From 17850c644c14b7972453d03b5975ba1f14f99a45 Mon Sep 17 00:00:00 2001 From: woutdenolf Date: Fri, 9 Feb 2024 18:56:46 +0100 Subject: [PATCH 1/2] first refactored NXxas template --- applications/NXxas_new.nxdl.xml | 230 +++++++++++++++++++++++++ base_classes/NXelectron_level.nxdl.xml | 61 +++++++ base_classes/NXelement.nxdl.xml | 171 ++++++++++++++++++ 3 files changed, 462 insertions(+) create mode 100644 applications/NXxas_new.nxdl.xml create mode 100644 base_classes/NXelectron_level.nxdl.xml create mode 100644 base_classes/NXelement.nxdl.xml diff --git a/applications/NXxas_new.nxdl.xml b/applications/NXxas_new.nxdl.xml new file mode 100644 index 0000000000..e6864bdb83 --- /dev/null +++ b/applications/NXxas_new.nxdl.xml @@ -0,0 +1,230 @@ + + + + + + + The symbol(s) listed here will be used below to coordinate datasets with the same shape. + + + Number of energy data points + + + Number of electronic transitions + + + + This is an application definition for X-ray absorption spectroscopy. + + + + Official NeXus NXDL schema to which this file conforms. TODO: replace NXxas + + + + + + + + + + TODO + + + + + TODO total or partial fluorescence yield + + + + + TODO high energy resolution fluorescence detected + + + + + TODO total or partial electron yield + + + + + TODO + + + + + TODO + + + + + TODO + + + + + TODO + + + + + TODO + + + + + TODO + + + + + + Excited element + + + + Excited electron level + + + + + Emission lines relevant when :ref:`mode </NXxas_new/ENTRY/mode-field>` is + `fluorescence yield` or `herfd`. + + The emission lines are described as a list of names of the form + *"INITIAL-FINAL"* where *INITAL* and *FINAL* are electron levels + as listed for :ref:`here </NXelectron_level/name-field>`. + + + + + + + TODO + + + + + + TODO + + + + + + TODO + + + + + + + Descriptive name of the sample + + + + + Description on how :ref:`energy </NXxas_new/ENTRY/energy-field>` + and :ref:`intensity </NXxas_new/ENTRY/intensity-field>` were obtained + from the raw data. + + + + + + + + + + + + + + + + + + + + + spacing between crystal planes of the reflection + + + Type or material of monochromating substance (Si, Ge, Multilayer). + + + Miller indices (hkl) values of nominal reflection + + + + + + + + + + + + + + + + + + + + + XAS intensity versus energy plot + + + + + + Table like data structure common in the XAS domain. + + + + + + + + + + + + + + + + + + + diff --git a/base_classes/NXelectron_level.nxdl.xml b/base_classes/NXelectron_level.nxdl.xml new file mode 100644 index 0000000000..97ed107ee6 --- /dev/null +++ b/base_classes/NXelectron_level.nxdl.xml @@ -0,0 +1,61 @@ + + + + + TODO ??? levels of electrons in atoms. + + + TODO Name of the atomic orbital in IUPAC or X-ray notation. + + The corresponding atomic notation *nlj* is also given, where *n* the principal quantum number, + *l* the orbital angular momentum quantum number (expressed with letters s, p, d, ...) and *j = l + s* + (*s=±½* the spin quantum number). + + + 1s1/2 + 2s1/2 + 2p1/2 + 2p3/2 + 3s1/2 + 3p1/2 + 3p3/2 + 3d3/2 + 3d5/2 + 4s1/2 + 4p1/2 + 4p3/2 + 4d3/2 + 4d5/2 + 4f5/2 + 4f7/2 + + + diff --git a/base_classes/NXelement.nxdl.xml b/base_classes/NXelement.nxdl.xml new file mode 100644 index 0000000000..19237a8d29 --- /dev/null +++ b/base_classes/NXelement.nxdl.xml @@ -0,0 +1,171 @@ + + + + + Definition of a chemical element. + + + For each symbol, the atomic number, common English name, and standard atomic weight are also given. + + + Z=1, name="hydrogen", standard_atomic_weight=1.0078 + Z=2, name="helium", standard_atomic_weight=4.0026 + Z=3, name="lithium", standard_atomic_weight=6.94 + Z=4, name="beryllium", standard_atomic_weight=9.0122 + Z=5, name="boron", standard_atomic_weight=10.81 + Z=6, name="carbon", standard_atomic_weight=12.011 + Z=7, name="nitrogen", standard_atomic_weight=14.007 + Z=8, name="oxygen", standard_atomic_weight=15.999 + Z=9, name="fluorine", standard_atomic_weight=18.9984 + Z=10, name="neon", standard_atomic_weight=20.1797 + Z=11, name="sodium", standard_atomic_weight=22.9898 + Z=12, name="magnesium", standard_atomic_weight=24.305 + Z=13, name="aluminum", standard_atomic_weight=26.9815 + Z=14, name="silicon", standard_atomic_weight=28.085 + Z=15, name="phosphorus", standard_atomic_weight=30.9738 + Z=16, name="sulfur", standard_atomic_weight=32.06 + Z=17, name="chlorine", standard_atomic_weight=35.453 + Z=18, name="argon", standard_atomic_weight=39.948 + Z=19, name="potassium", standard_atomic_weight=39.0983 + Z=20, name="calcium", standard_atomic_weight=40.078 + Z=21, name="scandium", standard_atomic_weight=44.9559 + Z=22, name="titanium", standard_atomic_weight=47.867 + Z=23, name="vanadium", standard_atomic_weight=50.9415 + Z=24, name="chromium", standard_atomic_weight=51.996 + Z=25, name="manganese", standard_atomic_weight=54.938 + Z=26, name="iron", standard_atomic_weight=55.845 + Z=27, name="cobalt", standard_atomic_weight=58.9332 + Z=28, name="nickel", standard_atomic_weight=58.6934 + Z=29, name="copper", standard_atomic_weight=63.546 + Z=30, name="zinc", standard_atomic_weight=65.38 + Z=31, name="gallium", standard_atomic_weight=69.72 + Z=32, name="germanium", standard_atomic_weight=72.63 + Z=33, name="arsenic", standard_atomic_weight=74.9216 + Z=34, name="selenium", standard_atomic_weight=78.971 + Z=35, name="bromine", standard_atomic_weight=79.904 + Z=36, name="krypton", standard_atomic_weight=83.798 + Z=37, name="rubidium", standard_atomic_weight=85.4678 + Z=38, name="strontium", standard_atomic_weight=87.62 + Z=39, name="yttrium", standard_atomic_weight=88.9058 + Z=40, name="zirconium", standard_atomic_weight=91.224 + Z=41, name="niobium", standard_atomic_weight=92.9064 + Z=42, name="molybdenum", standard_atomic_weight=95.95 + Z=43, name="technetium", standard_atomic_weight=97.907 + Z=44, name="ruthenium", standard_atomic_weight=101.07 + Z=45, name="rhodium", standard_atomic_weight=102.906 + Z=46, name="palladium", standard_atomic_weight=106.42 + Z=47, name="silver", standard_atomic_weight=107.868 + Z=48, name="cadmium", standard_atomic_weight=112.414 + Z=49, name="indium", standard_atomic_weight=114.818 + Z=50, name="tin", standard_atomic_weight=118.71 + Z=51, name="antimony", standard_atomic_weight=121.76 + Z=52, name="tellurium", standard_atomic_weight=127.6 + Z=53, name="iodine", standard_atomic_weight=126.905 + Z=54, name="xenon", standard_atomic_weight=131.293 + Z=55, name="cesium", standard_atomic_weight=132.905 + Z=56, name="barium", standard_atomic_weight=137.327 + Z=57, name="lanthanum", standard_atomic_weight=138.905 + Z=58, name="cerium", standard_atomic_weight=140.116 + Z=59, name="praseodymium", standard_atomic_weight=140.908 + Z=60, name="neodymium", standard_atomic_weight=144.242 + Z=61, name="promethium", standard_atomic_weight=145.0 + Z=62, name="samarium", standard_atomic_weight=150.36 + Z=63, name="europium", standard_atomic_weight=151.96 + Z=64, name="gadolinium", standard_atomic_weight=157.25 + Z=65, name="terbium", standard_atomic_weight=158.925 + Z=66, name="dysprosium", standard_atomic_weight=162.5 + Z=67, name="holmium", standard_atomic_weight=164.93 + Z=68, name="erbium", standard_atomic_weight=167.259 + Z=69, name="thulium", standard_atomic_weight=168.934 + Z=70, name="ytterbium", standard_atomic_weight=173.045 + Z=71, name="lutetium", standard_atomic_weight=174.967 + Z=72, name="hafnium", standard_atomic_weight=178.49 + Z=73, name="tantalum", standard_atomic_weight=180.948 + Z=74, name="tungsten", standard_atomic_weight=183.84 + Z=75, name="rhenium", standard_atomic_weight=186.207 + Z=76, name="osmium", standard_atomic_weight=190.23 + Z=77, name="iridium", standard_atomic_weight=192.217 + Z=78, name="platinum", standard_atomic_weight=195.084 + Z=79, name="gold", standard_atomic_weight=196.967 + Z=80, name="mercury", standard_atomic_weight=200.592 + Z=81, name="thallium", standard_atomic_weight=204.383 + Z=82, name="lead", standard_atomic_weight=207.2 + Z=83, name="bismuth", standard_atomic_weight=208.98 + Z=84, name="polonium", standard_atomic_weight=209.0 + Z=85, name="astatine", standard_atomic_weight=210.0 + Z=86, name="radon", standard_atomic_weight=222.0 + Z=87, name="francium", standard_atomic_weight=223.0 + Z=88, name="radium", standard_atomic_weight=226.0 + Z=89, name="actinium", standard_atomic_weight=227.0 + Z=90, name="thorium", standard_atomic_weight=232.038 + Z=91, name="protactinium", standard_atomic_weight=231.036 + Z=92, name="uranium", standard_atomic_weight=238.029 + Z=93, name="neptunium", standard_atomic_weight=237.048 + Z=94, name="plutonium", standard_atomic_weight=239.052 + Z=95, name="americium", standard_atomic_weight=243.0 + Z=96, name="curium", standard_atomic_weight=247.0 + Z=97, name="berkelium", standard_atomic_weight=247.0 + Z=98, name="californium", standard_atomic_weight=251.0 + Z=99, name="einsteinium", standard_atomic_weight=252 + Z=100, name="fermium", standard_atomic_weight=257 + Z=101, name="mendelevium", standard_atomic_weight=258 + Z=102, name="nobelium", standard_atomic_weight=259 + Z=103, name="lawrencium", standard_atomic_weight=266 + Z=104, name="rutherfordium", standard_atomic_weight=267 + Z=105, name="dubnium", standard_atomic_weight=268 + Z=106, name="seaborgium", standard_atomic_weight=269 + Z=107, name="bohrium", standard_atomic_weight=270 + Z=108, name="hassium", standard_atomic_weight=269 + Z=109, name="meitnerium", standard_atomic_weight=278 + Z=110, name="darmstadtium", standard_atomic_weight=281 + Z=111, name="roentgenium", standard_atomic_weight=282 + Z=112, name="copernicium", standard_atomic_weight=285 + Z=113, name="nihonium", standard_atomic_weight=286 + Z=114, name="flerovium", standard_atomic_weight=289 + Z=115, name="moscovium", standard_atomic_weight=290 + Z=116, name="livermorium", standard_atomic_weight=293 + Z=117, name="tennessine", standard_atomic_weight=294 + Z=118, name="oganesson", standard_atomic_weight=294 + + + + The charge number *Z* of the atomic nucleus. + + + + *Relative atomic mass* of the element in *amu*. It can be but is not restricted to the + *standard atomic weight* (using the natural abundance of isotopes). + + + + The charge of the atom after ionic approximation of its heteronuclear bonds. + + From c6dc90cdbf0b81b782e1a380038f42c2ad66b1f4 Mon Sep 17 00:00:00 2001 From: woutdenolf Date: Sun, 11 Feb 2024 17:03:06 +0100 Subject: [PATCH 2/2] improve NXelectron_level --- base_classes/NXelectron_level.nxdl.xml | 28 +++++++++++++++++--------- 1 file changed, 19 insertions(+), 9 deletions(-) diff --git a/base_classes/NXelectron_level.nxdl.xml b/base_classes/NXelectron_level.nxdl.xml index 97ed107ee6..7025489043 100644 --- a/base_classes/NXelectron_level.nxdl.xml +++ b/base_classes/NXelectron_level.nxdl.xml @@ -30,32 +30,42 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd" > - TODO ??? levels of electrons in atoms. + Electron energy levels in atoms for spectroscopy. - TODO Name of the atomic orbital in IUPAC or X-ray notation. + Electron energy level for spectroscopy in IUPAC notation. - The corresponding atomic notation *nlj* is also given, where *n* the principal quantum number, - *l* the orbital angular momentum quantum number (expressed with letters s, p, d, ...) and *j = l + s* - (*s=±½* the spin quantum number). + The corresponding *nlj* notation is also given, where *n* the principal quantum number (shell), + *l* the azimuthal quantum number (subshell, expressed with letters *s=0*, *p=1*, *d=2*, ...) + and *j = l + s* (*s=±½* the spin quantum number). - 1s1/2 - 2s1/2 + 1s + 2s 2p1/2 2p3/2 - 3s1/2 + 3s 3p1/2 3p3/2 3d3/2 3d5/2 - 4s1/2 + 4s 4p1/2 4p3/2 4d3/2 4d5/2 4f5/2 4f7/2 + 5s + 5p1/2 + 5p3/2 + 5d3/2 + 5d5/2 + 5f5/2 + 5f7/2 + 6s + 6p1/2 + 6p3/2