Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry

[Lowry, Roy K.]

Superb outcome. Cheers, Roy.


Please note that I partially retired on 01/11/2015. I am now only working 7.5 
hours a week and can only guarantee e-mail response on Wednesdays, my day in 
the office. All vocabulary queries should be sent to enquir...@bodc.ac.uk. 
Please also use this e-mail if your requirement is urgent.



From: CF-metadata  on behalf of Durack, Paul 
J. 
Sent: 13 April 2017 18:35
To: cf-metadata@cgd.ucar.edu
Subject: Re: [CF-metadata] New standard names for OMIP biogeochemistry and 
chemistry

Ok great this simplifies things considerably. So, we can drop the request for 
these separate “surface_” names, which cleans up the 51 names that Alison was 
questioning. I believe in the OMIP data request these variables are uniquely 
names (e.g. dissic vs dissicos [surface is last]), so only the standard_names 
require updating in the google sheet.

Alison, what other open questions remain unanswered from your comprehensive 
email dated 29th March 2017? I believe we are close to the finish line on this 
large standard name request.

Cheers,

P

On 4/11/17, 4:00 AM, "CF-metadata on behalf of James Orr" 
 wrote:

Paul,

> So, use a single standard_name (for the identical quantity), and keep
> the second 2D (CMOR) variable (as is the status of the current CMIP6
> data request). I believe this solution would solve many of the 51
> “surface” variables that Alison highlighted, as these requests could
> be dropped in favor of their 3D (existing) names.

Your suggestion is excellent.  Using the same standard-name but a
different "CMIP name" to indicate the surface variable would be a
fine solution.

> As an aside, the “depth0m” current CMOR_dimension is not correct
> either. I assume these variables will be reported for the top ocean
> level, which in CMIP5 was 0-10m reported as 5m for many models, and
> for CMIP6 will be varied across the model suite. Jim/John, should this
> be clarified? Martin, would you care to comment here?

Yes, for these "sea surface" variables, we mean the top layer of the
ocean model.  In CMIP6, the thickness of that layer will indeed vary
among ocean models. Any ideas for clarification are welcome although
most ocean modelers should not need it.

Best,

Jim

On Thu, 6 Apr 2017, Durack, Paul J. wrote:

> To answer the “surface” question raised by Alison, and posed by Jim (the 
bottom of this email) - apologies for the tardy response.
>
> The analogue in the physical domain are the tos and sos variables which 
are the “surface” (or more correctly top model level) 2D equivalents of their 
counterpart 3D variables thetao and so.
>
> In this instance, we could have two variables with the same standard_name 
and differing “CMIP name”, so for example:
>
> The originally proposed variables and standard_names (see biogeochemistry 
sheet: https://goo.gl/Fyr6QW)
>
> dissicos – CF_standard_name: 
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water; 
CMOR_dimensions: longitude latitude time depth0m (Omon line 7)
> dissic – CF_standard_name: 
mole_concentration_of_dissolved_inorganic_carbon_in_sea_water; CMOR_dimensions: 
longitude latitude olevel time (Omon line 60)
>
> Could be finalized as:
>
> dissicos – CF_standard_name: 
mole_concentration_of_dissolved_inorganic_carbon_in_sea_water; CMOR_dimensions: 
longitude latitude time depth0m
> dissic – CF_standard_name: 
mole_concentration_of_dissolved_inorganic_carbon_in_sea_water; CMOR_dimensions: 
longitude latitude olevel time
>
> So, use a single standard_name (for the identical quantity), and keep the 
second 2D (CMOR) variable (as is the status of the current CMIP6 data request). 
I believe this solution would solve many of the 51 “surface” variables that 
Alison highlighted, as these requests could be dropped in favor of their 3D 
(existing) names.
>
>
> As an aside, the “depth0m” current CMOR_dimension is not correct either. 
I assume these variables will be reported for the top ocean level, which in 
CMIP5 was 0-10m reported as 5m for many models, and for CMIP6 will be varied 
across the model suite. Jim/John, should this be clarified? Martin, would you 
care to comment here?
>
>
> Cheers,
>
> P
>
> On 4/6/17, 10:51 AM, "CF-metadata on behalf of martin.juc...@stfc.ac.uk" 
 wrote:
>
>Hello All,
>
>I'd like to support Alison on point 4 (see 
http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2017/059357.html ), regarding 
the proposal for new standard names for near surface tracer fields.
>
>The statement 'The surface called "surface" means the lower boundary 
of the 

Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry

[Durack, Paul J.]

Ok great this simplifies things considerably. So, we can drop the request for 
these separate “surface_” names, which cleans up the 51 names that Alison was 
questioning. I believe in the OMIP data request these variables are uniquely 
names (e.g. dissic vs dissicos [surface is last]), so only the standard_names 
require updating in the google sheet.

Alison, what other open questions remain unanswered from your comprehensive 
email dated 29th March 2017? I believe we are close to the finish line on this 
large standard name request.

Cheers,

P

On 4/11/17, 4:00 AM, "CF-metadata on behalf of James Orr" 
 wrote:

Paul,

> So, use a single standard_name (for the identical quantity), and keep 
> the second 2D (CMOR) variable (as is the status of the current CMIP6 
> data request). I believe this solution would solve many of the 51 
> “surface” variables that Alison highlighted, as these requests could 
> be dropped in favor of their 3D (existing) names.

Your suggestion is excellent.  Using the same standard-name but a 
different "CMIP name" to indicate the surface variable would be a
fine solution.

> As an aside, the “depth0m” current CMOR_dimension is not correct 
> either. I assume these variables will be reported for the top ocean 
> level, which in CMIP5 was 0-10m reported as 5m for many models, and 
> for CMIP6 will be varied across the model suite. Jim/John, should this 
> be clarified? Martin, would you care to comment here?

Yes, for these "sea surface" variables, we mean the top layer of the 
ocean model.  In CMIP6, the thickness of that layer will indeed vary 
among ocean models. Any ideas for clarification are welcome although 
most ocean modelers should not need it.

Best,

Jim

On Thu, 6 Apr 2017, Durack, Paul J. wrote:

> To answer the “surface” question raised by Alison, and posed by Jim (the 
bottom of this email) - apologies for the tardy response.
>
> The analogue in the physical domain are the tos and sos variables which 
are the “surface” (or more correctly top model level) 2D equivalents of their 
counterpart 3D variables thetao and so.
>
> In this instance, we could have two variables with the same standard_name 
and differing “CMIP name”, so for example:
>
> The originally proposed variables and standard_names (see biogeochemistry 
sheet: https://goo.gl/Fyr6QW)
>
> dissicos – CF_standard_name: 
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water; 
CMOR_dimensions: longitude latitude time depth0m (Omon line 7)
> dissic – CF_standard_name: 
mole_concentration_of_dissolved_inorganic_carbon_in_sea_water; CMOR_dimensions: 
longitude latitude olevel time (Omon line 60)
>
> Could be finalized as:
>
> dissicos – CF_standard_name: 
mole_concentration_of_dissolved_inorganic_carbon_in_sea_water; CMOR_dimensions: 
longitude latitude time depth0m
> dissic – CF_standard_name: 
mole_concentration_of_dissolved_inorganic_carbon_in_sea_water; CMOR_dimensions: 
longitude latitude olevel time
>
> So, use a single standard_name (for the identical quantity), and keep the 
second 2D (CMOR) variable (as is the status of the current CMIP6 data request). 
I believe this solution would solve many of the 51 “surface” variables that 
Alison highlighted, as these requests could be dropped in favor of their 3D 
(existing) names.
>
>
> As an aside, the “depth0m” current CMOR_dimension is not correct either. 
I assume these variables will be reported for the top ocean level, which in 
CMIP5 was 0-10m reported as 5m for many models, and for CMIP6 will be varied 
across the model suite. Jim/John, should this be clarified? Martin, would you 
care to comment here?
>
>
> Cheers,
>
> P
>
> On 4/6/17, 10:51 AM, "CF-metadata on behalf of martin.juc...@stfc.ac.uk" 
 wrote:
>
>Hello All,
>
>I'd like to support Alison on point 4 (see 
http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2017/059357.html ), regarding 
the proposal for new standard names for near surface tracer fields.
>
>The statement 'The surface called "surface" means the lower boundary 
of the atmosphere' occurs in many standard name definitions: introducing a new 
set of names in which "surface" means "near surface" introduces an unnecessary 
ambiguity.
>
>I also note that some of these variables have already been requested 
in CMIP5, using the approach described by Karl.
>
>regards,
>Martin
>
> On 3/31/17, 9:04 AM, "CF-metadata on behalf of Jonathan Gregory" 
 wrote:
>
>Dear Alison
>
>I second Jim Orr's vote of 

Re: [CF-metadata] WG: proposal for two new standard_names and an additional chemical species

[alison.pamment]

Dear Roy and Beate,

Thank you both for your replies (and for educating me about sea water partial 
pressures!)

The two new names are accepted as proposed:

partial_pressure_of_carbon_dioxide_in_sea_water (Pa)
'The partial pressure of a dissolved gas in sea water is the partial pressure 
in air with which it would be in equilibrium. 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.'

partial_pressure_of_methane_in_sea_water (Pa)
'The partial pressure of a dissolved gas in sea water is the partial pressure 
in air with which it would be in equilibrium. 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 
methane is CH4.'

These will be added at the next update of the standard name table, scheduled 
for 24th April.

Best wishes,
Alison

--
Alison Pamment   Tel: +44 
1235 778065
Centre for Environmental Data Analysis Email: alison.pamm...@stfc.ac.uk
STFC Rutherford Appleton Laboratory 
R25, 2.22
Harwell Campus, Didcot, OX11 0QX, U.K.


From: Lowry, Roy K. [mailto:r...@bodc.ac.uk] 
Sent: 30 March 2017 11:38
To: Pamment, Alison (STFC,RAL,RALSP); beate.ge...@hzg.de; 
cf-metadata@cgd.ucar.edu
Subject: Re: [CF-metadata] WG: proposal for two new standard_names and an 
additional chemical species

Hi Alison,

The 'in equilibrium' in pCO2 definition refers to the air in the analytical 
equipment and so has nothing to do with air-sea interface equilibrium. pCO2 is 
measured by using something like a shower-head or a column full of marbles to 
equilibrate the water sample with a stream of air that is then passed into a 
gas analyser. Consequently, the Standard Name makes no statement about the 
depth from which the water was taken. The same would apply to methane.

Whilst it is usual to measure pCO2 in surface waters, I have come across 
measurements on water bottle samples collected at depth.

Cheers, Roy.

Please note that I partially retired on 01/11/2015. I am now only working 7.5 
hours a week and can only guarantee e-mail response on Wednesdays, my day in 
the office. All vocabulary queries should be sent to enquir...@bodc.ac.uk. 
Please also use this e-mail if your requirement is urgent.


From: CF-metadata  on behalf of 
alison.pamm...@stfc.ac.uk 
Sent: 29 March 2017 12:34
To: beate.ge...@hzg.de; cf-metadata@cgd.ucar.edu
Subject: Re: [CF-metadata] WG: proposal for two new standard_names and an 
additional chemical species 
 
Dear Beate,

Thank you for your proposals.

As you have pointed out, we have an existing name 
'surface_partial_pressure_of_carbon_dioxide_in_sea_water'. I completely agree 
that we should remove the sentence
' "Water" means water in all phases, including frozen i.e. ice and snow' from 
the definition as it really isn't necessary for this name. I will make that 
change in the April update to the standard name table.

The definition of the existing name includes the sentence 'The partial pressure 
of a dissolved gas in sea water is the partial pressure in air with which it 
would be in equilibrium' so clearly this is talking about equilibrium of 
partial pressures across the air-sea interface, i.e. at the surface. For the 
proposed name partial_pressure_of_carbon_dioxide_in_sea_water do you mean 
partial pressures at some arbitrary depth below the sea surface, even if these 
are not actually in physical contact with the surface itself? If so, then I 
agree we do need a new name.

For the methane name I would ask the same question. Certainly we can introduce 
a methane partial pressure name, but I'd like to understand whether it's at the 
surface or at some arbitrary depth.

Best wishes,
Alison

--
Alison Pamment   Tel: +44 
1235 778065
Centre for Environmental Data Analysis Email: alison.pamm...@stfc.ac.uk
STFC Rutherford Appleton Laboratory 
R25, 2.22
Harwell Campus, Didcot, OX11 0QX, U.K.


From: CF-metadata [mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of 
beate.ge...@hzg.de
Sent: 20 February 2017 08:30
To: cf-metadata@cgd.ucar.edu
Subject: [CF-metadata] WG: proposal for two new standard_names and an 
additional chemical species

Dear all and especially the cf-metadata crew,

My colleagues and I apply for an expansion of the table of chemical species 
(http://cfconventions.org/Data/cf-standard-names/docs/guidelines.html#id2799094):
 methane.

We apply to include partial_pressure_of_methane_in_sea_water (units: Pa)
with following description:
The partial pressure of a dissolved gas in sea water is the partial pressure in 
air with which it would be in 

Re: [CF-metadata] New standard names for NEMO ocean model output

[alison.pamment]

Dear Jonathan and Sebastien,

Thank you both for your comments. I think we are now agreed on the following 
names (with definitions as given in my previous email 
http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2017/059392.html):

1. sea_water_mass_per_unit_area_expressed_as_thickness (m)
2. ocean_mixed_layer_thickness_defined_by_vertical_tracer_diffusivity_threshold 
(m)
2a. The existing name 
ocean_mixed_layer_thickness_defined_by_vertical_tracer_diffusivity will become 
an alias of 
ocean_mixed_layer_thickness_defined_by_vertical_tracer_diffusivity_deficit (m).
6. ratio_of_sea_water_potential_temperature_anomaly_to_relaxation_timescale (K 
s-1)
7. ratio_of_sea_water_practical_salinity_anomaly_to_relaxation_timescale (s-1)
8. integral_of_sea_water_practical_salinity_wrt_depth (m)

These names are accepted for publication in the standard name table and will be 
added at the next update, scheduled for 24th April.

I think we have also agreed to drop proposal (9) 
integral_of_sea_water_practical_salinity_wrt_total_depth (m) because it is the 
same quantity as (8).

For the 'steric' names, Jonathan feels these should indicate that the term 
relates to a change in local sea level, rather than simply water column 
thickness, and Sebastien is keen that we adopt a common approach for all three 
names. We have a number of "sea_surface_height_above_X" names where X is 
variously "geoid", "reference_ellipsoid", etc. Based on this syntax I would 
then suggest the following names:

3. steric_change_in_sea_surface_height_above_sea_floor (m)
' "Sea surface height" is a time-varying quantity. The steric change in sea 
surface height is the change in height a water column of standard temperature 
T=0°C and practical salinity S=35.0 would undergo when its temperature and 
salinity are changed to the observed values. The sum of the quantities with 
standard names thermosteric_change_in_sea_surface_height_above_sea_floor and 
halosteric_change_in_sea_surface_height_above_sea_floor is the total steric 
change in the water column height, which has the standard name of 
steric_change_in_sea_surface_height_above_sea_floor. The sum of the quantities 
with standard names sea_water_mass_per_unit_area_expressed_as_thickness and 
steric_change_in_sea_surface_height_above_sea_floor is the total thickness of 
the sea water column.'

4. halosteric_change_in_sea_surface_height_above_sea_floor (m)
' "Sea surface height" is a time-varying quantity. The halosteric change in sea 
surface height is the change in height a water column of standard practical 
salinity S=35.0 would undergo when its salinity is changed to the observed 
value. The sum of the quantities with standard names 
thermosteric_change_in_sea_surface_height_above_sea_floor and 
halosteric_change_in_sea_surface_height_above_sea_floor is the total steric 
change in the water column height, which has the standard name of 
steric_change_in_sea_surface_height_above_sea_floor.'

5. thermosteric_change_in_sea_surface_height_above_sea_floor (m)
' "Sea surface height" is a time-varying quantity. The thermosteric change in 
sea surface height is the change in height a water column of standard 
temperature T=0°C would undergo when its temperature is changed to the observed 
value. The sum of the quantities with standard names 
thermosteric_change_in_sea_surface_height_above_sea_floor and 
halosteric_change_in_sea_surface_height_above_sea_floor is the total steric 
change in the water column height, which has the standard name of 
steric_change_in_sea_surface_height_above_sea_floor.'

Are these better?

Best wishes,
Alison

--
Alison Pamment   Tel: +44 
1235 778065
Centre for Environmental Data Analysis Email: alison.pamm...@stfc.ac.uk
STFC Rutherford Appleton Laboratory 
R25, 2.22
Harwell Campus, Didcot, OX11 0QX, U.K.



> -Original Message-
> From: CF-metadata [mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of
> Sebastien Villaume
> Sent: 05 April 2017 11:51
> To: cf-metadata@cgd.ucar.edu
> Subject: Re: [CF-metadata] New standard names for NEMO ocean model output
> 
> 
> Dear Alison et al,
> 
> we are happy with your suggestions/modifications.
> 
> I also understand from your comments to
> integral_of_sea_water_practical_salinity_wrt_depth that my proposal to
> rename
> integral_of_sea_water_potential_temperature_wrt_depth_expressed_as_heat_
> content for consistency is no longer required.
> 
> 
> Regarding Jonathan comments, I think we (Eric, Kevin, myself) are fine with
> "thickness", "thickness_change", "height" or "height_change" for the steric,
> halosteric and thermosteric contributions as long as it is consistent for the
> three standard names and other related names.
> 
> In the future, we may want to produce the steric, halosteric and thermosteric
> contributions of each water cell of the column, not only for the whole water
> column. The definitions of the present standard names and the