm 2

43
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@ -93,6 +93,37 @@ can be given in order to allow for several scan variables.
the mode currently configured active in the scan object is used.
</UL>
</p>
<h2>Fastscan</h2>
<p>
At some instruments there is a fastscan facility. This scan starts a
motor and the counter. As often as possible or configured, the scan
module will calculate the difference to the previous count, normalize
it to the monitor difference and print it. This is usually faster then
doing a step scan. There are limitations, though:
<ul>
<li>Fastscans are restricted to one motor. There is no way that a
coordinated movement of several motors can be enforced by fastscan
without mechanical coupling.
<li>Due to the volatile nature of the beam at SINQ, this type of scans
come into problems when the beam is off. A warning is printed, but...
<li>If the motor is driving to fast, there might not be enough
neutrons around even in the peak to be registered.
</ul>
Basically, <b>if you see a feauture in fastscan, it is there, if not,
that does not mean anything!</b>. Fastscan comes into its own for
alignment scans or when searching peaks. The syntax is:
<dl>
<dt>fastscan motor start stop speed
<dd>Runs a fastscan on motor between start and stop. Speed is the
speed with which the motor is run. The motors speed is reset to the
original value when fastscan finishes.
<dt>diffscan skip val
<dd>If fastscan produces to much output on to short intervalls,
increasing the skip parameter allows to control that. Skip is the
number of SICS cyles to skip between measurements. Thus this value is
highly dependent on the overall performance of SICS.
</dl>
</p>
<h2>Peak And Center</h2>
<p>
These two commands are related to the scan command insofar as they act upon
@ -107,5 +138,17 @@ the position, FWHM and maximum value of the peak in the last scan. The
The two points are interpolated from the data and the peak position
calculated as the middle point between the two halfheight points.
</p>
<h2>PSD scans</h2>
<p>
Some instrument wish to perform scans with position sensitive
detectors. In such cases the scan mode can be switched between PSD and
normal mode. This is done through the commands:
<dl>
<dt>scan2d
<dd>Switches PSAD detetcor scanning on.
<dt>scan1d
<dd>Switches back to normal scan mode on a single counter.
</dl>
</p>
</body>
</html>

41
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@ -14,27 +14,11 @@ to be solved are:
<li>Measure a couple of reflections.
<li>Furthermore there are some specialities.
</ul>
There are two ways to achieve all this:
The older way uses some built in SICS functionality plus some external
programs inherited from the ILL. This is called the ILL operation.
Then a complete
four circle package called DIFRAC from P. White and Eric Gabe was
integrated into SICS.
This is The Difrac way of operation.
</p>
<h2>DIFRAC</h2>
<p>
The DIFRAC commands are accessed by prepending the difrac commands
with <b>dif</b>. For example: "dif td" calls the difrac td
command. For more information on DIFRAC commands see the separate
<a href="diftrics.htm">DIFRAC manual</a>.
</p>
<h2>ILL operation</h2>
<h3>Locate Reflections</h3>
<p>
If you know x-ray single crystal diffractometers you'll expect sophisticated
reflection search procedures here. Nothing is available in this field in
reflection search procedures here. Little is available in this field in
SICS. It was deemed inapropriate for neutron research. The first reflections
must be found by hand. Something which may help in this is a quick scan
facility which allows to run a motor and print counts while the motor is
@ -54,12 +38,27 @@ But it may help to locate the aproximate position of a peak.
</p>
<p>
Once a peak has been found, its position can be optimised and centered with the
<a href="optimise.htm">peak optimiser</a>.
<a href="optimise.htm">peak optimiser</a>. Dor not forget to put all
collimators in and to close all slits before optimizing. This is in
order to improve accuracy.
</p>
<p>
Once one reflection has been located, others might be located using the
<a href="Conescan.html">conescan</a> method when the lattice constants
are known. Do not forget to open all slits and to remove all
collimators for this.
</p>
<p>
If two reflections and the cell constants are known, a provisional UB
matrix may be <a href="ubcalc.htm">calculated</a> with the UBCALC
module. UBCALC can also calculate the UB matrix from three reflections
from scratch.
</p>
<P>
The next thing to do is to store the reflection and find other ones. Once a
few reflections have been found, the need to be written to disk. This can be
accomplished with the object rliste which has the following subcommands:
With a prvisional UB matrix determined it is advisable to locate and
optimise another 20 reflections in order to do UB matrix
refinement. During this time, reflections may be stored using the
rliste module:
<DL>
<DT>rliste clear
<DD> clears all entries from the list

11
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@ -18,7 +18,7 @@
\begin{huge}
TRICS--Reference Manual \\
\end{huge}
Version July, 2001\\
\today\\
Dr. Mark K\"onnecke \\
Labor f\"ur Neutronenstreuung\\
Paul Scherrer Institut\\
@ -41,12 +41,14 @@ Switzerland\\
%html logbook.htm 2
%html commandlog.htm 2
%html macro.htm 1
%html buffer.htm 1
%html exeman.htm 3
%html buffer.htm 2
%html hkl.htm 2
%html config.htm 1
%html system.htm 1
%html tricsingle.htm 1
%html optimise.htm 2
\section{External FORTRAN 77 Programs}
\subsection{INDEX}
@ -338,6 +340,8 @@ H H L
3 : 2H + L = 4n
\end{verbatim}
%html Conescan.html 2
%html ubcalc.htm 2
%html mesure.htm 2
%html hklscan.htm 2
@ -349,7 +353,4 @@ H H L
%html trscan.htm 2
%html psddata.htm 1
%html xds.htm 2
%html auto.htm 2
%html autocloud.htm 3
\end{document}

85
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@ -71,6 +71,13 @@ The log files show you all commands given and all the responses of the system.
safely ignored, SICS fixes this condition.
</dl>
</p>
<h2>Restarting SICS</h2>
<p>
All of SICS can be restarted through the command:
<pre>
monit restart all
</pre>
</p>
<h2>Starting SICS</h2>
<p>
An essential prerequisite of SICS is that the server is up
@ -79,7 +86,7 @@ fails. Only after a reboot or when the keepalive processes were killed (see
below) the SICServer must be restarted. This is done for all instruments by
typing:
<pre>
startsics
monit
</pre>
at the command prompt. startsics actually starts two programs: one is
the replicator application which is responsible for the automatic
@ -95,9 +102,10 @@ everything the server process must be killed. This can be accomplished either m
</p>
<h2>Stopping SICS</h2>
<p>
All SICS processes can be stopped through the command:
All SICS processes can be stopped through the commands:
<pre>
killsics
monit stop all
monit quit
</pre>
given at the unix command line. You must be the instrument user
(for example DMC) on the instrument computer for this to work properly.
@ -123,81 +131,40 @@ can not be resolved by simple means.
<p>
Sometimes it happens that the SICServer hangs while starting up or hardware
components are not properly initialized. In such cases it is useful to
look at the SICS servers startup messages. In order to do so, both the
SICServer and its keepalive process must be killed first. On the instrument
acount issue the command:
look at the SICS servers startup messages.
On the instrument account issue the commands:
<pre>
ps -A | grep SICS
monit stop sicsserver
cd inst_sics
./SICServer inst.tcl | more
</pre>
A message like this will be printed:
Replace inst with the name of the appropriate instrument in lower case.
For example, from the home directory of the hrpt account on the computer hrpt:
<pre>
23644 ?? I 0:00.00 ksh keepalive SICServer focus.tcl
23672 ?? R 59:24.05 SICServer focus.tcl
7119 ttyp6 S + 0:00.00 grep SICS
cd
monit stop sicsserver
cd hrpt_sics
./SICServer hrpt.tcl | more
</pre>
Remember the numbers in the first columns (the PID's) and kill both
programs by issuing the command:
<pre>
kill -9 pid pid
</pre>
Example:
<pre>
kill -9 23644 23672
</pre>
Note, the numbers are those displayed with the ps -A command.
Then cd into the bin directory of the instrument account and issue
the unix command:
<pre>
SICServer inst.tcl | more
</pre>
Replace inst.tcl with the name of the appropriate instrument initialisation
file. This allows to page through SICS startup messages and will help to
This allows to page through SICS startup messages and will help to
identify the troublesome component. The proceed to check the component and
the connections to it.
</p>
<h2>Getting New SICS Software</h2>
<p>
Sometimes you might want to be sure that you have the latest SICS software.
This is how to get it:
<ol>
<li>Login to the instrument account.
<li>If you are no there type cd to get into the home directory.
<li>Type <b>killsics</b> at the unix prompt in order to stop the SICS server.
<li>Type <b>sicsinstall exe</b> at the unix prompt for copying new
SICS software from the general distribution area.
<li>Type <b> startsics</b> to restart the SICS software.
</ol>
</p>
<h2>Hot Fixes</h2>
<p>
When there is trouble with SICS you may be asked by one of the SICS
programmers to copy the most recent development reason of the SICS server
to your machine. This is done as follows:
<ol>
<li>Login to the instrument account.
<li>cd into the bin directory, for example: /home/DMC/bin.
<li>Type <b> killsics</b> at the unix prompt in order to stop the SICS server.
<li>Type <b>cp /data/koenneck/src/sics/SICServer .</b> at the unix prompt.
<li>Type <b> startsics</b> to restart the SICS software.
</ol>
<b>!!!!!! WARNING !!!!!!!. Do this only when advised to do so by a competent
SICS programmer. Otherwise you might be copying a SICS server in an
instable experimental state!</b>
</p>
<h2> HELP debugging!!!!</h2>
<p>
The SICS server hanging or crashing should not happen. In order to sort such
problems out it is very helpful if any available debugging information is
saved and presented to the programmers. Information available are the log
files as written continously by the SICS server and posssible core files
lying around. They have just this name: core. In order to save them create a
lying around. They have just this name: core.pid, where pid is the process identification number.
In order to save them create a
new directory (for example dump2077) and copy the stuff in there. This looks
like:
<pre>
/home/DMC> mkdir dump2077
/home/DMC> cp log/*.log dump2077
/home/DMC> cp core dump2077
/home/DMC> cp core.2077 dump2077
</pre>
The <tt>/home/DMC> </tt> is just the command prompt. Please note, that core
files are only available after crashes of the server. These few commands

36
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@ -4,8 +4,23 @@
</HEAD>
<BODY>
<H1>PSD-TRICS Count and Tricsscan Command</H1>
<h2>New Commands</h2>
<p>
As of 2005, the normal SICS scan command can be used for TRICS. There is
now a special command:
<pre>
scan2d
</pre>
which switches to PSD scan mode. Switching to single detector mode is
achieved through:
<pre>
scan1d
</pre>
H, k and l are now virtual motors in SICS and can be scanned normally.
</p>
<h2>Obsolete Commands</h2>
<P>
Two special commands have been defined for TRICS with a PSD:
Several special commands have been defined for TRICS with a PSD:
<dl>
<dt>count <tt>mode preset </tt>
<dd>counts with all three detectors. The parameter mode defines which
@ -26,9 +41,24 @@ Two special commands have been defined for TRICS with a PSD:
<dd>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.
preset. These parameters have the same meaning as described above. If the
{\bf hkl nb 1} command has been given before the invocation of this scan,
reflections will be searched in normal beam geometry. psdrefscan, however,
will only print the normal four circle angles, though.
<dt>detscan start step np mode preset
<dd>Detscan performs a scan in two theta. This may be useful for detector
calibrations. Arguments as described above.
<dt>phscan start step np mode preset
<dd>Phscan performs a scan in phi. This can be usefule for orienting a
crystal. Arguments as described above.
<dt>o2tscan2d start step np mode preset
<dd>O2tscan2d performs a omega - two-theta scan with the PSD.
Arguments as described above.
<dt>hklscan2d
<dd> For a scan in reciprocal space with the PSD, see the
documentation for <a href="hklscan.htm">hklscan</a>. Please note that
for a PSD HKL scan, all commans have to start with hklscan2d.
</dl>
</P>
</BODY>
</HTML>

70
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@ -0,0 +1,70 @@
<HTML>
<HEAD>
<TITLE>The Online UB Calculation Routine</TITLE>
</HEAD>
<BODY>
<H1>The Online UB Calculation Routine</H1>
<P>
This module allows to calculate the UB matrix from either two reflections and the
cell constants or standalone from three reflections. A little aid for
indexing is implemented too. As usual when dealing with calculations
the common rule: shit in, shit out holds true. In this case this
means that the quality of the UB matrix obtained increases when:
<ul>
<li>Reflections have been centered as accuratly as possible, i.e. with
slits closed and collimators in.
<li>Two theta has been calibrated against a standard beforehand.
<li> The crystal under investigation has been properly centered.
<li>Cell constants and wavelength are accurate.
</ul>
This module is for classic four circle diffraction only.
</P>
<p>
A range of commands allows for reflection and data input and
calculations. For the following discussion it is assumed that the UB
matrix calculation object has been configured into the system under
the name ubcalc.
<dl>
<dt>ubcalc ref1, ref2, ref3 h k l two_theta omega chi phi
<dd>Reflection input for up to three reflections. Miller indices must
be given. When angles are not given, the current position of motors
stt, om, chi, phi is read.
<dt>ubcalc cell a b c alpha beta gamma
<dd>Input of cell constants
<dt>ubcalc ub2ref
<dt>Calculate the UB matrix from ref1, ref2 and the cell constants.
<dt>ubcalc ub3ref
<dd>Calculate the UB matrix from the three reflections ref1, ref2 and
ref3.
<dt>ubcalc listub
<dd>Print the calculated UB matrix
<dt>ubcalc cellub
<dd>Caclulate and print the cell constants as calculated from the UB matrix.
<dt>ubcalc activate
<dd>Copies the UB matrix to the hkl module. The positions of new
reflections can then be calculated with hkl.
<dt>ubcalc index two_theta
<dd>Makes suggestions for possible miller indices matching
two_theta. If two_theta is omitted, the current value of two theta is
read from the motor stt. A brute force search through the space of
possible indices is undertaken using the cell constants given and the
wavelength from the hkl module. This routine is controlled by three
parameters within ubcalc:
<ul>
<li>difftheta, The maximum permissible difference in two_theta
<li>maxindex, The maximum value for miller indices in any direction.
<li>maxlist, The maximum number of suggestions to list.
</ul>
<dt>ubcalc difftheta, maxindex, maxlist value
<dd>Inquire or set the above parameters. For inquiry, give no value,
for setting the parameter give tha name and the value.
<dt>ubcalc list
<dd>Print all the data in ubcalc.
<dt>ubcalc listcell
<dd>Print the cell constants.
<dt>ubcalc listref1, listref2, listref2
<dd>Print reflections 1, 2 or 3
</dl>
</p>
</BODY>
</HTML>

11
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@ -29,6 +29,7 @@ Switzerland\\
\clearpage
\tableofcontents
\clearpage
\clearpage
\chapter{Introduction}
This is the master user manual for SICS. It gives an overview over all
@ -40,13 +41,14 @@ SICS built in scripting language. Only the most common of such
commands are listed here.
\chapter{System Commands and Concepts}
%html sicsinvoc.htm 2
%html basic.htm 2
%html sicsinvoc.htm 2
%html logging.htm 2
%html logbook.htm 3
%html commandlog.htm 3
%html batch.htm 2
%html macro.htm 3
%html exeman.htm 3
%html buffer.htm 3
%html token.htm 2
%html system.htm 2
@ -63,13 +65,12 @@ commands are listed here.
%html count.htm 2
%html histogram.htm 2
%html samenv.htm 2
%html ctrl.htm 2
%html ../manager/rs232.htm 2
%html velocity.htm 2
%html velolambda.htm 2
\chapter{Common User Commands}
%html topscan.htm 2
%html hkl.htm 2
%html optimise.htm 2
%html xytable.htm 2
%html lowmax.htm 2
@ -85,8 +86,10 @@ commands are listed here.
%html amortof.htm 3
\section{TRICS Specific Commands}
%html hklscan.htm 3
%html trscan.htm 3
%html hklscan.htm 3
%html hkl.htm 3
%html ubcalc.htm 3
%html mesure.htm 3
%html nextrics.htm 3
%html peaksearch.htm 3

2
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@ -51,6 +51,8 @@ is set, without the current value is printed.
<DT> nvs loss
<DD> Starts a loss current measurement on the velocity selector and prints the
result.
<DT>nvs forbidden
<DD>Prints a list of forbidden speed regions for this selector.
<DT>nvs status
<DD>Prints a status summary of the velocity selector.
</DL>