lots of edits

docs/automation.rst

@@ -47,8 +47,8 @@ differences in the columns corresponding to the different instruments.
 
 Make sure you are using the most up-to-date version of the spreadsheet.
 
-.. note:: The current spreadsheet version is **13**, as of 29
-          February, 2024.  You should *always* use a current
+.. note:: The current spreadsheet version is **14**, as of 14
+          November, 2024.  You should *always* use a current
           spreadsheet.
 
 .. caution:: Spreadsheets with version number earlier 13 **will not
@@ -68,19 +68,31 @@ indicated measurements.  In :numref:`Figure %s
 green background.  All rows underneath the green line are used to
 describe individual measurements.
 
-For an individual measurement, if a white cell is left blank, the
-default value from the corresponding green cell will be used.  If a
-white cell is filled in, that value will be used for that measurement.
+For each individual measurement:
+
++ If a white cell is left blank, the default value from the
+  corresponding green cell will be used.  
++ If a white cell is filled in, that value will be used for that
+  measurement.
 
 Experimenters
 ~~~~~~~~~~~~~
 
-The other green part of the spreadsheet is a cell for entering the
-names of all the experimenters involved in the measurement.
+.. note::
+
+   As of summer 2024, with the implementation of data security, the
+   beamline now has access to some information about the proposal and
+   SAF.  It is no longer necessary to specify the names of the
+   experimenters.  All names on the proposal will be put in the
+   metadata of every scan.
 
-This should **always** be filled in.  Doing so allows for the
-possibility of searching BMM's master database for data associated
-with a particular user.
+..
+  The other green part of the spreadsheet is a cell for entering the
+  names of all the experimenters involved in the measurement.
+
+  This should **always** be filled in.  Doing so allows for the
+  possibility of searching BMM's master database for data associated
+  with a particular user.
 
 .. _spreadsheet_options:
 
@@ -91,14 +103,11 @@ Beneath the experimenter cell, there are three drop-down menus for
 setting aspects of the sequence of measurements described on the
 spreadsheet tab.
 
-#. A yes/no menu for forcing Bluesky to run the ``change_edge()``
-   command at the beginning of the measurement sequence.
-
 #. A yes/no menu for telling Bluesky to close the shutter at the end
    of the measurement sequence.
 
 #. A menu of options for modifying filenames to contain information
-   about things like absorber element, edge symbol, LInkam stage
+   about things like absorber element, edge symbol, Linkam stage
    temperature, and so on.  This simplifies data entry into the
    ``filename`` column of the spreadsheet.
 
@@ -107,6 +116,21 @@ spreadsheet tab.
    "repetitions", which specifies the number of repeated XAS scans of
    the sample in that row of the spreadsheet.  
 
+Detector position
+~~~~~~~~~~~~~~~~~
+
+On the right hand side of each spreadsheet, there is a column for
+specifying the position of the fluorescence detector.  A smaller value
+is closer to the sample.
+
+The detector position is set on a sample-by-sample basis, allowing the
+best possible measurement |nd| not saturating the detector while
+maximizing the signal for samples of different absorber concentrations
+|nd| for each sample.  For many experiments, most of the set up work
+involves moving from sample to sample and setting the values of this
+column.
+
+
 Fine tuning sample position and slits
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -130,7 +154,7 @@ the centers of the spinners.
 
 
 Selecting a spreadsheet
-~~~~~~~~~~~~~~~~~~~~~~~
+-----------------------
 
 All spreadsheets are imported using the :file:`xlsx()` command.  The
 spreadsheets are self-identifying.  Every spreadsheet has an
@@ -140,6 +164,9 @@ pink background.
 .. caution:: **Never** change the text in the pink cell or your
              spreadsheet will likely be interpreted incorrectly.
 
+Import a spreadsheet
+~~~~~~~~~~~~~~~~~~~~
+
 To convert a spreadsheet into a macro then run the macro, do the
 following:
 
@@ -240,9 +267,9 @@ are aligned.
    diameter holes.  The rings on the double wheel are 26 mm apart
    (center to center of slots/holes).
 
-The automation concept is that each slot on the sample wheel is
-described by a row in the spreadsheet.  Each column of the spreadsheet
-carries one parameter of the XAFS scan.  
+The automation concept is that a measurement at an edge on a slot on
+the sample wheel is described by a row in the spreadsheet.  Each
+column of the spreadsheet carries one parameter of the XAFS scan.
 
 
 .. _fig-doublewheel-spreadsheet:
@@ -265,8 +292,8 @@ the INI file |nd| file name, element, edge, and so on.
 The green cell in the first row is used to input the names of all the
 people involved in the experiment, as explained above.
 
-As explained above, row 6, row with an entirely green background, is
-used to specify the default values for all the parameters.  The
+As explained above, row 6, the row with the lime-green background,
+is used to specify the default values for all the parameters.  The
 concept here is to try to avoid having to input repetitive
 information.  For instance, in this case, all measurements will be
 made at the Fe K edge.  The element and edge are all specified in the
@@ -325,6 +352,8 @@ explicit arguments for the filled-in spreadsheet cells.
    yield from xafs('MnFewheel.ini', filename='Fe-Spessartine', sample='Mn3Al2(SiO4)3', comment='Grants Mining District; New Mexico')
    close_last_plot()
 
+   ## and so on....
+
 .. _auto_linkam:
 
 Linkam stage automation
@@ -418,7 +447,9 @@ measurement.  And there is a column for specifying the holding time
 after arriving at temperature before beginning the XAFS measurement.
 
 There is a column for specifying the power level of the heater in the
-cryostat.  There are three power settings.
+cryostat.  There are three power settings.  You probably want to use
+the high power setting.  The controller is pretty well tuned for the
+cryostat.  It is unlikely to overshoot the when raising temperature.
 
 .. _fig-lakeshore-spreadsheet:
 .. figure::  _images/lakeshore_spreadsheet.png
@@ -549,5 +580,15 @@ spreadsheet is identical to the *ex situ* sample wheel spreadsheet.
    <https://github.com/NSLS-II-BMM/profile_collection/raw/master/startup/xlsx/grid.xlsx>`_.
 
 
-.. caution:: Spreadsheets with version number earlier 13 **will not
-	     work** as of 1 March, 2024.
+.. admonition:: Future Tech!
+
+   Spreadsheets for:
+
+   + Electrochemistry experiments using the BioLogic potentiostat
+   + Chemistry experiments using the gas cart, including its mass flow
+     controllers, valves, temperature controller, and mass spectrometer.
+
+
+
+.. caution:: Spreadsheets with version number earlier than 13 **will
+	     not work** as of 1 March, 2024.

docs/before.rst

@@ -252,6 +252,11 @@ to the first day of the beamtime to check in at `the GUV Center
 <https://www.bnl.gov/guv/>`__ and to complete beamline specific
 training.
 
+The GUV Center opens at `7 a.m. on weekdays
+<https://www.bnl.gov/guv/check-in.php>`__, so it is possible to obtain
+badges and access cards prior to the 8 a.m. start date of your
+experiment.
+
 Please consult `NSLS-II user guide <https://www.bnl.gov/ps/userguide/>`__
 or contact BMM beamline staff for more information.
 

docs/instruments.rst

@@ -54,13 +54,15 @@ photons, this versatility of setup is occasionally very helpful.
    silicon drift detector.
 
 
-.. 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. 
+.. note:: 
+   Thanks to funding from the CHIPS Act, BMM now has a new
+   7-element SDD!
+
+   It has been calibrated and fully integrated into the Bluesky data
+   acquisition system.
 
-   It arrived on 23 August, 2024!  Installation and commissioning to
-   start soon!  Still waiting on the new XYZ stage.
+   The new XYZ stage has also arrived and will be integrated during
+   the 2024-2025 winter shutdown.
 
    .. _fig-7element:
    .. figure:: _images/7element.jpg
@@ -69,7 +71,17 @@ photons, this versatility of setup is occasionally very helpful.
       :align: center
 
 
+Electron yield detector
+-----------------------
+
+.. todo::
+
+   Document this!
+
+.. todo::
 
+   Better scheme in Bluesky for specifying that the yield detector is
+   in use and that its signal should be plotted in real time.
 
 
 Area detector
@@ -204,18 +216,21 @@ folder (Section %s) <data>`.
    potentiostat.  This limits the level of automation and integration
    with the rest of the beamline.
 
-   We hope to implement external triggering and collection of current
-   and voltage values over the August 2024 shutdown.  This may become
-   available in the 2024-3 cycle.
+   DSSI has implemented external triggering and collection of current
+   and voltage using the `Quantum Detectors PandABox
+   <https://quantumdetectors.com/products/pandabox/>`__.  This may
+   become available to BMM users sometime in 2025.
 
 BMM does not provide electrochemical cells.  The user is expected to
-bring their own cells.
+bring their own cells.  Ideally, the electrochemistry has been tested
+in the cells intended for use at the beamline and are known to produce
+reliable electrochemical results.
 
 
 Temperature control
 -------------------
 
-BMM has two options for experiments as elevated or reduced temperature.
+BMM has two options for experiments at elevated or reduced temperature.
 
 
 Linkam stage

docs/manage.rst

@@ -38,15 +38,15 @@ chores.
 
 The ``name`` should be the PI's full name, preferably transliterated
 into normal ASCII.  The ``date`` should be the starting day of the
-experiment in the ``YYYY-MM-DD`` format.  The ```GUP`` and ``SAF``
+experiment in the ``YYYY-MM-DD`` format.  The ``GUP`` and ``SAF``
 numbers can be found on the posted safety approval form.
 
 Once the experiment is finished, run this command::
 
   BMMuser.end_experiment()
 
-This will reset the logger and the ``DATA`` variable and unset the GUP
-and SAF numbers.
+This will reset the logger and the ``BMMuser.folder`` variable and
+unset the GUP and SAF numbers.
 
 
 

docs/motors.rst

@@ -151,14 +151,6 @@ are the same for all sample stage motors.
    To see the available foils, do ``%se`` or look at the value of
    ``xafs_ref.mapping``.
 
-   BMM has foils or stable oxides for each of these elements::
-
-      Sc Ti V  Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Zr Nb Mo Pt Au Pb Bi Sr Y
-      Cs La Ce Pr Nd Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Rb Ba Hf Ta W  Re Os Ir Ru
-
-   (A few of these |nd| Ba, Os, Ir |nd| are missing as of 2
-   November, 2023.  We are working to obtain the missing ones.)
-
    :numref:`See Section %s for a full explanation of the the reference wheel contents. <reference-wheel>`
 
    `Here is a complete list of standards

docs/pds.rst

@@ -109,7 +109,8 @@ The ``change_edge()`` command does this automatically, so long as the
 target edge is available on the reference holder.
 
 The reference wheel content is configured as a python dictionary.  See
-``xafs_ref.mapping``.
+``xafs_ref.mapping``, `defined here
+<https://github.com/NSLS-II-BMM/profile_collection/blob/master/startup/BMM/user_ns/instruments.py#L323>`__.
 
 This dictionary identifies the positions in ``xafs_ref`` and
 ``xafs_refx`` for each reference sample.  It also identifies the form

docs/xafs.rst

@@ -761,14 +761,14 @@ elsewhere is captured in the output XDI file.
 .. todo:: Document use of ``XDI_record`` dictionary to control which
 	  xafs motors and/or temperatures get recorded in the XDI header
 
-.. admonition:: New as of 27 February, 2024 (broken 22 July)
+.. admonition:: New as of Fall 2024
 
    There is a new XDI header in use in BMM's datafiles:
-   ``Scan.hdf5file``.  This captures the name of the associated HDF5
-   file for fluorescence XAS measurements.
+   ``Scan.xspress3_hdf5_file``.  This captures the name of the
+   associated HDF5 file for fluorescence XAS measurements.
 
-   The path and file name are given relative to the assets location on
-   central storage: ``/nsls2/data3/bmm/assets/xspress3/``.
+   The value is the path to the asset location beneath the current
+   proposal folder.
 
 .. code-block:: text
 
@@ -1186,14 +1186,14 @@ sample being measured, of course).
    Outer 21        Pb              foil                    Inner 21        Re              |Reoxide|
    Outer 22        Bi              |Bioxide|               Inner 22        Os              *<absent>*
    Outer 23        Sr              |Srtitanate|            Inner 23        Sc              metal powder
-   Outer 24        Y               |Yoxide|                Inner 24        Ru              |Ruoxide|
+   Outer 24        Y               foil                    Inner 24        Ru              |Ruoxide|
    ============   ========        ===================     ============    ========        ===============
 
-+ For Th L3: Bi will be used (outer 20)
-+ For U L3: Y will be used (outer 24)
-+ For Pu L3: Zr will be used (outer 16)
++ For Th L\ :sub:`3`: Bi\ :sub:`1` will be used (outer 22)
++ For U L\ :sub:`3`: Y K will be used (outer 24)
++ For Pu L\ :sub:`3`: Zr K will be used (outer 16)
 
-The missing elements (Ba, W, & Os, Ir) will be added when they are acquired.
+Four elements are missing: Ba, W, & Os, and Ir.
 
 See also `BMM's complete list of standard materials
 <https://nsls-ii-bmm.github.io/bmm-standards/BMM-standards.html>`__.