New Extension: SpeciesType #180

DavidSagan · 2018-02-06T17:29:20Z

This pull request has a new file for standardizing the names of particle species.

Implements issue: #176

Description

This convention is for standardizing the names of particle species, e.g. in particle physics.

Affected Components

new extension: SpeciesType

Logic Changes

A new optional string attribute speciesType can now be present at mesh record and particle group level.

Writer Changes

openPMD-api (upcoming): Add to writer and reader API.

Reader Changes

Readers can if they want read the new attribute (if it exists) and propose e.g. groups, accumulations, etc. on it.

openPMD-validator: Validate it's a string if present New Attribute: speciesType openPMD-validator#38
openPMD-viewer: https://github.com/openPMD/openPMD-viewer/...
yt: https://github.com/yt-project/yt/...
VisIt: https://github.com/openPMD/openPMD-visit-plugin
openPMD-api (upcoming): https://github.com/openPMD/openPMD-api/...

Data Updater

New optional extension with optional attribute. No update of existing data needed.
Edit: update needed for ED-PIC extension: #192

ax3l · 2018-02-06T17:34:38Z

Left-over to do's from #177:

hardons: define protons & anti-protons
separate anti-particles by , instead of putting them in brackets
remove extension-ID (2.0.0)

DavidSagan · 2018-02-20T05:00:41Z

@ax3l There also should be a version number associated with this. I assume it should be 1.0.0 .

ax3l · 2018-02-20T08:31:20Z

@DavidSagan the version number will simply be the one of the standard it gets in with.

DavidSagan · 2018-02-20T12:50:20Z

@ax3l

the version number will simply be the one of the standard it gets in with.

OK just to make sure I understand: Say in the future changes to an extension necessitates that it is to be bumped up a version. Then even if the base standard has not changed it will be bumped up too? Yes?

ax3l · 2018-02-20T12:58:50Z

Exactly.
Admittedly, up to now the major changes were triggered by the base standard.

ax3l · 2018-02-26T13:21:15Z

@RemiLehe @marcguetg hi, do you want to give your review comments on this PR? From my side I think it's already in quite good shape.

ax3l · 2018-02-26T13:22:56Z

EXT_SpeciesType.md

+Additional Record Attribute
+---------------------------
+
+The following additional attribute for openPMD `records` is defined in this


oh wait, I think it should read:

... mesh records and particle groups ...

How about simply:

The following attribute for openPMD is defined ...

Sure, but I think for reader tools it is good to know where to look for it, no?
I currently only see these two locations as useful and relaxing later on is always possible.

OK I did not realize that this was defining where the info should go. How about adding a definition for mesh record and particle group in the Standard?

good, this aspect is moved to #187

RemiLehe · 2018-03-29T13:56:12Z

@ax3l Should we merge this?

ax3l · 2018-04-03T13:45:43Z

ok, I addressed the last inline comment about the location of the SpeciesType attribute, so reader implementors know where to expect it

DavidSagan · 2018-04-03T13:54:32Z

Minor detail: Since neutron is a common standard name do we want to use neutron, anti-neutron rather than other:neutron, other:anti-neutron?

ax3l · 2018-04-03T14:00:19Z

Sure, we can do that. It's just not too common for us since it's neutral ;-)

I did just draw a line (arbitrarily) since (anti-)protons are the only stable free hadrons.

- file renamed to `EXT_SpeciesType.md` - extension name: `SpeciesType` with extension-ID `4` (`1` is used and we reserved `2`$ - formatting unified - defined `SpeciesType` as attribute: *recommended* if extension is declared - allowed `lists`, e.g. for a local *summed charge density* in a non-equilibrium plasma - atoms & isotopes: reference to IUPAC namings

Reference to the new extension `SpeciesType` in the base standard

- optional by default - clarify annotations

Not needed (yet)

Add pointers

ax3l · 2018-04-03T14:10:12Z

@DavidSagan moved (anti-)neutron to "common" and added sigma baryon as another example. now we draw the line at the nucleus :D

ax3l · 2018-04-03T14:18:00Z

EXT_SpeciesType.md

+The following additional attribute for openPMD `mesh records` and
+`particle groups` is defined in this extension:
+
+- `SpeciesType`


wait, why is this upper-case in the first letter? Aren't we starting all attributes with a lowercase letter? Will update for consistency.

currently, all attributes start lower case.

ax3l · 2018-04-03T15:06:24Z

@RemiLehe @DavidSagan I think this can be merged now :)

zerothi · 2021-10-18T06:45:42Z

EXT_SpeciesType.md

+An example would be `Si` for silicon.
+
+Specifications of isotopes are denoted by a pound symbol `#` followed
+by the isotopic number followed by the chemical symbol, e.g.: `#3He`


Could we add a mention on how to mention #2H2#15O? It isn't fully clear how this works in this flow?

ax3l requested review from ax3l and RemiLehe February 6, 2018 17:30

ax3l added the EXT: SpeciesType physical particle species extension label Feb 6, 2018

ax3l added this to the openPMD 2.X milestone Feb 6, 2018

ax3l mentioned this pull request Feb 6, 2018

Added ParticleSpeciesNames.md #177

Closed

ax3l changed the title ~~New particle id standard~~ New particle type standard Feb 6, 2018

ax3l changed the title ~~New particle type standard~~ Extension: Particle Species Type Feb 6, 2018

ax3l changed the title ~~Extension: Particle Species Type~~ Extension: Species Type Feb 6, 2018

ax3l changed the title ~~Extension: Species Type~~ New Extension: Species Type Feb 6, 2018

ax3l force-pushed the New-ParticleID-Standard branch from 85ed6e1 to 02320b7 Compare February 20, 2018 08:52

ax3l mentioned this pull request Feb 20, 2018

Ext: Species Type openPMD/openPMD-api#85

Open

ax3l approved these changes Feb 20, 2018

View reviewed changes

ax3l added the minor change backwards-compatible change label Feb 20, 2018

ax3l reviewed Feb 26, 2018

View reviewed changes

RemiLehe approved these changes Mar 29, 2018

View reviewed changes

DavidSagan and others added 3 commits April 3, 2018 16:01

Added ParticleSpeciesNames.md

c4b9e04

EXT SpeciesType: Reference in Std

7a2756d

Reference to the new extension `SpeciesType` in the base standard

ax3l and others added 7 commits April 3, 2018 16:01

EXT SpeciesType: Update

a676245

- optional by default - clarify annotations

Remove Prefixes

b6b32d8

Not needed (yet)

Fix Typos

6935749

Clarification Charge State

585537b

Add pointers

Elementary Particles & Gauge+Higgs Bosons

734da1c

Format, Proton, No Ext-ID

8467f34

Location of SpeciesType Attribute

c5c4733

ax3l force-pushed the New-ParticleID-Standard branch from 8e781f6 to c5c4733 Compare April 3, 2018 14:02

Neutron: Common Particle :)

a7711ee

ax3l mentioned this pull request Apr 3, 2018

ED-PIC: Remove proton/neutron Number? #191

Open

ax3l requested changes Apr 3, 2018

View reviewed changes

speciesType: lower case

161956f

currently, all attributes start lower case.

ax3l approved these changes Apr 3, 2018

View reviewed changes

ax3l mentioned this pull request Apr 3, 2018

New Attribute: speciesType openPMD/openPMD-validator#38

Merged

ax3l changed the title ~~New Extension: Species Type~~ New Extension: SpeciesType Apr 3, 2018

RemiLehe merged commit 7457b4e into openPMD:upcoming-2.0.0 Apr 3, 2018

zerothi reviewed Oct 18, 2021

View reviewed changes

DavidSagan deleted the New-ParticleID-Standard branch September 14, 2023 16:28

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

New Extension: SpeciesType #180

New Extension: SpeciesType #180

DavidSagan commented Feb 6, 2018 •

edited by ax3l

Loading

ax3l commented Feb 6, 2018 •

edited

Loading

DavidSagan commented Feb 20, 2018

ax3l commented Feb 20, 2018

DavidSagan commented Feb 20, 2018 •

edited

Loading

ax3l commented Feb 20, 2018 •

edited

Loading

ax3l commented Feb 26, 2018 •

edited

Loading

ax3l Feb 26, 2018

DavidSagan Feb 26, 2018

ax3l Feb 26, 2018 •

edited

Loading

DavidSagan Feb 26, 2018

ax3l Apr 3, 2018 •

edited

Loading

RemiLehe commented Mar 29, 2018

ax3l commented Apr 3, 2018

DavidSagan commented Apr 3, 2018

ax3l commented Apr 3, 2018 •

edited

Loading

ax3l commented Apr 3, 2018 •

edited

Loading

ax3l Apr 3, 2018 •

edited

Loading

ax3l commented Apr 3, 2018

zerothi Oct 18, 2021

New Extension: SpeciesType #180

New Extension: SpeciesType #180

Conversation

DavidSagan commented Feb 6, 2018 • edited by ax3l Loading

Description

Affected Components

Logic Changes

Writer Changes

Reader Changes

Data Updater

ax3l commented Feb 6, 2018 • edited Loading

DavidSagan commented Feb 20, 2018

ax3l commented Feb 20, 2018

DavidSagan commented Feb 20, 2018 • edited Loading

ax3l commented Feb 20, 2018 • edited Loading

ax3l commented Feb 26, 2018 • edited Loading

ax3l Feb 26, 2018

Choose a reason for hiding this comment

DavidSagan Feb 26, 2018

Choose a reason for hiding this comment

ax3l Feb 26, 2018 • edited Loading

Choose a reason for hiding this comment

DavidSagan Feb 26, 2018

Choose a reason for hiding this comment

ax3l Apr 3, 2018 • edited Loading

Choose a reason for hiding this comment

RemiLehe commented Mar 29, 2018

ax3l commented Apr 3, 2018

DavidSagan commented Apr 3, 2018

ax3l commented Apr 3, 2018 • edited Loading

ax3l commented Apr 3, 2018 • edited Loading

ax3l Apr 3, 2018 • edited Loading

Choose a reason for hiding this comment

ax3l commented Apr 3, 2018

zerothi Oct 18, 2021

Choose a reason for hiding this comment

DavidSagan commented Feb 6, 2018 •

edited by ax3l

Loading

ax3l commented Feb 6, 2018 •

edited

Loading

DavidSagan commented Feb 20, 2018 •

edited

Loading

ax3l commented Feb 20, 2018 •

edited

Loading

ax3l commented Feb 26, 2018 •

edited

Loading

ax3l Feb 26, 2018 •

edited

Loading

ax3l Apr 3, 2018 •

edited

Loading

ax3l commented Apr 3, 2018 •

edited

Loading

ax3l commented Apr 3, 2018 •

edited

Loading

ax3l Apr 3, 2018 •

edited

Loading