From b3090a7758620e9412935bfd1312f13e93f7fad7 Mon Sep 17 00:00:00 2001 From: David Sagan Date: Tue, 30 Jan 2018 16:28:23 -0500 Subject: [PATCH 1/8] Added ParticleSpeciesNames.md --- ParticleSpeciesNames.md | 47 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 ParticleSpeciesNames.md diff --git a/ParticleSpeciesNames.md b/ParticleSpeciesNames.md new file mode 100644 index 0000000..68d9d59 --- /dev/null +++ b/ParticleSpeciesNames.md @@ -0,0 +1,47 @@ +Convention for Specifying Particle Species +------------------------------------------ + +This convention is for standardizing the names of particle species. + +SubAtomic Particle Names +---------------------------------- + + - Subatomic particle names: + - antimuon + - antiproton + - bottom + - charm-antiquark + - charm-quark + - deuteron + - down-antiquark + - down-quark + - electron + - electron-neutrino + - gluon + - graviton + - higgs-boson + - muon + - muon-neutrino + - neutron + - photon + - pion + - positron + - proton + - strange-antiquark + - strange-quark + - tao-antiquark + - tao-quark + - tao-neutrino + - top-antiquark + - top-quark + - up-antiquark + - up-quark + - w-boson + - z-boson + + +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. + From c4635da60081ea1106fadbda8e64208a42ad8de6 Mon Sep 17 00:00:00 2001 From: David Sagan Date: Thu, 1 Feb 2018 16:07:54 +0100 Subject: [PATCH 2/8] Update Draft of SpeciesType Extension - 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 --- EXT_SpeciesType.md | 80 +++++++++++++++++++++++++++++++++++++++++ ParticleSpeciesNames.md | 47 ------------------------ 2 files changed, 80 insertions(+), 47 deletions(-) create mode 100644 EXT_SpeciesType.md delete mode 100644 ParticleSpeciesNames.md diff --git a/EXT_SpeciesType.md b/EXT_SpeciesType.md new file mode 100644 index 0000000..a372c9b --- /dev/null +++ b/EXT_SpeciesType.md @@ -0,0 +1,80 @@ +Convention for Specifying Particle Species +========================================== + +openPMD extension name: `SpeciesType` + +openPMD extension ID: `4` + + +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: *recommended* + - description: particle species in this record, 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`). + +### SubAtomic Particle Names + + - `antimuon` + - `antiproton` + - `bottom` + - `charm-antiquark` + - `charm-quark` + - `deuteron` + - `down-antiquark` + - `down-quark` + - `electron` + - `electron-neutrino` + - `gluon` + - `graviton` + - `higgs-boson` + - `muon` + - `muon-neutrino` + - `neutron` + - `photon` + - `pion` + - `positron` + - `proton` + - `strange-antiquark` + - `strange-quark` + - `tao-antiquark` + - `tao-quark` + - `tao-neutrino` + - `top-antiquark` + - `top-quark` + - `up-antiquark` + - `up-quark` + - `w-boson` + - `z-boson` + +### 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. +Element namings follow the abbreviated namings of the periodic table, defined by *The International Union of Pure and Applied Chemistry* (IUPAC). + +### Molecules + +Use standard chemical notation, e.g.: `H20`. diff --git a/ParticleSpeciesNames.md b/ParticleSpeciesNames.md deleted file mode 100644 index 68d9d59..0000000 --- a/ParticleSpeciesNames.md +++ /dev/null @@ -1,47 +0,0 @@ -Convention for Specifying Particle Species ------------------------------------------- - -This convention is for standardizing the names of particle species. - -SubAtomic Particle Names ----------------------------------- - - - Subatomic particle names: - - antimuon - - antiproton - - bottom - - charm-antiquark - - charm-quark - - deuteron - - down-antiquark - - down-quark - - electron - - electron-neutrino - - gluon - - graviton - - higgs-boson - - muon - - muon-neutrino - - neutron - - photon - - pion - - positron - - proton - - strange-antiquark - - strange-quark - - tao-antiquark - - tao-quark - - tao-neutrino - - top-antiquark - - top-quark - - up-antiquark - - up-quark - - w-boson - - z-boson - - -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. - From e0c830d7db9ab8e8b00b4e9a890026ba0fba4ef7 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Thu, 1 Feb 2018 16:09:40 +0100 Subject: [PATCH 3/8] EXT SpeciesType: Reference in Std Reference to the new extension `SpeciesType` in the base standard --- STANDARD.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/STANDARD.md b/STANDARD.md index 9524470..ad4ccf8 100644 --- a/STANDARD.md +++ b/STANDARD.md @@ -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 From d2fe6428932a6af0fb9a517c542af926a027db55 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Thu, 1 Feb 2018 16:49:18 +0100 Subject: [PATCH 4/8] EXT SpeciesType: Update - optional by default - clarify annotations --- EXT_SpeciesType.md | 86 ++++++++++++++++++++++++++-------------------- 1 file changed, 48 insertions(+), 38 deletions(-) diff --git a/EXT_SpeciesType.md b/EXT_SpeciesType.md index a372c9b..ed6ef18 100644 --- a/EXT_SpeciesType.md +++ b/EXT_SpeciesType.md @@ -21,8 +21,10 @@ extension: - `SpeciesType` - type: *(string)* - - scope: *recommended* - - description: particle species in this record, semicolon-separated list + - 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 @@ -36,45 +38,53 @@ extension: This attribute can be used with any `record` (including `mesh records`). -### SubAtomic Particle Names - - - `antimuon` - - `antiproton` - - `bottom` - - `charm-antiquark` - - `charm-quark` - - `deuteron` - - `down-antiquark` - - `down-quark` - - `electron` - - `electron-neutrino` - - `gluon` - - `graviton` - - `higgs-boson` - - `muon` - - `muon-neutrino` - - `neutron` - - `photon` - - `pion` - - `positron` - - `proton` - - `strange-antiquark` - - `strange-quark` - - `tao-antiquark` - - `tao-quark` - - `tao-neutrino` - - `top-antiquark` - - `top-quark` - - `up-antiquark` - - `up-quark` - - `w-boson` - - `z-boson` +### SubAtomic Particles + + - `subatomic:antimuon` + - `subatomic:antiproton` + - `subatomic:bottom` + - `subatomic:charm-antiquark` + - `subatomic:charm-quark` + - `subatomic:deuteron` + - `subatomic:down-antiquark` + - `subatomic:down-quark` + - `subatomic:electron` + - `subatomic:electron-neutrino` + - `subatomic:gluon` + - `subatomic:graviton` + - `subatomic:higgs-boson` + - `subatomic:muon` + - `subatomic:muon-neutrino` + - `subatomic:neutron` + - `subatomic:photon` + - `subatomic:pion` + - `subatomic:positron` + - `subatomic:proton` + - `subatomic:strange-antiquark` + - `subatomic:strange-quark` + - `subatomic:tao-antiquark` + - `subatomic:tao-quark` + - `subatomic:tao-neutrino` + - `subatomic:top-antiquark` + - `subatomic:top-quark` + - `subatomic:up-antiquark` + - `subatomic:up-quark` + - `subatomic:w-boson` + - `subatomic:z-boson` ### 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. -Element namings follow the abbreviated namings of the periodic table, defined by *The International Union of Pure and Applied Chemistry* (IUPAC). +Element namings follow the abbreviated namings of the periodic table, defined +by *The International Union of Pure and Applied Chemistry* (IUPAC). +They are prefixed with `element:`, e.g. `element:Si`. + +Closer specifications of isotopes are denoted by a `isotope:` prefix followed +by the isotopic number followed by the chemical symbol, e.g.: `isotope:3He` +for Helium-3. + +Charge states shall not be specified here but rather in `attributes` +(`mesh record`) or `records` or a `particle species`. ### Molecules -Use standard chemical notation, e.g.: `H20`. +Use standard chemical notation with a `molecule:` prefix, e.g.: `molecule:H20`. From 9cb0d47c03d0bbf14b66e3e52e8cd10778475d9b Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Thu, 1 Feb 2018 16:57:25 +0100 Subject: [PATCH 5/8] Remove Prefixes Not needed (yet) --- EXT_SpeciesType.md | 74 ++++++++++++++++++++++++---------------------- 1 file changed, 39 insertions(+), 35 deletions(-) diff --git a/EXT_SpeciesType.md b/EXT_SpeciesType.md index ed6ef18..5b5ba47 100644 --- a/EXT_SpeciesType.md +++ b/EXT_SpeciesType.md @@ -40,46 +40,46 @@ This attribute can be used with any `record` (including `mesh records`). ### SubAtomic Particles - - `subatomic:antimuon` - - `subatomic:antiproton` - - `subatomic:bottom` - - `subatomic:charm-antiquark` - - `subatomic:charm-quark` - - `subatomic:deuteron` - - `subatomic:down-antiquark` - - `subatomic:down-quark` - - `subatomic:electron` - - `subatomic:electron-neutrino` - - `subatomic:gluon` - - `subatomic:graviton` - - `subatomic:higgs-boson` - - `subatomic:muon` - - `subatomic:muon-neutrino` - - `subatomic:neutron` - - `subatomic:photon` - - `subatomic:pion` - - `subatomic:positron` - - `subatomic:proton` - - `subatomic:strange-antiquark` - - `subatomic:strange-quark` - - `subatomic:tao-antiquark` - - `subatomic:tao-quark` - - `subatomic:tao-neutrino` - - `subatomic:top-antiquark` - - `subatomic:top-quark` - - `subatomic:up-antiquark` - - `subatomic:up-quark` - - `subatomic:w-boson` - - `subatomic:z-boson` + - `antimuon` + - `antiproton` + - `bottom` + - `charm-antiquark` + - `charm-quark` + - `deuteron` + - `down-antiquark` + - `down-quark` + - `electron` + - `electron-neutrino` + - `gluon` + - `graviton` + - `higgs-boson` + - `muon` + - `muon-neutrino` + - `neutron` + - `photon` + - `pion` + - `positron` + - `proton` + - `strange-antiquark` + - `strange-quark` + - `tao-antiquark` + - `tao-quark` + - `tao-neutrino` + - `top-antiquark` + - `top-quark` + - `up-antiquark` + - `up-quark` + - `w-boson` + - `z-boson` ### Atoms & Isotopes Element namings follow the abbreviated namings of the periodic table, defined by *The International Union of Pure and Applied Chemistry* (IUPAC). -They are prefixed with `element:`, e.g. `element:Si`. +An example would be `Si` for silicate. -Closer specifications of isotopes are denoted by a `isotope:` prefix followed -by the isotopic number followed by the chemical symbol, e.g.: `isotope:3He` +Closer 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. Charge states shall not be specified here but rather in `attributes` @@ -87,4 +87,8 @@ Charge states shall not be specified here but rather in `attributes` ### Molecules -Use standard chemical notation with a `molecule:` prefix, e.g.: `molecule:H20`. +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. From 57fece30651115dfad95adda5511e531ee7163ca Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Thu, 1 Feb 2018 17:05:28 +0100 Subject: [PATCH 6/8] Fix Typos --- EXT_SpeciesType.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/EXT_SpeciesType.md b/EXT_SpeciesType.md index 5b5ba47..ba0517f 100644 --- a/EXT_SpeciesType.md +++ b/EXT_SpeciesType.md @@ -76,14 +76,15 @@ This attribute can be used with any `record` (including `mesh records`). 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 silicate. +An example would be `Si` for silicon. -Closer specifications of isotopes are denoted by a pound symbol `#` followed +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. -Charge states shall not be specified here but rather in `attributes` -(`mesh record`) or `records` or a `particle species`. +Charge states shall not be encoded here. +An extension that specifies `charge` can further define its appropriate +location (e.g. `attribute` or `constant particle record`). ### Molecules From 0bb1615a4ad97e298ab3a237c28be41faf225b22 Mon Sep 17 00:00:00 2001 From: David Sagan Date: Thu, 1 Feb 2018 17:12:31 +0100 Subject: [PATCH 7/8] Clarification Charge State Add pointers --- EXT_SpeciesType.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/EXT_SpeciesType.md b/EXT_SpeciesType.md index ba0517f..01f7c1e 100644 --- a/EXT_SpeciesType.md +++ b/EXT_SpeciesType.md @@ -82,9 +82,8 @@ 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. -Charge states shall not be encoded here. -An extension that specifies `charge` can further define its appropriate -location (e.g. `attribute` or `constant particle record`). +The charge state is not encoded by the `SpeciesType` attribute. +Any extension using this standard can define how to specify the charge state. ### Molecules From 6563438e5c04e148e1dab47ff044d93e5da85d93 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Tue, 6 Feb 2018 14:39:31 +0100 Subject: [PATCH 8/8] Elementary Particles & Gauge+Higgs Bosons --- EXT_SpeciesType.md | 67 +++++++++++++++++++++++----------------------- 1 file changed, 34 insertions(+), 33 deletions(-) diff --git a/EXT_SpeciesType.md b/EXT_SpeciesType.md index 01f7c1e..05b9a9c 100644 --- a/EXT_SpeciesType.md +++ b/EXT_SpeciesType.md @@ -38,39 +38,40 @@ extension: This attribute can be used with any `record` (including `mesh records`). -### SubAtomic Particles - - - `antimuon` - - `antiproton` - - `bottom` - - `charm-antiquark` - - `charm-quark` - - `deuteron` - - `down-antiquark` - - `down-quark` - - `electron` - - `electron-neutrino` - - `gluon` - - `graviton` - - `higgs-boson` - - `muon` - - `muon-neutrino` - - `neutron` - - `photon` - - `pion` - - `positron` - - `proton` - - `strange-antiquark` - - `strange-quark` - - `tao-antiquark` - - `tao-quark` - - `tao-neutrino` - - `top-antiquark` - - `top-quark` - - `up-antiquark` - - `up-quark` - - `w-boson` - - `z-boson` +### 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`) + - `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