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Update documentation with historical background #310

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mnlevy1981 opened this issue Aug 20, 2018 · 0 comments
Open

Update documentation with historical background #310

mnlevy1981 opened this issue Aug 20, 2018 · 0 comments
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Sphinx Documentation This issue refers to the documentation generated by sphinx in docs/
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@mnlevy1981
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We have the following comments in marbl_mod.F90 and marbl_ciso_mod.F90:

  !  Multispecies ecosystem based on Doney et al. 1996, Moore et al., 2002
  !  Based on POP Global NCAR Nitrogen Ecosystem Model
  !  version 0.0 (June 15th, 1998) from S.C. Doney.
  !  Based on Doney et al., 1996 model.
  !  Climate and Global Dynamics, NCAR
  !  (doney@whoi.edu)
  !
  !  Version 1.0
  !  Multispecies, multiple limiting nutrient version of ecosystem
  !  based on mixed layer model of Moore et al.(2002).  Implemented here with
  !  fixed elemental ratios and including only the diatoms and small
  !  phytoplankton, with a parameterization of calcification,
  !  by Keith Lindsay and Keith Moore, Fall 2001 - Spring 2002.
  !  Calcification parameterization based on Moore et al. 2002.
  !
  !  Version 2.0, January 2003
  !    Adds diazotrophs as a phytoplankton group, (based on Moore et al., 2002a)
  !    Allows for variable fe/C for all phytoplankton groups
  !     Allows for variable si/C for the diatoms
  !     Adds explicit tracers for DON, DOP, DOFe
  !     variable remin length scale for detrital soft POM and bSi f(temperature)
  !     Extensive modifications to iron scavenging parameterization
  !     Addition of a sedimentary dissolved iron source,
  !        (implemented in ballast code as excess remin in bottom cell)
  !        coded by J.K. Moore, (jkmoore@uci.edu)
  !
  !   Version 2.01. March 2003
  !     corrected O2 bug
  !     corrected grazing parameter z_grz bug at depth
  !     dust dissolution at depth releases iron,
  !     increased length scale for dust diss., increased hard fraction dust
  !     no deep ocean reduction in scavenging rates,
  !     increase bSi OC/ballast ratio 0.3 -> 0.35,
  !     corrected bug in diazotroph photoadaptation, and diat and sp adapatation
  !
  !   Version 2.02.
  !     corrected bug in Fe_scavenge (units for dust), May 2003
  !     changed C/N/P ratios to 117/16/1 (Anderson & Sarmiento, 1994)
  !
  !   Version 2.03., July 2003
  !     Remin of DOM no longer temperature dependent,
  !     new iron scavenging parameterization added,
  !     some dissolution of hard fraction of ballast materials added
  !
  !   Version 2.1, September 2003
  !     modfied iron scavenging and dust dissolution at depth
  !
  !   Version 2.11, March 2004
  !     fixed bug in iron scavenging code, replace dust and POC flux_in w/ flux_out
  !
  !   Version 2.12, April 2004 - Final version for GBC paper revision,
  !     (Questions/comments, Keith Moore - jkmoore@uci.edu
  !
  !   References
  !   Doney, S.C., Glover, D.M., Najjar, R.G., 1996. A new coupled, one-dimensional
  !   biological-physical model for the upper ocean: applications to the JGOFS
  !   Bermuda Time-Series Study (BATS) site. Deep-Sea Res. II, 43: 591-624.
  !
  !   Moore, JK, Doney, SC, Kleypas, JA, Glover, DM, Fung, IY, 2002. An intermediate
  !   complexity marine ecosystem model for the global domain. Deep-Sea Res. II, 49:
  !   403-462.
  !
  !   Moore, JK, Doney, SC, Glover, DM, Fung, IY, 2002. Iron cycling and nutrient
  !   limitation patterns in surface waters of the world ocean. Deep-Sea Res. II,
  !   49: 463-507.

and

  !-----------------------------------------------------------------------
  !  Carbon 13 module and biotic 14C module
  !  13C code is based on code form G. Xavier, ETH, 2010, which
  !  was written for pop1 (CCSM3)
  !  This code needs the ecosystem model to run, as it uses several
  !  variables computed there.
  !  This module adds 7 carbon pools for 13C and another 7 for 14C
  !
  !   References
  !   Jahn, A., K. Lindsay, X. Giraud, N. Gruber, B. L. Otto-Bliesner, Z. Liu,
  !   E. C. Brady, 2015. Carbon isotopes in the ocean model of the Community
  !   Earth System Model (CESM1). Geosci. Model Dev., 8: 2419-2434.
  !   doi:10.5194/gmd-8-2419-2015
  !-----------------------------------------------------------------------

With the changes coming from #308 to address #86, it seems clear that comments like these belong in the sphinx documentation rather than in the Fortran code. Perhaps on the landing page for the scientific documentation?

@mnlevy1981 mnlevy1981 added this to the MARBL1.0.0 milestone Aug 24, 2018
@mnlevy1981 mnlevy1981 added PR updates documentation Sphinx Documentation This issue refers to the documentation generated by sphinx in docs/ and removed PR updates documentation labels Aug 24, 2018
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