NXapm_paraprobe_results_ranger

Status:

application definition, extends NXobject

Description:

Results 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_ions: The total number of ions in the reconstruction.

n_ivec: The maximum number of atoms per molecular ion type.

Groups cited:

NXcoordinate_system_set, NXcs_computer, NXcs_cpu, NXcs_gpu, NXcs_io_obj, NXcs_io_sys, NXcs_mm_sys, NXcs_profiling_event, NXcs_profiling, NXentry, NXfabrication, NXion, NXprocess, NXtransformations, NXuser

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.

Obligatory value: NXapm_paraprobe_results_ranger

program: (required) NX_CHAR

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 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.

analysis_identifier: (optional) NX_CHAR

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.

time_stamp: (required) NX_DATE_TIME

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

config_filename: (required) NX_CHAR

The absolute path and name of the config file for this analysis.

@version: (required) NX_CHAR

At least SHA256 strong hash of the specific config_file for tracking provenance.

USER: (recommended) NXuser

If used, contact information and eventually details of at least the person who performed this analysis.

name: (required) NX_CHAR

affiliation: (recommended) NX_CHAR

address: (optional) NX_CHAR

email: (recommended) NX_CHAR

orcid: (recommended) NX_CHAR

orcid_platform: (recommended) NX_CHAR

telephone_number: (optional) NX_CHAR

role: (recommended) NX_CHAR

social_media_name: (optional) NX_CHAR

social_media_platform: (optional) NX_CHAR

COORDINATE_SYSTEM_SET: (optional) NXcoordinate_system_set

Details about the coordinate system conventions used.

TRANSFORMATIONS: (required) NXtransformations

The individual coordinate systems which used. fields should be prefixed with a prefix taken from an enumeration which details the individual coordinate systems:

  • lab

  • specimen

  • laser

  • leap

  • detector

  • recon

PROCESS: (optional) NXprocess

use_existent_ranging: (optional) NXprocess

Paraprobe-ranger loads the iontypes and evaluates for each ion on which iontype it matches. If it matches on none, the ion is considered of the default unknown type with a 0 as its respective value in the iontypes array.

iontypes: (required) NX_UINT (Rank: 1, Dimensions: [n_ions]) {units=NX_UNITLESS}

The iontype ID for each ion that was best matching, stored in the order of the evaporation sequence ID.

ION: (required) NXion

isotope_vector: (required) NX_UINT

nuclid_list: (recommended) NX_UINT

charge_state: (required) NX_INT

mass_to_charge_range: (required) NX_FLOAT

molecular_ion_search: (optional) NXprocess

Paraprobe-ranger performs a combinatorial search over all possible or a reduced set of nuclids to identify into which ions these can be composed.

isotope_vector_matrix: (required) NX_UINT (Rank: 2, Dimensions: [i, 32]) {units=NX_UNITLESS}

The main result is the list of molecular ions, here formatted according to the definitions of a set of isotope_vectors as detailed in NXion.

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

The mass-to-charge-state ratio of each molecular ion without considering relativistic or quantum effects.

mass: (optional) NX_FLOAT (Rank: 1, Dimensions: [i]) {units=NX_ANY}

The mass of each molecular ion without considering relativistic or quantum effects.

charge_state: (required) NX_UINT (Rank: 1, Dimensions: [i]) {units=NX_CHARGE}

The charge_state of each molecular ion.

natural_abundance_product: (optional) NX_FLOAT (Rank: 1, Dimensions: [i]) {units=NX_DIMENSIONLESS}

The product of the natural abundance of the isotopes building each molecular ion. Further details are available in NXapm_paraprobe_config_ranger.

composition_product: (optional) NX_FLOAT (Rank: 1, Dimensions: [i]) {units=NX_DIMENSIONLESS}

The product of the natural abundance of the isotopes building each molecular ion. Further details are available in NXapm_paraprobe_config_ranger.

number_of_disjoint_nuclids: (optional) NX_POSINT (Rank: 1, Dimensions: [i]) {units=NX_UNITLESS}

The number of disjoint nuclids for each molecular ion.

number_of_nuclids: (optional) NX_POSINT (Rank: 1, Dimensions: [i]) {units=NX_UNITLESS}

The number of nuclids for each molecular ion.

performance: (recommended) NXcs_profiling

command_line_call: (optional) NX_CHAR

start_time: (recommended) NX_DATE_TIME

end_time: (recommended) NX_DATE_TIME

total_elapsed_time: (required) NX_NUMBER

number_of_processes: (required) NX_POSINT

number_of_threads: (required) NX_POSINT

number_of_gpus: (required) NX_POSINT

CS_COMPUTER: (recommended) NXcs_computer

name: (recommended) NX_CHAR

operating_system: (required) NX_CHAR

@version: (required) NX_CHAR

uuid: (optional) NX_CHAR

CS_CPU: (optional) NXcs_cpu

name: (optional) NX_CHAR

FABRICATION: (recommended) NXfabrication

identifier: (optional) NX_CHAR

capabilities: (optional) NX_CHAR

CS_GPU: (optional) NXcs_gpu

name: (optional) NX_CHAR

FABRICATION: (recommended) NXfabrication

identifier: (optional) NX_CHAR

capabilities: (optional) NX_CHAR

CS_MM_SYS: (optional) NXcs_mm_sys

total_physical_memory: (required) NX_NUMBER

CS_IO_SYS: (optional) NXcs_io_sys

CS_IO_OBJ: (required) NXcs_io_obj

technology: (required) NX_CHAR

max_physical_capacity: (required) NX_NUMBER

name: (optional) NX_CHAR

FABRICATION: (recommended) NXfabrication

identifier: (optional) NX_CHAR

capabilities: (optional) NX_CHAR

CS_PROFILING_EVENT: (required) NXcs_profiling_event

start_time: (optional) NX_DATE_TIME

end_time: (optional) NX_DATE_TIME

description: (required) NX_CHAR

elapsed_time: (required) NX_NUMBER

number_of_processes: (required) NX_POSINT

Specify if it was different from the number_of_processes in the NXcs_profiling super class.

number_of_threads: (required) NX_POSINT

Specify if it was different from the number_of_threads in the NXcs_profiling super class.

number_of_gpus: (required) NX_POSINT

Specify if it was different from the number_of_threads in the NXcs_profiling super class.

max_virtual_memory_snapshot: (recommended) NX_NUMBER

max_resident_memory_snapshot: (recommended) NX_NUMBER

Hypertext Anchors

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

NXDL Source:

https://github.com/FAIRmat-Experimental/nexus_definitions/tree/fairmat/contributed_definitions/NXapm_paraprobe_results_ranger.nxdl.xml