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Add sub-application definition NXmpes_liquid #104

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Add sub-application definition NXmpes_liquid #104

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fca5092
Latest liquidjet definitions
domna Nov 3, 2023
d548ad1
Add mpes_liquid to docs
domna Nov 3, 2023
2b39845
Replace NX_SAMPLE with NXsample
domna Nov 3, 2023
1700b47
Removes composite units
domna Nov 3, 2023
9eff698
Corrects typo in depends_on
domna Nov 3, 2023
c6e089f
Removes liquidjet base class
domna Nov 3, 2023
eb97fd2
Adds jet_direction and leaf_normal
domna Nov 8, 2023
2ff8fa9
Further transformation refinements
domna Nov 13, 2023
263c872
Adds changes from Uwes and Stephans comments
domna Nov 21, 2023
9ad5e73
Adds docstring extensions for gas_pressure and temperature in NXsample
domna Nov 22, 2023
8999792
adjust to recent changes in NXmpes
lukaspie Jul 12, 2024
21c27da
fix nyaml nxdl incosistency
lukaspie Jul 12, 2024
681d4c6
fix mpes-structure.rst
lukaspie Jul 12, 2024
511d755
change sample enviroments to NXenvironment
rettigl Sep 10, 2024
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251 changes: 251 additions & 0 deletions contributed_definitions/NXmpes_liquid.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="NXmpes_liquid" extends="NXmpes" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<doc>
This is the application definition for multidimensional photoelectron spectroscopy on liquids.
It extends the NXmpes application definition by metadata for characterizing liquidjet composition
and geometry.
</doc>
<group type="NXentry">
<field name="definition">
<attribute name="version"/>
<enumeration>
<item value="NXmpes_liquid"/>
</enumeration>
</field>
<group type="NXinstrument">
<group name="instrument_orientation" type="NXtransformations" optional="true">
<doc>
Transformations describing base geometry in the experiment.
Usually defaults to the beam in z direction and gravity in -y direction.
</doc>
<field name="analyzer_optical_axis" type="NX_NUMBER" recommended="true">
<doc>
The coordinate system frame of the analyzer.
If no direction attribute is specified,
the optical axis of the analyzer follows the positive z-direction.
</doc>
<attribute name="gravity">
<doc>
Direction of gravity in the analyzer coordinate system.
</doc>
</attribute>
<attribute name="beam_direction">
<doc>
Direction of the photon beam in the analyzer coordinate system.
</doc>
</attribute>
<attribute name="direction">
<doc>
The direction of the analyzer optical axis.
If this is not specified the optical axis points
in the positive jet direction.
It is recommended to always specify the axis
direction explicitly (even for the default case).
</doc>
</attribute>
</field>
</group>
</group>
<group type="NXsample">
<field name="thickness" type="NX_FLOAT" recommended="true" units="NX_LENGTH">
<doc>
Thickness of the sample in normal direction to the surface that is probed,
e.g., diameter of capillary (round jets) or thickness of the leaf (flat jets).
</doc>
</field>
<field name="flow_rate" type="NX_FLOAT" recommended="true" units="NX_ANY">
<doc>
Flow rate of the liquid into the chamber, i.e.,
through the microjet capillary (or in case of a flat jet: both capillaries).
Unit should be NX_VOLUME / NX_TIME.
</doc>
</field>
<field name="shape" type="NX_CHAR">
<enumeration>
<item value="round"/>
<item value="flat"/>
</enumeration>
</field>
<field name="nozzle_material" type="NX_CHAR" recommended="true">
<doc>
Material the microjet nozzle is made of
(users are encouraged to expand on that in group history/sample_preparation).
</doc>
</field>
<group name="temperature_env" type="NXenvironment" optional="true">
<doc>
The temperature set for the liquid jet or the injection assembly.
Details may be added through instances of NXsensor/NXactuator the how this temperature
value is obtained (whether a chiller unit was used, point of cooling, temperature reading
etc.) and where this value would be expected (estimate for the jet assembly, the liquid
prior to injection, or at the interaction point taking into account evaporative cooling etc.).
</doc>
</group>
<group name="gas_pressure_env" type="NXenvironment" optional="true">
<doc>
Pressure in the interaction chamber under operation conditions and actuators/sensors
controlling/measuring it.
</doc>
</group>
<field name="depends_on" recommended="true">
<doc>
Connects this liquidjet to its transformation chain.
</doc>
</field>
<group name="liquidjet_orientation" type="NXtransformations">
<doc>
Transformations describing the transformation chain of the liquid jet flow direction
and optionally the flat jet normal. The vector of the major flow direction of the
liquid jet from the point of injection into the chamber.
Along the cylinder axis for single, cylindrical jets, and parallel to the leaf plane for flatjets.
</doc>
<field name="jet_direction" type="NX_NUMBER" units="NX_ANGLE">
<doc>
The coordinate system frame of the liquid jet direction.
If no direction attribute is specified,
the jet points in the positive z-direction.
</doc>
<attribute name="gravity" type="NX_NUMBER" recommended="true">
<doc>
The direction of gravity in the coordinate system
of `jet_direction`.
</doc>
<dimensions rank="1">
<dim index="1" value="3"/>
</dimensions>
</attribute>
<attribute name="transformation_type" type="NX_CHAR">
<enumeration>
<item value="rotation"/>
</enumeration>
</attribute>
<attribute name="direction" type="NX_NUMBER" recommended="true">
<doc>
The direction of the liqud jet.
If this is not specified the jet points
in the positive jet direction.
It is recommended to always specify the jet
direction explicitly (even for the default case).
</doc>
<dimensions rank="1">
<dim index="1" value="3"/>
</dimensions>
</attribute>
</field>
<field name="leaf_normal" type="NX_NUMBER" units="NX_ANGLE">
<doc>
Coordinate frame for the surface normal of the first leaf on the side of solvent #1.
If no direction is specified,
the surface leaf normal vector points in the positive z-direction.
The value of this field is the angle between the
analyzer optical axis and the leaf normal.
If you only want to collect the angle between the leaf normal
and the analyzer optical axis the `depends_on` attribute may be omitted.
If a transformation chain is provided (with the `depends_on` attribute)
it should depend on the analyzer optical axis or the jet direction depending
on the use case.
</doc>
<attribute name="transformation_type">
<enumeration>
<item value="rotation"/>
</enumeration>
</attribute>
<attribute name="direction" type="NX_NUMBER" recommended="true">
<doc>
Direction of surface normal vector of the first leaf on the side of solvent #1.
If this is not specified it defaults to the positve z-direction which should
be parallel to the detection direction.
It is recommended to always specify the leaf normal direction
explicitly (even for the default case).
</doc>
<dimensions rank="1">
<dim index="1" value="3"/>
</dimensions>
</attribute>
</field>
</group>
<group name="solventSOLVENT" type="NXsample_component">
<doc>
Solvent substance of the liquid jet.
For flat jets, this group may appear more than once.
If a mixture of solvents is used,
the one with the highest mol fraction should be designated solvent,
and the other(s) solute(s) (see solute group).
</doc>
<field name="description" type="NX_CHAR" recommended="true"/>
<field name="name" type="NX_CHAR"/>
<field name="chemical_formula" type="NX_CHAR">
<doc>
Molecular or structural formula of the solvent.
</doc>
</field>
<field name="chem_id_cas" type="NX_CHAR" recommended="true"/>
<field name="ph_value" type="NX_FLOAT" optional="true" units="NX_UNITLESS">
<doc>
Measured pH value of the solution.
</doc>
</field>
<field name="ph_adjustment" type="NX_BOOLEAN" optional="true">
<doc>
Whether or not agents for pH adjustment were added to the solution.
In this case, users are encouraged to expand on that in the ``history`` group
or add a corresponding solute group.
</doc>
</field>
<field name="mol_fraction" type="NX_FLOAT" optional="true" units="NX_ANY">
<doc>
Molarity of the solvent in the solution.
Unit should be 1 / NX_VOLUME.
</doc>
</field>
</group>
<group name="soluteSOLUTE" type="NXsample_component">
<doc>
Solute substance solved in a given solvent.
This also accounts for multiple solutes if more than one is given.
</doc>
<field name="description" type="NX_CHAR" recommended="true"/>
<field name="name" type="NX_CHAR"/>
<field name="chemical_formula" type="NX_CHAR">
<doc>
Molecular or structural formula of the solute.
</doc>
</field>
<field name="chem_id_cas" type="NX_CHAR" recommended="true"/>
<field name="mol_fraction" type="NX_FLOAT" recommended="true" units="NX_ANY">
<doc>
Molarity of the solute in the solution.
Unit should be 1 / NX_VOLUME
</doc>
</field>
<field name="solvent" type="NX_CHAR">
<doc>
Specifies the parent solvent entry of the solution.
</doc>
</field>
</group>
</group>
</group>
</definition>
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