From eedb091199104bd2f57f18bea2b93014f8d7be1e Mon Sep 17 00:00:00 2001 From: Pete R Jemian Date: Sat, 17 Feb 2024 18:49:39 -0600 Subject: [PATCH 01/10] MNT #1355 recover missing definition --- utils/update_copyright_date.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/utils/update_copyright_date.py b/utils/update_copyright_date.py index 261b1933a3..01d7bee769 100755 --- a/utils/update_copyright_date.py +++ b/utils/update_copyright_date.py @@ -12,12 +12,19 @@ import os, sys import mimetypes -from build_preparation import ROOT_DIR_EXPECTED_RESOURCES import datetime YEAR = datetime.datetime.now().year LEFT_SIDE_TEXT_MATCH = "Copyright (C) " RIGHT_SIDE_TEXT_MATCH = " NeXus International Advisory Committee (NIAC)" +ROOT_DIR_EXPECTED_RESOURCES = { + "files": """COPYING LGPL.txt Makefile NXDL_VERSION + nxdl.xsd nxdlTypes.xsd README.md + """.split(), + "subdirs": """applications base_classes contributed_definitions manual + package utils www impatient-guide + """.split(), +} def update(filename): From 307e6a7c0f8be7c46e85764a9533b80f67cd9dd3 Mon Sep 17 00:00:00 2001 From: Pete R Jemian Date: Sat, 17 Feb 2024 18:50:27 -0600 Subject: [PATCH 02/10] MNT #1355 update NeXus copyright notices --- Makefile | 2 +- applications/NXarchive.nxdl.xml | 2 +- applications/NXarpes.nxdl.xml | 2 +- applications/NXcanSAS.nxdl.xml | 2 +- applications/NXdirecttof.nxdl.xml | 2 +- applications/NXfluo.nxdl.xml | 2 +- applications/NXindirecttof.nxdl.xml | 2 +- applications/NXiqproc.nxdl.xml | 2 +- applications/NXlauetof.nxdl.xml | 2 +- applications/NXmonopd.nxdl.xml | 2 +- applications/NXmx.nxdl.xml | 2 +- applications/NXrefscan.nxdl.xml | 2 +- applications/NXreftof.nxdl.xml | 2 +- applications/NXsas.nxdl.xml | 2 +- applications/NXsastof.nxdl.xml | 2 +- applications/NXscan.nxdl.xml | 2 +- applications/NXspe.nxdl.xml | 2 +- applications/NXsqom.nxdl.xml | 2 +- applications/NXstxm.nxdl.xml | 2 +- applications/NXtas.nxdl.xml | 2 +- applications/NXtofnpd.nxdl.xml | 2 +- applications/NXtofraw.nxdl.xml | 2 +- applications/NXtofsingle.nxdl.xml | 2 +- applications/NXtomo.nxdl.xml | 2 +- applications/NXtomophase.nxdl.xml | 2 +- applications/NXtomoproc.nxdl.xml | 2 +- applications/NXxas.nxdl.xml | 2 +- applications/NXxasproc.nxdl.xml | 2 +- applications/NXxbase.nxdl.xml | 2 +- applications/NXxeuler.nxdl.xml | 2 +- applications/NXxkappa.nxdl.xml | 2 +- applications/NXxlaue.nxdl.xml | 2 +- applications/NXxlaueplate.nxdl.xml | 2 +- applications/NXxnb.nxdl.xml | 2 +- applications/NXxrot.nxdl.xml | 2 +- applications/nxdlformat.xsl | 2 +- base_classes/NXaperture.nxdl.xml | 2 +- base_classes/NXattenuator.nxdl.xml | 2 +- base_classes/NXbeam.nxdl.xml | 2 +- base_classes/NXbeam_stop.nxdl.xml | 2 +- base_classes/NXbending_magnet.nxdl.xml | 2 +- base_classes/NXcapillary.nxdl.xml | 2 +- base_classes/NXcite.nxdl.xml | 2 +- base_classes/NXcollection.nxdl.xml | 2 +- base_classes/NXcollimator.nxdl.xml | 2 +- base_classes/NXcrystal.nxdl.xml | 2 +- base_classes/NXcylindrical_geometry.nxdl.xml | 2 +- base_classes/NXdata.nxdl.xml | 2 +- base_classes/NXdetector.nxdl.xml | 2 +- base_classes/NXdetector_channel.nxdl.xml | 2 +- base_classes/NXdetector_group.nxdl.xml | 2 +- base_classes/NXdetector_module.nxdl.xml | 2 +- base_classes/NXdisk_chopper.nxdl.xml | 2 +- base_classes/NXentry.nxdl.xml | 2 +- base_classes/NXenvironment.nxdl.xml | 2 +- base_classes/NXevent_data.nxdl.xml | 2 +- base_classes/NXfermi_chopper.nxdl.xml | 2 +- base_classes/NXfilter.nxdl.xml | 2 +- base_classes/NXflipper.nxdl.xml | 2 +- base_classes/NXfresnel_zone_plate.nxdl.xml | 2 +- base_classes/NXgeometry.nxdl.xml | 2 +- base_classes/NXgrating.nxdl.xml | 2 +- base_classes/NXguide.nxdl.xml | 2 +- base_classes/NXinsertion_device.nxdl.xml | 2 +- base_classes/NXinstrument.nxdl.xml | 2 +- base_classes/NXlog.nxdl.xml | 2 +- base_classes/NXmirror.nxdl.xml | 2 +- base_classes/NXmoderator.nxdl.xml | 2 +- base_classes/NXmonitor.nxdl.xml | 2 +- base_classes/NXmonochromator.nxdl.xml | 2 +- base_classes/NXnote.nxdl.xml | 2 +- base_classes/NXobject.nxdl.xml | 2 +- base_classes/NXoff_geometry.nxdl.xml | 2 +- base_classes/NXorientation.nxdl.xml | 2 +- base_classes/NXparameters.nxdl.xml | 2 +- base_classes/NXpdb.nxdl.xml | 2 +- base_classes/NXpinhole.nxdl.xml | 2 +- base_classes/NXpolarizer.nxdl.xml | 2 +- base_classes/NXpositioner.nxdl.xml | 2 +- base_classes/NXprocess.nxdl.xml | 2 +- base_classes/NXroot.nxdl.xml | 2 +- base_classes/NXsample.nxdl.xml | 2 +- base_classes/NXsample_component.nxdl.xml | 2 +- base_classes/NXsensor.nxdl.xml | 2 +- base_classes/NXshape.nxdl.xml | 2 +- base_classes/NXslit.nxdl.xml | 2 +- base_classes/NXsource.nxdl.xml | 2 +- base_classes/NXsubentry.nxdl.xml | 2 +- base_classes/NXtransformations.nxdl.xml | 2 +- base_classes/NXtranslation.nxdl.xml | 2 +- base_classes/NXuser.nxdl.xml | 2 +- base_classes/NXvelocity_selector.nxdl.xml | 2 +- base_classes/NXxraylens.nxdl.xml | 2 +- base_classes/nxdlformat.xsl | 2 +- contributed_definitions/NXaberration.nxdl.xml | 2 +- contributed_definitions/NXaberration_model.nxdl.xml | 2 +- contributed_definitions/NXaberration_model_ceos.nxdl.xml | 2 +- contributed_definitions/NXaberration_model_nion.nxdl.xml | 2 +- contributed_definitions/NXadc.nxdl.xml | 2 +- contributed_definitions/NXaperture_em.nxdl.xml | 2 +- contributed_definitions/NXapm.nxdl.xml | 2 +- .../NXapm_composition_space_results.nxdl.xml | 2 +- contributed_definitions/NXapm_input_ranging.nxdl.xml | 2 +- contributed_definitions/NXapm_input_reconstruction.nxdl.xml | 2 +- .../NXapm_paraprobe_config_clusterer.nxdl.xml | 2 +- .../NXapm_paraprobe_config_distancer.nxdl.xml | 2 +- .../NXapm_paraprobe_config_intersector.nxdl.xml | 2 +- .../NXapm_paraprobe_config_nanochem.nxdl.xml | 2 +- contributed_definitions/NXapm_paraprobe_config_ranger.nxdl.xml | 2 +- .../NXapm_paraprobe_config_selector.nxdl.xml | 2 +- .../NXapm_paraprobe_config_spatstat.nxdl.xml | 2 +- .../NXapm_paraprobe_config_surfacer.nxdl.xml | 2 +- .../NXapm_paraprobe_config_tessellator.nxdl.xml | 2 +- .../NXapm_paraprobe_config_transcoder.nxdl.xml | 2 +- .../NXapm_paraprobe_results_clusterer.nxdl.xml | 2 +- .../NXapm_paraprobe_results_distancer.nxdl.xml | 2 +- .../NXapm_paraprobe_results_intersector.nxdl.xml | 2 +- .../NXapm_paraprobe_results_nanochem.nxdl.xml | 2 +- contributed_definitions/NXapm_paraprobe_results_ranger.nxdl.xml | 2 +- .../NXapm_paraprobe_results_selector.nxdl.xml | 2 +- .../NXapm_paraprobe_results_spatstat.nxdl.xml | 2 +- .../NXapm_paraprobe_results_surfacer.nxdl.xml | 2 +- .../NXapm_paraprobe_results_tessellator.nxdl.xml | 2 +- .../NXapm_paraprobe_results_transcoder.nxdl.xml | 2 +- contributed_definitions/NXbeam_path.nxdl.xml | 2 +- contributed_definitions/NXbeam_splitter.nxdl.xml | 2 +- contributed_definitions/NXcalibration.nxdl.xml | 2 +- contributed_definitions/NXcg_alpha_complex.nxdl.xml | 2 +- contributed_definitions/NXcg_cylinder_set.nxdl.xml | 2 +- contributed_definitions/NXcg_ellipsoid_set.nxdl.xml | 2 +- contributed_definitions/NXcg_face_list_data_structure.nxdl.xml | 2 +- contributed_definitions/NXcg_geodesic_mesh.nxdl.xml | 2 +- contributed_definitions/NXcg_grid.nxdl.xml | 2 +- contributed_definitions/NXcg_half_edge_data_structure.nxdl.xml | 2 +- contributed_definitions/NXcg_hexahedron_set.nxdl.xml | 2 +- contributed_definitions/NXcg_marching_cubes.nxdl.xml | 2 +- contributed_definitions/NXcg_parallelogram_set.nxdl.xml | 2 +- contributed_definitions/NXcg_point_set.nxdl.xml | 2 +- contributed_definitions/NXcg_polygon_set.nxdl.xml | 2 +- contributed_definitions/NXcg_polyhedron_set.nxdl.xml | 2 +- contributed_definitions/NXcg_polyline_set.nxdl.xml | 2 +- contributed_definitions/NXcg_roi_set.nxdl.xml | 2 +- contributed_definitions/NXcg_sphere_set.nxdl.xml | 2 +- contributed_definitions/NXcg_tetrahedron_set.nxdl.xml | 2 +- contributed_definitions/NXcg_triangle_set.nxdl.xml | 2 +- contributed_definitions/NXcg_triangulated_surface_mesh.nxdl.xml | 2 +- contributed_definitions/NXcg_unit_normal_set.nxdl.xml | 2 +- contributed_definitions/NXchamber.nxdl.xml | 2 +- contributed_definitions/NXchemical_composition.nxdl.xml | 2 +- contributed_definitions/NXcircuit_board.nxdl.xml | 2 +- contributed_definitions/NXclustering.nxdl.xml | 2 +- contributed_definitions/NXcollectioncolumn.nxdl.xml | 2 +- contributed_definitions/NXcontainer.nxdl.xml | 2 +- contributed_definitions/NXcoordinate_system_set.nxdl.xml | 2 +- contributed_definitions/NXcorrector_cs.nxdl.xml | 2 +- contributed_definitions/NXcs_computer.nxdl.xml | 2 +- contributed_definitions/NXcs_cpu.nxdl.xml | 2 +- contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml | 2 +- contributed_definitions/NXcs_gpu.nxdl.xml | 2 +- contributed_definitions/NXcs_io_obj.nxdl.xml | 2 +- contributed_definitions/NXcs_io_sys.nxdl.xml | 2 +- contributed_definitions/NXcs_mm_sys.nxdl.xml | 2 +- contributed_definitions/NXcs_prng.nxdl.xml | 2 +- contributed_definitions/NXcs_profiling.nxdl.xml | 2 +- contributed_definitions/NXcs_profiling_event.nxdl.xml | 2 +- contributed_definitions/NXcsg.nxdl.xml | 2 +- contributed_definitions/NXcxi_ptycho.nxdl.xml | 2 +- contributed_definitions/NXdac.nxdl.xml | 2 +- contributed_definitions/NXdeflector.nxdl.xml | 2 +- contributed_definitions/NXdelocalization.nxdl.xml | 2 +- contributed_definitions/NXdispersion.nxdl.xml | 2 +- contributed_definitions/NXdispersion_function.nxdl.xml | 2 +- .../NXdispersion_repeated_parameter.nxdl.xml | 2 +- contributed_definitions/NXdispersion_single_parameter.nxdl.xml | 2 +- contributed_definitions/NXdispersion_table.nxdl.xml | 2 +- contributed_definitions/NXdispersive_material.nxdl.xml | 2 +- contributed_definitions/NXdistortion.nxdl.xml | 2 +- contributed_definitions/NXebeam_column.nxdl.xml | 2 +- contributed_definitions/NXelectronanalyser.nxdl.xml | 2 +- contributed_definitions/NXelectrostatic_kicker.nxdl.xml | 2 +- contributed_definitions/NXellipsometry.nxdl.xml | 2 +- contributed_definitions/NXem.nxdl.xml | 2 +- contributed_definitions/NXem_ebsd.nxdl.xml | 2 +- contributed_definitions/NXem_ebsd_conventions.nxdl.xml | 2 +- .../NXem_ebsd_crystal_structure_model.nxdl.xml | 2 +- contributed_definitions/NXenergydispersion.nxdl.xml | 2 +- contributed_definitions/NXevent_data_em.nxdl.xml | 2 +- contributed_definitions/NXevent_data_em_set.nxdl.xml | 2 +- contributed_definitions/NXfabrication.nxdl.xml | 2 +- contributed_definitions/NXfiber.nxdl.xml | 2 +- contributed_definitions/NXgraph_edge_set.nxdl.xml | 2 +- contributed_definitions/NXgraph_node_set.nxdl.xml | 2 +- contributed_definitions/NXgraph_root.nxdl.xml | 2 +- contributed_definitions/NXibeam_column.nxdl.xml | 2 +- contributed_definitions/NXimage_set.nxdl.xml | 2 +- contributed_definitions/NXimage_set_em_adf.nxdl.xml | 2 +- contributed_definitions/NXimage_set_em_kikuchi.nxdl.xml | 2 +- contributed_definitions/NXion.nxdl.xml | 2 +- contributed_definitions/NXisocontour.nxdl.xml | 2 +- contributed_definitions/NXiv_temp.nxdl.xml | 2 +- .../NXlab_electro_chemo_mechanical_preparation.nxdl.xml | 2 +- contributed_definitions/NXlab_sample_mounting.nxdl.xml | 2 +- contributed_definitions/NXlens_em.nxdl.xml | 2 +- contributed_definitions/NXlens_opt.nxdl.xml | 2 +- contributed_definitions/NXmagnetic_kicker.nxdl.xml | 2 +- contributed_definitions/NXmanipulator.nxdl.xml | 2 +- contributed_definitions/NXmatch_filter.nxdl.xml | 2 +- contributed_definitions/NXmpes.nxdl.xml | 2 +- contributed_definitions/NXms.nxdl.xml | 2 +- contributed_definitions/NXms_feature_set.nxdl.xml | 2 +- contributed_definitions/NXms_score_config.nxdl.xml | 2 +- contributed_definitions/NXms_score_results.nxdl.xml | 2 +- contributed_definitions/NXms_snapshot.nxdl.xml | 2 +- contributed_definitions/NXms_snapshot_set.nxdl.xml | 2 +- contributed_definitions/NXopt.nxdl.xml | 2 +- contributed_definitions/NXoptical_system_em.nxdl.xml | 2 +- contributed_definitions/NXorientation_set.nxdl.xml | 2 +- contributed_definitions/NXpeak.nxdl.xml | 2 +- contributed_definitions/NXpid.nxdl.xml | 2 +- contributed_definitions/NXpolarizer_opt.nxdl.xml | 2 +- contributed_definitions/NXprogram.nxdl.xml | 2 +- contributed_definitions/NXpulser_apm.nxdl.xml | 2 +- contributed_definitions/NXpump.nxdl.xml | 2 +- contributed_definitions/NXquadric.nxdl.xml | 2 +- contributed_definitions/NXquadrupole_magnet.nxdl.xml | 2 +- contributed_definitions/NXreflectron.nxdl.xml | 2 +- contributed_definitions/NXregion.nxdl.xml | 2 +- contributed_definitions/NXregistration.nxdl.xml | 2 +- contributed_definitions/NXscanbox_em.nxdl.xml | 2 +- contributed_definitions/NXsensor_scan.nxdl.xml | 2 +- contributed_definitions/NXseparator.nxdl.xml | 2 +- contributed_definitions/NXsimilarity_grouping.nxdl.xml | 2 +- contributed_definitions/NXslip_system_set.nxdl.xml | 2 +- contributed_definitions/NXsolenoid_magnet.nxdl.xml | 2 +- contributed_definitions/NXsolid_geometry.nxdl.xml | 2 +- contributed_definitions/NXspatial_filter.nxdl.xml | 2 +- contributed_definitions/NXspectrum_set.nxdl.xml | 2 +- contributed_definitions/NXspectrum_set_em_eels.nxdl.xml | 2 +- contributed_definitions/NXspectrum_set_em_xray.nxdl.xml | 2 +- contributed_definitions/NXspin_rotator.nxdl.xml | 2 +- contributed_definitions/NXspindispersion.nxdl.xml | 2 +- contributed_definitions/NXstage_lab.nxdl.xml | 2 +- contributed_definitions/NXsubsampling_filter.nxdl.xml | 2 +- contributed_definitions/NXtransmission.nxdl.xml | 2 +- contributed_definitions/NXwaveplate.nxdl.xml | 2 +- contributed_definitions/NXxpcs.nxdl.xml | 2 +- contributed_definitions/nxdlformat.xsl | 2 +- manual/source/copyright.rst | 2 +- manual/source/examples/NX__template__.nxdl.xml | 2 +- manual/source/examples/NXwoni.nxdl.xml | 2 +- nxdl.xsd | 2 +- nxdlTypes.xsd | 2 +- utils/create_release_notes.py | 2 +- utils/update_copyright_date.py | 2 +- 254 files changed, 254 insertions(+), 254 deletions(-) diff --git a/Makefile b/Makefile index eefdcb3a9b..3a882c2568 100644 --- a/Makefile +++ b/Makefile @@ -114,7 +114,7 @@ nyaml: # NeXus - Neutron and X-ray Common Data Format # -# Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC) +# Copyright (C) 2008-2024 NeXus International Advisory Committee (NIAC) # # This library is free software; you can redistribute it and/or # modify it under the terms of the GNU Lesser General Public diff --git a/applications/NXarchive.nxdl.xml b/applications/NXarchive.nxdl.xml index 79b41857b1..6f0de71726 100644 --- a/applications/NXarchive.nxdl.xml +++ b/applications/NXarchive.nxdl.xml @@ -3,7 +3,7 @@ + + + + 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 cba83c551a7062067df2d0befcb196103b5365ed Mon Sep 17 00:00:00 2001 From: woutdenolf Date: Sun, 11 Feb 2024 17:03:06 +0100 Subject: [PATCH 07/10] 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 From 762870d9a8a2395bf75a8ddb9b0eb398bd8f03f7 Mon Sep 17 00:00:00 2001 From: woutdenolf Date: Tue, 13 Feb 2024 11:43:12 +0100 Subject: [PATCH 08/10] use X-ray level --- applications/NXxas_new.nxdl.xml | 4 ++-- ...electron_level.nxdl.xml => NXxray_level.nxdl.xml} | 12 +++++++++--- 2 files changed, 11 insertions(+), 5 deletions(-) rename base_classes/{NXelectron_level.nxdl.xml => NXxray_level.nxdl.xml} (85%) diff --git a/applications/NXxas_new.nxdl.xml b/applications/NXxas_new.nxdl.xml index e6864bdb83..449859d32f 100644 --- a/applications/NXxas_new.nxdl.xml +++ b/applications/NXxas_new.nxdl.xml @@ -110,7 +110,7 @@ Excited element - + Excited electron level @@ -121,7 +121,7 @@ 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>`. + as listed for :ref:`here </NXxray_level/name-field>`. diff --git a/base_classes/NXelectron_level.nxdl.xml b/base_classes/NXxray_level.nxdl.xml similarity index 85% rename from base_classes/NXelectron_level.nxdl.xml rename to base_classes/NXxray_level.nxdl.xml index 7025489043..3160791153 100644 --- a/base_classes/NXelectron_level.nxdl.xml +++ b/base_classes/NXxray_level.nxdl.xml @@ -22,7 +22,7 @@ # For further information, see http://www.nexusformat.org --> - Electron energy levels in atoms for spectroscopy. + + The electronic state of an atom occurring as initial or final state of a process involving the absorption or emission of x-ray radiation. + - Electron energy level for spectroscopy in IUPAC notation. + Name of the *X-ray level* as recommended by `IUPAC <https://doi.org/10.1002/xrs.1300200308>`_. 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*, ...) @@ -66,6 +68,10 @@ 6s 6p1/2 6p3/2 + 6d3/2 + 6d5/2 + 6f5/2 + 6f7/2 From a4244fa47884324daa708fe21b797fc09acfd1dc Mon Sep 17 00:00:00 2001 From: woutdenolf Date: Wed, 14 Feb 2024 00:35:13 +0100 Subject: [PATCH 09/10] add more documentation --- base_classes/NXxray_level.nxdl.xml | 83 +++++++++++++++++------------- 1 file changed, 48 insertions(+), 35 deletions(-) diff --git a/base_classes/NXxray_level.nxdl.xml b/base_classes/NXxray_level.nxdl.xml index 3160791153..7ef382915b 100644 --- a/base_classes/NXxray_level.nxdl.xml +++ b/base_classes/NXxray_level.nxdl.xml @@ -31,47 +31,60 @@ xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd" > - The electronic state of an atom occurring as initial or final state of a process involving the absorption or emission of x-ray radiation. + The electronic state of an atom occurring as initial or final state of a process + involving the absorption or emission of X-ray radiation. + + The energy of an atom with one missing electron is referred to as an *X-ray level*. It is a + multi-electronic state which occurs as a result of the photoemission of one electron. - Name of the *X-ray level* as recommended by `IUPAC <https://doi.org/10.1002/xrs.1300200308>`_. + The *X-ray level* name as recommended by `IUPAC <https://doi.org/10.1002/xrs.1300200308>`_. + + The corresponding :math:`nl_{j}^{-1}` notation of the electron configuration is also provided: + + * *n* the principal quantum number (shell) + * *l* the orbital angular momentum quantum number (subshell, expressed with letters *s=0*, *p=1*, *d=2*, ...) + * *j = l + s* the total angular momentum (spin-orbit splitting) + * *s=±½* the spin angular momentum quantum number + * :math:`^{-1}` refers to one missing electron - 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). + The subshell energy levels are split due to the unpaired electron left behind after photoemission of + one electron, that may have a parallel or antiparallel alignment to the orbital momentum. - 1s - 2s - 2p1/2 - 2p3/2 - 3s - 3p1/2 - 3p3/2 - 3d3/2 - 3d5/2 - 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 - 6d3/2 - 6d5/2 - 6f5/2 - 6f7/2 + :math:`1s^{-1}` + :math:`2s^{-1}` + :math:`2p_{1/2}^{-1}` + :math:`2p_{3/2}^{-1}` + :math:`3s^{-1}` + :math:`3p_{1/2}^{-1}` + :math:`3p_{3/2}^{-1}` + :math:`3d_{3/2}^{-1}` + :math:`3d_{5/2}^{-1}` + :math:`4s^{-1}` + :math:`4p_{1/2}^{-1}` + :math:`4p_{3/2}^{-1}` + :math:`4d_{3/2}^{-1}` + :math:`4d_{5/2}^{-1}` + :math:`4f_{5/2}^{-1}` + :math:`4f_{7/2}^{-1}` + :math:`5s^{-1}` + :math:`5p_{1/2}^{-1}` + :math:`5p_{3/2}^{-1}` + :math:`5d_{3/2}^{-1}` + :math:`5d_{5/2}^{-1}` + :math:`5f_{5/2}^{-1}` + :math:`5f_{7/2}^{-1}` + :math:`5g_{7/2}^{-1}` + :math:`5g_{9/2}^{-1}` + :math:`6s^{-1}` + :math:`6p_{1/2}^{-1}` + :math:`6p_{3/2}^{-1}` + :math:`6d_{3/2}^{-1}` + :math:`6d_{5/2}^{-1}` + :math:`6f_{5/2}^{-1}` + :math:`6f_{7/2}^{-1}` From 6c3c95145bd2386d486cb321f5c84f98641ee11c Mon Sep 17 00:00:00 2001 From: Marius Retegan Date: Wed, 29 May 2024 08:44:51 +0200 Subject: [PATCH 10/10] Remove NXxray_level base class --- base_classes/NXxray_level.nxdl.xml | 90 ------------------------------ 1 file changed, 90 deletions(-) delete mode 100644 base_classes/NXxray_level.nxdl.xml diff --git a/base_classes/NXxray_level.nxdl.xml b/base_classes/NXxray_level.nxdl.xml deleted file mode 100644 index 7ef382915b..0000000000 --- a/base_classes/NXxray_level.nxdl.xml +++ /dev/null @@ -1,90 +0,0 @@ - - - - - - The electronic state of an atom occurring as initial or final state of a process - involving the absorption or emission of X-ray radiation. - - The energy of an atom with one missing electron is referred to as an *X-ray level*. It is a - multi-electronic state which occurs as a result of the photoemission of one electron. - - - - The *X-ray level* name as recommended by `IUPAC <https://doi.org/10.1002/xrs.1300200308>`_. - - The corresponding :math:`nl_{j}^{-1}` notation of the electron configuration is also provided: - - * *n* the principal quantum number (shell) - * *l* the orbital angular momentum quantum number (subshell, expressed with letters *s=0*, *p=1*, *d=2*, ...) - * *j = l + s* the total angular momentum (spin-orbit splitting) - * *s=±½* the spin angular momentum quantum number - * :math:`^{-1}` refers to one missing electron - - The subshell energy levels are split due to the unpaired electron left behind after photoemission of - one electron, that may have a parallel or antiparallel alignment to the orbital momentum. - - - :math:`1s^{-1}` - :math:`2s^{-1}` - :math:`2p_{1/2}^{-1}` - :math:`2p_{3/2}^{-1}` - :math:`3s^{-1}` - :math:`3p_{1/2}^{-1}` - :math:`3p_{3/2}^{-1}` - :math:`3d_{3/2}^{-1}` - :math:`3d_{5/2}^{-1}` - :math:`4s^{-1}` - :math:`4p_{1/2}^{-1}` - :math:`4p_{3/2}^{-1}` - :math:`4d_{3/2}^{-1}` - :math:`4d_{5/2}^{-1}` - :math:`4f_{5/2}^{-1}` - :math:`4f_{7/2}^{-1}` - :math:`5s^{-1}` - :math:`5p_{1/2}^{-1}` - :math:`5p_{3/2}^{-1}` - :math:`5d_{3/2}^{-1}` - :math:`5d_{5/2}^{-1}` - :math:`5f_{5/2}^{-1}` - :math:`5f_{7/2}^{-1}` - :math:`5g_{7/2}^{-1}` - :math:`5g_{9/2}^{-1}` - :math:`6s^{-1}` - :math:`6p_{1/2}^{-1}` - :math:`6p_{3/2}^{-1}` - :math:`6d_{3/2}^{-1}` - :math:`6d_{5/2}^{-1}` - :math:`6f_{5/2}^{-1}` - :math:`6f_{7/2}^{-1}` - - -