3.3.3.21. NXapm_paraprobe_config_ranger

Status:

application definition (contribution), extends NXobject

Description:

Configuration of a paraprobe-ranger tool run in atom probe microscopy.

Symbols:

The symbols used in the schema to specify e.g. dimensions of arrays.

n_isotopes: The number of isotopes to consider as building blocks for searching molecular ions.

n_composition: The number of compositions to consider for molecular ion search tasks.

Groups cited:

NXapm_input_ranging, NXapm_input_reconstruction, NXcg_cylinder_set, NXcg_ellipsoid_set, NXcg_face_list_data_structure, NXcg_hexahedron_set, NXcs_filter_boolean_mask, NXcs_profiling, NXentry, NXmatch_filter, NXprocess, NXspatial_filter, NXsubsampling_filter

Structure:

ENTRY: (required) NXentry

@version: (required) NX_CHAR

Version specifier of this application definition.

definition: (required) NX_CHAR ⤆

Official NeXus NXDL schema with which this file was written. ...

Official NeXus NXDL schema with which this file was written.

Obligatory value: NXapm_paraprobe_config_ranger

program: (required) NX_CHAR

Given name of the program/software/tool with which this NeXus ...

Given name of the program/software/tool with which this NeXus (configuration) file was generated.

@version: (required) NX_CHAR

Ideally program version plus build number, or commit hash or description ...

Ideally program version plus build number, or commit hash or description of ever persistent resources where the source code of the program and build instructions can be found so that the program can be configured ideally in such a manner that the result of this computational process is recreatable in the same deterministic manner.

time_stamp: (required) NX_DATE_TIME

ISO 8601 formatted time code with local time zone offset to UTC ...

ISO 8601 formatted time code with local time zone offset to UTC information included when this configuration file was created.

analysis_identifier: (required) NX_CHAR

Ideally, a (globally persistent) unique identifier for referring ...

Ideally, a (globally persistent) unique identifier for referring to this analysis.

analysis_description: (optional) NX_CHAR

Possibility for leaving a free-text description about this analysis.

results_path: (optional) NX_CHAR

Path to the directory where the tool should store NeXus/HDF5 results ...

Path to the directory where the tool should store NeXus/HDF5 results of this analysis. If not specified results will be stored in the current working directory.

number_of_processes: (required) NX_UINT {units=NX_UNITLESS}

How many task to perform?

PROCESS: (optional) NXprocess ⤆

apply_existent_ranging: (optional) NXprocess

dataset: (required) NXapm_input_reconstruction

filename: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

dataset_name_reconstruction: (required) NX_CHAR ⤆

dataset_name_mass_to_charge: (required) NX_CHAR ⤆

iontypes: (required) NXapm_input_ranging

filename: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

group_name_iontypes: (required) NX_CHAR ⤆

spatial_filter: (optional) NXspatial_filter

windowing_method: (required) NX_CHAR ⤆

CG_ELLIPSOID_SET: (optional) NXcg_ellipsoid_set ⤆

dimensionality: (required) NX_POSINT ⤆

cardinality: (required) NX_POSINT ⤆

identifier_offset: (required) NX_INT ⤆

center: (required) NX_NUMBER ⤆

half_axes_radii: (required) NX_NUMBER ⤆

orientation: (required) NX_NUMBER ⤆

CG_CYLINDER_SET: (optional) NXcg_cylinder_set ⤆

dimensionality: (required) NX_POSINT ⤆

cardinality: (required) NX_POSINT ⤆

identifier_offset: (required) NX_INT ⤆

center: (required) NX_NUMBER ⤆

height: (required) NX_NUMBER ⤆

radii: (required) NX_NUMBER ⤆

CG_HEXAHEDRON_SET: (optional) NXcg_hexahedron_set ⤆

dimensionality: (required) NX_POSINT ⤆

cardinality: (required) NX_POSINT ⤆

identifier_offset: (required) NX_INT ⤆

hexahedra: (required) NXcg_face_list_data_structure ⤆

CS_FILTER_BOOLEAN_MASK: (optional) NXcs_filter_boolean_mask ⤆

number_of_objects: (required) NX_UINT ⤆

bitdepth: (required) NX_UINT ⤆

mask: (required) NX_UINT ⤆

identifier: (required) NX_UINT ⤆

evaporation_id_filter: (optional) NXsubsampling_filter

iontype_filter: (optional) NXmatch_filter

hit_multiplicity_filter: (optional) NXmatch_filter

molecular_ion_search: (optional) NXprocess

assumed_composition_isotopes: (optional) NX_UINT (Rank: 2, Dimensions: [n_composition, 2]) {units=NX_UNITLESS}

A list of pairs of number of protons and either the value 0 (per row) ...

A list of pairs of number of protons and either the value 0 (per row) or the mass number for all those isotopes which are assumed present in a virtual specimen. The purpose of this field is to compute also composition-weighted products to yield a simple estimation which could potentially help scientists to judge if certain molecular ions are to be expected. The corresponding setting store_composition_weighted_product should be activated.

isotope_whitelist: (required) NX_UINT (Rank: 2, Dimensions: [n_isotopes, 2]) {units=NX_UNITLESS}

A list of pairs of number of protons and mass number for all isotopes ...

A list of pairs of number of protons and mass number for all isotopes to consider that can be composed into (molecular) ions, during the recursive molecular_ion_search.

mass_to_charge_interval: (required) NX_FLOAT (Rank: 1, Dimensions: [2]) {units=NX_ANY}

The mass-to-charge-state ratio interval in which ...

The mass-to-charge-state ratio interval in which all molecular ions are searched.

maximum_charge: (required) NX_UINT {units=NX_UNITLESS}

The maximum charge that a molecular ion should have.

maximum_number_of_isotopes: (required) NX_UINT {units=NX_UNITLESS}

The maximum number of isotopes of which the molecular ion ...

The maximum number of isotopes of which the molecular ion should be composed. Currently this must not be larger than 32.

Users should be warned that the larger the maximum_charge and especially the larger the maximum_number_of_isotopes is chosen, the eventually orders of magnitude more costly the search becomes.

This is because paraprobe-ranger computes really all (at least) theoretically possible combinations that would have likely a mass-to-charge-state ratio in the specified mass_to_charge_interval. It is the challenge in atom probe to judge which of these (molecular) ions are feasible and also practically possible. This tool does not answer this question.

Namely, which specific molecular ion will evaporate, remain stable during flight and becomes detected is a complicated and in many cases not yet in detail understood phenomenon. The ab-initio conditions before and during launch, the local environment, arrangement and field as well as the flight phase in an evacuated but not analysis chamber with a complex electrical field, eventual laser pulsing in place, temperature and remaining atoms or molecules all can have an effect which iontypes are really physically evaporating and detected.

store_atomic_mass_sum: (required) NX_BOOLEAN

Report the accumulated atomic mass from each isotope building the ion. ...

Report the accumulated atomic mass from each isotope building the ion. Accounts for each identified ion. Relatistic effects are not accounted for.

store_natural_abundance_product: (required) NX_BOOLEAN

Report the product of the natural abundances from each isotope building ...

Report the product of the natural abundances from each isotope building the ion. Accounts for each identified ion.

The value zero indicates it is not possible to build such molecular ion from nuclids which are all observationally stable. Very small values can give an idea/about how likely such a molecular ion is expected to form assuming equal probabilities.

However in atom probe experiments this product has to be modified by the (spatially-correlated) local composition in the region from which the ions launch because the formation of a molecular ion depends as summarized under maximum_number_of_isotopes on the specific quantum-mechanical configuration and field state upon launch or/and (early state) of flight respectively. We are aware that this modified product can have a substantially different value than the natural_abundance_product.

Natural abundancies folded with the estimated compositions of the specimen can differ by orders of magnitude.

store_charge_state: (required) NX_BOOLEAN

Report the charge state of the ions.

store_disjoint_isotopes: (required) NX_BOOLEAN

Report if identified ions should be characterized ...

Report if identified ions should be characterized wrt to their number of disjoint isotopes.

check_existent_ranging: (optional) NXprocess

iontypes: (required) NXapm_input_ranging

filename: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

group_name_iontypes: (required) NX_CHAR ⤆

performance: (required) NXcs_profiling

current_working_directory: (required) NX_CHAR ⤆

Hypertext Anchors

List of hypertext anchors for all groups, fields, attributes, and links defined in this class.

NXDL Source:

https://github.com/nexusformat/definitions/blob/main/contributed_definitions/NXapm_paraprobe_config_ranger.nxdl.xml