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Application definition for XPS #249

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merged 15 commits into from
Jul 4, 2024
Merged

Application definition for XPS #249

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4d8cffb
draft for NXxps
lukaspie Jun 19, 2024
8416504
add image of XPS CS
lukaspie Jun 19, 2024
f07112a
image of xps cs with white background
lukaspie Jun 19, 2024
75498be
regenerate nxdl and nyaml files
lukaspie Jun 19, 2024
5a8d2f9
rearrange order of transformations, add docs to depends_on
lukaspie Jun 20, 2024
befbc10
fix typo in NXxps
lukaspie Jun 24, 2024
44e59fc
add x,y,z for coordinate system
lukaspie Jun 27, 2024
ccac378
ellipticals in xps cs drawing
lukaspie Jun 28, 2024
27b0337
fix component transformations
lukaspie Jun 28, 2024
06da11a
update coordinate transformations
lukaspie Jun 28, 2024
2b2f2e5
typo fix
lukaspie Jun 28, 2024
a9f5a2e
make example a code block
lukaspie Jun 28, 2024
e13d329
add NXxps to mpes-stucture
lukaspie Jun 28, 2024
adb8895
use right handed rotations
lukaspie Jul 3, 2024
2f06550
fix mpes-structure.rst
lukaspie Jul 4, 2024
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319 changes: 319 additions & 0 deletions contributed_definitions/NXxps.nxdl.xml
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<?xml version='1.0' encoding='UTF-8'?>
<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
<!--
# NeXus - Neutron and X-ray Common Data Format
#
# Copyright (C) 2014-2024 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
# License as published by the Free Software Foundation; either
# version 3 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# For further information, see http://www.nexusformat.org
-->
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="application" type="group" name="NXxps" extends="NXmpes" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<doc>
This is the application definition for X-ray photoelectron spectroscopy.
</doc>
<group type="NXentry">
<field name="definition" type="NX_CHAR">
<enumeration>
<item value="NXxps"/>
</enumeration>
</field>
<field name="method">
<doc>
A name of the experimental method according to `Clause 11`_ of
the `ISO 18115-1:2023`_ specification.

Examples for XPS-related experiments include:
* X-ray photoelectron spectroscopy (XPS)
* angle-resolved X-ray photoelectron spectroscopy (ARXPS)
* ultraviolet photoelectron spectroscopy (UPS)
* hard X-ray photoemission spectroscopy (HAXPES)
* near ambient pressure X-ray photoelectron spectroscopy (NAPXPS)
* electron spectroscopy for chemical analysis (ESCA)

.. _ISO 18115-1:2023: https://www.iso.org/standard/74811.html
.. _Clause 11: https://www.iso.org/obp/ui/en/#iso:std:iso:18115:-1:ed-3:v1:en:sec:11
</doc>
</field>
<group name="geometries" type="NXcoordinate_system_set">
<group name="xps_coordinate_system" type="NXcoordinate_system" optional="true">
<doc>
In traditional surface science, the coordinate system is defined such that the positive z-axis
points along the normal of the sample stage, and the x- and y-axes lie in the plane of the sample stage.
However, in NeXus, a coordinate system that is the same as `McStas`_ is used. `xps_coordinate_system`
gives the user the opportunity to work in the traditional base coordinate system.

.. _McStas: http://mcstas.org/

.. image:: xps/xps_cs.png
:width: 40%
</doc>
<field name="origin">
<enumeration>
<item value="sample stage"/>
</enumeration>
</field>
<field name="handedness">
<enumeration>
<item value="left_handed"/>
</enumeration>
</field>
<field name="z_direction">
<enumeration>
<item value="sample stage normal"/>
</enumeration>
</field>
<field name="x">
<enumeration>
<item value="[-1, 0, 0]"/>
</enumeration>
</field>
<field name="y">
<enumeration>
<item value="[0, 1, 0]"/>
</enumeration>
</field>
<field name="z">
<enumeration>
<item value="[0, 0, 1]"/>
</enumeration>
</field>
<field name="depends_on" type="NX_CHAR">
<doc>
Link to transformations defining the XPS base coordinate system,
which is defined such that the positive z-axis points along the sample stage normal, and the
x- and y-axes lie in the plane of the sample stage.
</doc>
</field>
<group name="coordinate_system_transformations" type="NXtransformations">
<doc>
Set of transformations, describing the orientation of the XPS coordinate system
with respect to the beam coordinate system (.).
</doc>
</group>
</group>
</group>
<group type="NXinstrument">
<doc>
Description of the XPS spectrometer and its individual parts.

This concept is related to term `12.58`_ of the ISO 18115-1:2023 standard.

.. _12.58: https://www.iso.org/obp/ui/en/#iso:std:iso:18115:-1:ed-3:v1:en:term:12.58
</doc>
<group name="sourceTYPE" type="NXsource">
<field name="power" type="NX_FLOAT" units="NX_POWER" recommended="true"/>
</group>
<group name="beamTYPE" type="NXbeam">
<field name="depends_on" recommended="true">
<doc>
Reference to the transformation describing the orientation of the beam
relative to a defined coordinate system.
</doc>
</field>
<group name="transformations" type="NXtransformations" recommended="true">
<field name="beam_azimuth_angle" type="NX_NUMBER" units="NX_ANGLE">
<doc>
Azimuthal tilt of the beam from the y-direction towards the operator, defined
by the sample stage.
</doc>
<attribute name="transformation_type">
<enumeration>
<item value="rotation"/>
</enumeration>
</attribute>
<attribute name="vector">
<enumeration>
<item value="[0, 0, -1]"/>
</enumeration>
</attribute>
<attribute name="depends_on">
<enumeration>
<item value="beam_polar_angle_of_incidence"/>
</enumeration>
</attribute>
</field>
<field name="beam_polar_angle_of_incidence" type="NX_NUMBER" units="NX_ANGLE">
<doc>
Incidence angle of the beam with respect to the upward z-direction, defined by
the sample stage.
</doc>
<attribute name="transformation_type">
<enumeration>
<item value="rotation"/>
</enumeration>
</attribute>
<attribute name="vector">
<enumeration>
<item value="[1, 0, 0]"/>
</enumeration>
</attribute>
<attribute name="depends_on">
<doc>
This should point to the last element of the coordinate system transformations defined in
/entry/geometries/xps_coordinate_system/coordinate_system_transformations.
</doc>
</attribute>
</field>
</group>
</group>
<group type="NXelectronanalyser">
<field name="work_function" type="NX_FLOAT"/>
<group name="transmission_function" type="NXdata" recommended="true"/>
<group type="NXcollectioncolumn">
<field name="magnification" type="NX_FLOAT" recommended="true" units="NX_DIMENSIONLESS"/>
</group>
<group type="NXenergydispersion">
<field name="diameter" type="NX_NUMBER" recommended="true" units="NX_LENGTH"/>
<field name="energy_scan_mode"/>
</group>
<field name="depends_on" recommended="true">
<doc>
Reference to the transformation describing the orientation of the analyzer
relative to a defined coordinate system.
</doc>
</field>
<group name="transformations" type="NXtransformations" recommended="true">
<field name="analyser_take_off_azimuth_angle" type="NX_NUMBER" units="NX_ANGLE">
<doc>
Azimuthal tilt of the analyser from the y-direction towards the operator,
defined by the sample stage.
</doc>
<attribute name="transformation_type">
<enumeration>
<item value="rotation"/>
</enumeration>
</attribute>
<attribute name="vector">
<enumeration>
<item value="[0, 0, -1]"/>
</enumeration>
</attribute>
<attribute name="depends_on">
<enumeration>
<item value="analyser_take_off_polar_angle"/>
</enumeration>
</attribute>
</field>
<field name="analyser_take_off_polar_angle" type="NX_NUMBER" units="NX_ANGLE">
<doc>
Polar tilt of the analyser with respect to the upward z-direction, defined by
the sample stage.
</doc>
<attribute name="transformation_type">
<enumeration>
<item value="rotation"/>
</enumeration>
</attribute>
<attribute name="vector">
<enumeration>
<item value="[1, 0, 0]"/>
</enumeration>
</attribute>
<attribute name="depends_on">
<doc>
This should point to the last element of the coordinate system transformations defined in
/entry/geometries/xps_coordinate_system/coordinate_system_transformations.
</doc>
</attribute>
</field>
</group>
</group>
</group>
<group type="NXprocess_mpes">
<group name="energy_referencing" type="NXcalibration" recommended="true"/>
<group name="transmission_correction" type="NXcalibration" recommended="true"/>
</group>
<group type="NXsample">
<field name="depends_on" recommended="true">
<doc>
Reference to the transformation describing the orientation of the sample
relative to a defined coordinate system.
</doc>
</field>
<group name="transformations" type="NXtransformations" recommended="true">
<field name="sample_rotation_angle" type="NX_NUMBER" units="NX_ANGLE">
<doc>
Clockwise rotation about the sample normal.
</doc>
<attribute name="transformation_type">
<enumeration>
<item value="rotation"/>
</enumeration>
</attribute>
<attribute name="vector">
<enumeration>
<item value="[0, 0, -1]"/>
</enumeration>
</attribute>
<attribute name="depends_on">
<enumeration>
<item value="sample_normal_tilt_azimuth_angle"/>
</enumeration>
</attribute>
</field>
<field name="sample_normal_tilt_azimuth_angle" type="NX_NUMBER" units="NX_ANGLE">
<doc>
Azimuthal tilt of the sample from the y-direction towards the operator, defined
by the sample stage.
</doc>
<attribute name="transformation_type">
<enumeration>
<item value="rotation"/>
</enumeration>
</attribute>
<attribute name="vector">
<enumeration>
<item value="[0, 0, -1]"/>
</enumeration>
</attribute>
<attribute name="depends_on">
<enumeration>
<item value="sample_normal_polar_angle_of_tilt"/>
</enumeration>
</attribute>
</field>
<field name="sample_normal_polar_angle_of_tilt" type="NX_NUMBER" units="NX_ANGLE">
<doc>
Polar tilt of the sample with respect to the upward z-direction, defined by the
sample stage.
</doc>
<attribute name="transformation_type">
<enumeration>
<item value="rotation"/>
</enumeration>
</attribute>
<attribute name="vector">
<enumeration>
<item value="[1, 0, 0]"/>
</enumeration>
</attribute>
<attribute name="depends_on">
<doc>
This should point to the last element of the coordinate system transformations defined in
/entry/geometries/xps_coordinate_system/coordinate_system_transformations.
</doc>
</attribute>
</field>
</group>
</group>
<group name="data" type="NXdata">
<field name="energy" type="NX_NUMBER"/>
<attribute name="energy_indices"/>
<attribute name="energy_depends" recommended="true"/>
</group>
</group>
</definition>
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