From 0d76fb6c1e7d5fcb996b9f93fb8d722ff850375b Mon Sep 17 00:00:00 2001 From: Alice DuVivier Date: Mon, 1 Oct 2018 13:29:43 -0600 Subject: [PATCH 1/4] adding CMIP variable documentation --- doc/source/user_guide/ug_case_settings.rst | 2 +- doc/source/user_guide/ug_implementation.rst | 23 ++++++++++++++++----- 2 files changed, 19 insertions(+), 6 deletions(-) diff --git a/doc/source/user_guide/ug_case_settings.rst b/doc/source/user_guide/ug_case_settings.rst index c8eba51f6..027769437 100755 --- a/doc/source/user_guide/ug_case_settings.rst +++ b/doc/source/user_guide/ug_case_settings.rst @@ -354,7 +354,7 @@ Table of namelist options "``trestore``", "integer", "sst restoring time scale (days)", "" "``restore_ice``", "true/false", "restore ice state along lateral boundaries", "" "", "", "", "" - "*icefields_tracer_nml*", "", "", "" + "*icefields_nml*", "", "", "" "", "", "*History Fields*", "" "``f_``", "string", "frequency units for writing ```` to history", "" "", "``y``", "write history every ``histfreq_n`` years", "" diff --git a/doc/source/user_guide/ug_implementation.rst b/doc/source/user_guide/ug_implementation.rst index bf8767139..47f9788e2 100644 --- a/doc/source/user_guide/ug_implementation.rst +++ b/doc/source/user_guide/ug_implementation.rst @@ -743,8 +743,10 @@ History files Model output data is averaged over the period(s) given by `histfreq` and `histfreq\_n`, and written to binary or  files prepended by `history\_file` -in **ice\_in**. That is, if `history\_file` = ‘iceh’ then the filenames -will have the form **iceh.[timeID].nc** or **iceh.[timeID].da**, +in **ice\_in**. These settings for history files are set in the +**setup\_nml** section of **ice\_in** (see :ref:`tabnamelist`). +If `history\_file` = ‘iceh’ then the +filenames will have the form **iceh.[timeID].nc** or **iceh.[timeID].da**, depending on the output file format chosen in **comp\_ice** (set `IO\_TYPE`). The  history files are CF-compliant; header information for data contained in the  files is displayed with the command `ncdump -h @@ -752,9 +754,10 @@ filename.nc`. Parallel  output is available using the PIO library; the attribute `io\_flavor` distinguishes output files written with PIO from those written with standard netCDF. With binary files, a separate header file is written with equivalent information. Standard fields are output -according to settings in the **icefields\_nml** namelist in **ice\_in**. +according to settings in the **icefields\_nml** section of **ice\_in** +(see :ref:`tabnamelist`). The user may add (or subtract) variables not already available in the -namelist by following the instructions in section :ref:`addhist`. +namelist by following the instructions in section :ref:`addhist`. With this release, the history module has been divided into several modules based on the desired formatting and on the variables @@ -779,7 +782,7 @@ with a given `histfreq` value, or if an element of `histfreq\_n` is 0, then no file will be written at that frequency. The output period can be discerned from the filenames. -For example, in namelist: +For example, in the namelist: :: @@ -832,6 +835,16 @@ another that is multiplied by :math:`a_i`, representing an average over the grid cell area. Our naming convention attaches the suffix “\_ai" to the grid-cell-mean variable names. +In this version of CICE, history variables requested by the Sea Ice Model Intercomparison +Project (SIMIP) have been added as possible history output variables (e.g. +`f_sithick`, `f_sidmassgrowthbottom`, etc.). A full list of SIMIP variables is +available at the following site +. +Additionally, a new history output variable, `f_CMIP`, has been added. When `f_CMIP` +is added to the **icefields\_nml** section of **ice\_in** then all SIMIP variables +will be turned on for output at the frequency specified by `f_CMIP`. + + **************** Diagnostic files **************** From 146f9f26aa238244d8d2e600eb1928b96336fca3 Mon Sep 17 00:00:00 2001 From: Alice DuVivier Date: Mon, 1 Oct 2018 20:21:43 -0600 Subject: [PATCH 2/4] updating references --- doc/source/master_list.bib | 222 +++++++++----------- doc/source/science_guide/sg_modelcomps.rst | 6 +- doc/source/user_guide/ug_implementation.rst | 11 +- doc/source/user_guide/ug_testing.rst | 28 ++- 4 files changed, 121 insertions(+), 146 deletions(-) diff --git a/doc/source/master_list.bib b/doc/source/master_list.bib index 0e2f96cb5..071c864cd 100644 --- a/doc/source/master_list.bib +++ b/doc/source/master_list.bib @@ -45,12 +45,14 @@ @string{JPD @string{NTN = {NCAR Tech. Note}} @string{BGC = {Biogeochemistry}} @string{EFM = {Eng. Fract. Mech.}} +@string{GMD = {Geosci. Model Dev.}} +@string{CRST = {Cold Reg. Sci. Technol.}} -% Individual entries (roughly sequential, then alphabetical but first-author’s last name) +% Individual entries (roughly sequential, then alphabetical but first-author last name) @incollection{Assur58, author = "A. Assur", title = "Composition of sea ice and its tensile strength", - booktitle = "Arctic sea ice; conference held at Easton, Maryland, February 24–27, 1958", + booktitle = "Arctic sea ice; conference held at Easton, Maryland, February 24-€“27, 1958", publisher = "Publs. Natl. Res. Coun. Wash.", address = "Washington, D.C.", year = "1958", @@ -178,7 +180,7 @@ @Article{Maykut82 @incollection{SP86 author = "G. Siedler and H. Peters", title = "Physical properties (general) of sea water", - booktitle = "Landolt-Börnstein: Numerical data and functional relationships in science and technology, New Series V/3a", + booktitle = "Landolt-Barnstein: Numerical data and functional relationships in science and technology, New Series V/3a", publisher = "Springer", year = "1986", pages = {233-264}, @@ -292,6 +294,16 @@ @Manual{SKM95 year = "1995", url = {https://github.com/CICE-Consortium/CICE/blob/master/doc/PDF/LAUR-95-1146.pdf} } +@article{ZvS95, + author = "F.W. Zwiers and H. von Storch", + title = {Taking serial correlation into account in tests of the mean}, + journal = JC, + year = {1995}, + volume = {8}, + number = {2}, + pages = {336-351}, + url = {https://doi.org/10.1175/1520-0442(1995)008<0336:TSCIAI>2.0.CO;2} +} @Article{Murray96 author = "R.J. Murray", title = "{Explicit generation of orthogonal grids for ocean models}", @@ -373,7 +385,7 @@ @Book{vSZ99 publisher = "Cambridge University Press", note = "Cambridge, UK", year = "1999", - pages = {484 pp}, + pages = {484 pp} } @Article{DB00 author = "J.K. Dukowicz and J.R. Baumgardner", @@ -420,6 +432,16 @@ @Article{Schulson01 pages = {1839-1887}, url = {http://dx.doi.org/10.1016/S0013-7944(01)00037-6} } +@article{Taylor01, + author = "K.E. Taylor", + title = {Summarizing multiple aspects of model performance in a single diagram}, + journal = JGRA, + year = "2001", + volume = {106}, + number = {D7}, + pages = {7183-7192}, + url = {https://doi.org/10.1029/2000JD900719} +} @Article{TWMH01 author = "H.J. Trodahl and S.O.F. Wilkinson and M.J. McGuinness and T.G. Haskeel", title = "{Thermal conductivity of sea ice: dependence on temperature and depth}", @@ -431,7 +453,7 @@ @Article{TWMH01 } @Article{HD02 author = "E.C. Hunke and J.K. Dukowicz", - title = "{The Elastic-Viscous-Plastic sea ice dynamics model in general orthogonal curvilinear coordinates on a sphere—Effect of metric terms}", + title = "{The Elastic-Viscous-Plastic sea ice dynamics model in general orthogonal curvilinear coordinates on a sphere - Incorporation of metric terms}", journal = MWR, year = "2002", volume = {130}, @@ -517,7 +539,7 @@ @Article{LDM05 } @Book{Notz05 author = "D. Notz", - title = "Thermodynamic and Fluid-Dynamical Processes in Sea Ice", + title = "{Thermodynamic and Fluid-Dynamical Processes in Sea Ice}", publisher = "University of Cambridge, UK", note = "PhD thesis", year = "2005", @@ -550,6 +572,14 @@ @incollection{GLBA06 year = "2006", volume = {4}, } +@article{HRHPSL06, + author = "W.D. Hibler and A. Roberts and P. Heil and A.Y. Proshutinsky and H.L. Simmons and J. Lovick", + title = "{Modeling M2 tidal variability in Arctic sea-ice drift and deformation}", + journal = AG, + volume = {44}, + year = {2006}, + url = {https://doi.org/10.3189/172756406781811178} +} @Article{WF06 author = "A.V. Wilchinsky and D.L. Feltham", title = "{Modelling the rheology of sea ice as a collection of diamond-shaped floes}", @@ -565,7 +595,7 @@ @Book{Wilks06 publisher = "Academic Press", note = "2nd ed.", year = "2006", - pages = {627 pp}, + pages = {627 pp} } @Manual{BL07 author = "B.P. Briegleb and B. Light", @@ -646,6 +676,15 @@ @Article{FFT10 number = {C8}, url = {http://dx.doi.org/10.1029/2009JC005568} } +@Article{KH2010 + author = "C. Konig Beatty and D.M. Holland", + title = "{Modeling landfast ice by adding tensile strength}", + journal = JPO, + year = "2010", + volume = {40}, + pages = {185-198}, + url = {https://doi.org/10.1175/2009JPO4105.1} +} @Article{ABTH11 author = "K.C. Armour and C.M. Bitz and L. Thompson and E.C. Hunke", title = "{Controls on Arctic sea ice from first-year and multi-year ice survivability}", @@ -700,8 +739,17 @@ @Article{HBBLH12 pages = {1413-1430}, url = {http://dx.doi.org/10.1175/JCLI-D-11-00078.1} } +@article{LOSF12, + author = "M. Lepparanta and A. Oikkonen and K. Shirasawa and Y. Fukamachi", + title = "{A treatise on frequency spectrum of drift ice velocity}", + journal = CRST, + year = {2012}, + volume = {76-77}, + pages = {83-91}, + url= {https://doi.org/10.1016/j.coldregions.2011.12.005} +} @Article{LGHA12 - author = "C. Lüpkes and V.M. Gryanik and J. Hartmann and E.L. Andreas", + author = "C. Lupkes and V.M. Gryanik and J. Hartmann and E.L. Andreas", title = "{A parametrization, based on sea ice morphology, of the neutral atmospheric drag coefficients for weather prediction and climate models}", journal = JGRA, year = "2012", @@ -727,6 +775,15 @@ @Article{HHL13 pages = {26-42}, url = {http://dx.doi.org/10.1016/j.ocemod.2012.11.008} } +@article{Irving2015, + author = "D. Irving", + title = {A minimum standard for publishing computational results in the weather and climate sciences}, + journal = BAMS, + number = {97}, + pages = {1149-1158}, + year = {2015}, + url = {https://doi.org/10.1175/BAMS-D-15-00010.1} +} @Article{TFW13 author = "M. Tsamados and D.L. Feltham and A.V. Wilchinsky", title = "{Impact of a new anisotropic rheology on simulations of Arctic sea ice}", @@ -754,128 +811,45 @@ @Article{TFSFFKLB14 pages = {1329-1353}, url = {https://doi.org/10.1175/JPO-D-13-0215.1} } - -@Article{KH2010 - author = "C. Konig Beatty and D.M. Holland", - title = "{Modeling landfast ice by adding tensile strength}", - journal = JPO, - year = "2010", - volume = {40}, - pages = {185-198}, - url = {https://doi.org/10.1175/2009JPO4105.1} +@article{RCWODHNCB15, + author = "A.F. Roberts and A.P. Craig and W. Maslowski and R. Osinski and A.K. DuVivier and M. Hughes and B. Nijssen and J.J. Cassano and M. Brunke", + title = "{Simulating transient ice -€“ ocean Ekman transport in the Regional Arctic System Model and Community Earth System Model}", + journal = AG, + year = "2015", + volume = {56}, + number = {69}, + pages = {211-228}, + url = {https://doi.org/10.3189/2015AoG69A760} } - -@Article{Lemieux2016 - author = "J.F. Lemieux and F.Dupont and P. Blain and F. Roy and G.C. Smith and G.M. Flato", - title = "{Improving the simulation of landfast ice by combining tensile strength and a parameterization for -grounded ridges,}", +@Article{LDBRSF16 + author = "J.F. Lemieux and F. Dupont and P. Blain and F. Roy and G.C. Smith and G.M. Flato", + title = "{Improving the simulation of landfast ice by combining tensile strength and a parameterization for grounded ridges}", journal = JGRO, year = "2016", volume = {121}, - pages = {}, + pages = {7354-7368}, url = {https://doi.org/10.1002/2016JC012006} } - -@article{Hunke2018, - author = {Hunke, Elizabeth and Roberts, Andrew and Allard, Richard and Lemieux, Jean-Fran{\c{c}}ois and Turner, Matthew and Craig, Tony and DuVivier, Alice and Bailey, David and Holland, Marika and Winton, Michael and Dupont, Frederic and Grumbine, Robert}, - title = {{The CICE Consortium Sea Ice Modeling Suite}}, - journal = {}, - year = {In Prep.} -} - -@article{Roberts2015, - author = {Roberts, Andrew F. and Craig, Anthony and Maslowski, Wieslaw and Osinski, Robert and Duvivier, Alice and Hughes, Mimi and Nijssen, Bart and Cassano, John J. and Brunke, Michael}, - doi = {10.3189/2015AoG69A760}, - journal = {Ann. Glaciol.}, - 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} -} - -@article{Taylor2001, - author = {Taylor, Karl E}, - journal = {J. Geophys. Res.}, - number = {D7}, - pages = {7183--7192}, - title = {{Summarizing multiple aspects of model performance}}, - volume = {106}, - year = {2001} -} - -@article{HiblerIII2006, - author = {Hibler, III, W. D. and Roberts, Andrew F. and Heil, Petra and Proshutinsky, A Y and Simmons, H L and Lovick, J}, - doi = {10.3189/172756406781811178}, - journal = {Ann. Glaciol.}, - pages = {418--428}, - title = {{Modeling M2 tidal variability in Arctic sea-ice drift and deformation}}, - volume = {44}, - year = {2006} -} - -@article{Hibler2006, - author = {Hibler, W.D. and Roberts, A. and Heil, P. and Proshutinsky, A.Y. and Simmons, H.L. and Lovick, J.}, - doi = {10.3189/172756406781811178}, - journal = {Ann. Glaciol.}, - title = {{Modeling M2 tidal variability in Arctic sea-ice drift and deformation}}, - volume = {44}, - year = {2006} -} - -@article{Zwiers1995, - author = {Zwiers, Francis W. and von Storch, Hans}, - doi = {10.1175/1520-0442(1995)008<0336:TSCIAI>2.0.CO;2}, - journal = {J. Clim.}, - number = {2}, - pages = {336--351}, - title = {{Taking serial correlation into account in tests of the mean}}, - volume = {8}, - year = {1995} +@Article{NJHHMSTV16 + author = "D. Notz and A. Jahn and E. Hunke and F. Massonnet and J. Stroeve and B. Tremblay and M. Vancoppenolle", + title = "{The CMIP6 Sea-Ice Model Intercomparison Project (SIMIP): understanding sea ice through climate-model simulations}", + journal = GMD, + year = "2016", + volume = {9}, + pages = {3427-3446}, + url = {https://doi.org/10.5194/gmd-9-3427-2016} } - -@book{VonStorch1999, - author = {von Storch, Hans and Zwiers, Francis W}, - pages = {484}, - publisher = {Cambridge University Press}, - title = {{Statistical Analysis in Climate Research}}, - year = {1999} +@article{HRALTCDBHWDG18, + author = {E.C. Hunke and A. Roberts and R. Allard and J.F. Lemieux and M. Turner, and A.P. Craig and A.K. DuVivier and D. Bailey and M.M. Holland and M. Winton and F. Dupont and R. Grumbine}, + title = "{The CICE Consortium Sea Ice Modeling Suite}", + journal = {In Prep.}, + year = {2018 - In Prep.}, + url = {https://doi.org} } - @article{Roberts2018, - author = {Roberts, A. and Maslowski, W. and Hunke, E. and Osinski, R. and Cassano, J. and DuVivier, A. and Hughes, M. and Seefeldt, M. and Nijssen, B. and Hamman, J. and Hutchings, J. and Tsamados, M. and Feltham, D.}, - journal = {Prep.}, - title = {{Inter-comparison of isotropic and anisotropic sea-ice mechanics in a high-resolution fully coupled climate model}}, - year = {2018} -} - -@article{Irving2015, - author = {Irving, Damien}, - doi = {10.1175/BAMS-D-15-00010.1}, - journal = {Bull. Am. Meteorol. Soc.}, - number = {July}, - pages = {151007152952002}, - title = {{A minimum standard for publishing computational results in the weather and climate sciences}}, - year = {2015} -} - -@article{Lepparanta2012, - author = {Lepp{\"{a}}ranta, Matti and Oikkonen, Annu and Shirasawa, Kunio and Fukamachi, Yasushi}, - doi = {10.1016/j.coldregions.2011.12.005}, - journal = {Cold Reg. Sci. Technol.}, - month = {jun}, - pages = {83--91}, - title = {{A treatise on frequency spectrum of drift ice velocity}}, - volume = {76-77}, - year = {2012} -} - -@book{Wilks2006, - author = {Wilks, Daniel S}, - edition = {2nd}, - pages = {627}, - publisher = {Academic Press}, - title = {{Statistical methods in the atmospheric sciences}}, - year = {2006} -} - + author = {A. Roberts and W. Maslowski and E.C. Hunke and R. Osinski and J.J. Cassano and A.K. DuVivier and M. Hughes and M. Seefeldt and B. Nijssen and J. Hamman and J. Hutchings and M. Tsamados and D. Feltham}, + title = "{Inter-comparison of isotropic and anisotropic sea-ice mechanics in a high-resolution fully coupled climate model}", + journal = {In Prep.}, + year = {2018 - In Prep.}, + url = {https://doi.org} +} \ No newline at end of file diff --git a/doc/source/science_guide/sg_modelcomps.rst b/doc/source/science_guide/sg_modelcomps.rst index 7e92f2418..773960e35 100644 --- a/doc/source/science_guide/sg_modelcomps.rst +++ b/doc/source/science_guide/sg_modelcomps.rst @@ -1439,7 +1439,7 @@ where :math:`m` is the combined mass of ice and snow per unit area and :math:`\vec{\tau}_a` and :math:`\vec{\tau}_w` are wind and ocean stresses, respectively. The term :math:`\vec{\tau}_b` is a seabed stress (also referred to as basal stress) that represents the grounding of pressure -ridges in shallow water :cite:`Lemieux2016`. The strength of the ice is represented by the +ridges in shallow water :cite:`LDBRSF16`. The strength of the ice is represented by the internal stress tensor :math:`\sigma_{ij}`, and the other two terms on the right hand side are stresses due to Coriolis effects and the sea surface slope. The parameterization for the wind and ice–ocean stress @@ -1537,7 +1537,7 @@ pending further testing. Seabed stress *************** -The parameterization for the seabed stress is described in :cite:`Lemieux2016`. The components of the basal seabed stress are +The parameterization for the seabed stress is described in :cite:`LDBRSF16`. The components of the basal seabed stress are :math:`\tau_{bx}=C_bu` and :math:`\tau_{by}=C_bv`, where :math:`C_b` is a coefficient expressed as .. math:: @@ -1590,7 +1590,7 @@ is therefore simply equal to :math:`-\sigma_1/2`. *Elastic-Viscous-Plastic* In the EVP model the internal stress tensor is determined from a -regularized version of the VP constitutive law. Following the approach of :cite:`KH2010` (see also :cite:`Lemieux2016`), the +regularized version of the VP constitutive law. Following the approach of :cite:`KH2010` (see also :cite:`LDBRSF16`), the elliptical yield curve can be modified such that the ice has isotropic tensile strength. The tensile strength :math:`T_p` is expressed as a fraction of the ice strength :math:`P`, that is :math:`T_p=k_t P` where :math:`k_t` should be set to a value between 0 and 1. The constitutive law is therefore diff --git a/doc/source/user_guide/ug_implementation.rst b/doc/source/user_guide/ug_implementation.rst index 47f9788e2..dc94774a1 100644 --- a/doc/source/user_guide/ug_implementation.rst +++ b/doc/source/user_guide/ug_implementation.rst @@ -836,10 +836,13 @@ the grid cell area. Our naming convention attaches the suffix “\_ai" to the grid-cell-mean variable names. In this version of CICE, history variables requested by the Sea Ice Model Intercomparison -Project (SIMIP) have been added as possible history output variables (e.g. -`f_sithick`, `f_sidmassgrowthbottom`, etc.). A full list of SIMIP variables is -available at the following site -. +Project (SIMIP) :cite:`NJHHMSTV16` have been added as possible history output variables (e.g. +`f_sithick`, `f_sidmassgrowthbottom`, etc.). The lists of +`monthly `_ and +`daily `_ +requested SIMIP variables provide the names of possible history fields in CICE. +However, each of the additional variables can be output at any temporal frequency +specified in the **icefields\_nml** section of **ice\_in** as detailed above. Additionally, a new history output variable, `f_CMIP`, has been added. When `f_CMIP` is added to the **icefields\_nml** section of **ice\_in** then all SIMIP variables will be turned on for output at the frequency specified by `f_CMIP`. diff --git a/doc/source/user_guide/ug_testing.rst b/doc/source/user_guide/ug_testing.rst index 0adc61572..0fd4753b9 100644 --- a/doc/source/user_guide/ug_testing.rst +++ b/doc/source/user_guide/ug_testing.rst @@ -534,7 +534,7 @@ and CICE have not significantly altered simulated ice volume using previous mode configurations. Here we describe the CICE testing tools, which are applies to output from five-year gx-1 simulations that use the standard CICE atmospheric forcing. A scientific justification of the testing is provided in -:cite:`Hunke2018`. +:cite:`HRALTCDBHWDG18`. .. _paired: @@ -550,7 +550,7 @@ approximated as :math:`\bar{h}_{d}=\tfrac{1}{n}\sum_{i=1}^n (h_{ai}{-}h_{bi})` for :math:`n` paired samples of ice thickness :math:`h_{ai}` and :math:`h_{bi}` in each grid cell of the gx-1 mesh. Following -:cite:`Wilks2006`, the associated :math:`t`-statistic +:cite:`Wilks06`, the associated :math:`t`-statistic expects a zero mean, and is therefore .. math:: @@ -582,15 +582,15 @@ equations (:eq:`t-distribution`). That is: \bar{h}_d=\frac{1}{n} \sum \limits_{i=1}^{n} {h}_{di} :label: short-means -Following :cite:`Zwiers1995`, the effective sample size is +Following :cite:`ZvS95`, the effective sample size is limited to :math:`n_{eff}\in[2,n]`. This definition of :math:`n_{eff}` assumes ice thickness evolves as an AR(1) process -:cite:`VonStorch1999`, which can be justified by analyzing +:cite:`vSZ99`, which can be justified by analyzing the spectral density of daily samples of ice thickness from 5-year -records in CICE Consortium member models :cite:`Hunke2018`. +records in CICE Consortium member models :cite:`HRALTCDBHWDG18`. The AR(1) approximation is inadmissible for paired velocity samples, because ice drift possesses periodicity from inertia and tides -:cite:`Hibler2006,Lepparanta2012,Roberts2015`. Conversely, +:cite:`HRHPSL06,LOSF12,RCWODHNCB15`. Conversely, tests of paired ice concentration samples may be less sensitive to ice drift than ice thickness. In short, ice thickness is the best variable for CICE Consortium quality control (QC), and for the test of the mean @@ -599,7 +599,7 @@ in particular. Care is required in analyzing mean sea ice thickness changes using (:eq:`t-distribution`) with :math:`N{=}n_{eff}{-}1` degrees of freedom. -:cite:`Zwiers1995` demonstrate that the :math:`t`-test in +:cite:`ZvS95` demonstrate that the :math:`t`-test in (:eq:`t-distribution`) becomes conservative when :math:`n_{eff} < 30`, meaning that :math:`H_0` may be erroneously confirmed for highly auto-correlated series. Strong autocorrelation @@ -607,7 +607,7 @@ frequently occurs in modeled sea ice thickness, and :math:`r_1>0.99` is possible in parts of the gx-1 domain for the five-year QC simulations. In the event that :math:`H_0` is confirmed but :math:`2\leq n_{eff}<30`, the :math:`t`-test progresses to the ‘Table Lookup Test’ of -:cite:`Zwiers1995`, to check that the first-stage test +:cite:`ZvS95`, to check that the first-stage test using (:eq:`t-distribution`) was not conservative. The Table Lookup Test chooses critical :math:`t` values :math:`|t| Date: Mon, 1 Oct 2018 21:16:59 -0600 Subject: [PATCH 3/4] cleaning up the documentation --- .../developer_guide/dg_documentation.rst | 2 +- doc/source/developer_guide/dg_driver.rst | 4 +- doc/source/developer_guide/dg_dynamics.rst | 5 +- doc/source/developer_guide/dg_scripts.rst | 6 +-- doc/source/master_list.bib | 51 ++++++++++--------- doc/source/science_guide/sg_modelcomps.rst | 2 +- doc/source/user_guide/ug_case_settings.rst | 1 + doc/source/user_guide/ug_running.rst | 4 +- 8 files changed, 41 insertions(+), 34 deletions(-) diff --git a/doc/source/developer_guide/dg_documentation.rst b/doc/source/developer_guide/dg_documentation.rst index e5c46a2c4..ac62de0f2 100755 --- a/doc/source/developer_guide/dg_documentation.rst +++ b/doc/source/developer_guide/dg_documentation.rst @@ -142,7 +142,7 @@ Here are some resources for using RST files: Building documentation ~~~~~~~~~~~~~~~~~~~~~~ -Once you've committed and pushed changes to the documentation *.rst files on your personal development fork. +Once you've committed and pushed changes to the documentation `*.rst` files on your personal development fork. Go to your readthedocs.org site and then select your project "Overview". Whenever you commit to your fork the documents will automatically build. There is also an option to "Build a Version". Choose "latest" and then click the green "Build version" button. diff --git a/doc/source/developer_guide/dg_driver.rst b/doc/source/developer_guide/dg_driver.rst index 076c77252..266f2a702 100755 --- a/doc/source/developer_guide/dg_driver.rst +++ b/doc/source/developer_guide/dg_driver.rst @@ -14,7 +14,7 @@ coupled. Within the **cicecore/drivers/cice/** directory, the following files a **CICE.F90** is the top level program file and that calls CICE_Initialize, CICE_Run, and CICE_Finalize methods. **CICE_InitMod.F90** contains the CICE_Initialize method and other next level source code. **CICE_RunMod.F90** contains the CICE_Run method and other next level source code. -**CICE_FinalMod.F90 ** contains the CICE_Finalize method and other next level source code. +**CICE_FinalMod.F90** contains the CICE_Finalize method and other next level source code. Other **cicecore/drivers/** directories are similarly implemented with a top level coupling layer, that is largely specified by an external coupled system and then some version of the **CICE_InitMod.F90**, @@ -87,4 +87,4 @@ The run sequence within a time loop looks something like:: call coupling_prep (iblk) enddo ! iblk -See a **CICE_RunMod.F90** file for the latest. \ No newline at end of file +See a **CICE_RunMod.F90** file for the latest. diff --git a/doc/source/developer_guide/dg_dynamics.rst b/doc/source/developer_guide/dg_dynamics.rst index d86b9145f..d1c1f6666 100755 --- a/doc/source/developer_guide/dg_dynamics.rst +++ b/doc/source/developer_guide/dg_dynamics.rst @@ -70,7 +70,10 @@ block size and tracer count. Those block sizes and tracer counts are defined in **cice.settings** file, are passed to the build script as CPPs, like :: -ftn -c ... -DNXGLOB=100 -DNYGLOB=116 -DBLCKX=25 -DBLCKY=29 -DMXBLCKS=4 -DNICELYR=7 -DNSNWLYR=1 -DNICECAT=5 -DTRAGE=1 -DTRFY=1 -DTRLVL=1 -DTRPND=1 -DTRBRI=0 -DNTRAERO=1 -DTRZS=0 -DNBGCLYR=7 -DTRALG=0 -DTRBGCZ=0 -DTRDOC=0 -DTRDOC=0 -DTRDIC=0 -DTRDON=0 -DTRFED=0 -DTRFEP=0 -DTRZAERO=0 -DTRBGCS=0 -DNUMIN=11 -DNUMAX=99 ... + ftn -c ... -DNXGLOB=100 -DNYGLOB=116 -DBLCKX=25 -DBLCKY=29 -DMXBLCKS=4 -DNICELYR=7 + -DNSNWLYR=1 -DNICECAT=5 -DTRAGE=1 -DTRFY=1 -DTRLVL=1 -DTRPND=1 -DTRBRI=0 -DNTRAERO=1 + -DTRZS=0 -DNBGCLYR=7 -DTRALG=0 -DTRBGCZ=0 -DTRDOC=0 -DTRDOC=0 -DTRDIC=0 -DTRDON=0 + -DTRFED=0 -DTRFEP=0 -DTRZAERO=0 -DTRBGCS=0 -DNUMIN=11 -DNUMAX=99 ... and then those CPPs replace variable strings in the file **cicecore/shared/ice_domain_size.F90**. Data in **ice_domain_size.F90** provides parameters for static array allocations throughout CICE. diff --git a/doc/source/developer_guide/dg_scripts.rst b/doc/source/developer_guide/dg_scripts.rst index e73ee3d28..befcdd321 100755 --- a/doc/source/developer_guide/dg_scripts.rst +++ b/doc/source/developer_guide/dg_scripts.rst @@ -29,7 +29,7 @@ The directory structure under configure/scripts is as follows. | **parse_namelist.sh** replaces namelist with command-line configuration | **parse_namelist_from_settings.sh** replaces namelist with values from cice.settings | **parse_settings.sh** replaces settings with command-line configuration -| **setup_run_dirs.csh creates the case run directories +| **setup_run_dirs.csh** creates the case run directories | **set_version_number.csh** updates the model version number from the **cice.setup** command line | **tests/** scripts for configuring and running basic tests @@ -51,7 +51,7 @@ The file **cice.settings** specifies a set of env defaults for the case. The fi **ice_in** defines the namelist input for the cice driver. -.. _dev_options: +.. _dev_preset_options: Preset Case Options --------------------- @@ -89,7 +89,7 @@ One other files will need to be changed to support a port, that is **configuration/scripts/cice.batch.csh**. To port to a new machine, see :ref:`porting`. -.. _dev_options: +.. _dev_test_options: Test Options --------------- diff --git a/doc/source/master_list.bib b/doc/source/master_list.bib index 071c864cd..bb7e82389 100644 --- a/doc/source/master_list.bib +++ b/doc/source/master_list.bib @@ -48,11 +48,11 @@ @string{EFM @string{GMD = {Geosci. Model Dev.}} @string{CRST = {Cold Reg. Sci. Technol.}} -% Individual entries (roughly sequential, then alphabetical but first-author last name) +% Individual entries (roughly sequential, then alphabetical by first-author's last name) @incollection{Assur58, author = "A. Assur", title = "Composition of sea ice and its tensile strength", - booktitle = "Arctic sea ice; conference held at Easton, Maryland, February 24-€“27, 1958", + booktitle = "Arctic sea ice; conference held at Easton, Maryland, February 24-27, 1958", publisher = "Publs. Natl. Res. Coun. Wash.", address = "Washington, D.C.", year = "1958", @@ -180,7 +180,7 @@ @Article{Maykut82 @incollection{SP86 author = "G. Siedler and H. Peters", title = "Physical properties (general) of sea water", - booktitle = "Landolt-Barnstein: Numerical data and functional relationships in science and technology, New Series V/3a", + booktitle = "Landolt-Börnstein: Numerical data and functional relationships in science and technology, New Series V/3a", publisher = "Springer", year = "1986", pages = {233-264}, @@ -385,7 +385,7 @@ @Book{vSZ99 publisher = "Cambridge University Press", note = "Cambridge, UK", year = "1999", - pages = {484 pp} + pages = {484 pp}, } @Article{DB00 author = "J.K. Dukowicz and J.R. Baumgardner", @@ -453,7 +453,7 @@ @Article{TWMH01 } @Article{HD02 author = "E.C. Hunke and J.K. Dukowicz", - title = "{The Elastic-Viscous-Plastic sea ice dynamics model in general orthogonal curvilinear coordinates on a sphere - Incorporation of metric terms}", + title = "{The Elastic-Viscous-Plastic sea ice dynamics model in general orthogonal curvilinear coordinates on a sphere—Effect of metric terms}", journal = MWR, year = "2002", volume = {130}, @@ -539,7 +539,7 @@ @Article{LDM05 } @Book{Notz05 author = "D. Notz", - title = "{Thermodynamic and Fluid-Dynamical Processes in Sea Ice}", + title = "Thermodynamic and Fluid-Dynamical Processes in Sea Ice", publisher = "University of Cambridge, UK", note = "PhD thesis", year = "2005", @@ -595,7 +595,7 @@ @Book{Wilks06 publisher = "Academic Press", note = "2nd ed.", year = "2006", - pages = {627 pp} + pages = {627 pp}, } @Manual{BL07 author = "B.P. Briegleb and B. Light", @@ -676,7 +676,7 @@ @Article{FFT10 number = {C8}, url = {http://dx.doi.org/10.1029/2009JC005568} } -@Article{KH2010 +@Article{KH10 author = "C. Konig Beatty and D.M. Holland", title = "{Modeling landfast ice by adding tensile strength}", journal = JPO, @@ -704,7 +704,7 @@ @Article{DJEHMJ11 url = {http://dx.doi.org/10.1029/2010JC006409} } @Article{LLCL11 - author = "P. Lu and Z. Li and B. Cheng and M. Lepparanta", + author = "P. Lu and Z. Li and B. Cheng and M. Lepp{\"{a}}ranta", title = "{A parametrization fo the ice-ocean drag coefficient}", journal = JGRO, year = "2011", @@ -740,16 +740,16 @@ @Article{HBBLH12 url = {http://dx.doi.org/10.1175/JCLI-D-11-00078.1} } @article{LOSF12, - author = "M. Lepparanta and A. Oikkonen and K. Shirasawa and Y. Fukamachi", + author = "M. Lepp{\"{a}}ranta and A. Oikkonen and K. Shirasawa and Y. Fukamachi", title = "{A treatise on frequency spectrum of drift ice velocity}", + year = "2012", journal = CRST, - year = {2012}, volume = {76-77}, pages = {83-91}, - url= {https://doi.org/10.1016/j.coldregions.2011.12.005} + doi = {https://doi.org/10.1016/j.coldregions.2011.12.005} } @Article{LGHA12 - author = "C. Lupkes and V.M. Gryanik and J. Hartmann and E.L. Andreas", + author = "C. Lüpkes and V.M. Gryanik and J. Hartmann and E.L. Andreas", title = "{A parametrization, based on sea ice morphology, of the neutral atmospheric drag coefficients for weather prediction and climate models}", journal = JGRA, year = "2012", @@ -775,15 +775,6 @@ @Article{HHL13 pages = {26-42}, url = {http://dx.doi.org/10.1016/j.ocemod.2012.11.008} } -@article{Irving2015, - author = "D. Irving", - title = {A minimum standard for publishing computational results in the weather and climate sciences}, - journal = BAMS, - number = {97}, - pages = {1149-1158}, - year = {2015}, - url = {https://doi.org/10.1175/BAMS-D-15-00010.1} -} @Article{TFW13 author = "M. Tsamados and D.L. Feltham and A.V. Wilchinsky", title = "{Impact of a new anisotropic rheology on simulations of Arctic sea ice}", @@ -813,9 +804,9 @@ @Article{TFSFFKLB14 } @article{RCWODHNCB15, author = "A.F. Roberts and A.P. Craig and W. Maslowski and R. Osinski and A.K. DuVivier and M. Hughes and B. Nijssen and J.J. Cassano and M. Brunke", - title = "{Simulating transient ice -€“ ocean Ekman transport in the Regional Arctic System Model and Community Earth System Model}", + title = "{Simulating transient ice-ocean Ekman transport in the Regional Arctic System Model and Community Earth System Model}", + year = "2015", journal = AG, - year = "2015", volume = {56}, number = {69}, pages = {211-228}, @@ -846,10 +837,20 @@ @article{HRALTCDBHWDG18 year = {2018 - In Prep.}, url = {https://doi.org} } + @article{Roberts2018, - author = {A. Roberts and W. Maslowski and E.C. Hunke and R. Osinski and J.J. Cassano and A.K. DuVivier and M. Hughes and M. Seefeldt and B. Nijssen and J. Hamman and J. Hutchings and M. Tsamados and D. Feltham}, + author = "A. Roberts and W. Maslowski and E.C. Hunke and R. Osinski and J.J. Cassano and A.K. DuVivier and M. Hughes and M. Seefeldt and B. Nijssen and J. Hamman and J. Hutchings and M. Tsamados and D. Feltham", title = "{Inter-comparison of isotropic and anisotropic sea-ice mechanics in a high-resolution fully coupled climate model}", journal = {In Prep.}, year = {2018 - In Prep.}, url = {https://doi.org} +} +@article{Irving2015, + author = "D. Irving", + title = "{A minimum standard for publishing computational results in the weather and climate sciences}", + year = "2015", + journal = BAMS, + number = {97}, + pages = {1149-1158}, + url = {https://doi.org/10.1175/BAMS-D-15-00010.1} } \ No newline at end of file diff --git a/doc/source/science_guide/sg_modelcomps.rst b/doc/source/science_guide/sg_modelcomps.rst index 773960e35..6009369cb 100644 --- a/doc/source/science_guide/sg_modelcomps.rst +++ b/doc/source/science_guide/sg_modelcomps.rst @@ -1590,7 +1590,7 @@ is therefore simply equal to :math:`-\sigma_1/2`. *Elastic-Viscous-Plastic* In the EVP model the internal stress tensor is determined from a -regularized version of the VP constitutive law. Following the approach of :cite:`KH2010` (see also :cite:`LDBRSF16`), the +regularized version of the VP constitutive law. Following the approach of :cite:`KH10` (see also :cite:`LDBRSF16`), the elliptical yield curve can be modified such that the ice has isotropic tensile strength. The tensile strength :math:`T_p` is expressed as a fraction of the ice strength :math:`P`, that is :math:`T_p=k_t P` where :math:`k_t` should be set to a value between 0 and 1. The constitutive law is therefore diff --git a/doc/source/user_guide/ug_case_settings.rst b/doc/source/user_guide/ug_case_settings.rst index 027769437..6a7c4968f 100755 --- a/doc/source/user_guide/ug_case_settings.rst +++ b/doc/source/user_guide/ug_case_settings.rst @@ -94,6 +94,7 @@ Table of namelist options :header: "variable", "options/format", "description", "recommended value" :widths: 15, 15, 30, 15 + "", "", "", "" "*setup_nml*", "", "", "" "", "", "*Time, Diagnostics*", "" "``days_per_year``", "``360`` or ``365``", "number of days in a model year", "365" diff --git a/doc/source/user_guide/ug_running.rst b/doc/source/user_guide/ug_running.rst index dc437abe9..e99d43381 100644 --- a/doc/source/user_guide/ug_running.rst +++ b/doc/source/user_guide/ug_running.rst @@ -182,7 +182,9 @@ Some of the options are ``bgc*`` which turns of various bgc configurations -and there are others. These may change as needed. Use ``cice.setup --help`` to see the latest. To add a new option, just add the appropriate file in **configuration/scripts/options**. For more information, see :ref:`dev_options` +and there are others. These may change as needed. Use ``cice.setup --help`` to see the latest. +To add a new option, just add the appropriate file in **configuration/scripts/options**. +For more information, see :ref:`dev_test_options` Examples ~~~~~~~~~ From 843f9c9fb9468a1efe0e8c2ee15fd214f20e875b Mon Sep 17 00:00:00 2001 From: Alice DuVivier Date: Mon, 1 Oct 2018 21:21:35 -0600 Subject: [PATCH 4/4] fixing bibliography typos --- doc/source/master_list.bib | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/master_list.bib b/doc/source/master_list.bib index bb7e82389..96741caef 100644 --- a/doc/source/master_list.bib +++ b/doc/source/master_list.bib @@ -296,9 +296,9 @@ @Manual{SKM95 } @article{ZvS95, author = "F.W. Zwiers and H. von Storch", - title = {Taking serial correlation into account in tests of the mean}, + title = "{Taking serial correlation into account in tests of the mean}", journal = JC, - year = {1995}, + year = "1995", volume = {8}, number = {2}, pages = {336-351}, @@ -853,4 +853,4 @@ @article{Irving2015 number = {97}, pages = {1149-1158}, url = {https://doi.org/10.1175/BAMS-D-15-00010.1} -} \ No newline at end of file +}