Added ParticleSpeciesNames.md by DavidSagan · Pull Request #177 · openPMD/openPMD-standard

DavidSagan · 2018-01-30T21:52:45Z

This pull request has a new file for standardizing the names of particle species. See #176 .

Affected Components: None.
Writer/Reader/Data converter Changes: At this point none since the present standard does not reference particle species names.

ax3l · 2018-01-30T22:23:51Z

+Names for Atoms and Molecules
+-------------------
+
+ - Atoms and molecules: Use standard chemical notation. Eg: "H20". Isotopes are denoted by a pound symbol "#" followed by the isotopic number followed by the chemical symbol. Eg: "#3He" for Helium-3.


maybe that's a stupid question, but is there some kind of ISO naming already for this on which we can rely on?

I looked but I could not find anything unfortunately.

I see, thanks for checking.
And something from PDG (the particle data group), maybe? Just that we don't miss something that already defines spellings.

(besides that insecurity of mine about accidentally re-inventing something, I like the proposed spellings)

I had looked at the PDG as well without luck.

ax3l

We will need to add:

an extension ID 4 for 1.1.0 (because it will first be removed in 2.0.0)
mention it in the base standard in the extensions section
add the name for the new record attribute
define if this attribute is optional/recommended/required if the extension is declared for a file
define if it is allowed to have more than one particle name per record, e.g. one could store a mesh with "summed charge density" of all ions and electrons -> list?

DavidSagan · 2018-01-31T12:15:44Z

I realize I forgot to specify how to write atom and molecular charge states. So how about something like:

The charge state is denoted by a suffix with either:

Some number of plus or minus signs. Example: "H2O++"
A plus or minus sign with a following integer. Example: "CO+3"

ax3l · 2018-01-31T12:22:32Z

I wonder if we want to record charge states really in the species type name.

We usually have them as a record in the species anyway and for constant charge state as a constant record. Maybe other domains would do the same?

DavidSagan · 2018-01-31T12:28:37Z

@ax3l: Having the charge state separately specified would be fine.

- 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

ax3l · 2018-02-01T15:10:12Z

Changes I applied:

file renamed to EXT_SpeciesType.md
extension name: SpeciesType with extension-ID 4 (1 is used and we reserved 2 in the past)
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 in base standard

ax3l · 2018-02-01T15:26:25Z

+
+- `SpeciesType`
+  - type: *(string)*
+  - scope: *recommended*


offline discussion: maybe better optional here, it's weird for e.g. "E fields" or arbitrary other records

Later on, in the ED-PIC extension or the BeamPhysics extension one can still specify, that it is recommended for e.g. particle species.

DavidSagan · 2018-02-01T15:26:45Z

+- `SpeciesType`
+  - type: *(string)*
+  - scope: *recommended*
+  - description: particle species in this record, semicolon-separated list


Replace "semicolon-separated list" with "If there are multiple species to be specified, they can be specified using a semicolon separated list."

ax3l · 2018-02-01T15:27:38Z

+
+This attribute can be used with any `record` (including `mesh records`).
+
+### SubAtomic Particle Names


Unify headline: SubAtomic Particles

DavidSagan · 2018-02-01T15:30:11Z

+
+### Atoms & Isotopes
+
+Isotopes are denoted by a pound symbol `#` followed by the isotopic number followed by the chemical symbol, e.g.: `#3He` for Helium-3.


Switch order sentences. That is, start this section with "Element namings...".

ax3l · 2018-02-01T15:30:32Z

+
+Isotopes are denoted by a pound symbol `#` followed by the isotopic number followed by the chemical symbol, e.g.: `#3He` for Helium-3.
+Element namings follow the abbreviated namings of the periodic table, defined by *The International Union of Pure and Applied Chemistry* (IUPAC).
+


Should we mention that the most abundant isotope can just be short-handed as He (for #4He)? It's somehow missing, but would allow ambiguity.

Is D ok for #2H or shall it be forced to the latter?

I would say that the standard should assume that "He" is equivalent to "#4He".

Deuterium would be "#2H"

excellent, so we keep the abbreviations to a minimum: regular elements in the IUPAC periodic table

DavidSagan · 2018-02-01T15:39:56Z

+
+### Molecules
+
+Use standard chemical notation, e.g.: `H20`.


The isotope prefix can be used with molecules. Example "#2H2O" for two deuterium and "#2HHO" for one deuterium.

idea: we prefix the allowed values with the sections, e.g. subatomic:, atom:/isotope:, molecule:, ...

- optional by default - clarify annotations

ax3l · 2018-02-01T15:50:35Z

+
+openPMD extension name: `SpeciesType`
+
+openPMD extension ID: `4`


note: this will be removed in 2.0.0 but we have to assign it since we are still in 1.X

ax3l · 2018-02-01T15:54:00Z

+
+### SubAtomic Particles
+
+  - `subatomic:antimuon`


offline discussion: we won't collide (yet) and if we should later one we can still add prefixes and convert known ones.

Not needed (yet)

Add pointers

ax3l · 2018-02-01T16:18:20Z

@RemiLehe we finished our proposal and you can now add your comments & review! :)

We tried to document all ideas and steps during our review today inline in comments, so if you like you can just un-collapse them for curiosity.

ax3l · 2018-02-05T09:20:50Z

@RemiLehe ping :)

RemiLehe · 2018-02-05T22:33:26Z

+  - `strange-quark`
+  - `tao-antiquark`
+  - `tao-quark`
+  - `tao-neutrino`


Shouldn't this be tau-neutrino (and adding tau-antineutrino) instead of tao-neutrino ? In addition, we should probably add tau as a particle (for the counterpart of muon and electron).

Yes. The change should be made.

RemiLehe · 2018-02-05T22:39:28Z

+  - `muon-neutrino`
+  - `neutron`
+  - `photon`
+  - `pion`


Is there a reason to standardize the name of the pion, but not of all the other mesons?
(If the reason is that the pion is the most common, I am fine with this ; I am definitely not a specialist... I was just wondering.)

The list I came up with was meant to get the discussion going rather then being complete (I am definitely not a specialist either). Do you have a list of names for the other mesons? By all means let us put them in.

RemiLehe · 2018-02-05T22:40:26Z

+
+### SubAtomic Particles
+
+  - `antimuon`


Should we add antitau? (See remark below on the tau lepton.)

Yes we should add antitau. And tao is a typo. Should be tau everywhere.

RemiLehe · 2018-02-05T22:40:38Z

+### SubAtomic Particles
+
+  - `antimuon`
+  - `antiproton`


Should we add antineutron?

RemiLehe · 2018-02-05T22:41:59Z

+
+  - `antimuon`
+  - `antiproton`
+  - `bottom`


Shouldn't this be bottom-quark and bottom-antiquark for consistency?

RemiLehe · 2018-02-05T22:43:53Z

+  - `bottom`
+  - `charm-antiquark`
+  - `charm-quark`
+  - `deuteron`


It seems that deuteron could be expressed as #2H. Using the convention below. Therefore, I suggest that we remove it from this list.

Correct that deuteron is the same as #2H with a charge state of 1. In terms of having the name in the standard I don't care either way. @ax3l: Do you have an opinion?

sure, Deuterium should not be here

RemiLehe · 2018-02-05T22:44:48Z

+  - `strange-antiquark`
+  - `strange-quark`
+  - `tao-antiquark`
+  - `tao-quark`


Also, I am not sure whether a tao-quark and tao-antiquark exist in the standard model... (If I remember well, the quarks of the standard model are up, down, strange, charm, bottom, top.)

Correct. That is a typo and should be removed.

RemiLehe · 2018-02-05T22:46:12Z

+by the isotopic number followed by the chemical symbol, e.g.: `#3He`
+for Helium-3.
+
+The charge state is not encoded by the `SpeciesType` attribute.


By charge state, do we mean ionization state? Could charge state be considered ambiguous for some users?

Imho, charge state is the more general concept while ionization state only applies to atoms & molecules. This section just says we do not express it in this extension.

OK, sounds good.

I concur with Alex.

RemiLehe · 2018-02-05T22:47:33Z

Sorry for my late review! I added a couple of comments/questions.

RemiLehe · 2018-02-05T22:48:27Z

+  - `down-antiquark`
+  - `down-quark`
+  - `electron`
+  - `electron-neutrino`


Should we add electron-antineutrino?

RemiLehe · 2018-02-05T22:48:45Z

+  - `graviton`
+  - `higgs-boson`
+  - `muon`
+  - `muon-neutrino`


Should we add muon_antineutrino?

And I thought you wanted to point to Majorana neutrinos here ;)

ax3l · 2018-02-06T09:40:50Z

Sorry, I totally forgot to swipe through the subatomic particle list again in review.

I would suggest to make one list with elementary particles of the standard model (and their anti-partners), Gauge bosons and the higgs boson.

There is a plethora of namings for composite particles that are only used in elementary particle physics, especially Hadrons such as Mesons and Baryons, and should imho not be tried to be defined here (besides the obvious ones we need such below for atoms), but instead reference e.g. the particle data group. Also, actual particle detector people think of jets and channels with particles which are again composites of the above. As far as we have no detector people here that suggest a naming I would also keep this free. Likely they would also use group identifiers #163

DavidSagan · 2018-02-06T13:15:18Z

@ax3l

I would suggest to make one list with elementary particles of the standard model (and their anti-partners), Gauge bosons and the higgs boson.

Sounds good to me.

ax3l · 2018-02-06T13:40:45Z

I updated the PR accordingly.

I would suggest to move this PR to 2.0.0 and close the 1.1.0 merge window so we do not merge it in last-minute and can take more time for it. Is that ok? I would then prepare the last clean-ups for 1.1.0 now.

ax3l · 2018-02-06T13:46:02Z

+
+Leptons:
+  - `electron` (`positron`)
+  - `electron-neutrino` (`anti-electron-neutrino`)


anti-neutrinos: who knows, maybe they turn out to be the same particles. but until now it seems that calling them anti-neutrinos is common

DavidSagan · 2018-02-06T14:49:28Z

@ax3l:

I would suggest to move this PR to 2.0.0 and close the 1.1.0 merge window so we do not merge it in last-minute and can take more time for it. Is that ok?

Fine with me.

RemiLehe · 2018-02-06T14:53:51Z

I really like the reorganized version of the file.
Thanks for editing the PR!

DavidSagan · 2018-02-06T15:28:30Z

Yes I like the reorg too.
Minor stylistic suggestion: Use a comma instead of parenthesis. For example, Instead of:
electron ( positron )
write:
electron, positron

DavidSagan · 2018-02-06T15:42:38Z

I know we don't want to in general get into trying to define names of mesons but thinking about it I would make an exception for proton and anti-proton since these are commonly used in experiments.

ax3l · 2018-02-06T15:59:19Z

I am ok with both suggestions, just need to find a place to put anti-proton and maybe to say that H and proton are the same thing? Actually they might not be the same, a user might want to refer to the element (atom) H...

DavidSagan · 2018-02-06T16:03:33Z

I am ok with both suggestions, just need to find a place to put anti-proton and maybe to say that H and proton are the same thing? Actually they might not be the same, a user might want to refer to the element (atom) H...

It could be added that #1H is the same as proton if the charge is specified as +1.

ax3l · 2018-02-06T16:05:36Z

I might just have been thinking loudly. proton is just more specific than H and that is fine, imho. No reason to explain more I think.

ax3l · 2018-02-06T17:25:28Z

we will re-open this PR for further review into upcoming-2.0.0

ax3l · 2018-02-06T17:31:35Z

Re-opened for 2.0.0 inclusion in #180

Added ParticleSpeciesNames.md

b3090a7

ax3l added the EXT: SpeciesType physical particle species extension label Jan 30, 2018

ax3l self-assigned this Jan 30, 2018

ax3l requested review from RemiLehe and ax3l January 30, 2018 22:22

ax3l reviewed Jan 30, 2018

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DavidSagan and others added 2 commits February 1, 2018 16:07

EXT SpeciesType: Reference in Std

e0c830d

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

ax3l reviewed Feb 1, 2018

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DavidSagan commented Feb 1, 2018

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DavidSagan commented Feb 1, 2018

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EXT SpeciesType: Update

d2fe642

- optional by default - clarify annotations

ax3l reviewed Feb 1, 2018

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ax3l added 2 commits February 1, 2018 16:57

Remove Prefixes

9cb0d47

Not needed (yet)

Fix Typos

57fece3

ax3l force-pushed the New-ParticleID-Standard branch from dd7005c to 57fece3 Compare February 1, 2018 16:06

Clarification Charge State

0bb1615

Add pointers

RemiLehe requested changes Feb 5, 2018

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Elementary Particles & Gauge+Higgs Bosons

6563438

ax3l force-pushed the New-ParticleID-Standard branch from 273db25 to 6563438 Compare February 6, 2018 13:44

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ax3l added the do not merge pull requests that are not yet finished or will collide label Feb 6, 2018

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ax3l closed this Feb 6, 2018

ax3l mentioned this pull request Feb 6, 2018

New Extension: SpeciesType #180

Merged

6 tasks


		This attribute can be used with any `record` (including `mesh records`).

		### SubAtomic Particle Names


		### Atoms & Isotopes

		Isotopes are denoted by a pound symbol `#` followed by the isotopic number followed by the chemical symbol, e.g.: `#3He` for Helium-3.


		Isotopes are denoted by a pound symbol `#` followed by the isotopic number followed by the chemical symbol, e.g.: `#3He` for Helium-3.
		Element namings follow the abbreviated namings of the periodic table, defined by The International Union of Pure and Applied Chemistry (IUPAC).


		openPMD extension name: `SpeciesType`

		openPMD extension ID: `4`

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