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fixed many typos
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bruceravel committed Nov 15, 2024
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25 changes: 12 additions & 13 deletions docs/commonchores.rst
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,8 @@ Search the Hutch

The buttons on the hutch interlock panel are labeled with black
stickers with white numbers. Those labels correspond to the numbering
in these lists:
in these lists. Note that there is no step #4 when opening the hutch
and no step #2 when closing.

To OPEN the hutch
~~~~~~~~~~~~~~~~~
Expand All @@ -47,6 +48,7 @@ the buttons. The serach **is not** a team sport!

1. Complete the hutch search

+ Wait for others to exit the hutch
+ Look in the mirror to see that no one is behind the table
+ Press search button 1
+ Visually inspect the length of the hutch, verifying that it is empty of people
Expand Down Expand Up @@ -78,7 +80,7 @@ Change energy and prepare for fluorescence measurements
-------------------------------------------------------

In this example, we are using Fe as the example. That is, we assume
your are moving the beamline to the state in which it is ready to
you are moving the beamline to the state in which it is ready to
measure at the Fe K edge. For any other edge, simply change ``Fe`` to
the appropriate element in the following example.

Expand All @@ -100,7 +102,7 @@ Once the hutch is secured and you are back at the computer:
with ``xafs_det.limits``.

#. Measure an XRF spectra: ``%xrf``. Remember that you want the OCR
(total count rate) to be 200,000 or less on each of the four
(total count rate) to be 200,000 or less on each of the seven
channels.

#. Adjust the detector position ``RE(mv(xafs_det, <value>))``.
Expand Down Expand Up @@ -137,17 +139,17 @@ Align the *ex situ* sample wheel

The attractive feature of the *ex situ* sample wheel is that it makes
it easy to move from sample to sample. Once the wheel is properly
aligned in the beam, the command ``RE(slot(#))``,
``RE(xafs_wheel.inner())``, and ``RE(xafs_wheel.inner())`` are all
aligned in the beam, the commands ``RE(slot(#))``,
``RE(xafs_wheel.inner())``, and ``RE(xafs_wheel.outer())`` are all
that's needed to move from sample to sample.

For this to work, the wheel has to be properly aligned in the frist
place.

Once the rotation stage is in place and a wheel is mounted on the
stage, place a phosphor screen in front of any slot *on the outer
ring*. It is essential that the initial alignment be done of the
outer ring.
ring*. The alignment procedure assumes that the initial alignment be
done of the outer ring.

#. Rotate the wheel such that the phosphor screen is in the beam path
using ``RE(slot(#))``, where # is between 1 and 24.
Expand All @@ -160,12 +162,11 @@ outer ring.
beam on the phosphor screen when looking through one of the
cameras. Use ``RE(mvr(xafs_x, <amount>))`` and ``RE(mvr(xafs_y,
<amount>))`` to move the stage in X and Y. ``<amount>`` is a
*number* |nd| some sensible distance in millimeters, something like
5 is often a good choice.
*number* |nd| some sensible distance in millimeters.

#. Using ``RE(mvr(xafs_x, <amount>))`` and ``RE(mvr(xafs_y,
<amount>))``, move the stage such that the beam is approximately in
position to go through a slot on the outer ring.
position to go through the middle of a slot on the outer ring.

#. Rotate the stage to an empty slot using ``RE(slot(#))``.

Expand All @@ -185,8 +186,6 @@ outer ring.
``xafs_x`` and ``xafs_y``.




This procedure sets a parameter specifying the ``xafs_x`` position of
the outer ring. The inner ring is known to be 26 mm away. Thus, the
positions of both rings are set. This is why it is important to run
Expand Down Expand Up @@ -336,7 +335,7 @@ Filling the 25 liter LN2 dewar
#. Do not remove glasses, face shield, lab coat, or gloves from the
hutch.

#. Open main LN2 valve. Use the button on the "06BM utilities" CSS
#. Close main LN2 valve. Use the button on the "06BM utilities" CSS
screen or at the bsui command line do ``ln2.close()``.

#. Press the :green:`Front Right Maglock` button. The green light should be
Expand Down
83 changes: 45 additions & 38 deletions docs/manage.rst
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Expand Up @@ -204,16 +204,16 @@ that you started at with the other crystal set and run a rocking curve
scan.

Note that some of these motions can be a bit surprising in the sense
that the monochromator will end up outside the normal operating range
of the beamline. They will, however, eventually return to sensible
places.
that the monochromator will briefly report itself as being outside the
normal operating range of the beamline. They will, however,
eventually return to sensible places.


Change XAS |harr| XRD
Change XAS |larr| XRD
---------------------

Begin this transition by leaving the I0 chamber in place to monitor
the incidence flux. In most cases, this should do the trick:
To move the photon delivery system to delivery of focused beam to the
goniometer:

.. code-block:: python
Expand All @@ -238,18 +238,19 @@ To do all of that by hand, you would do the follow commands:
RE(slit_height())
This change of mode should have the beam in good focus at the position
of the goniometer. 8000 eV is the nominal operating energy for the
of the goniometer. 8600 eV is the nominal operating energy for the
goniometer. If a higher energy is required, substitute the correct
energy for ``8600`` in the second line.

.. note:: The I\ :sub:`0` chamber should be left in place. This will
facilitate changing energy while doing scattering
experiments. The flight path can be put in place at any time.

.. todo:: Determine look-up table for lower energy operations using
both M2 and M3. This will require a new XAFS table and
adjustments to the limit switches on ``m3_ydo`` and
``m3_ydi``.

Once the photon delivery system is set, remove the ion chambers and
insert the XRD flight path into its place.


.. _use333:

Expand Down Expand Up @@ -511,8 +512,13 @@ We use the `BioLogic EC_lab software
the `VSP-300 potentiostat
<https://www.biologic.net/products/vsp-300/>`__. Since there is not a
dedicated Windows machine at BMM, EC-Lab is run on a virtual machine
that is spun up when needed. Here are the instructions for starting
and interacting with the the VM.
that is spun up when needed.

Similarly, Hiden's control software is a Window's only produce. It is
run on the same firtual machine.

Here are the instructions for starting and interacting with the
the VM.

Starting the virtual machine
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -524,10 +530,10 @@ Starting the virtual machine
+ The Windows desktop might start with a full-screen management
application that looks like the figure below. You can close
or minimize that window.
+ Double-click on the EC-lab icon.
+ Do some electrochemistry.
+ Save your electrochemistry data to the assets folder as explained
below.
+ Double-click on the EC-lab or Hiden icon.
+ Do some electrochemistry or mass spectrometry.
+ Save your electrochemistry or mass spectrometry data to the assets
folder as explained below.

.. _fig-winvm:
.. figure:: _images/Winvm_startup.png
Expand All @@ -537,11 +543,12 @@ Starting the virtual machine

VM management window. You can minimize or close this.

Storing echem data
~~~~~~~~~~~~~~~~~~
Storing electrochemistry or mass spectrometry data
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The Windows VM has permission to connect to central storage with
permissions to write files from EC-lab to the correct location.
permissions to write files from EC-lab or the Hiden software to the
correct location.

To start a new experiment, you first have to disconnect the old drive
(if connected). This is likely mounted as the ``Z:`` drive.
Expand Down Expand Up @@ -609,18 +616,22 @@ The new network drive can now be clicked into.
Configure EC-lab to write its data files into the
``assets\vsp300-1`` folder.

Configure the Hiden software to write its data files into the
``assets\hpr20-1`` folder.

.. _fig-winsassetsfolder:
.. figure:: _images/Windows_assets_folder.png
:target: _images/Windows_assets_folder.png
:width: 70%
:align: center

The ``assets\vsp300-1`` folder is the correct place for data from
EC-lab to be written.
EC-lab to be written. The ``assets\hpr20-1`` folder is the correct
place for data from the Hiden to be written.

By following this procedure, the electrochemistry data from EC-lab
will be available to the user in the
:numref:`same manner as their XAS data (Section %s) <data>`.
By following this procedure, the electrochemistry data from EC-lab and
mass spectrometry data from the Hiden will be available to the user in
the :numref:`same manner as their XAS data (Section %s) <data>`.



Expand Down Expand Up @@ -812,31 +823,27 @@ storage.
Manage Silicon Drift Detectors
------------------------------

.. note::
Thanks to funding from the CHIPS Act, BMM is
procuring a new 7-element SDD! Look for that in late 2024 or
early 2025.

The assumption is that one of the three detectors will be the primary
detector in an experiment. At the bsui command line (or in queue
server) the ``xs`` symbol should point at the correct detector. Also,
a parameter is set in Redis allowing other processes (such as the
Kafka plotting agent) to know which detector to be paying attention to.
The assumption in the data acquisition system is that one of the three
silicon drift detectors will be the primary detector in an experiment.
At the bsui command line (or in queue server) the ``xs`` symbol should
point at the correct detector. Also, a parameter is set in Redis
allowing other processes (such as the Kafka plotting agent) to know
which detector to be paying attention to.


.. code-block:: python
xs = xspress3_set_detector(4)
xs = xspress3_set_detector(7)
where the argument to ``xspress3_set_detector`` is 1, 4, or 7
where the argument to ``xspress3_set_detector`` is 1, 4, or 7. Since
October 2024, use of the seven element detector is the default.

This sets ``xs`` to the selected detector object |nd| ``xs1``,
``xs4``, or ``xs7``. The default at startup is to use the 4-element
detector. That will change soon to the new 7-element.
``xs4``, or ``xs7``.

Also set is the Redis parameter ``BMM:xspress3``, which is set to 1,
4, or 7 (and represented as a b-string).

.. code-block:: python
int(rkvs.get('BMM:xspress3'))
n_elements = int(rkvs.get('BMM:xspress3'))
2 changes: 1 addition & 1 deletion docs/prolog.rst
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
.. |plus| unicode:: U+002B .. PLUS SIGN
.. |checkmark| unicode:: U+2713 .. CHECK MARK
.. |xmark| unicode:: U+2717 .. BALLOT X
.. |harr| unicode:: U+02194 .. LEFT RIGHT ARROW
.. |larr| unicode:: U+02192 .. LEFT ARROW
.. |ast| unicode:: U+002A .. ASTERISK
.. |verbar| unicode:: U+007C .. VERTICAL LINE
.. |mquad| unicode:: U+2001 .. EM QUAD
Expand Down

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