Skip to content
Closed
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
95 changes: 95 additions & 0 deletions EXT_SpeciesType.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,95 @@
Convention for Specifying Particle Species
==========================================

openPMD extension name: `SpeciesType`

openPMD extension ID: `4`
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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



Introduction
------------

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


Additional Record Attribute
---------------------------

The following additional attribute for openPMD `records` is defined in this
extension:

- `SpeciesType`
- type: *(string)*
- scope: *optional*
- description: particle species in this record. If there are multiple
species to be specified, they can be specified using a
semicolon separated list.
- allowed values:
- *see the lists below* and additionally
- `other` if none of the ones below applies, user are free to append a
free text after a colon, e.g. `other:neutralino` or `other:cherry`
- examples:
- `electron` (e.g. on an electron `particle record` or an electron
density `mesh record`)
- `electron;proton;#12C` (e.g. on a `mesh record` for a plasma's
local charge density)
- `other:apple;other:orange` (for a `record` mixing apples & oranges)

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

### Elementary Particles

Namings for fundamental fermions and their anti-matter particles.

Quarks:
- `up` (`anti-up`)
- `down` (`anti-down`)
- `charm` (`anti-charm`)
- `strange` (`anti-strange`)
- `top` (`anti-top`)
- `bottom` (`anti-bottom`)

Leptons:
- `electron` (`positron`)
- `electron-neutrino` (`anti-electron-neutrino`)
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

- `muon` (`anti-muon`)
- `muon-neutrino` (`anti-muon-neutrino`)
- `tau` (`anti-tau`)
- `tau-neutrino` (`anti-tau-neutrino`)

Gauge & Higgs Bosons:
- `photon`
- `gluon`
- `w-boson`
- `z-boson`
- `higgs`

### Hadrons and Jets

We currently do not define spellings of hadrons besides the commonly used ones
below and suggest for this version to use `other:` with namings from the
[particle data group (PDG)](http://pdg.lbl.gov/). Other means of grouping e.g.
jets can be used, e.g. additional attributes outside of the definition of this
extension.

### Atoms & Isotopes

Element namings follow the abbreviated namings of the periodic table, defined
by *The International Union of Pure and Applied Chemistry* (IUPAC).
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`
for Helium-3.

The charge state is not encoded by the `SpeciesType` attribute.
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Copy link
Member

@ax3l ax3l Feb 5, 2018

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

OK, sounds good.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I concur with Alex.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

*Axel ;-)

Any extension using this standard can define how to specify the charge state.

### Molecules

Use standard chemical notation, e.g.: `H20`.

The isotope prefix can be used with molecules as well.
Examples for heavy water: `#2H2O` for two deuterium and `#2HHO` for one
deuterium.
2 changes: 2 additions & 0 deletions STANDARD.md
Original file line number Diff line number Diff line change
Expand Up @@ -730,6 +730,8 @@ defined:

- **ED-PIC**: electro-dynamic/static particle-in-cell codes,
see [EXT_ED-PIC.md](EXT_ED-PIC.md).
- **SpeciesType**: naming lists for particle species,
see [EXT_SpeciesType.md](EXT_SpeciesType.md).

Extensions to similar domains such as fluid, finite-element or
molecular-dynamics simulations, CCD images or other particle and/or mesh-based
Expand Down