Dear Jonathan,
You raise some good points, and like you I'm sure I'd benefit from one
of Alison's careful summaries before taking this discussion further.
I'm sure I'll be happy with whatever Alison recommends either way on this.
cheers,
Karl
On 3/23/17 9:59 AM, Jonathan Gregory wrote:
> Dear Karl
>
> I'm sure this question has been discussed before. I agree it seems surprising
> to have special names for surface quantities which also appear in 3D. I think
> there are two reasons why this is the right thing to do in some cases:
>
> * There is more than one way that "the" surface i.e. the bottom of the
> atmosphere can be defined by a coordinate. It is height=0 m, depth=0 m,
> over the sea it is quite near to altitude=0 m, it is approximately 1000 hPa
> air pressure, and in all sorts of different atmosphere and ocean model
> vertical coordinates it is described in different ways e.g. sigma=1 in the
> atmosphere. Any of these might legitimately be used as the vertical variable
> within the medium, so there are consequently lots of synonymous ways to label
> the surface quantity. Generic software would have to know about and look for
> all of them, and that's not really practical or convenient. To label them in
> the standard name is much easier and clearer. Of course, if you have a 3D
> variable which *includes* the surface as one of its levels, that's fine -
> you can use the non-surface standard name with the coordinate (whatever it
> is) indicating the surface. Also if the generic software can be sure which
> vertical coordinate is being used, again the non-surface standard name is fine,
> as for "surface air temperature", which is air_temperature with a height
> coordinate near the surface.
>
> * There are also plenty of standard names for quantities measured at other
> named levels, such as the toa, the tropopause, the sea floor and the cloud
> top. These are also geophysically defined, like the surface, but they can't
> be characterised by a coordinate value, so we have to label them in the
> standard name. It would be inconsistent to treat the bottom of the atmosphere
> differently.
>
> Having said that, I can't recall the discussion about the new OMIP surface
> names, so I think we should wait for Alison's summary.
>
> Best wishes
>
> Jonathan
>
> ----- Forwarded message from Karl Taylor <taylor13 at llnl.gov> -----
>
>> Date: Thu, 23 Mar 2017 09:27:08 -0700
>> From: Karl Taylor <taylor13 at llnl.gov>
>> To: alison.pamment at stfc.ac.uk, durack1 at llnl.gov
>> CC: j.m.gregory at reading.ac.uk
>> Subject: Re: [CF-metadata] New standard names for OMIP biogeochemistry and
>> chemistry
>> User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:45.0)
>> Gecko/20100101 Thunderbird/45.7.1
>>
>> Hi all,
>>
>> I haven't heard the arguments on how to treat the "surface" standard
>> names, but my thoughts are:
>>
>> 1) if the variable is found within a medium (e.g., ocean,
>> atmosphere, ice) and its value varies continuously as you move away
>> from the surface, then there is no need for a distinct
>> standard_name.
>>
>> 2) If the variable is a flux between two media at the surface (e.g.,
>> heat flux from atmos. to ocean) or is a property defined in terms of
>> a difference between the two media (e.g., CO2 partial pressure
>> difference between sea water and air at the surface), then the
>> standard name should include "surface".
>>
>> I know we may have made some exceptions to this in the past, so
>> perhaps these should be considered flexible "rules" we normally try
>> to follow (but not invariably).
>>
>> According to 1), all the "surface_mole_concentration" variables
>> could become simply "mole_concentration" and we would require a
>> scalar coordinate variable be defined as depth = 0. If a
>> concentration shows a sharp discontinuity at the surface, then there
>> would be good reason, perhaps, to include "surface" in its
>> standard_name.
>>
>> Hope this is helpful,
>> Karl
>>
>> On 3/23/17 4:07 AM, alison.pamment at stfc.ac.uk wrote:
>>> Hi Paul,
>>>
>>> Jonathan Gregory and Paul Griffies jointly submitted proposals for
>>> the OMIP physics names last year so they are already in my
>>> workflow. I don?t think they attracted any comments on the mailing
>>> list, so I guess it is up to me to work through them in my usual
>>> way. I am half way through writing a posting to the CF mailing
>>> list summarizing the status of all the remaining biogeochemistry
>>> names. I am accepting names where possible, getting others to a
>>> state where I just need you to give the ?OK? and they can be
>>> accepted, and for the rest I am pointing up any final unresolved
>>> issues so we can really focus the discussion on those. Further to
>>> my email yesterday, there are actually 61 ?surface? proposals, so
>>> clearing up that one question will allow about half the names to
>>> be agreed quite quickly. Please bear with me until I have posted
>>> my message to the list. I?ll then go through the physics names and
>>> we can discuss those in a second thread.
>>>
>>> I?m also in the process of looking through some non-CMIP
>>> oceanography names for the NEMO model, and have just accepted a
>>> bunch of wave names, so this is a good time to get as many ocean
>>> related names into the table as possible.
>>>
>>> Best wishes,
>>>
>>> Alison
>>>
>>> ------
>>>
>>> Alison Pamment
>>> Tel: +44 1235 778065
>>>
>>> Centre for Environmental Data Analysis Email:
>>> alison.pamment at stfc.ac.uk <mailto:J.A.Pamment at rl.ac.uk>
>>>
>>> STFC Rutherford Appleton Laboratory
>>>
>>> R25, 2.22
>>>
>>> Harwell Campus, Didcot, OX11 0QX, U.K.
>>>
>>> *From:*Durack, Paul J. [mailto:durack1 at llnl.gov]
>>> *Sent:* 22 March 2017 22:58
>>> *To:* Pamment, Alison (STFC,RAL,RALSP)
>>> *Cc:* Taylor, Karl E.; j.m.gregory at reading.ac.uk
>>> *Subject:* Re: [CF-metadata] New standard names for OMIP
>>> biogeochemistry and chemistry
>>>
>>> Thanks Alison, this is great news!
>>>
>>> I originally submitted 107 standard names for consideration
>>> (mostly the biogeochemical and chemical domains). There are also
>>> some physics (OMIP-physical, and FAFMIP) related names that were
>>> also appended, so I?ll have to collect all these amendments and
>>> then propagate them back to the google sheets where the master
>>> list is contained. Martin can then read these revised inputs, and
>>> the OMIP/ocean variable request will be updated.
>>>
>>> What would be the best way for me to capture all the submitted (so
>>> mine and the other separate ones) and then final standard names?
>>>
>>> Thanks again for pushing on this!
>>>
>>> P
>>>
>>> *From: *"alison.pamment at stfc.ac.uk
>>> <mailto:alison.pamment at stfc.ac.uk>" <alison.pamment at stfc.ac.uk
>>> <mailto:alison.pamment at stfc.ac.uk>>
>>> *Date: *Wednesday, March 22, 2017 at 4:37 AM
>>> *To: *"Taylor, Karl E." <taylor13 at llnl.gov
>>> <mailto:taylor13 at llnl.gov>>, "j.m.gregory at reading.ac.uk
>>> <mailto:j.m.gregory at reading.ac.uk>" <j.m.gregory at reading.ac.uk
>>> <mailto:j.m.gregory at reading.ac.uk>>
>>> *Cc: *"Durack, Paul J." <durack1 at llnl.gov <mailto:durack1 at llnl.gov>>
>>> *Subject: *RE: [CF-metadata] New standard names for OMIP
>>> biogeochemistry and chemistry
>>>
>>> Hi Karl,
>>>
>>> I think most of the OMIP names are in a pretty good state and some
>>> are already published. There are probably more that can be
>>> published quite quickly, so I will go through the list again and
>>> accept as many as possible so they will be included in the next
>>> standard name table update, which will be on Monday next week
>>> (postponed from this week because of the Copernicus wave names).
>>> The update will appear on the CF website on Tuesday.
>>>
>>> There is one group of names where there is a question regarding
>>> whether we need new surface quantities or whether we could manage
>>> with existing names. I need to post about those separately as I do
>>> feel the existing names should really be used, but some of the
>>> OMIP modellers wanted new names, and there wasn?t consensus in the
>>> discussion. I think it?s a straight forward either/or choice, so
>>> it?s not something that should take weeks to discuss, but I feel
>>> it needs to be highlighted again in order to respect the CF
>>> process. It affects about 30 of the names from recollection.
>>>
>>> For some time now I?ve been doing monthly updates to the table, so
>>> anything that isn?t included in the March update can go into the
>>> April one in another three or four weeks time. It is fine to go
>>> ahead and start using names once they have been accepted because
>>> they will then definitely be included in the next published
>>> version of the table. So from the OMIP point of view, the main
>>> thing is to make sure we can accept all the names. I think it?s
>>> perfectly realistic to say we can get to that point in the next
>>> two weeks, including reaching a decision on the
>>> surface/non-surface names.
>>>
>>> Best wishes,
>>>
>>> Alison
>>>
>>> ------
>>>
>>> Alison Pamment Tel: +44 1235 778065
>>>
>>> Centre for Environmental Data Analysis Email:
>>> alison.pamment at stfc.ac.uk <mailto:J.A.Pamment at rl.ac.uk>
>>>
>>> STFC Rutherford Appleton Laboratory
>>>
>>> R25, 2.22
>>>
>>> Harwell Campus, Didcot, OX11 0QX, U.K.
>>>
>>> *From:*Karl Taylor [mailto:taylor13 at llnl.gov]
>>> *Sent:* 21 March 2017 21:11
>>> *To:* Pamment, Alison (STFC,RAL,RALSP); Jonathan Gregory
>>> *Cc:* Durack, Paul J.
>>> *Subject:* Re: [CF-metadata] New standard names for OMIP
>>> biogeochemistry and chemistry
>>>
>>> Hi Alison and Jonathan,
>>>
>>> There appear to be 114 proposed standard names needing approval
>>> before the OMIP data request for CMIP6 can be completed. (For a
>>> list of these: http://cfeditor.ceda.ac.uk/proposals/1?status=active&namefilter=&proposerfilter=&descfilter=&unitfilter=&yearfilter=&commentfilter=OMIP&filter+and+display=Filter
>>> and eliminate 2 variables referencing "geoMIP").
>>>
>>> There are at least 2 groups on the verge of running their models
>>> and at the same time saving the data needed for CMIP6. There is
>>> now a real danger that these groups will fail to include the OMIP
>>> request (or rely on the current version of it, which is missing
>>> some very important variables). It is therefore urgent that we
>>> now approve the OMIP-proposed standard names immediately.
>>>
>>> Please let me know how I can help make this happen. Can we set a
>>> realistic deadline? Can CMIP6 just assume that all these standard
>>> names will eventually be approved and finalize our OMIP data
>>> request?
>>>
>>> thanks very much for all that you are doing.
>>>
>>> best regards,
>>> Karl
>>>
>>>
>>>
>>> On 3/16/17 11:15 AM, Durack, Paul J. wrote:
>>>
>>> Hi Alison,
>>>
>>> Sorry to nag, but I was just hoping to get some guidance from you
>>> about finalizing these OMIP standard names.
>>>
>>> If you can let me know what needs to be done, I?ll try and
>>> prioritize this!
>>>
>>> Cheers,
>>>
>>> P
>>>
>>> *From: *CF-metadata <cf-metadata-bounces at cgd.ucar.edu>
>>> <mailto:cf-metadata-bounces at cgd.ucar.edu> on behalf of "Durack,
>>> Paul J." <durack1 at llnl.gov> <mailto:durack1 at llnl.gov>
>>> *Date: *Wednesday, March 1, 2017 at 12:36 PM
>>> *To: *Alison Pamment <alison.pamment at stfc.ac.uk>
>>> <mailto:alison.pamment at stfc.ac.uk>
>>> *Cc: *"cf-metadata at cgd.ucar.edu" <mailto:cf-metadata at cgd.ucar.edu>
>>> <cf-metadata at cgd.ucar.edu> <mailto:cf-metadata at cgd.ucar.edu>,
>>> Stephen Griffies <stephen.griffies at noaa.gov>
>>> <mailto:stephen.griffies at noaa.gov>, "martin.juckes at stfc.ac.uk"
>>> <mailto:martin.juckes at stfc.ac.uk> <martin.juckes at stfc.ac.uk>
>>> <mailto:martin.juckes at stfc.ac.uk>, "gokhan at ucar.edu"
>>> <mailto:gokhan at ucar.edu> <gokhan at ucar.edu>
>>> <mailto:gokhan at ucar.edu>, "Taylor, Karl E." <taylor13 at llnl.gov>
>>> <mailto:taylor13 at llnl.gov>
>>> *Subject: *Re: [CF-metadata] New standard names for OMIP
>>> biogeochemistry and chemistry
>>>
>>> Hi Alison,
>>>
>>> I just checked the query of the OMIP standard name request at
>>> http://cfeditor.ceda.ac.uk/proposals/1?status=all&commentfilter=OMIP
>>> and it seems we still have some items under discussion.. How can
>>> we kick these along to get them finalized so I can get the
>>> information updated so Martin can finalize the OMIP/Ocean data
>>> request?
>>>
>>> Cheers,
>>>
>>> P
>>>
>>> *From: *John Dunne - NOAA Federal <john.dunne at noaa.gov>
>>> <mailto:john.dunne at noaa.gov>
>>> *Date: *Thursday, November 10, 2016 at 9:59 AM
>>> *To: *Alison Pamment <alison.pamment at stfc.ac.uk>
>>> <mailto:alison.pamment at stfc.ac.uk>
>>> *Cc: *"cf-metadata at cgd.ucar.edu" <mailto:cf-metadata at cgd.ucar.edu>
>>> <cf-metadata at cgd.ucar.edu> <mailto:cf-metadata at cgd.ucar.edu>,
>>> "Durack, Paul J." <durack1 at llnl.gov> <mailto:durack1 at llnl.gov>,
>>> Stephen Griffies <stephen.griffies at noaa.gov>
>>> <mailto:stephen.griffies at noaa.gov>, "gokhan at ucar.edu"
>>> <mailto:gokhan at ucar.edu> <gokhan at ucar.edu>
>>> <mailto:gokhan at ucar.edu>, James Orr <James.Orr at lsce.ipsl.fr>
>>> <mailto:James.Orr at lsce.ipsl.fr>
>>> *Subject: *Re: [CF-metadata] New standard names for OMIP
>>> biogeochemistry and chemistry
>>>
>>> Hi Alison,
>>>
>>> Thanks for following up! Some thoughts below...
>>>
>>> On Thu, Nov 10, 2016 at 12:00 PM, <alison.pamment at stfc.ac.uk
>>> <mailto:alison.pamment at stfc.ac.uk>> wrote:
>>>
>>> Dear All,
>>>
>>> Many thanks to all those who have commented in this
>>> discussion. I think we have reached, or are very close to
>>> reaching, agreement on many of the names. In this posting I
>>> have not addressed the "sea_surface" names which are proving
>>> to be the only contentious issue - I will deal with them in a
>>> separate message (to follow shortly). We need to raise the
>>> profile of that discussion in order to reach a fair and timely
>>> decision.
>>>
>>> The link to the full list of names with their units and
>>> definitions is
>>> http://cfeditor.ceda.ac.uk/proposals/1?status=active&namefilter=&proposerfilter=Durack&descfilter=&unitfilter=&yearfilter=&commentfilter=OMIP&filter+and+display=Filter.
>>> The list has been updated to show the latest status of the
>>> names. The next update to the published standard name table
>>> will take place on 15th November when all names marked as
>>> 'Accepted' will be added. Any names that are accepted before
>>> that date will be included in the update. Another update will
>>> take place in December.
>>>
>>> The numbering of the sections below refers to my previous summary:
>>>
>>> 1. The following names are now accepted for inclusion in the
>>> standard name table.
>>> >
>>> mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water,
>>> mol m-3
>>> >
>>> mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation,
>>> mol m-3
>>> >
>>> mole_concentration_of_dissolved_inorganic_silicon_in_sea_water,
>>> mol m-3
>>> >
>>> tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton,
>>> mol m-3 s-1
>>> > ocean_mass_content_of_dissolved_organic_carbon, kg m-2
>>> >
>>> ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon,
>>> kgm-2
>>> > mole_concentration_of_cfc11_in_sea_water, mol m-3
>>> > mole_concentration_of_cfc12_in_sea_water, mol m-3
>>> > surface_downward_mole_flux_of_cfc11, mol m-2 s-1
>>> > surface_downward_mole_flux_of_cfc12, mol m-2 s-1
>>>
>>> 2a. Phosporus names
>>> The following names are now accepted for inclusion in the
>>> standard name table.
>>> >
>>> mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water,
>>> mol m-3
>>> >
>>> tendency_of_ocean_mole_content_of_phosphorus_due_to_biological_production,
>>> mol m-2 s-1
>>>
>>> In addition, the spelling has now been corrected in all
>>> 'phosphorus' names.
>>>
>>> 2b. Definitions relating to new chemical species
>>> I agree with Roy's amendments to my suggested carbon13 and
>>> carbon14 definitions. The new chemical species definitions for
>>> carbon13, carbon 14 and sulfur_hexafluoride have been added to
>>> the appropriate names and the following four names are now
>>> accepted for inclusion in the standard name table:
>>> mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water,
>>> mol m-3
>>> mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water,
>>> mol m-3
>>> mole_concentration_of_sulfur_hexafluoride_in_sea_water, mol m-3
>>> surface_downward_mole_flux_of_sulfur_hexafluoride, mol m-3
>>>
>>> Looking at the carbon 13 and 14 names again, I suggest a
>>> slight amendment to the following two proposals:
>>> surface_downward_mass_flux_of_carbon13_dioxide_expressed_as_carbon_due_to_abiotic_component
>>> surface_downward_mass_flux_of_carbon14_dioxide_expressed_as_carbon_due_to_abiotic_component.
>>> I think these should be, respectively, expressed_as_carbon13
>>> and expressed_as_carbon14 rather than simply
>>> expressed_as_carbon. Is that right? Up to now we have always
>>> used the generic term 'expressed_as_carbon' in standard names
>>> which makes no distinction between isotopes but is that
>>> precise enough for these names?
>>>
>>> I'm conflicted. Jim, please make sure I have this right... On the
>>> one hand the names Alison proposes are more precise, but on the
>>> other hand my understanding is that calling abiotic 14C
>>> "expressed_as_carbon14" is technically incorrect by giving people
>>> the mistaken impression that the absolute concentration should
>>> be correct when in fact modeled 14C is referenced to a 14C:12C
>>> ratio of 1.0 rather than the real world reference (14C:12C ratio
>>> 1.17x10^-12). I thought was chosen to minimize numerical
>>> issues. In contrast, my understanding is that the proposed 13C
>>> tracer is in fact simulated as a true concentration such that
>>> model delta13C should be referenced to PeeDee Belemnite (13C:12C
>>> ratio = 0.0112372)... I have not implemented 13C, so I am not sure
>>> this is right. In any case, it seems like a clarification
>>> description would be helpful.
>>>
>>> 2c. tendency_of_ocean_mole_content_of_[in]organic_carbon names
>>>
>>> I wrote:
>>> >
>>> > My question here refers to the following five proposals:
>>> > tendency_of_ocean_mole_content_of_inorganic_carbon, mol m-2 s-1
>>> >
>>> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution,
>>> mol m-2 s-1
>>> >
>>> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation,
>>> mol m-2 s-1
>>> >
>>> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution,
>>> mol m-2 s-1
>>> >
>>> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation,
>>> mol m-2 s-1
>>> >
>>> > We have a couple of existing names for tendencies of
>>> inorganic carbon content,
>>> > both of which are for dissolved_inorganic_carbon. Am I
>>> correct in thinking that
>>> > your names also refer to dissolved amounts? If so, we should
>>> include it, e.g.
>>> > tendency_of_ocean_mole_content_of_inorganic_carbon should be
>>> >
>>> tendency_of_ocean_mole_content_of_dissolved_inorganic_carbon,
>>> and so on.
>>>
>>> John wrote:
>>> > These terms are intended to allow users to construct a
>>> complete carbon budget, and were not intended to distinguish
>>> between particulate and dissolved. Should we restrict > the
>>> definitions and add more terms? add "total" to the name before
>>> "inorganic"? Please note that the names listed above with
>>> "sedimentation" are incorrect. As they are
>>> > intended to represent loss from the ocean, they should not
>>> have "runoff_and". Like in Paul's spreadsheet, they should just be
>>> >
>>> "tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_sedimentation"
>>> and
>>> "tendency_of_ocean_mole_content_of_organic_carbon_due_to_sedimentation".
>>> > These are effectively both "particulate" since they just
>>> represent pelagic sinking in current models to my knowledge,
>>> though it is possible that models might include insitu
>>> > benthic organic production and/or inorganic precipitation
>>> which could be represented as a dissolved loss. Of course,
>>> "sediment dissolution" would be just dissolved, but
>>> > runoff could be either particulate or dissolved... did you
>>> want to distinguish between them?
>>>
>>> OK, thank you for the clarification. Since you intend to
>>> include both particulate and dissolved carbon, the names are
>>> in fact fine (I just wanted to check). In CF, an unqualified
>>> term is always interpreted as a 'total' amount and if only a
>>> component is intended, e.g. dissolved, particulate, it should
>>> be included in the name.
>>>
>>> Existing sedimentation names do not specify 'particulate' but
>>> it is included in the definition using the following sentence:
>>> ' "Sedimentation" is the sinking of particulate matter to the
>>> floor of a body of water.' Is that adequate? If we included an
>>> additional sentence 'Some models may also include insitu
>>> benthic organic production and/or inorganic precipitation',
>>> would that be useful or would it just confuse people?
>>>
>>> You say that some of the names themselves are listed
>>> incorrectly, so again just to clarify, is the following correct?
>>> tendency_of_ocean_mole_content_of_inorganic_carbon, mol m-2 s-1
>>> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution,
>>> mol m-2 s-1
>>> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_sedimentation,
>>> mol m-2 s-1
>>> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution,
>>> mol m-2 s-1
>>> tendency_of_ocean_mole_content_of_organic_carbon_due_to_sedimentation,
>>> mol m-2 s-1
>>>
>>> Yes.
>>>
>>> 2e. Limitation names
>>> Jonathan has suggested that we include the term 'growth' in
>>> these names, to which John has agreed. Also, Jonathan is
>>> suggesting the use of our well established "due_to" syntax for
>>> the solar irradiance names e.g.,
>>> growth_limitation_of_miscellaneous_phytoplankton_due_to_solar_irradiance.
>>> I think this is clear. So the names would then be as follows:
>>>
>>> growth_limitation_of_picophytoplankton_due_to_solar_irradiance
>>> (canonical units: 1)
>>> growth_limitation_of_calcareous_phytoplankton_due_to_solar_irradiance
>>> (canonical units: 1)
>>> growth_limitation_of_diazotrophs_due_to_solar_irradiance
>>> (canonical units: 1)
>>> growth_limitation_of_diatoms_due_to_solar_irradiance
>>> (canonical units: 1)
>>> growth_limitation_of_miscellaneous_phytoplankton_due_to_solar_irradiance
>>> (canonical units: 1)
>>> nitrogen_growth_limitation_of_picophytoplankton (canonical
>>> units: 1)
>>> nitrogen_growth_limitation_of_calcareous_phytoplankton
>>> (canonical units: 1)
>>> nitrogen_growth_limitation_of_diazotrophs (canonical units: 1)
>>> nitrogen_growth_limitation_of_diatoms (canonical units: 1)
>>> nitrogen_growth_limitation_of_miscellaneous_phytoplankton
>>> (canonical units: 1)
>>> iron_growth_limitation_of_picophytoplankton (canonical units: 1)
>>> iron_growth_limitation_of_calcareous_phytoplankton (canonical
>>> units: 1)
>>> iron_growth_limitation_of_diazotrophs (canonical units: 1)
>>> iron_growth_limitation_of_diatoms (canonical units: 1)
>>> iron_growth_limitation_of_miscellaneous_phytoplankton
>>> (canonical units: 1)
>>>
>>> OK?
>>>
>>> OK
>>>
>>> John asked a question about where the definition text should
>>> go - the answer is that it resides in the published standard
>>> name table:
>>> http://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html
>>> (click on a name to see its definition). (Almost) all standard
>>> names have definitions but they don't need to be reproduced in
>>> the data files. Those wishing to access the information can
>>> obtain it from a number of sources, namely the html table, the
>>> xml version (which is actually the 'master' copy of standard
>>> names)
>>> http://cfconventions.org/Data/cf-standard-names/current/src/cf-standard-name-table.xml
>>> or the NERC vocabulary server which is developed and
>>> maintained by the British Oceanographic Data Centre
>>> http://vocab.nerc.ac.uk/collection/P07/current/.
>>>
>>> Thanks, yes, now I understand.
>>>
>>> John suggested some refinements to the wording of the
>>> definitions, so taking these into account, my two examples
>>> would now be as follows.
>>>
>>> growth_limitation_of_miscellaneous_phytoplankton_due_to_solar_irradiance
>>> 'Phytoplankton are algae that live near the grow where there
>>> is sufficient light to support photosynthesis. "Miscellaneous
>>> phytoplankton" are all those phytoplankton that are not
>>> diatoms, diazotrophs, calcareous phytoplankton,
>>> picophytoplankton or other separately named components of the
>>> phytoplankton population. The specification of a physical
>>> process by the phrase "due_to_" process means that the
>>> quantity named is a single term in a sum of terms which
>>> together compose the general quantity named by omitting the
>>> phrase. "Irradiance" means the power per unit area (called
>>> radiative flux in other standard names), the area being normal
>>> to the direction of flow of the radiant energy. Solar
>>> irradiance is essential to the photosynthesis reaction and its
>>> presence promotes the growth of phytoplankton populations.
>>> "Growth limitation due to solar irradiance" means the ratio of
>>> the growth rate of a species population in the environment
>>> (where the amount of sunlight reaching a location may be
>>> limited) to the theoretical growth rate if there were no such
>>> limit on solar irradiance.'
>>>
>>> nitrogen_growth_limitation_of_diatoms
>>> 'Diatoms are phytoplankton with an external skeleton made of
>>> silica. Phytoplankton are algae that grow where there is
>>> sufficient light to support photosynthesis. Nitrogen is a
>>> nutrient essential to the growth of phytoplankton populations.
>>> "Nitrogen growth limitation" means the ratio of the growth
>>> rate of a species population in the environment (where there
>>> is a finite availability of nitrogen) to the theoretical
>>> growth rate if there were no such limit on nitrogen availability.'
>>>
>>> Are these OK?
>>>
>>> Those look fine to me.
>>>
>>> John, Jim and Paul, if you are happy with these names and
>>> sample definitions then I think the limitation names can all
>>> be accepted for publication. I will then construct definitions
>>> for them all, consistent with the examples.
>>>
>>> One final note about these phytoplankton names: Roy queried
>>> whether we have the best classification system for the
>>> different types of phytoplankton, i.e. we are currently mixing
>>> size and species as ways of delineating sections of the
>>> population. All I can say is that this is the system that was
>>> first proposed for CMIP5 and is being used again in CMIP6.
>>> Nothing else has ever been proposed. I agree that if new
>>> categories are ever proposed we will need to take account of
>>> the existing names, and in particular we may then need to
>>> think hard about the definition of 'miscellaneous
>>> phytoplankton'. However, in the time honoured tradition of CF,
>>> I propose to defer this discussion until such time as there is
>>> a clear need to change what we are doing. I hope that's OK.
>>>
>>> Fine with me.
>>>
>>> 2f. Natural/abiotic component names
>>>
>>> I confess that I have struggled somewhat to understand these
>>> names, although it's becoming gradually clearer. I do see now
>>> that we need both sets of names and that the "natural
>>> analogue" names are model diagnostics rather than forcing
>>> conditions.
>>>
>>> In John's most recent posting he suggests names and
>>> definitions of the form:
>>> mole_concentration_of_dissolved_inorganic_carbon_natural_analogue_in_sea_water
>>> Dissolved inorganic carbon (CO3+HCO3+H2CO3) concentration
>>> natural analogue forced by preindustrial atmospheric xCO2
>>>
>>> mole_concentration_of_dissolved_inorganic_carbon_abiotic_analogue_in_sea_water
>>> Dissolved inorganic carbon (CO3+HCO3+H2CO3) concentration
>>> abiotic analogue ignoring biological effects on carbon and
>>> alkalinity
>>>
>>> Certainly I think these names are a lot better and the
>>> terminology "natural analogue" and "abiotic analogue" is
>>> useful. We need to think about how this, or a similar, syntax
>>> will work in a standardised way with all the proposed natural
>>> and abiotic names. For example, how would we rewrite
>>> surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_natural_component?
>>> Perhaps we could replace the "due_to_X" in the current
>>> proposals with "X_analogue" at the end of the name or we could
>>> prepend it with "X_analogue_of". This would mean that the new
>>> names are consistent with many existing ones and would simply
>>> contain an additional qualification, e.g.
>>> [sea_]surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_natural_analogue
>>> or
>>> natural_analogue_of_[sea_]surface_
>>> mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water.
>>>
>>> How does that sound?
>>>
>>> I prefer:
>>>
>>> [sea_]surface_mole_concentration_of_carbonate_natural_analogue_expressed_as_carbon_in_sea_water
>>>
>>> If we can settle on a syntax, then the definitions shouldn't
>>> be too difficult to sort out. We'd need some explanatory words
>>> for the analogues, which should include some information about
>>> when these names might be used (for the benefit of the many CF
>>> users who will be totally unfamiliar with the OMIP
>>> experiments). Based on John's text I'd suggest the following:
>>> natural_analogue
>>> 'In ocean biogeochemistry models, a "natural analogue" is used
>>> to simulate the effect on a modelled variable of imposing
>>> preindustrial atmospheric carbon dioxide concentrations, even
>>> when the model as a whole may be subjected to varying forcings.'
>>> abiotic_analogue
>>> 'In ocean biogeochemistry models, an "abiotic analogue" is
>>> used to simulate the effect on a modelled variable when
>>> biological effects on ocean carbon concentration and
>>> alkalinity are ignored.'
>>>
>>> Based on the above, an example of a full definition would then
>>> be something like:
>>> surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_natural_analogue
>>> 'The surface called "surface" means the lower boundary of the
>>> atmosphere. The partial pressure of a gaseous constituent of
>>> air is the pressure which it alone would exert with unchanged
>>> temperature and number of moles per unit volume. The chemical
>>> formula for carbon dioxide is CO2. In ocean biogeochemistry
>>> models, a "natural analogue" is used to simulate the effect on
>>> a modelled variable of imposing preindustrial atmospheric
>>> carbon dioxide concentrations, even when the model as a whole
>>> may be subjected to varying forcings.'
>>>
>>> Any good?
>>>
>>> Those look good to me.
>>>
>>> Thanks again for all your help, John
>>>
>>>
>>> Best wishes,
>>> Alison
>>>
>>> > -----Original Message-----
>>> > From: CF-metadata [mailto:cf-metadata-bounces at cgd.ucar.edu
>>> <mailto:cf-metadata-bounces at cgd.ucar.edu>] On Behalf Of
>>> > alison.pamment at stfc.ac.uk <mailto:alison.pamment at stfc.ac.uk>
>>> > Sent: 19 October 2016 19:16
>>> > To: durack1 at llnl.gov <mailto:durack1 at llnl.gov>;
>>> cf-metadata at cgd.ucar.edu <mailto:cf-metadata at cgd.ucar.edu>
>>> > Cc: stephen.griffies at noaa.gov
>>> <mailto:stephen.griffies at noaa.gov>; gokhan at ucar.edu
>>> <mailto:gokhan at ucar.edu>
>>> > Subject: Re: [CF-metadata] New standard names for OMIP
>>> biogeochemistry and
>>> > chemistry
>>> >
>>>
>>> > Dear Paul, Jim and Jonathan,
>>> >
>>> > Thank you for all the proposals for OMIP biogeochemistry and
>>> chemistry names
>>> > and the discussion that has already begun on these.
>>> >
>>> > I have created entries for all the proposed names in the
>>> CEDA vocabulary
>>> > editor, available here:
>>> >
>>> http://cfeditor.ceda.ac.uk/proposals/1?status=active&namefilter=&proposerfilt
>>> >
>>> er=Durack&descfilter=&unitfilter=&yearfilter=&commentfilter=OMIP&filter+and
>>> > +display=Filter.
>>> > At the moment, the names themselves are all shown as
>>> originally proposed and
>>> > I have added standard definition text for consistency with
>>> existing names.
>>> > Please use the link to view the full list of names and
>>> definitions as it is easier
>>> > than reproducing it all in an email to the list.
>>> >
>>> > I think a number of the names look fine and could be
>>> published in their current
>>> > form (see item 1 below). Paul and Jim, please can you check
>>> the definitions that
>>> > I'm suggesting for these names and let me know if you're
>>> happy with them?
>>> > (Comments from others are of course welcome).
>>> >
>>> > For the groups of names where some discussion is still
>>> required my comments
>>> > are in item 2.
>>> >
>>> > 1. Names that I think can be approved, subject to checking
>>> of the definitions.
>>> >
>>> >
>>> mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water,
>>> mol m-3
>>> >
>>> mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturat
>>> > ion, mol m-3
>>> >
>>> mole_concentration_of_dissolved_inorganic_silicon_in_sea_water,
>>> mol m-3
>>> >
>>> tendency_of_mole_concentration_of_particulate_organic_matter_expressed_a
>>> > s_carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol
>>> m-3 s-1
>>> > ocean_mass_content_of_dissolved_organic_carbon, kg m-2
>>> >
>>> ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon,
>>> kg
>>> > m-2
>>> > mole_concentration_of_cfc11_in_sea_water, mol m-3
>>> > mole_concentration_of_cfc12_in_sea_water, mol m-3
>>> > surface_downward_mole_flux_of_cfc11, mol m-2 s-1
>>> > surface_downward_mole_flux_of_cfc12, mol m-2 s-1
>>> >
>>> > 2. Names requiring further discussion.
>>> >
>>> > a. Phosphorus names
>>> > Sorry that I didn't notice it when previewing the names, but
>>> I have realized that
>>> > 'phosphorus' is misspelled in the proposals, i.e., it should
>>> be 'phosphorus', not
>>> > 'phosphorous'. Subject to this correction and checking of
>>> the definitions, I think
>>> > the following names can be approved.
>>> >
>>> mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water,
>>> mol m-
>>> > 3
>>> >
>>> tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_product
>>> > ion, mol m-2 s-1
>>> >
>>> > I will also correct the spelling in three further phosphorus
>>> names which remain
>>> > under discussion due to other issues:
>>> >
>>> surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_wat
>>>
>>> > er, mol m-3
>>> > surface_mole_concentration_of_particulate_organic_matter_expressed_as_ph
>>> > osphorus_in_sea_water, mol m-3
>>> > surface_mole_concentration_of_phytoplankton_expressed_as_phosphorus_in_
>>> > sea_water, mol m-3
>>> >
>>> > b. Definitions relating to new chemical species
>>> > It is usual to include a sentence in the definition when a
>>> standard name refers
>>> > to a chemical species. There are three new species/isotopes
>>> in the current set
>>> > of proposals. I suggest adding a single sentence to the
>>> definitions of the
>>> > relevant names as follows:
>>> >
>>> > carbon13: ' "carbon13" means the naturally occurring isotope
>>> of carbon having
>>> > six protons and seven neutrons.'
>>> > carbon14: ' "carbon14" means the radioactive isotope of
>>> carbon having six
>>> > protons and eight neutrons, used in radiocarbon dating.'
>>> > sulfur_hexafluoride: 'The chemical formula of sulfur
>>> hexafluoride is SF6.'
>>> >
>>> > OK?
>>> >
>>> > c. tendency_of_ocean_mole_content_of_[in]organic_carbon names
>>> >
>>> > My question here refers to the following five proposals:
>>> > tendency_of_ocean_mole_content_of_inorganic_carbon, mol m-2 s-1
>>> > tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_s
>>> > ediment_dissolution, mol m-2 s-1
>>> > tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_s
>>> > edimentation, mol m-2 s-1
>>> > tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sed
>>> > iment_dissolution, mol m-2 s-1
>>> > tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sed
>>> > imentation, mol m-2 s-1
>>> >
>>> > We have a couple of existing names for tendencies of
>>> inorganic carbon content,
>>> > both of which are for dissolved_inorganic_carbon. Am I
>>> correct in thinking that
>>> > your names also refer to dissolved amounts? If so, we should
>>> include it, e.g.
>>> > tendency_of_ocean_mole_content_of_inorganic_carbon should be
>>> > tendency_of_ocean_mole_content_of_dissolved_inorganic_carbon,
>>> and so on.
>>> >
>>>
>>> > d. Surface concentration names
>>> > There are a lot of these: 42 surface_mole_concentration
>>> names (units of mol m-
>>> > 3), 6 surface_mass_concentration names (kg m-3) and I'm also
>>> including 2
>>> > surface_sea_water_alkalinity (mol m-3) names and 3
>>> surface_sea_water_ph
>>> > names in this section.
>>> >
>>> > My concern about these proposals is that the names and units
>>> are not
>>> > consistent. In CF standard names, "surface" means the lower
>>> boundary of the
>>> > atmosphere. It has no depth, so it is not meaningful to
>>> regard it as having a
>>> > mass or a volume. For this reason we can't assign units of
>>> kg m-3 or mol m-3 to
>>> > a 'surface' name. I assume that all these quantities are in
>>> fact "near surface"
>>> > values, i.e. representative of the top model layer, in which
>>> case there are two
>>> > possible ways to deal with this.
>>> >
>>> > The first solution is simply to remove 'surface' from all
>>> these names and
>>> > instead use a vertical coordinate or scalar coordinate and
>>> coordinate bounds to
>>> > indicate the location and thickness of the layer. This has
>>> the advantage that
>>> > many of the required names actually already exist, without
>>> the need to
>>> > introduce separate surface names. E.g, instead of adding a
>>> new name
>>> >
>>> surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water,
>>> > you could use the existing name
>>> > mole_concentration_of_dissolved_inorganic_carbon_in_sea_water
>>> > accompanied by suitable coordinate information to describe
>>> your quantity.
>>> >
>>> > The second solution, if you do feel that it is necessary to
>>> have distinct standard
>>> > names for all these near-surface quantities, would be to
>>> follow the approach
>>> > used in some existing sea_surface names such as
>>> sea_surface_temperature
>>> > and sea_surface_salinity. The names would then be
>>> 'sea_surface' names and
>>> > there would be an accompanying sentence in the definition to
>>> explain what that
>>> > means, i.e. that it refers to water close to the surface.
>>> You would still also need
>>> > to include the coordinate information and coordinate bounds
>>> to fully describe
>>> > your data. With this approach the proposed name
>>> >
>>> surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water
>>> > would become
>>> > sea_surface_mole_concentration_of_dissolved_inorganic_carbon.
>>> >
>>> > Either solution would be consistent with the proposed units
>>> and I'd be happy
>>> > with either. Please let me know how you prefer to proceed.
>>> >
>>> > As a final point in this section, the three proposed
>>> surface_sea_water_ph
>>> > names are dimensionless, but I imagine that these too are
>>> really intended to
>>> > represent the top model layer, in which case we should
>>> either drop 'surface' or
>>> > change them to 'sea_surface' names too.
>>> >
>>>
>>> > e. Limitation names
>>> > Jonathan has already raised the question of what 'limitation'
>>> means and also
>>> > what measure of the various phytoplankton populations is
>>> being limited. This is
>>> > a new concept in standard names so it's important to get the
>>> definitions right.
>>> >
>>> > John Dunne replied to Jonathan:
>>> > > With respect to the limitation terms, we currently have the
>>> definitions
>>> > explained in the "Resolved Comment" column as "Ratio of
>>> realizable
>>> > miscellaneous other
>>> > > phytoplankton growth rate under low nitrogen stress to
>>> theoretical rate
>>> > without such limitation".
>>> >
>>> > So from this, my understanding is that nitrogen and iron are
>>> nutrients whose
>>> > availability promotes the growth of phytoplankton, presumably
>>> by being
>>> > absorbed somehow into the organic matter, while solar
>>> irradiance is clearly the
>>> > energy source essential to the photosynthesis reaction.
>>> John's reply talks about
>>> > growth rate, so I assume that means the growth rate of the
>>> population of a
>>> > particular species (as opposed to the growth rate of
>>> individuals of that species).
>>> >
>>>
>>> > Based on this I've attempted a couple of example definitions.
>>> If we can agree
>>> > these, then I can go ahead and add the appropriate sentences
>>> to all the
>>> > limitation names.
>>> > nitrogen_limitation_of_diatoms (canonical units: 1)
>>> > 'Diatoms are single-celled phytoplankton with an external
>>> skeleton made of
>>> > silica. Phytoplankton are autotrophic prokaryotic or
>>> eukaryotic algae that live
>>> > near the water surface where there is sufficient light to
>>> support photosynthesis.
>>> > Nitrogen is a nutrient essential to the growth of
>>> phytoplankton populations.
>>> > "Nitrogen limitation" means the ratio of the growth rate of
>>> a species population
>>> > in the environment (where there is a finite availability of
>>> nitrogen) to the
>>> > theoretical growth rate if there were no such limit on
>>> nitrogen availability.'
>>> >
>>> > N.B. For the irradiance names, I suggest we make them
>>> 'solar_irradiance' to be
>>> > absolutely clear.
>>> > solar_irradiance_limitation_of_miscellaneous_phytoplankton
>>> (canonical
>>> > units:1)
>>> > 'Phytoplankton are autotrophic prokaryotic or eukaryotic
>>> algae that live near the
>>> > water surface where there is sufficient light to support
>>> photosynthesis.
>>> > "Miscellaneous phytoplankton" are all those phytoplankton
>>> that are not
>>> > diatoms, diazotrophs, calcareous phytoplankton,
>>> picophytoplankton or other
>>> > separately named components of the phytoplankton population.
>>> "Irradiance"
>>> > means the power per unit area (called radiative flux in
>>> other standard names),
>>> > the area being normal to the direction of flow of the
>>> radiant energy. Solar
>>> > irradiance is essential to the photosynthesis reaction and
>>> its presence
>>> > promotes the growth of phytoplankton populations. "Solar
>>> irradiance limitation"
>>> > means the ratio of the growth rate of a species population
>>> in the environment
>>> > (where the amount of sunlight reaching a location may be
>>> limited) to the
>>> > theoretical growth rate if there were no such limit on solar
>>> irradiance.'
>>> >
>>>
>>> > Comments and suggestions for improvement are welcome!
>>> >
>>> > f. Natural/abiotic component names
>>> > Thank you for the useful discussion that has already taken
>>> place about the 22
>>> > proposed natural_component and abiotic_component names. I hadn't
>>> > previously understood the details of how the OMIP experiments
>>> will be run.
>>> >
>>> > Reading through the discussion, I agree with Jonathan that the
>>> > natural_component names seem to be describing the forcing
>>> conditions for the
>>> > model, rather than being a separate set of diagnostics that
>>> represent the
>>> > effects of some process within the model. Hence I agree that
>>> it isn't necessary
>>> > to define separate standard names with
>>> due_to_natural_component and I'd
>>> > advocate leaving them out. Is that OK?
>>> >
>>> > I think we're agreed that the abiotic names are needed, and
>>> if I've understood
>>> > correctly we seem to have agreed to stick with
>>> due_to_abiotic_component
>>> > because it works for all the names where it's used, including
>>> ph names. Is that
>>> > right?
>>> >
>>>
>>> > Best wishes,
>>> > Alison
>>> >
>>>
>>> ------
>>> Alison Pamment Tel: +44 1235 778065
>>> <tel:%2B44%201235%20778065>
>>> Centre for Environmental Data Analysis Email:
>>> alison.pamment at stfc.ac.uk <mailto:alison.pamment at stfc.ac.uk>
>>> STFC Rutherford Appleton Laboratory
>>> R25, 2.22
>>> Harwell Campus, Didcot, OX11 0QX, U.K.
>>>
> ----- End forwarded message -----
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Received on Thu Mar 23 2017 - 13:05:41 GMT
