Doc compilation

configuration/driver/icedrv_constants.F90

@@ -67,7 +67,6 @@ module icedrv_constants
 
       real (kind=dbl_kind), parameter, public :: &
          omega     = 7.292e-5_dbl_kind, & ! angular velocity of earth (rad/sec)
-         radius    = 6.37e6_dbl_kind      ! earth radius (m)
 
       !-----------------------------------------------------------------
       ! numbers used outside the column package

doc/source/developer_guide/dg_col_phys.rst

@@ -16,7 +16,6 @@ The column physics source code contains the following files
 |    **icepack_algae.F90**         biogeochemistry
 |    **icepack_atmo.F90**          stability-based parameterization for calculation of turbulent ice–atmosphere fluxes
 |    **icepack_brine.F90**         evolves the brine height tracer
-|    **icepack_constants.F90**     physical and numerical constants required for column package
 |    **icepack_firstyear.F90**     handles most work associated with the first-year ice area tracer
 |    **icepack_flux.F90**          fluxes needed/produced by the model
 |    **icepack_intfc.F90**         interface routines for linking Icepack with a host sea ice model
@@ -29,7 +28,7 @@ The column physics source code contains the following files
 |    **icepack_mushy_physics.F90** physics routines for mushy thermodynamics
 |    **icepack_ocean.F90**         mixed layer ocean model
 |    **icepack_orbital.F90**       orbital parameters for Delta-Eddington shortwave parameterization
-|    **icepack_parameters.F90**    basic model parameters
+|    **icepack_parameters.F90**    basic model parameters including physical and numerical constants requried for column package
 |    **icepack_shortwave.F90**     shortwave and albedo parameterizations
 |    **icepack_therm_0layer.F90**  zero-layer thermodynamics of :cite:`Semtner76`
 |    **icepack_therm_bl99.F90**    multilayer thermodynamics of :cite:`BL99`
@@ -104,7 +103,7 @@ icepack_kinds module::
       use icepack_kinds, only: icepack_dbl_kind  => dbl_kind
       use icepack_kinds, only: icepack_r16_kind  => r16_kind
 
-icepack_tracers defines a handful of parameters constants that provide information
+icepack_tracers defines a handful of parameters that provide information
 about maximum array sizes for static dimensioning::
 
       use icepack_tracers,   only: icepack_max_nbtrcr => max_nbtrcr
@@ -116,28 +115,16 @@ about maximum array sizes for static dimensioning::
       use icepack_tracers,   only: icepack_max_aero   => max_aero
       use icepack_tracers,   only: icepack_nmodal1    => nmodal1
       use icepack_tracers,   only: icepack_nmodal2    => nmodal2
-      use icepack_constants, only: icepack_nspint     => nspint
+      use icepack_parameters, only: icepack_nspint     => nspint
 
-icepack_constants provides a list of static parameter constants::
-
-      use icepack_constants, only: c0 => c0
-
-icepack_constants provides init, query, write, and recompute methods to
-define constant values.  These constants have defaults that the caller
-can query or reset::
-
-      use icepack_constants, only: icepack_init_constants
-      use icepack_constants, only: icepack_query_constants
-      use icepack_constants, only: icepack_write_constants
-      use icepack_constants, only: icepack_recompute_constants
-
-icepack_parameters provides init, query, and write methods to
-define model parameters.  These parameters have defaults that the caller
-can query or reset::
+icepack_parameters provides init, query, write, and recompute methods to
+define constant values and model parameters.  These constants have defaults 
+that the caller can query or reset::
 
       use icepack_parameters, only: icepack_init_parameters
       use icepack_parameters, only: icepack_query_parameters
       use icepack_parameters, only: icepack_write_parameters
+      use icepack_parameters, only: icepack_recompute_constants
 
 icepack_tracers provides init, query, and write methods to
 define various tracer sizes, flags, indices, and numbers.  The
@@ -248,7 +235,6 @@ start driver
 
 initialize driver and read in driver namelist
 
-* call *icepack_init_constants*
 * call *icepack_init_parameters*
 * call *icepack_init_tracers_*
 * call *icepack_init_trcr*

doc/source/developer_guide/dg_driver.rst

@@ -43,4 +43,4 @@ to run 4 different gridcells on one processor with the same forcing used for all
 There is no MPI and no threading built into the icepack driver.  There is limited IO capabilities,
 no history files, and no netcdf restart files.  The model generally runs very quickly.
 
-Forcing data and details on these data are available in :ref:`testforce`.
+Forcing data and details on these data are available in :ref:`force`.

doc/source/icepack_index.rst

@@ -18,7 +18,6 @@ either Celsius or Kelvin units).
 
    "**A**", "", ""
    "a_rapid_mode", ":math:`\bullet` brine channel diameter", ""
-   "advection", ":math:`\bullet` type of advection algorithm used (‘remap’ or ‘upwind’)", "remap"
    "ahmax", ":math:`\bullet` thickness above which ice albedo is constant", "0.3m"
    "aice_init", "concentration of ice at beginning of timestep", ""
    "aice0", "fractional open water area", ""
@@ -33,8 +32,14 @@ either Celsius or Kelvin units).
    "albsnowi", ":math:`\bullet` near infrared, cold snow albedo", ""
    "albsnowv", ":math:`\bullet` visible, cold snow albedo", ""
    "algalN", "algal nitrogen concentration", mmol/m\ :math:`^3`
-   "alv(n)dr(f)", "albedo: visible (near IR), direct (diffuse)", ""
-   "alv(n)dr(f)_ai", "grid-box-mean value of alv(n)dr(f)", ""
+   "alndf", "albedo: near IR, diffuse", ""
+   "alndr", "albedo: near IR, direct", ""
+   "alvdf", "albedo: visible, diffuse", ""
+   "alvdr", "albedo: visible, direct", ""
+   "alndf_ai", "grid-box-mean value of alndf", ""
+   "alndr_ai", "grid-box-mean value of alndr", ""
+   "alvdf_ai", "grid-box-mean value of alvdf", ""
+   "alvdr_ai", "grid-box-mean value of alvdr", ""
    "amm", "ammonia/um concentration", "mmol/m\ :math:`^3`"
    "aparticn", "participation function", ""
    "apeff_ai", "grid-cell-mean effective pond fraction", ""
@@ -205,7 +210,6 @@ either Celsius or Kelvin units).
    "ice_stderr", "unit number for standard error output", ""
    "ice_ref_salinity", "reference salinity for ice–ocean exchanges", "4. ppt"
    "iceruf", "ice surface roughness", "5.\ :math:`\times`\ 10\ :math:`^{-4}` m"
-   "iceumask", "ice extent mask (U-cell)", ""
    "idate", "the date at the end of the current time step (yyyymmdd)", ""
    "idate0", "initial date", ""
    "igrid", "interface points for vertical bio grid", ""
@@ -273,7 +277,6 @@ either Celsius or Kelvin units).
    "nit", "nitrate concentration", "mmol/m\ :math:`^3`"
    "nlt_bgc_[chem]", "ocean sources and sinks for biogeochemistry", ""
    "nml_filename", "namelist file name", ""
-   "nprocs", ":math:`\bullet` total number of processors", ""
    "npt", ":math:`\bullet` total number of time steps (dt)", ""
    "nslyr", "number of snow layers in each category", ""
    "nspint", "number of solar spectral intervals", ""
@@ -329,7 +332,6 @@ either Celsius or Kelvin units).
    "PP_net", "total primary productivity per grid cell", "mg C/m\ :math:`^2`/s"
    "precip_units", ":math:`\bullet` liquid precipitation data units", ""
    "print_points", ":math:`\bullet` if true, print point data", "F"
-   "prs_sig", "replacement pressure", "N/m"
    "Pstar", "ice strength parameter", "2.75\ :math:`\times`\ 10\ :math:`^4`\ N/m"
    "puny", "a small positive number", "1\ :math:`\times`\ 10\ :math:`^{-11}`" 
    "**Q**", "", ""
@@ -348,7 +350,6 @@ either Celsius or Kelvin units).
    "R_snw", ":math:`\bullet` parameter for Delta-Eddington snow albedo", ""
    "r16_kind", "definition of quad precision", "selected_real_kind(26)", ""
    "Rac_rapid_mode", ":math:`\bullet` critical Rayleigh number", "10"
-   "radius", "earth radius", "6.37\ :math:`\times`\ 10\ :math:`^6` m"
    "rdg_conv", "convergence for ridging", "1/s"
    "rdg_shear", "shear for ridging", "1/s"
    "real_kind", "definition of single precision real", "selected_real_kind(6)"
@@ -386,7 +387,6 @@ either Celsius or Kelvin units).
    "shear", "strain rate II component", "1/s"
    "shlat", "southern latitude of artificial mask edge", "30\ :math:`^\circ`\ N"
    "shortwave", ":math:`\bullet` flag for shortwave parameterization ('default' or 'dEdd')", ""
-   "sig1(2)", "principal stress components (diagnostic)", ""
    "sil", "silicate concentration", "mmol/m\ :math:`^3`"
    "sk_l", "skeletal layer thickness", "0.03 m"
    "snoice", "snow-ice formation", "m"
@@ -411,7 +411,10 @@ either Celsius or Kelvin units).
    "strocnx(y)", "ice–ocean stress in the x(y)-direction (U-cell)", "N/m\ :math:`^2`"
    "strocnx(y)T", "ice–ocean stress, x(y)-dir. (T-cell)", "N/m\ :math:`^2`"
    "strtltx(y)", "surface stress due to sea surface slope", "N/m\ :math:`^2`"
-   "swv(n)dr(f)", "incoming shortwave radiation, visible (near IR), direct (diffuse)", "W/m\ :math:`^2`"
+   "swndf", "incoming shortwave radiation, near IR, diffuse", "W/m\ :math:`^2`"
+   "swndr", "incoming shortwave radiation, near IR, direct", "W/m\ :math:`^2`"
+   "swvdf", "incoming shortwave radiation, visible, diffuse", "W/m\ :math:`^2`"
+   "swvdr", "incoming shortwave radiation, visible, direct", "W/m\ :math:`^2`"
    "**T**", "", ""
    "Tair", "air temperature at 10 m", "K"
    "tday", "absolute day number", ""
@@ -449,7 +452,6 @@ either Celsius or Kelvin units).
    "TTTocn", "for saturated specific humidity over ocean", "5107.4 K"
    "**U**", "", ""
    "uatm", "wind velocity in the x direction", "m/s"
-   "umask", "land/boundary mask, velocity (U-cell)", ""
    "umin", "min wind speed for turbulent fluxes", "1. m/s"
    "uocn", "ocean current in the x-direction", "m/s"
    "update_ocn_f", ":math:`\bullet` if true, include frazil ice fluxes in ocean flux fields", ""
@@ -471,7 +473,6 @@ either Celsius or Kelvin units).
    "warmice", "value for constant albedo parameterization", "0.68"
    "warmsno", "value for constant albedo parameterization", "0.77"
    "wind", "wind speed", "m/s"
-   "write_ic", ":math:`\bullet` if true, write initial conditions", ""
    "write_restart", "if 1, write restart now", ""
    "**X**", "", ""
    "**Y**", "", ""

doc/source/intro/major_updates.rst

@@ -23,4 +23,6 @@ the code.  Icepack includes the simplified driver and scripts for configuring va
 column physics code in columnphysics/.
 
 Enhancements and bug fixes made to Icepack since the last numbered release can be found on the
-Icepack wiki https://github.com/CICE-Consortium/Icepack/wiki/Recent-changes.
+Icepack wiki https://github.com/CICE-Consortium/Icepack/wiki/Recent-changes. Major changes with
+each Icepack release (found here: https://github.com/CICE-Consortium/Icepack/releases) will
+be included as release notes.

doc/source/master_list.bib

@@ -48,6 +48,7 @@ @string{NTN
 @string{BGC = {Biogeochemistry}}
 @string{EFM = {Eng. Fract. Mech.}}
 @string{ANG = {Ann. Glaciol.}}
+@string{NOAA = {Natl. Ocn. and Atm. Admin}}
 
 % Individual entries (roughly sequential, then alphabetical but first-author’s last name)
 @incollection{Assur58,
@@ -333,6 +334,15 @@ @Article{GHA98
   pages = {21893-21913},
   url = {http://dx.doi.org/10.1029/98JC01258}
 }
+@Article{LIND98
+  author = "R.W. Lindsay",
+  title = "{Temporal variability of the energy balance of thick Arctic pack ice}",
+  journal = JC,
+  year = "1998",
+  volume = {11},
+  pages = {313-333},
+  url = {https://doi.org/10.1175/1520-0442(1998)011<0313:TVOTEB>2.0.CO;2 }
+}
 @Book{Lipscomb98
   author = "W.H. Lipscomb",
   title = "{Modeling the Thickness Distribution of Arctic Sea Ice}",
@@ -741,6 +751,23 @@ @Article{THB13
   pages = {2279-2294},
   url = {http://dx.doi.org/10.1002/jgrc.20171}
 }
+@Article{WOA13
+  author = "National Centers for Environmental Information",
+  title = "{World Ocean Atlas Version 2}",
+  journal = NOAA,
+  year = "2013",
+  url = {https://www.nodc.noaa.gov/OC5/woa13/}
+}
+@Article{JH14
+  author = "N. Jeffery and E.C. Hunke",
+  title = "{Modeling the winter-spring transition of first-year ice in the western Weddell Sea}",
+  journal = JGRO,
+  year = "2014",
+  volume = {119},
+  issue = {9},
+  pages = {5891-5920},
+  url = {http://dx.doi.org/10.1002/2013JC009634}
+}
 @Article{SAHA14
   author = "S. Saha and S. Moorthi and X. Wu and J. Wang and Coauthors",
   title = "{Two modes of sea-ice gravity drainage: a parameterization for large-scale modeling}",
@@ -761,12 +788,21 @@ @Article{TFSFFKLB14
 }
 @Article{Roberts2015,
   author = {A.F. Roberts and A. Craig and W. Maslowski and R. Osinski and A. Duvivier and M. Hughes and B. Nijssen and J.J. Cassano. and M. Brunke},
-  url = {https://doi.org/10.3189/2015AoG69A760},
+  title = {Simulating transient ice-ocean Ekman transport in the Regional Arctic System Model and Community Earth System Model},
   journal = ANG,
+  year = "2015",
+  volume = {56},
   number = {69},
   pages = {211--228},
-  title = {{Simulating transient ice-ocean Ekman transport in the Regional Arctic System Model and Community Earth System Model}},
-  volume = {56},
-  year = {2015}
+  url = {https://doi.org/10.3189/2015AoG69A760}
+}
+@Article{DUARTE17
+  author = "P. Duarte and Coauthors",
+  title = "{Sea ice thermohaline dynamics and biogeochemistry in the Arctic Ocean: Empirical and model results}",
+  journal = JGRB,
+  year = "2017",
+  volume = {122},
+  issue = {7},
+  pages = {1632-1654},
+  url = {https://doi.org/10.1002/2016JG003660}
 }
-

doc/source/user_guide/ug_case_settings.rst

@@ -225,8 +225,6 @@ column physics.
    "``oceanmixed_ice``", "true/false", "active ocean mixed layer calculation", "``.true.`` (if uncoupled)"
    "``ocn_data_type``", "``default``", "constant values defined in the code", ""
    "", "``ISPOL``", "ISPOL experiment data", ""
-   "``bgc_data_type``", "``default``", "constant values defined in the code", ""
-   "", "``ISPOL``", "ISPOL experiment data", ""
    "``oceanmixed_file``", "filename", "data file containing ocean forcing data", ""
    "``restore_ocn``", "true/false", "restore sst to data", ""
    "``trestore``", "integer", "sst restoring time scale (days)", ""
@@ -248,7 +246,10 @@ column physics.
    "``solve_zsal``", "true/false", "prognostic salinity tracer used with ktherm = 1", "``.false.``"
    "``restart_zsal``", "true/false", "restarts zsalinity", "``.false.``"
    "``bgc_data_dir``", "``/nitrate_and_silicate/forcing_directory/``", "", "'``/nitrate_and_silicate/forcing_directory/``'"
-   "``bgc_data_type``", "``default`` or ``NICE`` or ``ISPOL`` or ``clim``", "fixed, spatially homogeneous value for nitrate. 'clim' data file (see icedrv_forcing_bgc.F90) :cite:`GLBA06`", "``'default'``"
+   "``bgc_data_type``", "``default``", "fixed, spatially homogeneous constant values defined in the code", ""
+   "", "``clim``", "monthly climatology data file (see icedrv_forcing_bgc.F90) :cite:`GLBA06`", ""
+   "", "``NICE``", "NICE 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.``"

doc/source/user_guide/ug_implementation.rst

@@ -102,7 +102,7 @@ Initialization and Forcing
 
 Icepack’s parameters and variables are initialized in several
 steps. Many constants and physical parameters are set in
-**icepack\_constants.F90**. In the current driver implementation,
+**icepack\_parameters.F90**. In the current driver implementation,
 a namelist file is read to setup the model.
 Namelist values are given default
 values in the code, which may then be changed when the input file