Dear Alison,
Once again, you have done a very impressive job! Thanks so much for your
attention to detail. Please see below for my responses to your questions.
In particular see sections 2, 4, and 5.
On Wed, 29 Mar 2017, [email protected] wrote:
Dear All,
I have been reviewing the remaining biogeochemistry standard name
proposals for the CMIP6 OMIP experiment. Names that were previously
accepted have already been published in the standard name table. I
have now accepted some more names and these have been included in this
week's standard name table update.
Many discussion points have been resolved but there is one outstanding
question, affecting over 50 proposals, regarding whether some
quantities need new 'sea_surface' names or whether they should be
treated as full 3D quantities. Please see section 4 below for further
details. If we can reach a decision on this point then I think many
more of the remaining biogeochemistry proposals can be quickly
resolved.
This is a rather lengthy email as I've tried to cover all the
outstanding issues in one go. (I am aware of the thread discussing
"Silicate vs. dissolved inorganic silicon" and will address that
separately. I will also post separately regarding the physics standard
name proposals for OMIP).
1. tendency_of_ocean_mole_content_of_[in]organic_carbon names
...
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
...
These five names are accepted and have been included in this week's standard
name table update.
Excellent.
2. Natural/abiotic names
We have had an extended discussion on both the wording and the
definitions of these names. We have now reached agreement on names of
the form
mole_concentration_of_dissolved_inorganic_carbon_natural_analogue_in_sea_water
mole_concentration_of_dissolved_inorganic_carbon_abiotic_analogue_in_sea_water
in which the 'analogue' names are effectively part of the description of the
chemical species.
The corresponding definitions for the two above examples are as follows:
mole_concentration_of_dissolved_inorganic_carbon_natural_analogue_in_sea_water,
mol m-3
...
mole_concentration_of_dissolved_inorganic_carbon_abiotic_analogue_in_sea_water,
mol m-3
...
These two names are accepted and have been included in this week's standard
name table update.
Very good.
Following this pattern we then also have the following names:
mole_concentration_of_carbonate_abiotic_analogue_expressed_as_carbon_in_sea_water,
mol m-3
...
(Previously this one was
mole_concentration_of_abiotic_carbonate_expressed_as_carbon_in_sea_water)
mole_concentration_of_carbonate_natural_analogue_expressed_as_carbon_in_sea_water,
mol m-3
...
(This one was previously
mole_concentration_of_natural_carbonate_expressed_as_carbon_in_sea_water).
surface_downward_mass_flux_of_carbon_dioxide_abiotic_analogue_expressed_as_carbon,
kg m-2 s-1
...
(Previously this one was
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_abiotic_component)
surface_downward_mass_flux_of_carbon_dioxide_natural_analogue_expressed_as_carbon,
kg m-2 s-1
...
(This one was previously
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_natural_component).
These four names are accepted and have been included in this week's
standard name table update.
Very good as well.
We have also discussed and agreed that the analogue syntax can be
applied to carbon dioxide partial pressure names. It was pointed out
that the definitions should contain a sentence explaining the meaning
of partial pressure in sea water. For the partial pressure difference
names I have added a sentence about the sign convention. There are
four partial pressure names:
surface_partial_pressure_of_carbon_dioxide_natural_analogue_in_sea_water, Pa
'The surface called "surface" means the lower boundary of the
atmosphere. 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. 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.'
(This one was previously
surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_natural_component).
Since what is referred to here is the partial pressure in seawater, the last
sentence above should be deleted. It refers to the partial pressure in air.
surface_partial_pressure_of_carbon_dioxide_abiotic_analogue_in_sea_water, Pa
' The surface called "surface" means the lower boundary of the
atmosphere. The chemical formula for carbon dioxide is CO2. 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. 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.'
(This one was previously
surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_abiotic_component).
Again, the last sentence should be deleted.
surface_carbon_dioxide_natural_analogue_partial_pressure_difference_between_sea_water_and_air,
Pa
'The surface called "surface" means the lower boundary of the
atmosphere. 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. 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 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
difference between sea water and air is positive when the partial
pressure of the dissolved gas in sea water is greater than the partial
pressure in air.'
(This one was previously
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_natural_component).
The removed sentence from the previous variable description should be inserted
here as the second to last sentence. This is, the partial pressure in air needs
to be defined before describing the difference in partial pressure between air
and sea.
surface_carbon_dioxide_abiotic_analogue_partial_pressure_difference_between_sea_water_and_air,
Pa
'The surface called "surface" means the lower boundary of the
atmosphere. The chemical formula for carbon dioxide is CO2. 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. 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
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 difference between sea water and air is positive when the
partial pressure of the dissolved gas in sea water is greater than the
partial pressure in air.'
(This one was previously
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_abiotic_component)
Also, insert the same removed sentence as the second to last
sentence here.
These four names are accepted and have been included in this week's
standard name table update.
Good. Even better if my remarks for the 4 variables above could be taken into
account.
We have not so far discussed the proposed ph and alkalinity names, but
I think the analogue syntax could equally well be applied to these as
to the other natural/abiotic names. Paul, Jim and John, if you are
happy with the following three names and definitions then they can be
accepted and included in the April standard name table update.
sea_water_ph_natural_analogue_reported_on_total_scale,1
'sea_water_pH_reported_on_total_scale is the measure of acidity of sea
water, defined as the negative logarithm of the activity of dissolved
hydrogen ions plus bisulfate ions in a sea water medium; it can be
measured or calculated; when measured the scale is defined according
to a series of buffers prepared in artificial seawater containing
bisulfate. The quantity may be written as pH(total) = -log([H+](free)
+ [HSO4-]). 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.'
(Previously this one was
sea_water_ph_reported_on_total_scale_due_to_natural_component).
sea_water_ph_abiotic_analogue_reported_on_total_scale, 1
'sea_water_pH_reported_on_total_scale is the measure of acidity of sea water,
defined as the negative logarithm of the activity of dissolved hydrogen ions
plus bisulfate ions in a sea water medium; it can be measured or calculated;
when measured the scale is defined according to a series of buffers prepared
in artificial seawater containing bisulfate. The quantity may be written as
pH(total) = -log([H+](free) + [HSO4-]). 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.'
(Previously this one was
sea_water_ph_reported_on_total_scale_due_to_abiotic_component).
The two new "sea_water_ph_*" names are quite fine except for one word in each
description. That is, the word "activity" should be changed to "concentration".
In oceanography (e.g., on the total scale)
pH = -log10[H+]
where [H+] is the hydrogen ion concentration, not its activity. The H+ activity
is used in other definitions of pH, but not in oceangraphy, not nowadays anyway.
sea_water_alkalinity_natural_analogue_expressed_as_mole_equivalent, mol m-3
'sea_water_alkalinity_expressed_as_mole_equivalent is the total alkalinity
equivalent concentration (including carbonate, nitrogen, silicate, and borate
components). 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.'
(Previously this one was
sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component).
OK?
This modified name for "sea_water_alkalinity_natural_analogue*" is fine by me.
There are eight further 'natural' and 'abiotic' names still under discussion.
These are covered in sections 3 and 4 below because they are either carbon
isotope names or proposed 'surface' names.
3. Carbon13 and carbon14 names.
There was some discussion on the 'expressed_as' part of the carbon13 and
carbon14 names. Due to the formulation of the fluxes in the OMIP experiment it
was suggested that the names should take the following form:
surface_downward_mass_flux_of_carbon13_dioxide_expressed_as_carbon13_due_to_abiotic_component
surface_downward_mass_flux_of_carbon14_dioxide_expressed_as_carbon_due_to_abiotic_component.
Based on both the isotope discussion and the abiotic/natural discussion in (2)
above, I suggest now that these names and definitions should be:
surface_downward_mass_flux_of_carbon13_dioxide_abiotic_analogue_expressed_as_carbon13,
kg m-2 s-1
...
surface_downward_mass_flux_of_carbon14_dioxide_abiotic_analogue_expressed_as_carbon,
kg m-2 s-1
...
If you are happy with these names they can be accepted and included in the
April standard name table update.
I am happy with both of these new names.
4. When is a surface not a surface?
There are 3 proposed names for surface fluxes. Such names clearly refer to
conditions at the air/sea interface and it is correct to label them as surface
quantities. Those names are excluded from the discussion in this section.
There are 51 proposed names referring to 'surface_mole_concentration',
'surface_mass_concentration', 'surface_sea_water_ph' and
'surface_sea_water_alkalinity'. These are the names I want to discuss here. We
have already had some discussion of these names on the mailing list and there
has been some further on and off-list discussion over the last couple of days.
So far we have not arrived at consensus, but it is important that we try to do
so now to allow the majority of the remaining OMIP names to be accepted. I
will attempt to summarize the discussion and then make a recommendation as to
how I think we should proceed.
The reason for the discussion is that the surface concentration and alkalinity
names have all been proposed with units of mol m-3 or kg m-3, which indicates
that the named quantities are intended to represent 'near surface' layer
concentrations, i.e., the top one or two levels in an ocean model. Although
the ph names are dimensionless it is clear that these also are intended to
represent a near surface layer. In CF standard names it is inappropriate to
refer to these layer quantities simply as 'surface' quantities because the
term 'surface' is defined as 'the lower boundary of the atmosphere', i.e. it
is the exact interface between air and sea which therefore has no thickness or
volume and is therefore unsuitable for use with units of m-3.
At an earlier point in the discussion
(http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/059044.html) I
mentioned that we have a small number of existing sea_surface names - these
are near surface layer quantities and nearly all relate to specific
definitions of sea surface temperature, e.g., sea_surface_skin_temperature is
defined as 'the temperature within the conductive diffusion-dominated
sub-layer at a depth of approximately 10 - 20 micrometers below the air-sea
interface'. The only generic quantity is sea_surface_temperature which is a
deliberately vague term to cover different definitions of SST that have been
used historically, for example, when making temperature measurements using the
water in a ship's engine intake or by lowering a bucket over the side. These
are all in some sense 'near surface' values but the depth of measurement can
vary widely and in some cases may not even be recorded. I did toy with the
idea that for OMIP we could have 'sea_surface' names for near-surface
quantities because this would at least be consistent with the m-3 in the
units. However, I don't think this is the most satisfactory approach because
the OMIP quantities can perfectly well be described by using standard names
that can apply to quantities at any depth in conjunction with coordinate
variables and coordinate bounds to state the actual depth and thickness of the
surface layer. Even if we did introduce sea_surface names for OMIP it would
still be necessary to supply the coordinate information in other metadata
attributes to fully describe the location of the data, so it wouldn't do
anything to reduce the amount of metadata that would need to be provided. Not
to supply this metadata would render the data far less useful. Furthermore,
other contributors to the discussion (Roy, Jonathan) have clearly expressed
the view that we should not generalise the rather specialised
sea_surface_temperature approach to other variables.
In his most recent post, Jim has said that many fields will be output as 2D
quantities in order to reduce the amount of data generated for OMIP. Karl has
already explained that from a CMIP6 viewpoint this is perfectly consistent
with using standard names that could equally well apply to 3D quantities. It
is also consistent with usual practice in CF. There is no limitation on the
number of data variables in a CF-NetCDF file that can have the same standard
name and they do not all have to have the same dimensions, so it's even
possible to have 2D and 3D fields with the same standard name in the same
file. The important point for data users is not to rely solely on the standard
name to decide how to treat a variable, but also to examine many other
metadata attributes such as coordinate variables, coordinate bounds and
cell_methods. This is the always the correct way to work with CF metadata.
Indeed, I would argue that the most 'standard' way to record the OMIP
near-surface data in your files is to follow the practice I described earlier:
use standard names that can apply to any depth and supply coordinate variables
and coordinate bounds to state the actual depth and thickness of the surface
layer. I think users of the data are more likely to discover data named in
this way than if we introduce special sea_surface names for some quantities.
Also, this approach significantly reduces the number of new standard names
needed for OMIP. For example, the proposed name
[sea_]surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water
could be dropped in favour of using the existing name
mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water. Again, it is
standard practice in the CF community to avoid adding new standard names that
are not strictly necessary.
Based on the above arguments I recommend that we follow the second approach
and don't introduce separate sea_surface names. Please can those of you who
have been engaged in this discussion indicate whether you are in agreement. If
we can get consensus, or at least a clear majority on which approach to use,
then many of the outstanding names can be accepted very quickly. If we are
unable to reach a decision through this discussion, then I will need to call
on the CF committee to vote on their preferred approach. The committee's
decision will be final. This is in accordance with usual CF procedures.
It would be great if we could come to an agreement on this issue by ourselves,
without having to bother the CF committee.
If we adopt the idea to use the same name for variables whether they are 3-D
(full water column) or 2-D (sea surface only), that could confuse typical users
of the CMIP6 data. For CMIP5, users searched for available data files based on
variable names along with other criteria in the CMIP5 Data Reference Syntax
(DRS), which includes keywords for Institute, Model, Experiment, Frequency,
Realm, MIP Table, Ensemble, Version, Variable, and Temporal Subset. No keyword
currently exists for spatial dimensions. So removing "sea surface" from the
variable names would not be optimal unless a new keyword such as "Spatial
Domain" could be added to the CMIP6 DRS.
Paul, is this something that could be considered for CMIP6? Otherwise, I would
prefer to keep the "sea surface" prefix, as previously adopted for the physical
variables, 'sea surface temperature' and 'sea surface salinity' (tos, sos).
As for having 2 variables in the same file with the same name but different
shapes or dimensions, that would be confusing, both to users and to software
that is often used to analyze model output. Would CMIP6 even allow such a
practice. In any case, because the Temporal frequency of the 2 variables would
differ, that solution does not seem practical.
5. Miscellaneous questions
Apart from the discussions outlined in the preceding sections, there are a few
names about which I have specific questions.
a. surface_downward_mass_flux_of_carbon_dioxide (kg m-2 s-1)
We have an existing standard name,
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon (kg m-2 s-1)
defined as ' "Downward" indicates a vector component which is positive when
directed downward (negative upward). The phrase 'expressed_as' is used in the
construction A_expressed_as_B, where B is a chemical constituent of A. It
means that the quantity indicated by the standard name is calculated solely
with respect to the B contained in A, neglecting all other chemical
constituents of A. In accordance with common usage in geophysical disciplines,
"flux" implies per unit area, called "flux density" in physics. The surface
called "surface" means the lower boundary of the atmosphere. The chemical
formula for carbon dioxide is CO2.'
I think this existing name may be the one you need. Do you agree?
Yes, I would prefer to use the existing name instead, which implies that we are
referring to kg C m-2 s-1 instead of kg CO2 m-2 s-1.
b.
surface_mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_water
(mol m-3)
and
surface_mole_concentration_of_particulate_organic_matter_expressed_as_nitrogen_in_sea_water
(mol m-3)
We have existing 3D names for these, i.e., without the 'surface_' at the
beginning, so depending on the outcome of the discussion in section 4 we may
not actually need to introduce new names for these quantities. However, a
separate question relates to the definitions. Currently in standard names we
define organic detritus as 'particles of debris from decaying plants and
animals'. We don't have a definition for 'particulate_organic_matter' in sea
water. I'd like to understand the difference between 'organic_detritus' and
'particulate_organic_matter'. In the latter case, does it mean 'organic' in
the sense of organic chemistry, rather than biological life forms? That would
certainly be consistent with the way the term is used in atmosphere names.
Yes, 'organic' here should be thought of in the chemical (biogeochemical) sense.
That is, it is not inorganic.
c. tendency_of_ocean_mole_content_of_nitrogen_due_to_biological_production
What is meant here by 'nitrogen'? Does it mean atomic nitrogen, molecular
nitrogen, all chemical species containing nitrogen atoms, or something else?
I think John Dunne would be the best person to answer this question.
d.
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_remineralization
Please can you supply a (brief) explanation of the term 'remineralization'
that we can include in the definitions.
Remineralization is the degradation of organic matter into inorganic forms of
carbon, nitrogen, phosphorus and other micronutrients, which consumes oxygen and
releases energy.
e.
mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite
(mol m-3) and
mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite
(mol m-3)
Are we talking here about an equilibrium between dissolution and precipitation
of calcite and aragonite, i.e., mole concentrations in chemically saturated
solutions? If so, then we have existing names for these:
mole_concentration_of_aragonite_expressed_as_carbon_in_sea_water_at_saturation
(mol m-3)
' 'Mole concentration' means number of moles per unit volume, also
called"molarity", and is used in the construction
mole_concentration_of_X_in_Y, whereX is a material constituent of Y. A
chemical or biological species denoted by X may be described by a single term
such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Mole
concentration at saturation means the mole concentration in a saturated
solution. The phrase 'expressed_as' is used in the construction
A_expressed_as_B, where B is a chemical constituent of A. It means that the
quantity indicated by the standard name is calculated solely with respect to
the B contained in A, neglecting all other chemical constituents of A.
Aragonite is a mineral that is a polymorph of calcium carbonate. The chemical
formula of aragonite is CaCO3. Standard names also exist for calcite, another
polymorph of calcium carbonate.'
mole_concentration_of_calcite_expressed_as_carbon_in_sea_water_at_saturation
(mol m-3)
' 'Mole concentration' means number of moles per unit volume, also
called"molarity", and is used in the construction
mole_concentration_of_X_in_Y, whereX is a material constituent of Y. A
chemical or biological species denoted by X may be described by a single term
such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Mole
concentration at saturation means the mole concentration in a saturated
solution.The phrase 'expressed_as' is used in the construction
A_expressed_as_B, where B is a chemical constituent of A. It means that the
quantity indicated by the standard name is calculated solely with respect to
the B contained in A, neglecting all other chemical constituents of A. Calcite
is a mineral that is a polymorph of calcium carbonate. The chemical formula of
calcite is CaCO3. Standard names also exist for aragonite, another polymorph
of calcium carbonate.'
Do these look like the ones you need?
No. We are talking here about an equilibrium between dissolution and
precipitation of calcite and aragonite, i.e., mole concentrations in chemically
saturated solutions, but the existing names that you mention still do not work.
While carbonate ion (CO32-) is dissolved in seawater, aragonite and calcite (2
different forms of CaCO3) are not. Both calcite and aragonite are solids.
Once formed, they precipitate out. At a given salinity, the thermodynamic
equilibrium that is mentioned refers to that between dissolved carbonate ion and
CaCO3, a solid (pure aragonite and calcite).
Ca2+ + CO32- <-> CaCO3(s)
Therefore, we must refer to "mole_concentration_of_carbonate_*" and not to
"mole_concentration_of_aragonite_* and "mole_concentration_of_calcite_*".
Many thanks,
Jim
--
LSCE/IPSL, Laboratoire des Sciences du Climat et de l'Environnement
CEA-CNRS-UVSQ
LSCE/IPSL, CEA Saclay http://www.ipsl.jussieu.fr/~jomce
Bat. 712 - Orme mailto: [email protected]
Point courrier 132
F-91191 Gif-sur-Yvette Cedex Phone: (33) (0)1 69 08 39 73
FRANCE Fax: (33) (0)1 69 08 30 73
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