Beamline Device Layout and Motor Motions
Drawing of the layout of devices and motions at 12-ID-B
sav : sample vertical
sah : sample
horizontal (NOT in use)
sth : sample table
th : theta (the
incident angle in GISAXS)
phi : sample phi
angle (the sample azimuthal angle in GISAXS)
the main computer for beamline operation, and data collection.
run detectors' MDEM
- detector12 : The
inside the station B. Accessible from the monitor in the station and
from Purple through Remote Desktop Connection.
- sec12dt01 : For
data visualization and analysis. Accessible from Purple through Remote
- sec12dt02 : For
data analysis. Accessible from the monitor and keyboard at the right
end of the computer table.
to make a remote desktop connection from Linux computer:
xfreerdp -g 1920x1050 -u s12idb -d xray detector12.xray.aps.anl.gov
the data are on the network drive which can be accessed from any of the
above computers. However, user data transfer should be done through
It has multiple USB ports to use. User can copy
his/her whole data folder like "Z:\2018_1\zuoApr6" . Do NOT delete data
/ folders. Beamline staff regularly backup user's data which can be
SPEC Commands for Motor Motion and Data Acquisition
data acquisition software system is built mainly based on Epics.
users will face only SPEC, a command-line software program, and
home-built MATLAB codes during the experiment.
Spec, which has been used for many diffraction beamlines, has been
implemented for 12ID-B and serves as a kind of higher-level language,
which provides programming and minor plotting capability.
macros used for data acquisition at 12ID-B station.
filename exposuretime Nshot
filename exposuretime Nshot Period
takeshot bsa 1.0 30 3.0
thirty images for sample bsa with exposure time of 1.0 sec and period
of 3.0 sec. within the 3.0 sec period time, only 1.o sec for data
collection, the rest 2.0 sec is sleep time.
Nshot: number of shots
filename: should be readable but short
a motor to an absolute position
umv sth 20.5
move motor sth to postion 20.5
"Ctrl"+"c" combined key can abort the move
a motor by certain distance relative current position
umvr sav 1.5
move moter sav +1.5 mm relative to the currrent sav position
a sample angle and height to X-ray beam
automatically align the sample
the fast shutter
the fast shutter
motorname relativeleft relativeright Nshot expt
lup sth -2.0 3.0 40 0.1
scan sth motor in position range [- 2.0 +3.0] relative to current sth
position; measure for 40 positions, exposure time of 0.1 sec at each pos
on / off
Collection Python Interface: specGUI
is a python-based GUI program that can communicate with SPEC
operate motor move and data collection. Users can press
instead of typing commands on SPEC. It works only when SPEC
on server mode. See SPEC for how.
When SPEC is running, start specGUI by:
(1) Open a terminal. (2) Type, cd ~/python_codes;
(3) Type, startSpecGUI
mode: SAXS/ GISAXS/GIWAXS, different beamstop associated
with each mode.
scan: same as "lup" scan command, run with specific
scan: take image in the specified motor position range.
5. Creating New User
Folder for Data Collection
data folder is closely connected with the data collection and
processing programs. Changing data directory in SPEC or making new
arbitary directory will mess up data collection. Here is the correct
way to make a new user data directory:
(1) from "12IDB spec GUI", click "File" menu, then "New User Dir." A
window of "Make New User Directory" will pop up.
(2) fill fields in this window like below. Click "OK" to make
a new user directory.
The above window will make a user directory of :
The spec log file will be "xz05102018"
You will also see some print-out information in the SPEC window about
making the new directory.
If you cannot see your collected images/data, it could be caused by
wrong data directory. You can make a new user data directory
see if it solves the problem. Normally, the data transfer and
converting programs will follow the new user directory and you don't
have to do anything on that.
GISAXS Sample Alignment
- GISAXS measurement may require aligning the
top surface of a sample
- Exactly to the middle of beam (Half position)
- Parallel to the beam
- To do so, users need to align theta
- Looking at the sample on cameras, move the
sample vertically using umvr sav xxx or if
necessary, horizontally umvr sth xxx.
- When the vertical position is close to the
beam, type shopen to open the fast shutter.
- Keep eyes on the GISAXS photo diode counter
value and remember the full beam intensity that is the value with
sample below the beam.
- Move up the sample by typing umvr
sav 0.1 until the GI photo diode value becomes the half of
the full beam.
- Align the theta by typing lup th -1
1 50 .1.
- Find a tip of the lup scan and move theta
motor to the tip, for example 0.12, umv th 0.12.
- Set the theta position as 0, set th 0
- Repeat 4-7.
- When a sample was already aligned and a new
sample with almost the same substrate thickness is now mounted
replacing the old one,
- You can use centering
- To do so, keep in mind. the top surface of the
new sample should be within +- 2mm of the beam.
- Otherwise, set sav 0 after you manually bring
the top surface close to the beam.
- Align th and sav either manually or using
- lup sth -3 3 50 .1
- umvr chi 1 or umvr chi -1 depending on the
slope of the lup scan.
- zcent to align the sav again.
- repeat 2-4 until the slop of the lup scan