From 6df4ab1082e8a9b5c303f3934e7561f6dab894ab Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Thu, 7 Jun 2018 11:43:04 -0600 Subject: [PATCH 1/2] Add scientific description to docs --- docs/src/references.bib | 79 ++++++++++++++++++++++-- docs/src/sci-guide/index.rst | 1 + docs/src/sci-guide/light-attenuation.rst | 23 ++++--- docs/src/sci-guide/sci-description.rst | 30 +++++++++ 4 files changed, 117 insertions(+), 16 deletions(-) create mode 100644 docs/src/sci-guide/sci-description.rst diff --git a/docs/src/references.bib b/docs/src/references.bib index 9918fb6d..6cec8d4f 100644 --- a/docs/src/references.bib +++ b/docs/src/references.bib @@ -1,20 +1,91 @@ -@Article{Morel-Maritorena-2001, +@article{Moore-2008, + Author = {J. K. Moore and O. Braucher}, + Date-Added = {2018-06-07 17:29:42 +0000}, + Date-Modified = {2018-06-07 17:30:17 +0000}, + Journal = {Biogeosciences}, + Pages = {631--656}, + Title = {Sedimentary and mineral dust sources of dissolved iron to the world ocean}, + Volume = {5}, + Year = {2008}} + +@article{Moore-2007, + Author = {J. K. Moore and S. C. Doney}, + Date-Added = {2018-06-07 17:29:04 +0000}, + Date-Modified = {2018-06-07 17:29:35 +0000}, + Journal = {Global Biogeochem. Cycles}, + Title = {Iron availability limits the ocean nitrogen inventory stabilizing feedbacks between marine denitrification and nitrogen fixation}, + Volume = {21}, + Year = {2007}} + +@article{Moore-2004, + Author = {J. K. Moore and S. C. Doney and K. Lindsay}, + Date-Added = {2018-06-07 17:17:57 +0000}, + Date-Modified = {2018-06-07 17:18:35 +0000}, + Journal = {Global Biogeochem. Cycles}, + Title = {Upper ocean ecosystem dynamics and iron cycling in a global three-dimensional model}, + Volume = {18}, + Year = {2004}} + +@article{Moore-2002, + Author = {J. K. Moore and S. Doney and J. Kleypas and D. Glover and I. Fung}, + Date-Added = {2018-06-07 17:16:25 +0000}, + Date-Modified = {2018-06-07 17:17:17 +0000}, + Journal = {Deep-Sea Res. II}, + Pages = {403--462}, + Title = {An intermediate complexity marine ecosystem model for the global domain}, + Volume = {49}, + Year = {2002}} + +@article{Krishnamurthy-2007, + Author = {A. Krishnamurthy and J. K. Moore and C. S. Zender and C. Luo}, + Date-Added = {2018-06-07 17:13:45 +0000}, + Date-Modified = {2018-06-07 17:14:36 +0000}, + Journal = {J. Geophys. Res.}, + Title = {The effects of atmospheric inorganic nitrogen deposition on ocean biogeochemistry}, + Volume = {112}, + Year = {2007}} + +@article{Geider-1998, + Author = {R. Geider and H. MacIntyre and T. Kana}, + Date-Added = {2018-06-07 17:11:13 +0000}, + Date-Modified = {2018-06-07 17:12:03 +0000}, + Journal = {Limnology and Oceanography}, + Pages = {679--694}, + Title = {A dynamic regulatory model of phytoplankton acclimation to light, nutrients, and temperature}, + Volume = {43}, + Year = {1998}} + +@article{Doney-2009, + Author = {S. C. Doney and I. Lima and J.K. Moore and K. Lindsay and M.J. Behrenfeld and T.K. Westberry and N. Mahowald and D.M. Glover and T. Takahashi}, + Date-Added = {2018-06-07 17:01:30 +0000}, + Date-Modified = {2018-06-07 17:03:16 +0000}, + Journal = {J. Mar. Systems}, + Pages = {95--112}, + Title = {Skill metrics for confronting global upper ocean ecosystem-biogeochemistry models against field and remote sensing data}, + Volume = {76}, + Year = {2009}} + +@article{Morel-2001, Author = {Morel, Andr{\'e} and Maritorena, St{\'e}phane}, Doi = {10.1029/2000jc000319}, + Date-Modified = {2018-06-07 17:00:54 +0000}, Journal = {J. Geophys. Res.}, Month = {Apr}, Number = {C4}, Pages = {7163--7180}, Title = {Bio-optical properties of oceanic waters: A reappraisal}, Volume = {106}, - Year = {2001}} + Year = {2001}, + Bdsk-Url-1 = {https://dx.doi.org/10.1029/2000jc000319}} -@article{Morel-1998, +@article{Morel-1988, Author = {Morel, Andr{\'e}}, Doi = {10.1029/jc093ic09p10749}, + Date-Modified = {2018-06-07 16:57:25 +0000}, Journal = {J. Geophys. Res.}, Number = {C9}, Pages = {10749-10768}, Title = {{Optical modeling of the upper ocean in relation to its biogenous matter content (case I waters)}}, Volume = {93}, - Year = {1988}} + Year = {1988}, + Bdsk-Url-1 = {https://dx.doi.org/10.1029/jc093ic09p10749}} diff --git a/docs/src/sci-guide/index.rst b/docs/src/sci-guide/index.rst index a844189b..9ede688e 100644 --- a/docs/src/sci-guide/index.rst +++ b/docs/src/sci-guide/index.rst @@ -8,5 +8,6 @@ MARBL scientific documentation :maxdepth: 1 :caption: Contents: + sci-description.rst phytoplankton-growth.rst light-attenuation.rst diff --git a/docs/src/sci-guide/light-attenuation.rst b/docs/src/sci-guide/light-attenuation.rst index 2320edc2..5a7e0536 100644 --- a/docs/src/sci-guide/light-attenuation.rst +++ b/docs/src/sci-guide/light-attenuation.rst @@ -4,11 +4,11 @@ Light attenuation formulation =============================== -Starting point is equation 6 of :cite:`Morel-Maritorena-2001` +Starting point is equation 6 of :cite:`Morel-2001` .. math:: :label: ze_chl_tot - + Z_e = \begin{cases} 912.5 \left[ \mathrm{Chl_{tot}} \right]^{-0.839} & 10 < Z_e < 102 \\ @@ -24,9 +24,9 @@ averaged over the euphotic zone .. math:: :label: chl_tot_def - + \left[ \mathrm{Chl_{tot}} \right] = Z_e \overline{\left[ \mathrm{Chl} \right]} - + The crossover point :math:`Z_e=102` corresponds to :math:`\left[ \mathrm{Chl_{tot}} \right]=13.65`, which is equivalent to :math:`\overline{\left[ \mathrm{Chl} \right]}=0.1338`. @@ -39,12 +39,12 @@ and solving for :math:`Z_e` yields Z_e = \begin{cases} - 40.710 \overline{\left[ \mathrm{Chl} \right]}^{-0.4562} & \overline{\left[ \mathrm{Chl} \right]} > 0.1338 \\ - 50.105 \overline{\left[ \mathrm{Chl} \right]}^{-0.3536} & \overline{\left[ \mathrm{Chl} \right]} < 0.1338 + 40.710 \overline{\left[ \mathrm{Chl} \right]}^{-0.4562} & \overline{\left[ \mathrm{Chl} \right]} > 0.1338 \\ + 50.105 \overline{\left[ \mathrm{Chl} \right]}^{-0.3536} & \overline{\left[ \mathrm{Chl} \right]} < 0.1338 \end{cases} The euphotic zone depth is defined to be the depth where PAR is 1\% of its surface value -:cite:`Morel-1998`. +:cite:`Morel-1988`. We denote the attenuation coefficient of PAR as :math:`K`, and its effective average over the euphotic zone as :math:`\overline{K}`. @@ -67,7 +67,7 @@ solving for :math:`\overline{K}` yields .. math:: :label: Kbar_chl_avg - + \overline{K} = \begin{cases} 0.1131 \overline{\left[ \mathrm{Chl} \right]}^{0.4562} & \overline{\left[ \mathrm{Chl} \right]} > 0.1338 \\ @@ -85,7 +85,6 @@ The units of :math:`K` in equation :eq:`Kbar_chl_avg` are 1/m. Model units are cm, so the model implementation includes multiplication by 0.01. .. rubric:: References - -.. bibliography:: ../references.bib - :cited: - + +.. bibliography:: ../references.bib + :filter: docname in docnames diff --git a/docs/src/sci-guide/sci-description.rst b/docs/src/sci-guide/sci-description.rst new file mode 100644 index 00000000..2b6a32f4 --- /dev/null +++ b/docs/src/sci-guide/sci-description.rst @@ -0,0 +1,30 @@ +.. _sci-description: + +====================== +Scientific description +====================== + +The default MARBL configuration invokes the Biogeochemical Elemental Cycling (BEC) model :cite:`Moore-2004`. which is an ecosystem/biogeochemistry model designed to run within the ocean circulation component of CESM. + +The ecosystem includes multiple phytoplankton functional groups (diatoms, diazotrophs, small phytoplankton, and coccolithophores) and multiple potentially growth limiting nutrients (nitrate, ammonium, phosphate, silicate, and iron) :cite:`Moore-2002,Moore-2004`. +There is one zooplankton group, dissolved organic material (semi-labile), sinking particulate pools and explicit simulation of the biogeochemical cycling of key elements (C, N, P, Fe, Si, O, plus alkalinity) :cite:`Moore-2004`. +The ecosystem component is coupled with a carbonate chemistry module based on the Ocean Carbon Model Intercomparison Project (OCMIP) :cite:`Doney-2009` allowing dynamic computation of surface ocean pCO2 and air-sea CO2 flux. + +The model allows for water column denitrication, whereby nitrate is consumed during remineralization in place of O2 once ambient O2 concentrations fall below 4 micro-molar :cite:`Moore-2007`. +Photoadaptation is calculated as a variable phytoplankton ratio of chlorophyll to nitrogen based on :cite:`Geider-1998`. +The model allows for variable Fe/C and Si/C ratios with an optimum and minimum value prescribed. +As ambient Fe (or Si for diatoms) concentrations decline the phytoplankton lower their cellular quotas. +Phytoplankton N/P ratios are fixed at the Redfield value of 16, but the diazotroph group has a higher N/P atomic ratio of 50 (see detailed description of the model in :cite:`Moore-2002` and :cite:`Moore-2004`). +Thus, community N/P uptake varies with the phytoplankton community composition. + +The ecosystem model results have been compared extensively against in situ data (e.g., JGOFS time series stations) and SeaWiFS satellite ocean color observations in a global mixed layer only variant and coupled with a full-depth, global 3-D general circulation model :cite:`Moore-2002,Moore-2004,Doney-2009`. +In both cases, the simulated output is in generally good agreement with bulk ecosystem observations (e.g., total biomass, productivity, nutrients, export) across diverse ecosystems that include both macro-nutrient and iron-limited regimes as well as very different physical environments from high latitude sites to the mid-ocean gyres. +The model also incorporates the work of :cite:`Moore-2008`, who incorporated an improved sedimentary iron source and scavenging parameterization, greatly improving simulated iron fields relative to observations, and the work of :cite:`Krishnamurthy-2007`, who describe the impact of atmospheric deposition of nitrogen. + +.. note:: + This description is still under development. + +.. rubric:: References + +.. bibliography:: ../references.bib + :filter: docname in docnames From fb0c2396ba1fe204b37264e6aa53f59280688462 Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Thu, 7 Jun 2018 13:43:04 -0600 Subject: [PATCH 2/2] Move scientific description Description is now on the main science guide page --- docs/src/sci-guide/index.rst | 28 +++++++++++++++++++++- docs/src/sci-guide/light-attenuation.rst | 4 +++- docs/src/sci-guide/sci-description.rst | 30 ------------------------ 3 files changed, 30 insertions(+), 32 deletions(-) delete mode 100644 docs/src/sci-guide/sci-description.rst diff --git a/docs/src/sci-guide/index.rst b/docs/src/sci-guide/index.rst index 9ede688e..4ab94f10 100644 --- a/docs/src/sci-guide/index.rst +++ b/docs/src/sci-guide/index.rst @@ -4,10 +4,36 @@ MARBL scientific documentation ============================== +The default MARBL configuration invokes the Biogeochemical Elemental Cycling (BEC) model :cite:`Moore-2004`. which is an ecosystem/biogeochemistry model designed to run within the ocean circulation component of CESM. + +The ecosystem includes multiple phytoplankton functional groups (diatoms, diazotrophs, small phytoplankton, and coccolithophores) and multiple potentially growth limiting nutrients (nitrate, ammonium, phosphate, silicate, and iron) :cite:`Moore-2002,Moore-2004`. +There is one zooplankton group, dissolved organic material (semi-labile), sinking particulate pools and explicit simulation of the biogeochemical cycling of key elements (C, N, P, Fe, Si, O, plus alkalinity) :cite:`Moore-2004`. +The ecosystem component is coupled with a carbonate chemistry module based on the Ocean Carbon Model Intercomparison Project (OCMIP) :cite:`Doney-2009` allowing dynamic computation of surface ocean pCO2 and air-sea CO2 flux. + +The model allows for water column denitrication, whereby nitrate is consumed during remineralization in place of O2 once ambient O2 concentrations fall below 4 micro-molar :cite:`Moore-2007`. +Photoadaptation is calculated as a variable phytoplankton ratio of chlorophyll to nitrogen based on Geider et al. :cite:`Geider-1998`. +The model allows for variable Fe/C and Si/C ratios with an optimum and minimum value prescribed. +As ambient Fe (or Si for diatoms) concentrations decline the phytoplankton lower their cellular quotas. +Phytoplankton N/P ratios are fixed at the Redfield value of 16, but the diazotroph group has a higher N/P atomic ratio of 50 (see detailed description of the model in Moore et al., 2002 :cite:`Moore-2002`, and Moore et al., 2004 :cite:`Moore-2004`). +Thus, community N/P uptake varies with the phytoplankton community composition. + +The ecosystem model results have been compared extensively against in situ data (e.g., JGOFS time series stations) and SeaWiFS satellite ocean color observations in a global mixed layer only variant and coupled with a full-depth, global 3-D general circulation model :cite:`Moore-2002,Moore-2004,Doney-2009`. +In both cases, the simulated output is in generally good agreement with bulk ecosystem observations (e.g., total biomass, productivity, nutrients, export) across diverse ecosystems that include both macro-nutrient and iron-limited regimes as well as very different physical environments from high latitude sites to the mid-ocean gyres. +The model also incorporates the work of Moore and Braucher :cite:`Moore-2008`, who incorporated an improved sedimentary iron source and scavenging parameterization, greatly improving simulated iron fields relative to observations, and the work of Krishnamurthy et al. :cite:`Krishnamurthy-2007`, who describe the impact of atmospheric deposition of nitrogen. + +.. note:: + This description is still under development. + .. toctree:: :maxdepth: 1 :caption: Contents: - sci-description.rst phytoplankton-growth.rst light-attenuation.rst + +.. only:: html + + .. rubric:: References + +.. bibliography:: ../references.bib + :filter: docname in docnames diff --git a/docs/src/sci-guide/light-attenuation.rst b/docs/src/sci-guide/light-attenuation.rst index 5a7e0536..5c78880f 100644 --- a/docs/src/sci-guide/light-attenuation.rst +++ b/docs/src/sci-guide/light-attenuation.rst @@ -84,7 +84,9 @@ The units of :math:`K` in equation :eq:`Kbar_chl_avg` are 1/m. Model units are cm, so the model implementation includes multiplication by 0.01. -.. rubric:: References +.. only:: html + + .. rubric:: References .. bibliography:: ../references.bib :filter: docname in docnames diff --git a/docs/src/sci-guide/sci-description.rst b/docs/src/sci-guide/sci-description.rst deleted file mode 100644 index 2b6a32f4..00000000 --- a/docs/src/sci-guide/sci-description.rst +++ /dev/null @@ -1,30 +0,0 @@ -.. _sci-description: - -====================== -Scientific description -====================== - -The default MARBL configuration invokes the Biogeochemical Elemental Cycling (BEC) model :cite:`Moore-2004`. which is an ecosystem/biogeochemistry model designed to run within the ocean circulation component of CESM. - -The ecosystem includes multiple phytoplankton functional groups (diatoms, diazotrophs, small phytoplankton, and coccolithophores) and multiple potentially growth limiting nutrients (nitrate, ammonium, phosphate, silicate, and iron) :cite:`Moore-2002,Moore-2004`. -There is one zooplankton group, dissolved organic material (semi-labile), sinking particulate pools and explicit simulation of the biogeochemical cycling of key elements (C, N, P, Fe, Si, O, plus alkalinity) :cite:`Moore-2004`. -The ecosystem component is coupled with a carbonate chemistry module based on the Ocean Carbon Model Intercomparison Project (OCMIP) :cite:`Doney-2009` allowing dynamic computation of surface ocean pCO2 and air-sea CO2 flux. - -The model allows for water column denitrication, whereby nitrate is consumed during remineralization in place of O2 once ambient O2 concentrations fall below 4 micro-molar :cite:`Moore-2007`. -Photoadaptation is calculated as a variable phytoplankton ratio of chlorophyll to nitrogen based on :cite:`Geider-1998`. -The model allows for variable Fe/C and Si/C ratios with an optimum and minimum value prescribed. -As ambient Fe (or Si for diatoms) concentrations decline the phytoplankton lower their cellular quotas. -Phytoplankton N/P ratios are fixed at the Redfield value of 16, but the diazotroph group has a higher N/P atomic ratio of 50 (see detailed description of the model in :cite:`Moore-2002` and :cite:`Moore-2004`). -Thus, community N/P uptake varies with the phytoplankton community composition. - -The ecosystem model results have been compared extensively against in situ data (e.g., JGOFS time series stations) and SeaWiFS satellite ocean color observations in a global mixed layer only variant and coupled with a full-depth, global 3-D general circulation model :cite:`Moore-2002,Moore-2004,Doney-2009`. -In both cases, the simulated output is in generally good agreement with bulk ecosystem observations (e.g., total biomass, productivity, nutrients, export) across diverse ecosystems that include both macro-nutrient and iron-limited regimes as well as very different physical environments from high latitude sites to the mid-ocean gyres. -The model also incorporates the work of :cite:`Moore-2008`, who incorporated an improved sedimentary iron source and scavenging parameterization, greatly improving simulated iron fields relative to observations, and the work of :cite:`Krishnamurthy-2007`, who describe the impact of atmospheric deposition of nitrogen. - -.. note:: - This description is still under development. - -.. rubric:: References - -.. bibliography:: ../references.bib - :filter: docname in docnames