George's 8.3.1 Notes
edited 2/20/05
View last few
entries of luke.log
Various
Notes
Info on LUKE
Data Transfer and Archiving
Click
here for James's Notes on "Moving Data Around"
How
to use the "download" command: Example: Firewire on a Mac Computers
Firewire on Mac using "rsynch" (James's Notes)
Firewire
Drives for MS Windows (or click on
link above and scroll down)
Top
Trouble Shooting:
(Here's a link to a
text file of
other
problems and how they were solved. )
Here are a few common problems:
Please do NOT restart computers or nuke the system without calling
beamline support x2500!
- Problem: Can't control BLU-ICE:
- Cause: the "network" is "passive".
- Fix: On lower right status bar, next
to "Network" Click on "Passive" to toggle to "Active".
- Problem: Can't control BLU-ICE:
- Cause: Energy Scan aborted and restarted before
hutch has restored pre-scan set up.
- Fix: Kill
BLU-ICE and restart.
- Problem: Can't Abort, Reset, or Delete Runs in Collect.
- Cause: The "Network" is "Passive".
- Fix: On lower right status bar, next
to "Network" Click on "passive" to toggle to "Active".
- Problem: Can't move Stage, e.g. to HIGH MAG.
- Cause: Door Not Shut or Tray Table not retracted.
- Fix: Close Door and/or move
Tray back. Note: There should be a pop-up window on top of
BLU-ICE if this occurs, but the window will be moved to the background
if you Click the BLU-ICE window.
- Problem: BLU-ICE won't collect an image.
- Cause: The detector DHS is screwed up.
There'll be a "no_hw_host" error.
This will show up in the BLU-ICE log file which
streams past, at the bottom of the GUI. Scroll up the log to see
if this message was written, or press "collect" to see it again.
If you see that the "no_hw_host"
error came from "detector", then...
- Fix: "nuke" the system to restart the
detectorDHS software.
- Problem: BLU-ICE won't collect an image.
- Cause: There's a problem with the front end
computer. There'll be a "no_hw_host"
error. This will show up in the BLU-ICE log file which
streams past, at the bottom of the GUI. Scroll up the log to see
if this message was written, or press "collect" to see it again.
If you see that the "no_hw_host"
error came from "beamline", then...
- Fix: Use the KVM switch at "graphics1" to
change to "beamline". If there's a stopped motor controller, or
the system looks flakey, call x2500 and tell user support that you think
the "beamline" computer needs to be restarted.
Here's a link to a text file of
other
problems and how they were solved.
Fluorescence
Scans in Blu-ICE:
* Just click on SCAN -> Periodic Table -> the element's edge; The
scan's filename, range, step size, and optimization are done
automatically.
* Right click in the view area of the PLOT to see a menu of [file,
print, load, plot].
*Note all scans are printed out after they're done.
Direct
Beam
Note that the position of the beam on the detector changes with
detector distance. The data acquisition software takes this into
account and updates the coordinates of the beam center written to the
header of the image files. If you want to see what the current
mosflm/denzo beam center coordinates are, run direct_beam.com
in a terminal window.
There's usually enough "bleed through" to see the direct beam in the
images, but if you want to take a direct beam shot run find_direct_beam.com in a
terminal window. Here's what happens when you run this script:
- It will use the detector distance in the BLU-ICE collect tab if
no arguments are given, otherwise provide a distance 200mm, e.g., as an
argument.
- The script closes down the divergence to 0.02 X 0.02
- puts in all filters
- lowers the stage
- takes a 0.1 second exposure
- computes the location of beam center and reports where it is.
- By default, it will NOT write this NEW beam center into the
header file of each subsequent image. You'll need to run direct_beam.com
, with the adxv coordinates, reported in the step above, as an argument.
- Returns the hutch to it's inital state, BUT ...
- NOTE: BLU-ICE will have the exposure time and prefix
modified by this script. You need to change them (back) to
appropriate values.
Checking Beam
Alignment and Changing Pinholes
The beamline has an active feedback system and is quite stable over
time and wavelength changes: realignment is seldom necessary,
unless swapping pinholes. It should be obvious which pinhole is
being used: the 100 micron pinhole will have a beam defining circle of
~2.5 inches on the touch screen. The 30 micron pinhole will
be ~ 1 inch (and the total flux will be ~15% of the 100 micron pinhole).
To confirm the pinhole size, enter " grep pinhole
/data/log/change.log | tail -1 " in a terminal window. Please
don't change pinholes unless you've been shown how. Here are Seth
Harris's notes on how to do that. Below is a
description of realigning the beam.
- In a teminal window, enter " realign.com
". This will:
- move the collimator down
- move the goniometer stages to preset positions
- display pictures to help you put on the alignment jig correctly
- wait for you to proceed
- Now, place the special alignment jig (X-Ray fluorescent
YAG crystal with fine hair glued to end) onto the goniometer
shaft.
- If you want to change pinholes, and have been shown how, do so
now.
- Close the hutch door and press Photons
On button.
- Close the pictures displayed on the monitor and press <enter> in the terminal window. This
will cause the collimator to move up, and the script to continue.
- realign.com then does the
following:
- The jig will be centered automatically at Low, then High
Magnification.
- The Divergence will be set to (2.0, 0.35 milli-Rad) and Wave
Length (1.1 Angstrom).
- tuneup.com
will run and optomize the flux.
- The beam will be focused on the YAG with focus.com
then find_beam.com
will find the coordinates of the beam center and write those values to
/data/calibrations/beam_in_camera1.txt, to be used by find_axis.com,
later.
- The user is asked to set and/or confirm that the cross hairs on
the touch screen are centered and the beam defining circle
is the correct diameter. Make changes, if needed. The
script waits for <enter>.
Then, find_axis.com gets the
Vertical Collimator on to the Center of Rotation, and saves the new "up" position of the Vertical Collimator stage.
-
The user is then asked to confirm that this Center of Rotation
is correct. If it's not, the script will iterate from the tuneup.com step, above; otherwise it
continues:.
- tuneup.com is run again
with this new Vertical Collimator in
position.
- The feedback system is turned on after checking for false spots.
- The collimator moves down
- the goniometer is moved to its previous position.
- carefully remove the alignment jig and place it back in it's
vial.
Stopping
and Starting Software
* At the start (or end) of an indivual user's beamtime, type
"finished" to reset the beamline to default conditions.
* If you need to restart BLU-ICE, kill it by closing the window.
(Also kill adxv and the calculator, since go
will start all three running.)
* Type go to start BLU-ICE, adxv, and a
calculator. (Can also use dcs,ice, bluice, blu-ice,
blue-ice, start, session, ...)
* To kill and restart ALL data acquisition software, type nuke. PLEASE DON'T, with out consulting
with beamline support staff.
* (Staff only: To kill all data acquisition software , with out doing a
system wide restart type nuke die).
Scripts For Controlling
& Querying The Beamline
Most scripts are located on bl831.als.lbl.gov:/programs/beamline.
This list and the descriptions are far from complete.
Look in James's page for all the details, as well as the actual scripts.
Scripts that control the movement of a motor or actuator can be run
with no arguments: the state or the position of that particular device
will be returned. For example:
stage.com
returns the position of the Vertical Collimator Stage
shutter.com
returns the state of the fast shutter: open or closed
distance.com
returns the horizontal position of the detector
cover.com returns the position of the cover: on or off
beamstop.com returns the positon of the beamstop X-Y
stage
***************sample .com******************
sample.com returns the positon of the sample X-Y-Z stage.
Note: ALL coordinates are in millimeters.
Also, Regardless of goniometer rotation angle,
+X is opposite direction of beam, i.e. up stream or
towards the camera prism,
+Y is up,
+Z is away from goniometer.
If only one coordinate is entered it is assumed to
be X,
if two are entered they are assumed to be X and Y.
Note: there is a space between the command and each
coordinate.
sample.com X
Y Z - moves sample
stages by amounts X, Y, and Z
sample.com
0 .1
- moves sample stage Y by 100 microns.
sample.com
0 0 -1.0 - moves
sample stage Z by minus 1 millimeter.
sample.com to X
Y Z - moves sample stages to position X, Y, and Z
If in doubt about relative or absolute moves, you
can always use "by" or "to".
The defaults for sample.com
and beamstop.com are to move
the sample relative, or "by" the amount requested.
The defaults for stage.com
and phi.com are to move absolute,
or "to" the requested position.
*********************************
stage.com Y - moves the
Vertical Collimator to position Y
stage.com by Y - moves
the vertical collimator by amount Y
stage.com up - moves stage to
the "up" position
stage.com down - moves
stage to the "down" position
BEWARE: stage.com zero
- sets the current position to be the "up"
position
phi.com X - moves phi to angle
X
shutter.com [open/close] NOTE: at low MAG (Stage Down)
"watchdog.tcl" will CLOSE an open shutter.
cover.com [on/off]
diode.com [in/out]
backlight.com [in/out]this is
the polarized light source. It's light 2, whose intensity can be
adjusted by light.com.
light.com [1 or 2, 0-100]which
light, what % of full intensity.
blmotor.com easy way to send
commands to FRONT END computer (look here
to get complete list of commands recognized by labVIEW, the control
software.)
wave.com X - sets the photon
energy to wavelength X
divergence.com [Horizontal, Vertical];
units are in milli-radians , defalts are 2.00mr X 0.35mr.
flux.com [active]: - puts in
diode, opens shutter, auto-scales then reads I-end, closes shutter,
retracts diode (Stage must be UP)
focus.com (no parameters ) focuses
the object in the Hi Mag view (only).
tune_up.com - tunes the front-end
feedback.com [keep] -will
turn on feedback (after checking for false spots)
find_axis.com -finds the center
of rotation of the object in the HIGH MAG view, then calculates how far
the Vertical Collimator needs to move in order to have beam center on
the rotational axis.
find_beam.com -finds the
coordinates of the center of the beam on the YAG crystal in view.
center_wire.com -moves the object
in view (Hi or Low magnification) onto the Center of Rotation
eta.com -Calculates the time to
completion for the current run. (The script will run until killed
or collection stops. If collection hasn't started in runs and
quits)
Computers:
"graphics1": linux box on floor, to right of touch screen, usually used
for BLU-ICE
"graphics2": linux box at far right of work bench
"server"= is bl831.als.lbl.gov: central sever with RAID
array 600MBS of storage in each of /data and /data2
Penguin Computer in rack above far left side of work bench.
"crush1-16" dual processor cluster computers
Run Elves on CRUSH machines, run "o" on GRAPHICS#
"beamline" is bl831b.als.lbl.gov is the front end computer.
In C:/Beamline Controls/Log
Files, are files of EVERY motor move and the value of the
current amplifiers stored
every 10 seconds.
pmac1.als.lbl.gov controls the big end-station motors
pmac2.als.lbl.gov controls the goniometer, shutter, and fluorescence
counter
To Telnet to PMAC,
Logon to bl831, from there telnet to pmac1.als.lbl.gov 14001
This is only possible
if pmac DHS is not running.
Other
notes, mainly for staff...
Aligning High and Low mag cameras; Optimizing pin-hole
LabVIEW
Nuke and DHS
DVD
Robot for Dynamic backups and Archiving
Lots of logs are created. grep them to
extract information.
Info on configured runs and time
since last images were taken
Feedback settings on frontend
computer
BL8 Documentation" byAlastair
Starting "Monitoring" Software, and
others
Denzo Scripts from 8.2.1
8.3.1 Denzo
Site Def from James
On a linux box, to determine how many images
can be stored on the disk,
for a Q315 use df --block-size 18M
for a Q210 use df --block-size 8M