From 2b27a78aaecb3635d14b94464d918a67df750ff0 Mon Sep 17 00:00:00 2001 From: Tony Craig Date: Fri, 5 Jun 2020 16:41:47 -0700 Subject: [PATCH] Update documentation including namelist tables (#322) * update documentation including namelist tables * update version --- columnphysics/version.txt | 2 +- doc/source/conf.py | 4 +- doc/source/developer_guide/dg_other.rst | 28 + doc/source/developer_guide/index.rst | 1 + doc/source/master_list.bib | 18 + doc/source/user_guide/ug_case_settings.rst | 695 +++++++++++---------- 6 files changed, 432 insertions(+), 316 deletions(-) create mode 100644 doc/source/developer_guide/dg_other.rst diff --git a/columnphysics/version.txt b/columnphysics/version.txt index bbe568197..483b0ab91 100644 --- a/columnphysics/version.txt +++ b/columnphysics/version.txt @@ -1 +1 @@ -ICEPACK 1.2.1 +ICEPACK 1.2.2 diff --git a/doc/source/conf.py b/doc/source/conf.py index 0dd0b9343..5481da613 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -62,9 +62,9 @@ # built documents. # # The short X.Y version. -version = u'1.2.1' +version = u'1.2.2' # The full version, including alpha/beta/rc tags. -version = u'1.2.1' +version = u'1.2.2' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/doc/source/developer_guide/dg_other.rst b/doc/source/developer_guide/dg_other.rst new file mode 100644 index 000000000..ffdd287e7 --- /dev/null +++ b/doc/source/developer_guide/dg_other.rst @@ -0,0 +1,28 @@ +:tocdepth: 3 + +.. _adding: + +Other things +============= + + +.. _debugger: + +Running with a Debugger +------------------------- + +Availability and usage of interactive debuggers varies across machines. Contact your +system administrator for additional information about what’s available on your system. +To run with an interactive debugger, the following general steps should be taken. + +- Setup a case +- Modify the env file and Macros file to add appropriate modules and compiler/ linker flags +- Build the model +- Get interactive hardware resources as needed +- Open a csh shell +- Source the env.${machine} file +- Source cice.settings +- Change directories to the run directory +- Manually launch the executable thru the debugger + + diff --git a/doc/source/developer_guide/index.rst b/doc/source/developer_guide/index.rst index 49d0fca42..31757e2a6 100755 --- a/doc/source/developer_guide/index.rst +++ b/doc/source/developer_guide/index.rst @@ -16,3 +16,4 @@ Developer Guide dg_driver.rst dg_scripts.rst dg_adding_tracers.rst + dg_other.rst diff --git a/doc/source/master_list.bib b/doc/source/master_list.bib index fe237d1ef..ed4ef20cb 100644 --- a/doc/source/master_list.bib +++ b/doc/source/master_list.bib @@ -366,6 +366,15 @@ @Article{Taylor04 issue = {C12}, url = {http://dx.doi.org/10.1029/2004JC002361} } +@Article{Lavoie05, + author = "D. Lavoie and K. Denman and C. Michel", + title = "{Modeling ice algal growth and decline in a seasonally ice- covered region of the Arctic (Resolute Passage, Canadian Archipelago)}", + journal = JGRO, + year = {2005}, + volume = {110}, + issue = {C11}, + url = {http://dx.doi.org/10.1029/2005JC002922} +} @Book{Notz05 author = "D. Notz", title = "Thermodynamic and Fluid-Dynamical Processes in Sea Ice", @@ -462,6 +471,15 @@ @Article{Hunke09 issue = {CB}, url = {http://dx.doi.org/10.1029/2008JC005186} } +@Article{Tagliabue09, + author = "A. Tagliabue and L. Bopp and O. Aumont", + title = "{Evaluating the importance of atmospheric and sedimentary iron sources to Southern Ocean biogeochemistry}", + journal = GRL, + year = {2009}, + volume = {36}, + issue = {13}, + url = {http://dx.doi.org/10.1029/2009GL038914} +} @Article{Flocco10 author = "D. Flocco and D.L. Feltham and A.K. Turner", title = "{Incorporation of a physically based melt pond scheme into the sea ice component of a climate model}", diff --git a/doc/source/user_guide/ug_case_settings.rst b/doc/source/user_guide/ug_case_settings.rst index 0356d7d4b..fb9e072e8 100755 --- a/doc/source/user_guide/ug_case_settings.rst +++ b/doc/source/user_guide/ug_case_settings.rst @@ -15,62 +15,63 @@ for the icepack driver. Variables in both files are described below. Table of Icepack Settings -------------------------- -The **icepack.settings** file is reasonably well self documented. Several of -the variables defined in the file are not used in Icepack. They exist -to support the CICE model. +The **icepack.settings** file contains a number of environment variables that define +configuration, file system, run, and build settings. Several variables are set +by the **icepack.setup** script. This file is created on a case by case basis and +can be modified as needed. -.. csv-table:: *Icepack settings* - :header: "variable", "options/format", "description", "recommended value" +.. csv-table:: **Icepack settings** + :header: "variable", "options/format", "description", "default value" :widths: 15, 15, 25, 20 - "ICE_CASENAME", " ", "case name", "set by icepack.setup" - "ICE_SANDBOX", " ", "sandbox directory", "set by icepack.setup" - "ICE_MACHINE", " ", "machine name", "set by icepack.setup" - "ICE_COMPILER", " ", "environment name", "set by icepack.setup" - "ICE_MACHCOMP", " ", "machine_environment name", "set by icepack.setup" - "ICE_SCRIPTS", " ", "scripts directory", "set by icepack.setup" - "ICE_CASEDIR", " ", "case directory", "set by icepack.setup" - "ICE_RUNDIR", " ", "run directory", "set by icepack.setup" - "ICE_OBJDIR", " ", "compile directory", "${ICE_RUNDIR}/compile" - "ICE_RSTDIR", " ", "unused", "${ICE_RUNDIR}/restart" - "ICE_HSTDIR", " ", "unused", "${ICE_RUNDIR}/history" - "ICE_LOGDIR", " ", "log directory", "${ICE_CASEDIR}/logs" - "ICE_RSTPFILE", " ", "unused", "undefined" - "ICE_DRVOPT", " ", "unused", "icepack" - "ICE_IOTYPE", " ", "unused", "none" + "ICE_CASENAME", "string", "case name", "set by icepack.setup" + "ICE_SANDBOX", "string", "sandbox directory", "set by icepack.setup" + "ICE_MACHINE", "string", "machine name", "set by icepack.setup" + "ICE_COMPILER", "string", "environment name", "set by icepack.setup" + "ICE_MACHCOMP", "string", "machine_environment name", "set by icepack.setup" + "ICE_SCRIPTS", "string", "scripts directory", "set by icepack.setup" + "ICE_CASEDIR", "string", "case directory", "set by icepack.setup" + "ICE_RUNDIR", "string", "run directory", "set by icepack.setup" + "ICE_OBJDIR", "string", "compile directory", "${ICE_RUNDIR}/compile" + "ICE_RSTDIR", "string", "unused", "${ICE_RUNDIR}/restart" + "ICE_HSTDIR", "string", "unused", "${ICE_RUNDIR}/history" + "ICE_LOGDIR", "string", "log directory", "${ICE_CASEDIR}/logs" + "ICE_RSTPFILE", "string", "unused", "undefined" + "ICE_DRVOPT", "string", "unused", "icepack" + "ICE_IOTYPE", "string", "unused", "none" "ICE_CLEANBUILD", "true,false", "automatically clean before building", "true" - "ICE_CPPDEFS", " ", "user defined preprocessor macros for build", "null" + "ICE_CPPDEFS", "string", "user defined preprocessor macros for build", "null" "ICE_QUIETMODE", "true, false", "reduce build output to the screen", "false" "ICE_GRID", "col", "grid", "col" "ICE_NXGLOB", "4", "number of gridcells", "4" "ICE_NTASKS", "1", "number of tasks, must be set to 1", "1" "ICE_NTHRDS", "1", "number of threads per task, must be set to 1", "1" - "ICE_TEST", " ", "test setting if using a test", "set by icepack.setup" - "ICE_TESTNAME", " ", "test name if using a test", "set by icepack.setup" - "ICE_BASELINE", " ", "baseline directory name, associated with icepack.setup -bd", "set by icepack.setup" - "ICE_BASEGEN", " ", "baseline directory name for regression generation, associated with icepack.setup -bg ", "set by icepack.setup" - "ICE_BASECOM", " ", "baseline directory name for regression comparison, associated with icepack.setup -bc ", "set by icepack.setup" - "ICE_BFBCOMP", " ", "location of case for comparison, associated with icepack.setup -td", "set by icepack.setup" - "ICE_SPVAL", " ", "unused", "UnDeFiNeD" - "ICE_RUNLENGTH", " ", "batch run length default", " 00:10:00" - "ICE_ACCOUNT", " ", "batch account number", "set by icepack.setup or by default" - "ICE_QUEUE", "string", "batch queue name", "set by cice.setup or by default" + "ICE_TEST", "string", "test setting if using a test", "set by icepack.setup" + "ICE_TESTNAME", "string", "test name if using a test", "set by icepack.setup" + "ICE_BASELINE", "string", "baseline directory name, associated with icepack.setup -bd", "set by icepack.setup" + "ICE_BASEGEN", "string", "baseline directory name for regression generation, associated with icepack.setup -bg ", "set by icepack.setup" + "ICE_BASECOM", "string", "baseline directory name for regression comparison, associated with icepack.setup -bc ", "set by icepack.setup" + "ICE_BFBCOMP", "string", "location of case for comparison, associated with icepack.setup -td", "set by icepack.setup" + "ICE_SPVAL", "string", "unused", "UnDeFiNeD" + "ICE_RUNLENGTH", "string", "batch run length default", " 00:10:00" + "ICE_ACCOUNT", "string", "batch account number", "set by icepack.setup or by default" + "ICE_QUEUE", "string", "batch queue name", "set by icepack.setup or by default" "ICE_THREADED", "true,false", "force threading in compile, will always compile threaded if NTHRDS is gt 1", "false" - "NICELYR", " ", "number of vertical layers in the ice", "7" - "NSNWLYR", " ", "number of vertical layers in the snow", "1" - "NICECAT", " ", "number of ice thickness categories", "5" - "NFSDCAT", " ", "number of floe size categories", "12" + "NICELYR", "integer", "number of vertical layers in the ice", "7" + "NSNWLYR", "integer", "number of vertical layers in the snow", "1" + "NICECAT", "integer", "number of ice thickness categories", "5" + "NFSDCAT", "integer", "number of floe size categories", "12" "TRAGE", "0,1", "ice age tracer", "1" "TRFY", "0,1", "first-year ice area tracer", "1" "TRLVL", "0,1", "deformed ice tracer", "1" "TRPND", "0,1", "melt pond tracer", "1" - "NTRAERO", " ", "number of aerosol tracers", "1" - "NTRISO", " ", "number of water isotope tracers", "1" + "NTRAERO", "integer", "number of aerosol tracers", "1" + "NTRISO", "integer", "number of water isotope tracers", "1" "TRBRI", "0,1", "brine height tracer", "0" "TRZS", "0,1", "zsalinity tracer, needs TRBRI=1", "0" "TRBGCS", "0,1", "skeletal layer tracer, needs TRBGCZ=0", "0" "TRBGCZ", "0,1", "zbgc tracers, needs TRBGCS=0 and TRBRI=1", "0" - "NBGCLYR", " ", "number of zbgc layers", "7" + "NBGCLYR", "integer", "number of zbgc layers", "7" "TRZAERO", "0-6", "number of z aerosol tracers", "0" "TRALG", "0,1,2,3", "number of algal tracers", "0" "TRDOC", "0,1,2,3", "number of dissolved organic carbon", "0" @@ -87,322 +88,386 @@ to support the CICE model. Table of Namelist Inputs -------------------------- -Namelist is part of the icepack driver code and is used to setup testing of the -column physics. +The Icepack driver reads a namelist input file, **icepack_in**, consisting of several namelist groups. The tables below +summarize the different groups and the variables in each group. The variables are organized alphabetically +and the default values listed are the values defined in the source code. Those values will be +used unless overridden by the Icepack namelist file, **icepack_in**. The source code default values as listed +in the table are not necessarily the recommended production values. -.. _tab-namelist: +setup_nml +~~~~~~~~~~~~~~~~~~~~~~~~~ -.. csv-table:: *Namelist Inputs* - :header: "variable", "options/format", "description", "recommended value" - :widths: 20, 10, 25, 10 +.. csv-table:: **setup_nml namelist options** + :header: "variable", "options/format", "description", "default value" + :widths: 15, 15, 30, 15 - "*setup_nml*", "", "", "" - "", "", "**Time, Diagnostics**", "" - "``days_per_year``", "``360`` or ``365``", "number of days in a model year", "365" - "``use_leap_years``", "true/false", "if true, include leap days", "" - "``year_init``", "yyyy", "the initial year, if not using restart", "" - "``istep0``", "integer", "initial time step number", "0" - "``dt``", "seconds", "thermodynamics time step length", "3600." - "``npt``", "integer", "total number of time steps to take", "" - "``ndtd``", "integer", "number of dynamics/advection/ridging/steps per thermo timestep", "1" - "", "", "**Initialization/Restarting**", "" - "``ice_ic``", "``default``", "latitude and sst dependent", "default" - "", "``none``", "no ice", "" - "", "path/file", "restart file name", "" - "``restart_dir``", "path/", "path to restart directory", "" - "``dumpfreq``", "``y``", "write restart every ``dumpfreq_n`` years", "y" + "", "", "", "" + "``conserv_check``", "logical", "check conservation", "``.false.``" + "``cpl_bgc``", "logical", "couple bgc thru driver", "``.false.``" + "``days_per_year``", "integer", "number of days in a model year", "365" + "``diagfreq``", "integer", "frequency of diagnostic output in timesteps", "24" + "``diag_file``", "string", "diagnostic output filename", "'ice_diag'" + "``dumpfreq``", "``d``", "write restart every ``dumpfreq_n`` days", "``y``" "", "``m``", "write restart every ``dumpfreq_n`` months", "" - "", "``d``", "write restart every ``dumpfreq_n`` days", "" + "", "``y``", "write restart every ``dumpfreq_n`` years", "" "``dump_last``", "true/false", "write restart at end of run", "false" - "", "", "**Model Output**", "" - "``diagfreq``", "integer", "frequency of diagnostic output in ``dt``", "24" - "", "*e.g.*, 10", "once every 10 time steps", "" - "``diag_file``", "filename", "diagnostic output file (script may reset)", "" + "``dt``", "seconds", "thermodynamics time step length", "3600." + "``ice_ic``", "``default``", "latitude and sst dependent initial condition", "``default``" + "", "``none``", "no ice", "" + "", "'path/file'", "restart file name", "" + "``istep0``", "integer", "initial time step number", "0" + "``ndtd``", "integer", "number of dynamics/advection/ridging/steps per thermo timestep", "1" + "``npt``", "integer", "total number of time steps to take", "99999" + "``restart``", "logical", "initialize using restart file", "``.false.``" + "``restart_dir``", "string", "path to restart directory", "'./'" + "``restart_file``", "string", "output file prefix for restart dump", "'iced'" + "``use_leap_years``", "logical", "include leap days", "``.false.``" + "``year_init``", "integer", "the initial year if not using restart", "0" "", "", "", "" - "*grid_nml*", "", "", "" - "", "", "**Grid**", "" - "``kcatbound``", "``0``", "original category boundary formula", "0" - "", "``1``", "new formula with round numbers", "" + +grid_nml +~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. csv-table:: **grid_nml namelist options** + :header: "variable", "options/format", "description", "default value" + :widths: 15, 15, 30, 15 + + "", "", "", "" + "``kcatbound``", "``-1``", "single category formulation", "1" + "", "``0``", "old formulation", "" + "", "``1``", "new formulation with round numbers", "" "", "``2``", "WMO standard categories", "" - "", "``-1``", "one category", "" + "", "``3``", "asymptotic scheme", "" + "", "", "", "" + +tracer_nml +~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. csv-table:: **tracer_nml namelist options** + :header: "variable", "options/format", "description", "default value" + :widths: 15, 15, 30, 15 + + "", "", "", "" + "``tr_aero``", "logical", "aerosols", "``.false.``" + "``tr_fsd``", "logical", "floe size distribution", "``.false.``" + "``tr_FY``", "logical", "first-year ice area", "``.false.``" + "``tr_iage``", "logical", "ice age", "``.false.``" + "``tr_iso``", "logical", "isotopes", "``.false.``" + "``tr_lvl``", "logical", "level ice area and volume", "``.false.``" + "``tr_pond_cesm``", "logical", "CESM melt ponds", "``.false.``" + "``tr_pond_lvl``", "logical", "level-ice melt ponds", "``.false.``" + "``tr_pond_topo``", "logical", "topo melt ponds", "``.false.``" "", "", "", "" - "*tracer_nml*", "", "", "" - "", "", "**Tracers**", "" - "``tr_iage``", "true/false", "ice age", "" - "``tr_FY``", "true/false", "first-year ice area", "" - "``tr_lvl``", "true/false", "level ice area and volume", "" - "``tr_pond_cesm``", "true/false", "CESM melt ponds", "" - "``tr_pond_topo``", "true/false", "topo melt ponds", "" - "``tr_pond_lvl``", "true/false", "level-ice melt ponds", "" - "``tr_aero``", "true/false", "aerosols", "" - "``tr_iso``", "true/false", "water isotopes", "" - "``tr_fsd``", "true/false", "floe size distribution", "" + +thermo_nml +~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. csv-table:: **thermo_nml namelist options** + :header: "variable", "options/format", "description", "default value" + :widths: 15, 15, 30, 15 + "", "", "", "" - "*thermo_nml*", "", "", "" - "", "", "**Thermodynamics**", "" + "``a_rapid_mode``", "real", "brine channel diameter in m", "0.5e-3" + "``aspect_rapid_mode``", "real", "brine convection aspect ratio", "1.0" + "``conduct``", "``bubbly``", "conductivity scheme :cite:`Pringle07`", "``bubbly``" + "", "``MU71``", "conductivity :cite:`Maykut71`", "" + "``dSdt_slow_mode``", "real", "slow drainage strength parameter m/s/K", "-1.5e-7" "``kitd``", "``0``", "delta function ITD approximation", "1" "", "``1``", "linear remapping ITD approximation", "" - "``ktherm``", "``0``", "zero-layer thermodynamic model", "" + "``ksno``", "real", "snow thermal conductivity", "0.3" + "``ktherm``", "``-1``", "thermodynamic model disabled", "1" + "", "``0``", "zero-layer thermodynamic model", "" "", "``1``", "Bitz and Lipscomb thermodynamic model", "" "", "``2``", "mushy-layer thermodynamic model", "" - "``conduct``", "``Maykut71``", "conductivity :cite:`Maykut71`", "" - "", "``bubbly``", "conductivity :cite:`Pringle07`", "" - "``ksno``", "real", "Thermal conductivity of snow", "0.3 W/m/deg" - "``a_rapid_mode``", "real", "brine channel diameter", "0.5x10 :math:`^{-3}` m" - "``Rac_rapid_mode``", "real", "critical Rayleigh number", "10" - "``aspect_rapid_mode``", "real", "brine convection aspect ratio", "1" - "``dSdt_slow_mode``", "real", "drainage strength parameter", "-1.5x10 :math:`^{-7}` m/s/K" "``phi_c_slow_mode``", ":math:`0<\phi_c < 1`", "critical liquid fraction", "0.05" "``phi_i_mushy``", ":math:`0<\phi_i < 1`", "solid fraction at lower boundary", "0.85" + "``Rac_rapid_mode``", "real", "critical Rayleigh number", "10.0" "", "", "", "" - "*dynamics_nml*", "", "", "" - "", "", "**Dynamics**", "" + +dynamics_nml +~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. csv-table:: **dynamics_nml namelist options** + :header: "variable", "options/format", "description", "default value" + :widths: 15, 15, 30, 15 + + "", "", "", "" + "``Cf``", "real", "ratio of ridging work to PE change in ridging", "17.0" "``kstrength``", "``0``", "ice strength formulation :cite:`Hibler79`", "1" "", "``1``", "ice strength formulation :cite:`Rothrock75`", "" "``krdg_partic``", "``0``", "old ridging participation function", "1" "", "``1``", "new ridging participation function", "" "``krdg_redist``", "``0``", "old ridging redistribution function", "1" "", "``1``", "new ridging redistribution function", "" - "``mu_rdg``", "real", "e-folding scale of ridged ice", "" - "``Cf``", "real", "ratio of ridging work to PE change in ridging", "17." + "``mu_rdg``", "real", "e-folding scale of ridged ice for ``krdg_partic`` = 1 in m^0.5", "3.0" "", "", "", "" - "*shortwave_nml*", "", "", "" - "", "", "**Shortwave**", "" - "``shortwave``", "``ccsm3``", "NCAR CCSM3 distribution method", "'dEdd'" - "", "``dEdd``", "Delta-Eddington method", "" - "``albedo_type``", "``ccsm3``", "NCAR CCSM3 albedos", "'ccsm3'" + +shortwave_nml +~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. csv-table:: **shortwave_nml namelist options** + :header: "variable", "options/format", "description", "default value" + :widths: 15, 15, 30, 15 + + "", "", "", "" + "``ahmax``", "real", "albedo is constant above this thickness in meters", "0.3" + "``albedo_type``", "`ccsm3``", "NCAR CCSM3 albedo implementation", "``ccsm3``" "", "``constant``", "four constant albedos", "" - "``albicev``", ":math:`0<\alpha <1`", "visible ice albedo for thicker ice", "" - "``albicei``", ":math:`0<\alpha <1`", "near infrared ice albedo for thicker ice", "" - "``albsnowv``", ":math:`0<\alpha <1`", "visible, cold snow albedo", "" - "``albsnowi``", ":math:`0<\alpha <1`", "near infrared, cold snow albedo", "" - "``ahmax``", "real", "albedo is constant above this thickness", "0.3 m" - "``R_ice``", "real", "tuning parameter for sea ice albedo from Delta-Eddington shortwave", "" - "``R_pnd``", "real", "... for ponded sea ice albedo …", "" - "``R_snw``", "real", "... for snow (broadband albedo) …", "" - "``dT_mlt``", "real", ":math:`\Delta` temperature per :math:`\Delta` snow grain radius", "" - "``rsnw_mlt``", "real", "maximum melting snow grain radius", "" - "``kalg``", "real", "absorption coefficient for algae", "" + "``albicei``", ":math:`0<\alpha <1`", "near infrared ice albedo for thicker ice", "0.36" + "``albicev``", ":math:`0<\alpha <1`", "visible ice albedo for thicker ice", "0.78" + "``albsnowi``", ":math:`0<\alpha <1`", "near infrared, cold snow albedo", "0.70" + "``albsnowv``", ":math:`0<\alpha <1`", "visible, cold snow albedo", "0.98" + "``dT_mlt``", "real", ":math:`\Delta` temperature per :math:`\Delta` snow grain radius", "1.5" + "``kalg``", "real", "absorption coefficient for algae", "0.6" + "``rsnw_mlt``", "real", "maximum melting snow grain radius", "1500." + "``R_ice``", "real", "tuning parameter for sea ice albedo from Delta-Eddington shortwave", "0.0" + "``R_pnd``", "real", "tuning parameter for ponded sea ice albedo from Delta-Eddington shortwave", "0.0" + "``R_snw``", "real", "tuning parameter for snow (broadband albedo) from Delta-Eddington shortwave", "1.5" + "``shortwave``", "``ccsm3``", "NCAR CCSM3 shortwave distribution method", "``dEdd``" + "", "``dEdd``", "Delta-Eddington method", "" "", "", "", "" - "*ponds_nml*", "", "", "" - "", "", "**Melt Ponds**", "" - "``hp1``", "real", "critical ice lid thickness for topo ponds", "0.01 m" - "``hs0``", "real", "snow depth of transition to bare sea ice", "0.03 m" - "``hs1``", "real", "snow depth of transition to pond ice", "0.03 m" - "``dpscale``", "real", "time scale for flushing in permeable ice", ":math:`1\times 10^{-3}`" - "``frzpnd``", "``hlid``", "Stefan refreezing with pond ice thickness", "‘hlid’" - "", "``cesm``", "CESM refreezing empirical formula", "" - "``rfracmin``", ":math:`0 \le r_{min} \le 1`", "minimum melt water added to ponds", "0.15" - "``rfracmax``", ":math:`0 \le r_{max} \le 1`", "maximum melt water added to ponds", "1.0" + +ponds_nml +~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. csv-table:: **ponds_nml namelist options** + :header: "variable", "options/format", "description", "default value" + :widths: 15, 15, 30, 15 + + "", "", "", "" + "``dpscale``", "real", "time scale for flushing in permeable ice", "1.0" + "``frzpnd``", "``cesm``", "CESM pond refreezing forumulation", "``cesm``" + "", "``hlid``", "Stefan refreezing with pond ice thickness", "" + "``hp1``", "real", "critical ice lid thickness for topo ponds in m", "0.01" + "``hs0``", "real", "snow depth of transition to bare sea ice in m", "0.03" + "``hs1``", "real", "snow depth of transition to pond ice in m", "0.03" "``pndaspect``", "real", "aspect ratio of pond changes (depth:area)", "0.8" + "``rfracmax``", ":math:`0 \le r_{max} \le 1`", "maximum melt water added to ponds", "0.85" + "``rfracmin``", ":math:`0 \le r_{min} \le 1`", "minimum melt water added to ponds", "0.15" "", "", "", "" - "*forcing_nml*", "", "", "" - "", "", "**Forcing**", "" - "``formdrag``", "true/false", "calculate form drag", "" - "``atmbndy``", "``default``", "stability-based boundary layer", "‘default’" - "", "``constant``", "bulk transfer coefficients", "" - "``fyear_init``", "yyyy", "first year of atmospheric forcing data", "" - "``ycycle``", "integer", "number of years in forcing data cycle", "" - "``atm_data_type``", "``default``", "constant values defined in the code", "" - "", "``clim``", "monthly climatology (see :ref:`force`)", "" + +forcing_nml +~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. csv-table:: **forcing_nml namelist options** + :header: "variable", "options/format", "description", "default value" + :widths: 15, 15, 30, 15 + + "", "", "", "" + "``atmbndy``", "``constant``", "bulk transfer coefficients", "``default``" + "", "``default``", "stability-based boundary layer", "" + "``atmiter_conv``", "real", "convergence criteria for ustar", "0.0" + "``atm_data_file``", "string", "file containing atmospheric data", "' '" + "``atm_data_format``", "``bin``", "read direct access binary forcing files", "``bin``" + "``atm_data_type``", "``clim``", "monthly climatology (see :ref:`force`)", "``default``" "", "``CFS``", "CFS model output (see :ref:`force`)", "" + "", "``default``", "constant values defined in the code", "" "", "``ISPOL``", "ISPOL experiment data (see :ref:`force`)", "" "", "``NICE``", "N-ICE experiment data (see :ref:`force`)", "" - "``data_dir``", "path/", "path to forcing data directory", "" - "``atm_data_file``", "filename", "file containing atmospheric data", "" - "``ocn_data_file``", "filename", "file containing ocean data", "" - "``ice_data_file``", "filename", "file containing ice opening, closing data", "" - "``bgc_data_file``", "filename", "file containing biogeochemistry data", "" - "``calc_strair``", "true", "calculate wind stress and speed", "" - "", "false", "read wind stress and speed from files", "" - "``highfreq``", "true/false", "high-frequency atmo coupling", "" - "``natmiter``", "integer", "number of atmo boundary layer iterations", "" - "``atmiter_conv``", "real", "set a tolerance for convergence of ustar", "0.0d0" - "``calc_Tsfc``", "true/false", "calculate surface temperature", "``.true.``" - "``precip_units``", "``mks``", "liquid precipitation data units", "" - "", "``mm_per_month``", "", "" - "", "``mm_per_sec``", "(same as MKS units)", "" - "``tfrz_option``", "``minus1p8``", "constant ocean freezing temperature (:math:`-1.8^\circ C`)","" - "", "``linear_salt``","linear function of salinity (ktherm=1)","" - "", "``mushy``","matches mushy-layer thermo (ktherm=2)","" - "``default_season``","``winter``", "Sets initial values of forcing and is overwritten when forcing read in. Default is winter","" - "", "``summer``","typical summer values","" - "", "``spring``","typical spring values","" - "``ustar_min``", "real", "minimum value of ocean friction velocity", "0.0005 m/s" + "``bgc_data_file``", "string", "file containing biogeochemistry data", "' '" + "``bgc_data_format``", "``bin``", "read direct access binary forcing files", "``bin``" + "``bgc_data_type``", "``clim``", "bgc climatological data", "``default``" + "", "``default``", "constant values defined in the code", "" + "", "``ncar``", "POP ocean forcing data", "" + "``calc_strair``", "``.false.``", "read wind stress and speed from files", "``.true.``" + "", "``.true.``", "calculate wind stress and speed", "" + "``calc_Tsfc``", "logical", "calculate surface temperature", "``.true.``" + "``data_dir``", "string", "path to forcing data directory", "' '" + "``default_season``", "``summer``", "forcing initial summer values", "``winter``" + "", "``winter``", "forcing initial winter values", "" "``emissivity``", "real", "emissivity of snow and ice", "0.95" - "``fbot_xfer_type``", "``constant``", "constant ocean heat transfer coefficient", "" - "", "``Cdn_ocn``", "variable ocean heat transfer coefficient", "" - "``update_ocn_f``", "true", "include frazil water/salt fluxes in ocn fluxes", "" - "", "false", "do not include (when coupling with POP)", "" - "``l_mpond_fresh``", "true", "retain (topo) pond water until ponds drain", "" - "", "false", "release (topo) pond water immediately to ocean", "" - "``oceanmixed_ice``", "true/false", "active ocean mixed layer calculation", "``.true.`` (if uncoupled)" - "``wave_spec_file``", "filename", "file containing wave spectrum data for interaction with fsd","" - "``wave_spec_type``", "``none``", "no ocean wave spectrum data - no wave-ice interactions (not recommended with tr_fsd=.true.","" - "", "``constant``", "ocean wave spectrum data present*, sea surface height field generated using constant phase, fracture code not run to convergence, for testing FSD", "" - "", "``random``", "ocean wave spectrum data present*, sea surface height field generated using random phase, fracture code is run to convergence", "" - "``ocn_data_type``", "``default``", "constant values defined in the code", "" + "``fbot_xfer_type``", "``Cdn_ocn``", "variabler ocean heat transfer coefficient scheme", "``constant``" + "", "``constant``", "constant ocean heat transfer coefficient", "" + "``formdrag``", "logical", "calculate form drag", "``.false.``" + "``fyear_init``", "integer", "first year of atmospheric forcing data", "1998" + "``highfreq``", "logical", "high-frequency atmo coupling", "``.false.``" + "``ice_data_file``", "string", "file containing ice opening, closing data", "' '" + "``l_mpond_fresh``", "``.false.``", "release pond water immediately to ocean", "``.false.``" + "", "``true``", "retain (topo) pond water until ponds drain", "" + "``natmiter``", "integer", "number of atmo boundary layer iterations", "5" + "``oceanmixed_ice``", "logical", "active ocean mixed layer calculation", "``.false.``" + "``ocn_data_file``", "string", "file containing ocean data", "' ' " + "``ocn_data_format``", "``bin``", "read direct access binary forcing files", "``bin``" + "``ocn_data_type``", "``default``", "constant values defined in the code", "``default``" "", "``ISPOL``", "ISPOL experiment data (see :ref:`force`)", "" "", "``NICE``", "N-ICE experiment data (see :ref:`force`)", "" "", "``SHEBA``", "Opening/closing dataset from SHEBA", "" - "``oceanmixed_file``", "filename", "data file containing ocean forcing data", "" - "``restore_ocn``", "true/false", "restore sst to data", "" - "``trestore``", "integer", "sst restoring time scale (days)", "" + "``precip_units``", "``mks``", "liquid precipitation data units", "``mks``" + "", "``mm_per_month``", "", "" + "", "``mm_per_sec``", "(same as MKS units)", "" + "", "``m_per_sec``", "", "" + "``restore_ocn``", "logical", "restore sst to data", "``.false.``" + "``tfrz_option``", "``linear_salt``", "linear functino of salinity (ktherm=1)", "``mushy``" + "", "``minus1p8``", "constant ocean freezing temperature (:math:`-1.8^{\circ} C`)", "" + "", "``mushy``", "matches mushy-layer thermo (ktherm=2)", "" + "``trestore``", "integer", "sst restoring time scale (days)", "90" + "``update_ocn_f``", "``.false.``", "do not include frazil water/salt fluxes in ocn fluxes", "``.false.``" + "", "``true``", "include frazil water/salt fluxes in ocn fluxes", "" + "``ustar_min``", "real", "minimum value of ocean friction velocity in m/s", "0.005" + "``wave_spec_type``", "``constant``", "wave data file is provided, constant wave spectrum, for testing", "``none``" + "", "``none``", "no wave data provided, no wave-ice interactions", "" + "", "``profile``", "no wave data file is provided, use fixed dummy wave spectrum, for testing", "" + "", "``random``", "wave data file is provided, wave spectrum generated using random number", "" + "``ycycle``", "integer", "number of years in forcing data cycle", "1" "", "", "", "" - "*zbgc_nml*", "", "", "" - "", "", "**Biogeochemistry**", "" - "``tr_brine``", "true/false", "brine height tracer (needs TRBRI 1 in comp_ice)", "``.true.``" - "``restart_hbrine``", "true/false", "restart the brine height tracer (automatically turned on if restart = .true.)", "``.false.``" - "``tr_zaero``", "true/false", "turns on black carbon and dust aerosols", "``.false.``" - "``modal_aero``", "true/false", "turns on a modal aerosol option", "``.false.``" - "``conserv_check``", "true/false", "turns on conservation checks in the columnphysics", "``.false.``" - "``skl_bgc``", "true/false", "turns on a single bottom layer biogeochemistry. z_tracers and solve_zbgc must be false", "``.false.``" - "``z_tracers``", "true/false", "turns on a vertically resolved transport", "``.true.``" - "``dEdd_algae``", "true/false", "Include radiative impact of algae and aerosols in the delta-Eddington shortwave scheme. Requires shortwave = 'dEdd'.", "``.false.``" - "``solve_zbgc``", "true/false", "turns on the biochemistry using z_tracers (specify algal numbers in comp_ice TRALG)", "``.true.``" - "``bgc_flux_type``", "``Jin2006`` or ``default``", "ice–ocean flux type for bottom layer tracers only :cite:`Jin06`", "``Jin2006``" - "``restore_bgc``", "true/false", "restores upper ocean concentration fields to data values for nitrate and silicate", "``.false.``" - "``restart_bgc``", "true/false", "restarts biogeochemical tracers (automatically turned on if restart = .true.)", "``.false.``" - "``scale_bgc``", "true/false", "Initialize biogeochemical profiles to scale with prognosed salinity profile", "``.false.``" - "``solve_zsal``", "true/false", "prognostic salinity tracer used with ktherm = 1", "``.false.``" - "``restart_zsal``", "true/false", "restarts zsalinity", "``.false.``" - "``bgc_data_type``", "``default``", "fixed, spatially homogeneous constant values defined in the code", "" - "", "``clim``", "monthly climatology data file (see icedrv_forcing_bgc.F90) :cite:`Garcia06`", "" - "", "``NICE``", "N-ICE experiment data", "" - "", "``ISPOL``", "ISPOL experiment data", "" - "``tr_bgc_Nit``", "true/false", "nitrate tracer", "``.true.``" - "``tr_bgc_C``", "true/false", "dissolved organic carbon tracers and dissolved inorganic carbon tracers (not yet implemented)", "``.true.``" - "``tr_bgc_chl``", "true/false", "dummy variable for now. Chl is simply fixed ratio of algal Nitrogen", "``.false.``" - "``tr_bgc_Am``", "true/false", "Ammonium", "``.true.``" - "``tr_bgc_Sil``", "true/false", "Silicate", "``.true.``" - "``tr_bgc_DMS``", "true/false", "Three tracers: DMS dimethyl sulfide, DMSPp (particulate, assumed to be a fixed ratio of sulfur to algal nitrogen) and DMSPd (dissolved)", "``.true.``" - "``tr_bgc_PON``", "true/false", "passive purely mobile ice tracer with ocean concentration equivalent to nitrate", "``.false.``" - "``tr_bgc_hum``", "true/false", "refractory DOC or DON (units depend on the ocean source)", "``.true.``" - "``tr_bgc_DON``", "true/false", "dissolved organic nitrogen", "``.true.``" - "``tr_bgc_Fe``", "true/false", "dissolved iron and particulate iron", "``.true.``" - "``grid_o``", "real", "ice-ocean surface layer thickness (bgc transport scheme)", "0.006" - "``l_sk``", "real", "length scale in gravity drainage parameterization (bgc transport scheme)", "0.024" - "``grid_oS``", "real", "ice-ocean surface layer thickness (zsalinity transport scheme)", "0.0" - "``l_skS``", "real", "ice-atmosphere surface layer thickness (zsalinity transport scheme)", "0.028" - "``phi_snow``", "real", "snow porosity at the ice-snow interface. if :math:`<0` then phi_snow is computed from snow density", "-0.3" - "``initbio_frac``", "real", "for each bgc tracer, specifies the fraction of the ocean concentration that is retained in the ice during initial new ice formation", "0.8" - "``frazil_scav``", "real", "for each bgc tracer, specifies the fraction or multiple of the ocean concentration that is retained in the ice from frazil ice formation", "0.8" - "``ratio_si2N_diatoms``", "real", "algal Si to N (:math:`mol/mol`) for diatoms", "1.8" - "``ratio_si2N_sp``", "real", "algal Si to N (:math:`mol/mol`) for small phytoplankton", "0.0" - "``ratio_si2N_phaeo``", "real", "algal Si to N (:math:`mol/mol`) for phaeocystis", "0.0" - "``ratio_S2N_diatoms``", "real", "algal S to N (:math:`mol/mol`) for diatoms", "0.03" - "``ratio_S2N_sp``", "real", "algal S to N (:math:`mol/mol`) for small phytoplankton", "0.03" - "``ratio_S2N_phaeo``", "real", "algal S to N (:math:`mol/mol`) for phaeocystis", "0.03" - "``ratio_Fe2C_diatoms``", "real", "algal Fe to C (:math:`\mu mol/mol`) for diatoms", "0.0033" - "``ratio_Fe2C_sp``", "real", "algal Fe to C (:math:`\mu mol/mol`) for small phytoplankton", "0.0033" - "``ratio_Fe2C_phaeo``", "real", "algal Fe to C (:math:`\mu mol/mol`) for phaeocystis", "0.1" - "``ratio_Fe2N_diatoms``", "real", "algal Fe to N (:math:`\mu mol/mol`) for diatoms", "0.023" - "``ratio_Fe2N_sp``", "real", "algal Fe to N (:math:`\mu mol/mol`) for small phytoplankton", "0.023" - "``ratio_Fe2N_phaeo``", "real", "algal Fe to N (:math:`\mu mol/mol`) for phaeocystis", "0.7" - "``ratio_Fe2DON``", "real", "Fe to N of DON (:math:`nmol/mol`)", "0.023" - "``ratio_Fe2DOC_s``", "real", "Fe to C of DOC for saccharids (:math:`nmol/mol`)", "0.1" - "``ratio_Fe2DOC_l``", "real", "Fe to C of DOC for lipids (:math:`nmol/mol`)", "0.033" - "``fr_resp``", "real", "fraction of algal growth lost due to respiration", "0.05" - "``tau_min``", "real", "rapid mobile to stationary exchanges (:math:`s`)", "5200.0" - "``tau_max``", "real", "long time mobile to stationary exchanges (:math:`s`)", "1.73e5" - "``algal_vel``", "real", "0.5 :math:`cm/day (m/s)`", "1.11e-8" - "``R_dFe2dust``", "real", "g/g (3.5% content)", "0.035" - "``dustFe_sol``", "real", "solubility fraction", "0.005" - "``chlabs_diatoms``", "real", "diatoms chl absorption (:math:`1/m/(mg/m^3)`)", "0.03" - "``chlabs_sp``", "real", "small phytoplankton chl absorption (:math:`1/m/(mg/m^3)`)", "0.01" - "``chlabs_phaeo``", "real", "phaeocystis chl absorption (:math:`1/m/(mg/m^3)`)", "0.05" - "``alpha2max_low_diatoms``", "real", "diatoms light limitation (:math:`(W/m^2)^{-1}`)", "0.8" - "``alpha2max_low_sp``", "real", "small phytoplankton light limitation (:math:`(W/m^2)^{-1}`)", "0.67" - "``alpha2max_low_phaeo``", "real", "phaeocystis light limitation (:math:`(W/m^2)^{-1}`)", "0.67" - "``beta2max_diatoms``", "real", "diatoms light inhibition (:math:`(W/m^2)^{-1}`)", "0.018" - "``beta2max_sp``", "real", "small phytoplankton light inhibition (:math:`(W/m^2)^{-1}`)", "0.0025" - "``beta2max_phaeo``", "real", "phaeocystis light inhibition (:math:`(W/m^2)^{-1}`)", "0.01" - "``mu_max_diatoms``", "real", "diatoms maximum growth rate (:math:`day^{-1}`)", "1.2" - "``mu_max_sp``", "real", "small phytoplankton maximum growth rate (:math:`day^{-1}`)", "0.851" - "``mu_max_phaeo``", "real", "phaeocystis maximum growth rate (:math:`day^{-1}`)", "0.851" - "``grow_Tdep_diatoms``", "real", "diatoms Temperature dependence of growth (:math:`^o`\ C\ :math:`^{-1})`", "0.06" - "``grow_Tdep_sp``", "real", "small phytoplankton Temperature dependence of growth :math:`^o`\ C\ :math:`^{-1}`", "0.06" - "``grow_Tdep_phaeo``", "real", "phaeocystis Temperature dependence of growth :math:`^o`\ C\ :math:`^{-1}`", "0.06" - "``fr_graze_diatoms``", "real", "diatoms fraction grazed", "0.01" - "``fr_graze_sp``", "real", "small phytoplankton fraction grazed", "0.1" - "``fr_graze_phaeo``", "real", "phaeocystis fraction grazed", "0.1" - "``mort_pre_diatoms``", "real", "diatoms mortality (:math:`day^{-1}`)", "0.007" - "``mort_pre_sp``", "real", "small phytoplankton mortality (:math:`day^{-1}`)", "0.007" - "``mort_pre_phaeo``", "real", "phaeocystis mortality (:math:`day^{-1}`)", "0.007" - "``mort_Tdep_diatoms``", "real", "diatoms temperature dependence of mortality :math:`^o`\ C\ :math:`^{-1}`", "0.03" - "``mort_Tdep_sp``", "real", "small phytoplankton temperature dependence of mortality (:math:`^o`\ C\ :math:`^{-1}`)", "0.03" - "``mort_Tdep_phaeo``", "real", "phaeocystis temperature dependence of mortality (:math:`^o`\ C\ :math:`^{-1}`)", "0.03" - "``k_exude_diatoms``", "real", "diatoms algal exudation (:math:`day^{-1}`)", "0.0" - "``k_exude_sp``", "real", "small phytoplankton algal exudation (:math:`day^{-1}`)", "0.0" - "``k_exude_phaeo``", "real", "phaeocystis algal exudation (:math:`day^{-1}`)", "0.0" - "``K_Nit_diatoms``", "real", "datoms nitrate half saturation (:math:`mmol/m^3`)", "1.0" - "``K_Nit_sp``", "real", "small phytoplankton nitrate half saturation (:math:`mmol/m^3`)", "1.0" - "``K_Nit_phaeo``", "real", "phaeocystis nitrate half saturation (:math:`mmol/m^3`)", "1.0" - "``K_Am_diatoms``", "real", "diatoms ammonium half saturation (:math:`mmol/m^3`)", "0.3" - "``K_Am_sp``", "real", "small phytoplankton ammonium half saturation (:math:`mmol/m^3`)", "0.3" - "``K_Am_phaeo``", "real", "phaeocystis ammonium half saturation (:math:`mmol/m^3`)", "0.3" - "``K_Sil_diatoms``", "real", "diatoms silicate half saturation (:math:`mmol/m^3`)", "4.0" - "``K_Sil_sp``", "real", "small phytoplankton silicate half saturation (:math:`mmol/m^3`)", "0.0" - "``K_Sil_phaeo``", "real", "phaeocystis silicate half saturation (:math:`mmol/m^3`)", "0.0" - "``K_Fe_diatoms``", "real", "diatoms iron half saturation (:math:`nM`)", "1.0" - "``K_Fe_sp``", "real", "small phytoplankton iron half saturation (:math:`nM`)", "0.2" - "``K_Fe_phaeo``", "real", "phaeocystis iron half saturation (:math:`nM`)", "0.1" - "``f_don_protein``", "real", "fraction of spilled grazing to proteins", "0.6" - "``kn_bac_protein``", "real", "Bacterial degredation of DON (:math:`day^{-1}`)", "0.03" - "``f_don_Am_protein``", "real", "fraction of remineralized DON to ammonium", "0.25" - "``f_doc_s``", "real", "fraction of mortality to DOC saccharids", "0.4" - "``f_doc_l``", "real", "fraction of mortality to DOC lipids", "0.4" - "``f_exude_s``", "real", "fraction of exudation to DOC saccharids", "1.0" - "``f_exude_l``", "real", "fraction of exudation to DOC lipids", "1.0" - "``k_bac_s``", "real", "bacterial degredation of DOC (:math:`day^{-1}`) saccharids", "0.03" - "``k_bac_l``", "real", "bacterial degredation of DOC (:math:`day^{-1}`) lipids", "0.03" - "``T_max``", "real", "maximum temperature (:math:`^o`\ C)", "0.0" - "``fsal``", "real", "Salinity limitation (ppt)", "1.0" - "``op_dep_min``", "real", "Light attenuates for optical depths exceeding min", "0.1" - "``fr_graze_s``", "real", "fraction of grazing spilled or slopped", "0.5" + +zbgc_nml +~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. csv-table:: **zbgc_nml namelist options** + :header: "variable", "options/format", "description", "default value" + :widths: 15, 15, 30, 15 + + "", "", "", "" + "``algaltype_diatoms``", "real", "mobility type between stationary and mobile algal diatoms", "0.0" + "``algaltype_phaeo``", "real", "mobility type between stationary and mobile algal phaeocystis", "0.5" + "``algaltype_sp``", "real", "mobility type between stationary and mobile small plankton", "0.5" + "``algal_vel``", "real", ":cite:`Lavoie05`", "1.11e-8" + "``alpha2max_low_diatoms``", "real", "light limitation diatoms 1/(W/m^2)", "0.8" + "``alpha2max_low_phaeo``", "real", "light limitation phaeocystis 1/(W/m^2)", "0.67" + "``alpha2max_low_sp``", "real", "light limitation small plankton 1/(W/m^2)", "0.67" + "``ammoniumtype``", "real", "mobility type between stationary and mobile ammonium", "1.0" + "``beta2max_diatoms``", "real", "light inhibition diatoms 1/(W/m^2)", "0.18" + "``beta2max_phaeo``", "real", "light inhibition phaeocystis 1/(W/m^2)", "0.01" + "``beta2max_sp``", "real", "light inhibition small plankton 1/(W/m^2)", "0.0025" + "``bgc_data_type``", "``clim``", "bgc climatological data", "``default``" + "", "``default``", "constant values defined in the code", "" + "", "``ncar``", "POP ocean forcing data", "" + "``bgc_flux_type``", "``constant``", "constant ice–ocean flux velocity", "``Jin2006``" + "", "``Jin2006``", "ice–ocean flux velocity of :cite:`Jin06`", "" + "``chlabs_diatoms``", "real", "chl absorbtion diatoms 1/m/(mg/m^3)", "0.03" + "``chlabs_phaeo``", "real", "chl absorbtion phaeocystis 1/m/(mg/m^3)", "0.05" + "``chlabs_sp``", "real", "chl absorbtion small plankton 1/m/(mg/m^3)", "0.01" + "``dEdd_algae``", "logical", "", "``.false.``" + "``dmspdtype``", "real", "mobility type between stationary and mobile dmspd", "-1.0" + "``dmspptype``", "real", "mobility type between stationary and mobile dmspp", "0.5" + "``doctype_l``", "real", "mobility type between stationary and mobile doc lipids", "0.5" + "``doctype_s``", "real", "mobility type between stationary and mobile doc saccharids", "0.5" + "``dontype_protein``", "real", "mobility type between stationary and mobile don proteins", "0.5" + "``dustFe_sol``", "real", "solubility fraction", "0.005" + "``fedtype_1``", "real", "mobility type between stationary and mobile fed lipids", "0.5" + "``feptype_1``", "real", "mobility type between stationary and mobile fep lipids", "0.5" + "``frazil_scav``", "real", "increase in initial bio bracer from ocean scavenging", "1.0" + "``fr_dFe``", "real", "fraction of remineralized nitrogen in units of algal iron", "0.3" + "``fr_graze_diatoms``", "real", "fraction grazed diatoms", "0.01" "``fr_graze_e``", "real", "fraction of assimilation excreted", "0.5" + "``fr_graze_phaeo``", "real", "fraction grazed phaeocystis", "0.1" + "``fr_graze_s``", "real", "fraction of grazing spilled or slopped", "0.5" + "``fr_graze_sp``", "real", "fraction grazed small plankton", "0.1" "``fr_mort2min``", "real", "fractionation of mortality to Am", "0.5" - "``fr_dFe``", "real", "fraction of remineralized nitrogen (algal iron)", "0.3" - "``k_nitrif``", "real", "nitrification rate (:math:`day^{-1}`)", "0.0" - "``t_iron_conv``", "real", "desorption loss pFe to dFe (day)", "3065.0" - "``max_loss``", "real", "restrict uptake to % of remaining value", "0.9" - "``max_dfe_doc1``", "real", "max ratio of dFe to saccharides in the ice (:math:`nM Fe/\mu M C`)", "0.2" + "``fr_resp``", "real", "frac of algal growth lost due to respiration", "0.05" "``fr_resp_s``", "real", "DMSPd fraction of respiration loss as DMSPd", "0.75" + "``fsal``", "real", "salinity limitation ppt", "1.0" + "``F_abs_chl_diatoms``", "real", "scales absorbed radiation for dEdd chl diatoms", "2.0" + "``F_abs_chl_phaeo``", "real", "scales absorbed radiation for dEdd chl phaeocystis", "5.0" + "``F_abs_chl_sp``", "real", "scales absorbed radiation for dEdd small plankton", "4.0" + "``f_doc_l``", "real", "fraction of mortality to DOC lipids", "0.4" + "``f_doc_s``", "real", "fraction of mortality to DOC saccharides", "0.4" + "``f_don_Am_protein``", "real", "fraction of remineralized DON to ammonium", "0.25" + "``f_don_protein``", "real", "fraction of spilled grazing to proteins", "0.6" + "``f_exude_l``", "real", "fraction of exudation to DOC lipids", "1.0" + "``f_exude_s``", "real", "fraction of exudation to DOC saccharids", "1.0" + "``grid_o``", "real", "z biology for bottom flux", "5.0" + "``grid_oS``", "real", "z salinity for bottom flux", "5.0" + "``grow_Tdep_diatoms``", "real", "temperature dependence growth diatoms per degC", "0.06" + "``grow_Tdep_phaeo``", "real", "temperature dependence growth phaeocystis per degC", "0.06" + "``grow_Tdep_sp``", "real", "temperature dependence growth small plankton per degC", "0.06" + "``humtype``", "real", "mobility type between stationary and mobile hum", "1.0" + "``initbio_frac``", "real", "fraction of ocean trcr concentration in bio tracers", "1.0" + "``K_Am_diatoms``", "real", "ammonium half saturation diatoms mmol/m^3", "0.3" + "``K_Am_phaeo``", "real", "ammonium half saturation phaeocystis mmol/m^3", "0.3" + "``K_Am_sp``", "real", "ammonium half saturation small plankton mmol/m^3", "0.3" + "``k_bac_l``", "real", "Bacterial degredation of DOC lipids per day", "0.03" + "``k_bac_s``", "real", "Bacterial degredation of DOC saccharids per day", "0.03" + "``k_exude_diatoms``", "real", "algal exudation diatoms per day", "0.0" + "``k_exude_phaeo``", "real", "algal exudation phaeocystis per day", "0.0" + "``k_exude_sp``", "real", "algal exudation small plankton per day", "0.0" + "``K_Fe_diatoms``", "real", "iron half saturation diatoms nM", "1.0" + "``K_Fe_phaeo``", "real", "iron half saturation phaeocystis nM", "0.1" + "``K_Fe_sp``", "real", "iron half saturation small plankton nM", "0.2" + "``k_nitrif``", "real", "nitrification rate per day", "0.0" + "``K_Nit_diatoms``", "real", "nitrate half saturation diatoms mmol/m^3", "1.0" + "``K_Nit_phaeo``", "real", "nitrate half saturation phaeocystis mmol/m^3", "1.0" + "``K_Nit_sp``", "real", "nitrate half saturation small plankton mmol/m^3", "1.0" + "``K_Sil_diatoms``", "real", "silicate half saturation diatoms mmol/m^3", "4.0" + "``K_Sil_phaeo``", "real", "silicate half saturation phaeocystis mmol/m^3", "0.0" + "``K_Sil_sp``", "real", "silicate half saturation small plankton mmol/m^3", "0.0" + "``kn_bac_protein``", "real", "bacterial degradation of DON per day", "0.03" + "``l_sk``", "real", "characteristic diffusive scale in m", "7.0" + "``l_skS``", "real", "z salinity characteristic diffusive scale in m", "7.0" + "``max_dfe_doc1``", "real", "max ratio of dFe to saccharides in the ice in nm Fe / muM C", "0.2" + "``max_loss``", "real", "restrict uptake to percent of remaining value", "0.9" + "``modal_aero``", "logical", "modal aersols", "``.false.``" + "``mort_pre_diatoms``", "real", "mortality diatoms", "0.007" + "``mort_pre_phaeo``", "real", "mortality phaeocystis", "0.007" + "``mort_pre_sp``", "real", "mortality small plankton", "0.007" + "``mort_Tdep_diatoms``", "real", "temperature dependence of mortality diatoms per degC", "0.03" + "``mort_Tdep_phaeo``", "real", "temperature dependence of mortality phaeocystis per degC", "0.03" + "``mort_Tdep_sp``", "real", "temperature dependence of mortality small plankton per degC", "0.03" + "``mu_max_diatoms``", "real", "maximum growth rate diatoms per day", "1.2" + "``mu_max_phaeo``", "real", "maximum growth rate phaeocystis per day", "0.851" + "``mu_max_sp``", "real", "maximum growth rate small plankton per day", "0.851" + "``nitratetype``", "real", "mobility type between stationary and mobile nitrate", "-1.0" + "``op_dep_min``", "real", "light attenuates for optical depths exceeding min", "0.1" + "``phi_snow``", "real", "snow porosity for brine height tracer", "0.5" + "``ratio_chl2N_diatoms``", "real", "algal chl to N in mg/mmol diatoms", "2.1" + "``ratio_chl2N_phaeo``", "real", "algal chl to N in mg/mmol phaeocystis", "0.84" + "``ratio_chl2N_sp``", "real", "algal chl to N in mg/mmol small plankton", "1.1" + "``ratio_C2N_diatoms``", "real", "algal C to N in mol/mol diatoms", "7.0" + "``ratio_C2N_phaeo``", "real", "algal C to N in mol/mol phaeocystis", "7.0" + "``ratio_C2N_proteins``", "real", "algal C to N in mol/mol proteins", "7.0" + "``ratio_C2N_sp``", "real", "algal C to N in mol/mol small plankton", "7.0" + "``ratio_Fe2C_diatoms``", "real", "algal Fe to C in umol/mol diatoms", "0.0033" + "``ratio_Fe2C_phaeo``", "real", "algal Fe to C in umol/mol phaeocystis", "1.0" + "``ratio_Fe2C_sp``", "real", "algal Fe to C in umol/mol small plankton", "0.0033" + "``ratio_Fe2N_diatoms``", "real", "algal Fe to N in umol/mol diatoms", "0.23" + "``ratio_Fe2N_phaeo``", "real", "algal Fe to N in umol/mol phaeocystis", "0.7" + "``ratio_Fe2N_sp``", "real", "algal Fe to N in umol/mol small plankton", "0.23" + "``ratio_Fe2DOC_s``", "real", "Fe to C of DON saccharids nmol/umol", "1.0" + "``ratio_Fe2DOC_l``", "real", "Fe to C of DOC lipids nmol/umol", "0.033" + "``ratio_Fe2DON``", "real", "Fe to C of DON nmol/umol", "0.023" + "``ratio_Si2N_diatoms``", "real", "algal Si to N in mol/mol diatoms", "1.8" + "``ratio_Si2N_phaeo``", "real", "algal Si to N in mol/mol phaeocystis", "0.0" + "``ratio_Si2N_sp``", "real", "algal Si to N in mol/mol small plankton", "0.0" + "``ratio_S2N_diatoms``", "real", "algal S to N in mol/mol diatoms", "0.03" + "``ratio_S2N_phaeo``", "real", "algal S to N in mol/mol phaeocystis", "0.03" + "``ratio_S2N_sp``", "real", "algal S to N in mol/mol small plankton", "0.03" + "``restore_bgc``", "logical", "restore bgc to data", "``.false.``" + "``R_dFe2dust``", "real", "g/g :cite:`Tagliabue09`", "0.035" + "``scale_bgc``", "logical", "", "``.false.``" + "``silicatetype``", "real", "mobility type between stationary and mobile silicate", "-1.0" + "``skl_bgc``", "logical", "biogeochemistry", "``.false.``" + "``solve_zbgc``", "logical", "", "``.false.``" + "``solve_zsal``", "logical", "update salinity tracer profile", "``.false.``" + "``tau_max``", "real", "long time mobile to stationary exchanges", "1.73e-5" + "``tau_min``", "real", "rapid module to stationary exchanges", "5200." + "``tr_bgc_Am``", "logical", "ammonium tracer", "``.false.``" + "``tr_bgc_C``", "logical", "algal carbon tracer", "``.false.``" + "``tr_bgc_chl``", "logical", "algal chlorophyll tracer", "``.false.``" + "``tr_bgc_DMS``", "logical", "DMS tracer", "``.false.``" + "``tr_bgc_DON``", "logical", "DON tracer", "``.false.``" + "``tr_bgc_Fe``", "logical", "iron tracer", "``.false.``" + "``tr_bgc_hum``", "logical", "", "``.false.``" + "``tr_bgc_Nit``", "logical", "", "``.false.``" + "``tr_bgc_PON``", "logical", "PON tracer", "``.false.``" + "``tr_bgc_Sil``", "logical", "silicate tracer", "``.false.``" + "``tr_brine``", "logical", "brine height tracer", "``.false.``" + "``tr_zaero``", "logical", "vertical aerosol tracers", "``.false.``" + "``t_iron_conv``", "real", "desorption loss pFe to dFe in days", "3065." + "``t_sk_conv``", "real", "Stefels conversion time in days", "3.0" + "``t_sk_ox``", "real", "DMS oxidation time in days", "10.0" + "``T_max``", "real", "maximum temperature degC", "0.0" "``y_sk_DMS``", "real", "fraction conversion given high yield", "0.5" - "``t_sk_conv``", "real", "Stefels conversion time (:math:`day`)", "3.0" - "``t_sk_ox``", "real", "DMS oxidation time (:math:`day`)", "10.0" - "``algaltype_diatoms``", "real", "mobility type between stationary <--> mobile for diatoms", "0.0" - "``algaltype_sp``", "real", "mobility type between stationary <--> mobile for small phytoplankton", "0.5" - "``algaltype_phaeo``", "real", "mobility type between stationary <--> mobile for phaeocystis", "0.5" - "``nitratetype``", "real", "mobility type between stationary <--> mobile for nitrate", "-1.0" - "``ammoniumtype``", "real", "mobility type between stationary <--> mobile for ammonium", "1.0" - "``silicatetype``", "real", "mobility type between stationary <--> mobile for silicate", "-1.0" - "``dmspptype``", "real", "mobility type between stationary <--> mobile for DMSP particulate", "0.5" - "``dmspdtype``", "real", "mobility type between stationary <--> mobile for DMSP dissolved", "-1.0" - "``humtype``", "real", "mobility type between stationary <--> mobile for humic matter", "1.0" - "``doctype_s``", "real", "mobility type between stationary <--> mobile for DOC saccharids", "0.5" - "``doctype_l``", "real", "mobility type between stationary <--> mobile for DOC lipids", "0.5" - "``dontype_protein``", "real", "mobility type between stationary <--> mobile for proteins", "0.5" - "``fedtype_1``", "real", "mobility type between stationary <--> mobile for FeD", "0.5" - "``feptype_1``", "real", "mobility type between stationary <--> mobile for FeP", "0.5" - "``zaerotype_bc1``", "real","mobility type between stationary <--> mobile for zaerotype_bc1", "1.0" - "``zaerotype_bc2``", "real", "mobility type between stationary <--> mobile for zaerotype_bc2", "1.0" - "``zaerotype_dust1``", "real", "mobility type between stationary <--> mobile for dust1", "1.0" - "``zaerotype_dust2``", "real", "mobility type between stationary <--> mobile for dust2", "1.0" - "``zaerotype_dust3``", "real", "mobility type between stationary <--> mobile for dust3", "1.0" - "``zaerotype_dust4``", "real", "mobility type between stationary <--> mobile for dust4", "1.0" - "``ratio_C2N_diatoms``", "real", "diatom algal C to N ratio (:math:`mol/mol`)", "7.0" - "``ratio_C2N_sp``", "real", "small phytoplankton algal C to N ratio (:math:`mol/mol`)", "7.0" - "``ratio_C2N_phaeo``", "real", "phaeocystis algal C to N ratio (:math:`mol/mol`)", "7.0" - "``ratio_chl2N_diatoms``", "real", "diatom algal chlorophyll to N ratio (:math:`mg/mmol`)", "2.1" - "``ratio_chl2N_sp``", "real", "small phytoplankton algal chlorophyll to N ratio (:math:`mg/mmol`)", "1.1" - "``ratio_chl2N_phaeo``", "real", "phaeocystis algal chlorophyll to N ratio (:math:`mg/mmol`)", "0.84" - "``F_abs_chl_diatoms``", "real", "diatom scales absorbed radiation for dEdd", "2.0" - "``F_abs_chl_sp``", "real", "small phytoplankton scales absorbed radiation for dEdd", "4.0" - "``F_abs_chl_phaeo``", "real", "phaeocystis scales absorbed radiation for dEdd", "5.0" - "``ratio_C2N_proteins``", "real", "ratio of C to N in proteins (:math:`mol/mol`)", "7.0" + "``zaerotype_bc1``", "real", "mobility type between stationary and mobile zaero bc1", "1.0" + "``zaerotype_bc2``", "real", "mobility type between stationary and mobile zaero bc2", "1.0" + "``zaerotype_dust1``", "real", "mobility type between stationary and mobile zaero dust1", "1.0" + "``zaerotype_dust2``", "real", "mobility type between stationary and mobile zaero dust2", "1.0" + "``zaerotype_dust3``", "real", "mobility type between stationary and mobile zaero dust3", "1.0" + "``zaerotype_dust4``", "real", "mobility type between stationary and mobile zaero dust4", "1.0" + "``z_tracers``", "logical", "", "``.false.``" "", "", "", "" + .. commented out below .. "``dbug``", "true/false", "if true, write extra diagnostics", "``.false.``" .. "``atm_data_format``", "``nc``", "read  atmo forcing files", "" @@ -410,6 +475,10 @@ column physics. .. "", "``NICE``", "N-ICE experiment data", "" .. "", "``NICE``", "N-ICE experiment data", "" .. "", "``NICE``", "N-ICE experiment data", "" +.. "``grid_o_t``", "real", "z biology for top flux", "5.0" +.. "``restart_bgc``", "logical", "restart tracer values from file", "``.false.``" +.. "``restart_hbrine``", "logical", "", "``.false.``" +.. "``restart_zsal``", "logical", "", "``.false.``" * = If Icepack is run stand-alone and wave_spec_type is not set to none, then a fixed wave spectrum is defined in the code to use for testing. As with other input data, this spectrum should not be used for production runs or publications.