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Life and Fishery","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# UVic-updates-opem: Optimality-based Plankton Ecosystem Model (OPEM) for the UVic-ESCM\n\nMarkus Pahlow (mpahlow@geomar.de)\n\nUVic-updates-opem introduces optimality-based phytoplankton and zooplankton into the UVic-ESCM (version 2.9) with variable C:N:P(:Chl) stoichiometry for phytoplankton, diazotrophs, and detritus.  Code development started with and has incorporated updates provided by David Keller, Karin Kvale, and Levin Nickelsen.\n\n## Setup\n\n1. Clone the [UVic_ESCM-2.9](https://git.geomar.de/markus-pahlow/UVic_ESCM-2.9.git) to obtain the base code and data files\n2. Enter the `UVic_ESCM-2.9` folder and issue the commands `git submodule init`, `git submodule sync`, and `git submodule update`\n\nOPEM is activated via the compile-option `O_opem` and `Updates_Level = opem` in mk.in.  The first `Source_Directory` in mk.in must be set as `Source_Directory(1) = updates/opem/f90`.  A template [mk.in](mk.in) is provided in this project for compilation with ifort.  You must set the Version\\_Directory to the root folder of your UVic\\_ESCM-2.9 installation, i.e., where the mk executable and the run folder are.  Note that I also set Libraries, Compiler_F, etc. in mk.in.  Option `O_npzzd` switches on a second zooplankton compartment, but we have not used this yet.  Option `O_opem_chl` switches on dynamic chlorophyll tracers.  See also this [description of preprocessor options](options.md).  Here is a (still incomplete) commented [control.in](control.in).\n\n## Comments\n\n* Comment on O\u003csub\u003e2\u003c/sub\u003e and N\u003csub\u003e2\u003c/sub\u003e fixation: assimilatory nitrate reduction to ammonium releases 2 mol O\u003csub\u003e2\u003c/sub\u003e / mol N,\nHNO\u003csub\u003e3\u003c/sub\u003e + 1.5 H\u003csub\u003e2\u003c/sub\u003eO -\u003e NH\u003csub\u003e3\u003c/sub\u003e + 0.5 H\u003csub\u003e2\u003c/sub\u003eO + 2 O\u003csub\u003e2\u003c/sub\u003e, whereas N\u003csub\u003e2\u003c/sub\u003e fixation releases only 0.75 mol O\u003csub\u003e2\u003c/sub\u003e / mol N,\n0.5 N\u003csub\u003e2\u003c/sub\u003e + 1.5 H\u003csub\u003e2\u003c/sub\u003eO -\u003e NH\u003csub\u003e3\u003c/sub\u003e + 0.75 O\u003csub\u003e2\u003c/sub\u003e.  Thus, growth on N\u003csub\u003e2\u003c/sub\u003e fixation releases 1.25 mol O\u003csub\u003e2\u003c/sub\u003e less than growth on nitrate.\n* Fixed bug sometimes inflating negative concentrations: do not limit `tnpzd` to positive values in subroutine `tracer`, as this interferes with the flag mechanism in `npzd_src`.\n* If `timavgint=30`, i.e., not a divisor of a year (365 days), the first month will be skipped if starting at the beginning of the year and the year is not a multiple of 30.  -\u003e set `init_time_in = .true.` in namelist `ictime`.\n* Positive particulate tracers can be enforced by activating `O_fct_3d` and `O_opem_pos` in mk.in.\n\n## License\n\nThis work is published under the [GNU General Public License 3 (GPL-3.0)](http://opensource.org/licenses/GPL-3.0).  You may copy, distribute and modify the software as long as you track changes/dates of in source files and keep modifications under GPL. You can distribute your application using a GPL library commercially, but you must also provide the source code.\"\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/142805","html_url":"https://ost.ecosyste.ms/projects/142805"}