From 93b96534b1d05077168ad3359a430fb6328850fc Mon Sep 17 00:00:00 2001 From: David Bailey Date: Tue, 31 Oct 2017 15:19:45 -0600 Subject: [PATCH 1/6] Updated documentation --- _sources/cice_2_science_guide.rst.txt | 28 ++++----- _sources/cice_3_user_guide.rst.txt | 6 +- _sources/index.rst.txt | 2 +- _static/basic.css | 9 ++- _static/classic.css | 2 +- _static/doctools.js | 2 +- _static/searchtools.js | 2 +- _static/sidebar.js | 2 +- _static/websupport.js | 2 +- cice_1_introduction.html | 25 ++++---- cice_2_science_guide.html | 79 ++++++++++++------------ cice_3_user_guide.html | 89 +++++++++++++-------------- cice_4_index.html | 11 ++-- index.html | 11 ++-- search.html | 11 ++-- searchindex.js | 2 +- zreferences.html | 11 ++-- 17 files changed, 140 insertions(+), 154 deletions(-) diff --git a/_sources/cice_2_science_guide.rst.txt b/_sources/cice_2_science_guide.rst.txt index 5fb222326..b5156f683 100644 --- a/_sources/cice_2_science_guide.rst.txt +++ b/_sources/cice_2_science_guide.rst.txt @@ -199,9 +199,9 @@ stable and unstable atmosphere–ice boundary layers. Define the “stability” .. math:: - \Upsilon = {\kappa g z_\circ\over u^{*2}} - \left({\Theta^*\over\Theta_a\left(1+0.606Q_a\right)} + - {Q^*\over 1/0.606 + Q_a}\right), + \Upsilon = {\frac{\kappa g z_\circ}{u^{*2}}} + \left({\frac{\Theta^*}{\Theta_a\left(1+0.606Q_a\right)}} + + {\frac{Q^*}{\frac{1}{0.606} + Q_a}}\right), where :math:`\kappa` is the von Karman constant, :math:`g` is gravitational acceleration, and :math:`u^*`, :math:`\Theta^*` and @@ -225,7 +225,7 @@ Neglecting form drag,the exchange coefficients :math:`c_u`, :math:`c_\theta` and :math:`c_q` are initialized as .. math:: - \kappa\over \ln(z_{ref}/z_{ice}) + \frac{\kappa}{\ln(z_{ref}/z_{ice}}) and updated during a short iteration, as they depend upon the turbulent scales. The number of iterations is set by the namelist variable @@ -242,7 +242,7 @@ unstable (:math:`\Upsilon <0`) case are given by \begin{aligned} \psi_m = &\mbox{}&2\ln\left[0.5(1+\chi)\right] + \ln\left[0.5(1+\chi^2)\right] -2\tan^{-1}\chi + - {\pi\over 2}, \\ + {\frac{\pi}{2}}, \\ \psi_s = &\mbox{}&2\ln\left[0.5(1+\chi^2)\right].\end{aligned} In a departure from the parameterization used in @@ -257,8 +257,8 @@ The coefficients are then updated as .. math:: \begin{aligned} - c_u^\prime&=&{c_u\over 1+c_u\left(\lambda-\psi_m\right)/\kappa} \\ - c_\theta^\prime&=& {c_\theta\over 1+c_\theta\left(\lambda-\psi_s\right)/\kappa}\\ + c_u^\prime&=&{\frac{c_u}{1+c_u\left(\lambda-\psi_m\right)/\kappa}} \\ + c_\theta^\prime&=& {\frac{c_\theta}{1+c_\theta\left(\lambda-\psi_s\right)/\kappa}}\\ c_q^\prime&=&c_\theta^\prime\end{aligned} where :math:`\lambda = \ln\left(z_\circ/z_{ref}\right)`. The @@ -271,7 +271,7 @@ heat flux coefficients are computed, along with the wind stress: \nonumber C_l&=&\rho_a \left(L_{vap}+L_{ice}\right) u^* c_q \\ C_s&=&\rho_a c_p u^* c_\theta^* + 1, \\ - \vec{\tau}_a&=&{\rho_a u^{*2}\vec{U}_a\over |\vec{U}_a|},\end{aligned} + \vec{\tau}_a&=&{\rho_a \frac{u^{*2}\vec{U}_a}{|\vec{U}_a|}},\end{aligned} where :math:`L_{vap}` and :math:`L_{ice}` are latent heats of vaporization and fusion, :math:`\rho_a` is the density @@ -324,7 +324,7 @@ incorporates the cloud fraction and humidity through the atmospheric vapor pressure: .. math:: - F_{sw\downarrow} = {1353 \cos^2 Z \over {10^{-3}(\cos Z+2.7)e_a + 1.085\cos Z + 0.1}}\left(1-0.6 f_{cld}^3\right) > 0 + F_{sw\downarrow} = {\frac{1353 \cos^2 Z}{10^{-3}(\cos Z+2.7)e_a + 1.085\cos Z + 0.1}}\left(1-0.6 f_{cld}^3\right) > 0 where :math:`\cos Z` is the cosine of the solar zenith angle. @@ -733,7 +733,7 @@ ice volume :math:`v_{in}`, and snow volume :math:`v_{sn}` for each thickness category :math:`n` are .. math:: - {\partial\over\partial t} (a_{in}) + \nabla \cdot (a_{in} {\bf u}) = 0, + {\frac{\partial}{\partial t}} (a_{in}) + \nabla \cdot (a_{in} {\bf u}) = 0, :label: transport-ai .. math:: @@ -804,11 +804,11 @@ equations for pond area fraction :math:`a_{pnd}a_i` and pond volume :math:`h_{pnd}a_{pnd}a_i`, given the ice velocity :math:`\bf u`, are .. math:: - {\partial\over\partial t} (a_{pnd}a_{i}) + \nabla \cdot (a_{pnd}a_{i} {\bf u}) = 0, + {\frac{\partial}{\partial t}} (a_{pnd}a_{i}) + \nabla \cdot (a_{pnd}a_{i} {\bf u}) = 0, :label: transport-apnd .. math:: - {\partial\over\partial t} (h_{pnd}a_{pnd}a_{i}) + \nabla \cdot (h_{pnd}a_{pnd}a_{i} {\bf u}) = 0. + {\frac{\partial}{\partial t}} (h_{pnd}a_{pnd}a_{i}) + \nabla \cdot (h_{pnd}a_{pnd}a_{i} {\bf u}) = 0. :label: transport-hpnd (These equations represent quantities within one thickness category; @@ -3030,7 +3030,7 @@ the ridge potential energy is modified: .. math:: P = C_f \, C_p \, \beta \sum_{n=1}^{N_C} \left[ -a_{Pn} \, h_n^2 + \frac{a_{Pn}}{k_n} - \left( H_{\min}^2 + 2H_{\min}\lambda + 2 \lambda^2 \right) \right] % CHECK BRACES + \left( H_{\min}^2 + 2H_{\min}\lambda + 2 \lambda^2 \right) \right] :label: roth-strength1 The energy-based ice strength given by Equations :eq:`roth-strength0` or @@ -4293,7 +4293,7 @@ to the temperature, :math:`T`, and the brine volume, :math:`\phi`, by \begin{aligned} q =& \phi q_{br} &+\, (1-\phi) q_{i} =& \phi \rho_{w} c_{w} T &+\, (1-\phi) (\rho_i c_i T - \rho_i L_0) - \label{enthalpy_definition}\end{aligned} + \end{aligned} :label: enth-def where :math:`q_{br}` is the brine enthalpy, :math:`q_i` is the pure ice diff --git a/_sources/cice_3_user_guide.rst.txt b/_sources/cice_3_user_guide.rst.txt index 1c074a515..db2d4fd85 100644 --- a/_sources/cice_3_user_guide.rst.txt +++ b/_sources/cice_3_user_guide.rst.txt @@ -2329,10 +2329,10 @@ Table of namelist options "", "``2``", "mushy-layer thermodynamic model", "" "``conduct``", "``MU71``", "conductivity :cite:`MU71`", "" "", "``bubbly``", "conductivity :cite:`PETB07`", "" - "``a_rapid_mode``", "real", "brine channel diameter", "0.5x10\:math:`^{-3}` m" + "``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" + "``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" "", "", "", "" @@ -2431,7 +2431,7 @@ Table of namelist options "``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\degC`)", "" + "``tfrz_option``", "``minus1p8``", "constant ocean freezing temperature (:math:`-1.8^{\circ} C`)", "" "", "``linear_salt``", "linear function of salinity (ktherm=1)", "" "", "``mushy_layer``", "matches mushy-layer thermo (ktherm=2)", "" "``ustar_min``", "real", "minimum value of ocean friction velocity", "0.0005 m/s" diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt index 3c73abbeb..c6f42e413 100644 --- a/_sources/index.rst.txt +++ b/_sources/index.rst.txt @@ -1,4 +1,4 @@ -.. CICE-Consoritum documentation master file, created by +.. CICE-Consortium documentation master file, created by sphinx-quickstart on Thu Jun 29 13:47:09 2017. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. diff --git a/_static/basic.css b/_static/basic.css index 7ed0e58ed..6df76b0a6 100644 --- a/_static/basic.css +++ b/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -398,6 +398,13 @@ table.field-list td, table.field-list th { margin: 0; } +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + /* -- other body styles ----------------------------------------------------- */ ol.arabic { diff --git a/_static/classic.css b/_static/classic.css index 952274189..68efe0a2e 100644 --- a/_static/classic.css +++ b/_static/classic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- classic theme. * - * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/doctools.js b/_static/doctools.js index 816349563..565497723 100644 --- a/_static/doctools.js +++ b/_static/doctools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for all documentation. * - * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/searchtools.js b/_static/searchtools.js index bbfb3ac14..c82157380 100644 --- a/_static/searchtools.js +++ b/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/sidebar.js b/_static/sidebar.js index 4282fe91c..332bbf246 100644 --- a/_static/sidebar.js +++ b/_static/sidebar.js @@ -16,7 +16,7 @@ * Once the browser is closed the cookie is deleted and the position * reset to the default (expanded). * - * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/websupport.js b/_static/websupport.js index 98e7f40b6..53f6a4525 100644 --- a/_static/websupport.js +++ b/_static/websupport.js @@ -4,7 +4,7 @@ * * sphinx.websupport utilities for all documentation. * - * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/cice_1_introduction.html b/cice_1_introduction.html index 27d20dc08..1e4c35b19 100644 --- a/cice_1_introduction.html +++ b/cice_1_introduction.html @@ -1,16 +1,13 @@ + - - 1. Introduction - CICE5 — CICE-Consortium 0.0.1 documentation - - - + - + \ No newline at end of file diff --git a/cice_2_science_guide.html b/cice_2_science_guide.html index f79dbae81..7a9a94c65 100644 --- a/cice_2_science_guide.html +++ b/cice_2_science_guide.html @@ -1,16 +1,13 @@ + - - 2. Science Guide — CICE-Consortium 0.0.1 documentation - - - + - +

3.7. Table of namelist options

- - +
Table 8
+@@ -2684,12 +2774,12 @@

3.6.5.2. Practical Testing Procedure

- + - + @@ -2774,12 +2864,12 @@

3.6.5.2. Practical Testing Procedure

- + - + @@ -3000,7 +3090,7 @@

3.6.5.2. Practical Testing Procedure

+ @@ -3022,7 +3112,7 @@

3.6.5.2. Practical Testing Procedure

- + @@ -3032,7 +3122,7 @@

3.6.5.2. Practical Testing Procedure

- + @@ -3052,7 +3142,7 @@

3.6.5.2. Practical Testing Procedure

- + @@ -3419,12 +3509,47 @@

3.6.5.2. Practical Testing ProcedureTable Of Contents

Table 8
conduct MU71conductivity [50]conductivity [53]  
  bubblyconductivity [55]conductivity [58]  
a_rapid_modekstrength 0ice strength formulation [26]ice strength formulation [26] 1
  1ice strength formulation [57]ice strength formulation [61]  
krdg_partic``solve_zsal`
``solve_zsal` true/false update salinity tracer profile    climsilicate forcing from ocean climatology [23]silicate forcing from ocean climatology [23]  
nit_data_type  climnitrate forcing from ocean climatology [23]nitrate forcing from ocean climatology [23]  
 bgc_flux_type Jin2006ice–ocean flux velocity of [37]ice–ocean flux velocity of [39]  
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From eb375a6dc6ed7d9ee340ad61e3b95fbd0ca1b54b Mon Sep 17 00:00:00 2001 From: David Bailey Date: Fri, 1 Dec 2017 15:33:28 -0700 Subject: [PATCH 5/6] Update with Matt's documentation. --- _sources/cice_3_user_guide.rst.txt | 75 +++++++++++++++++++++++++++++- cice_3_user_guide.html | 69 +++++++++++++++++++++++++++ cice_4_index.html | 2 +- searchindex.js | 2 +- 4 files changed, 145 insertions(+), 3 deletions(-) diff --git a/_sources/cice_3_user_guide.rst.txt b/_sources/cice_3_user_guide.rst.txt index d70ca21d7..12a8be696 100644 --- a/_sources/cice_3_user_guide.rst.txt +++ b/_sources/cice_3_user_guide.rst.txt @@ -2262,7 +2262,80 @@ hemispheres, and must exceed a critical value nominally set to test and the Two-Stage test described in the previous section are provided in :cite:`Hunke2018`. - +In applying equations :eq:`t-distribution` through :eq:`short-means`, +we are accounting for the fact, however imperfectly, that a +:math:`t`-test should be a comparison of the means from two series of +independent samples. The typical affect of applying these equations to +sea ice model output is that :math:`n' \ll n`. For that reason, we need +a lengthy time series to narrow the range of acceptable values +in :eq:`t-crit`. There is little point in using more frequent output +from CICE than daily instantaneous values, since this would have little +impact on decreasing :math:`r_1` in :eq:`lag-1-auto-correlation`. + +Using these equations, a standard procedure in testing for +science-changing answers in CICE and Icepack is as follows: First, make +every attempt to obtain bit-for-bit reproducibility in the model code. +Once all available software-testing options have been exhausted, and the +source of the bit-for-bit test failure has been pinpointed, proceed with +the :math:`t`-test documented above if the expectation is that code +alterations should not be science-changing. +Equations :eq:`t-distribution` through :eq:`short-means` are +implemented in the reverse order from which they are presented here, and +applied individually to daily samples of :math:`h`, :math:`c`, :math:`u` +and :math:`v` from 5-year time series at every model grid point: i) +Calculate :math:`\bar{x}_{1:n-1}`, :math:`\bar{x}_{2:n}`, and +:math:`\bar{x}` in :eq:`short-means` for simulations :math:`a` and +:math:`b`; ii) Compute :eq:`lag-1-auto-correlation`, +:eq:`effective-sample-size` and :eq:`unbiased-sigma`, in that order, +for each simulation :math:`a` and :math:`b`, and finally; iii) Determine +whether the null hypothesis is true at each model grid point in +:eq:`t-crit` using equation :eq:`t-distribution` and a lookup +:math:`t`-distribution table. Should :math:`H_0` be confirmed at each +grid point, and for each variable :math:`h`, :math:`c`, :math:`u` and +:math:`v`, this test contributes to evidence that changes to CICE and +Icepack code are unlikely to alter scientific results. To guard against +the possibility of a Type II error, the test should be performed for +several different confidence intervals, nominally set at 68, 80 and 95%, +the first and last of these values corresponding to :math:`\sigma` and +:math:`2\sigma` tests. + +*************************** +Practical Testing Procedure +*************************** + +The CICE code compliance test is performed by running a python script (cice.t-test.py). +In order to run the script, the following requirements must be met: + +* Python v2.7 or later +* netCDF Python package +* numpy Python package + +In order to generate the files necessary for the compliance test, test cases should be +created with the ``ttest`` option (i.e., ``-s ttest``) when running create.case. This +option results in daily, non-averaged history files being written for a 5 year simulation. + +To run the compliance test: + +.. code-block:: bash + + cp configuration/scripts/tests/QC/cice.t-test.py . + ./cice.t-test.py /path/to/baseline/history /path/to/test/history + +The script will produce output similar to: + + | \INFO:__main__:Number of files: 1825 + | \INFO:__main__:Two-Stage Test Passed + | \INFO:__main__:Quadratic Skill Test Passed for Northern Hemisphere + | \INFO:__main__:Quadratic Skill Test Passed for Southern Hemisphere + | \INFO:__main__: + | \INFO:__main__:Quality Control Test PASSED + +Additionally, the exit code from the test (``echo $?``) will be 0 if the test passed, +and 1 if the test failed. + +Implementation notes: 1) Provide a pass/fail on each of the confidence +intervals, 2) Facilitate output of a bitmap for each test so that +locations of failures can be identified. .. _tabnamelist: diff --git a/cice_3_user_guide.html b/cice_3_user_guide.html index ed08ac17d..ac3abe050 100644 --- a/cice_3_user_guide.html +++ b/cice_3_user_guide.html @@ -2133,6 +2133,75 @@

3.6.4.6. Additional Details\(S_{crit}=0.99\) to pass the test. Practical illustrations of this test and the Two-Stage test described in the previous section are provided in [38].

+

In applying equations (1) through (4), +we are accounting for the fact, however imperfectly, that a +\(t\)-test should be a comparison of the means from two series of +independent samples. The typical affect of applying these equations to +sea ice model output is that \(n' \ll n\). For that reason, we need +a lengthy time series to narrow the range of acceptable values +in t-crit. There is little point in using more frequent output +from CICE than daily instantaneous values, since this would have little +impact on decreasing \(r_1\) in lag-1-auto-correlation.

+

Using these equations, a standard procedure in testing for +science-changing answers in CICE and Icepack is as follows: First, make +every attempt to obtain bit-for-bit reproducibility in the model code. +Once all available software-testing options have been exhausted, and the +source of the bit-for-bit test failure has been pinpointed, proceed with +the \(t\)-test documented above if the expectation is that code +alterations should not be science-changing. +Equations (1) through (4) are +implemented in the reverse order from which they are presented here, and +applied individually to daily samples of \(h\), \(c\), \(u\) +and \(v\) from 5-year time series at every model grid point: i) +Calculate \(\bar{x}_{1:n-1}\), \(\bar{x}_{2:n}\), and +\(\bar{x}\) in (4) for simulations \(a\) and +\(b\); ii) Compute lag-1-auto-correlation, +effective-sample-size and unbiased-sigma, in that order, +for each simulation \(a\) and \(b\), and finally; iii) Determine +whether the null hypothesis is true at each model grid point in +t-crit using equation (1) and a lookup +\(t\)-distribution table. Should \(H_0\) be confirmed at each +grid point, and for each variable \(h\), \(c\), \(u\) and +\(v\), this test contributes to evidence that changes to CICE and +Icepack code are unlikely to alter scientific results. To guard against +the possibility of a Type II error, the test should be performed for +several different confidence intervals, nominally set at 68, 80 and 95%, +the first and last of these values corresponding to \(\sigma\) and +\(2\sigma\) tests.

+

+
+

3.6.5.3. Practical Testing Procedure

+

The CICE code compliance test is performed by running a python script (cice.t-test.py). +In order to run the script, the following requirements must be met:

+ +

In order to generate the files necessary for the compliance test, test cases should be +created with the ttest option (i.e., -s ttest) when running create.case. This +option results in daily, non-averaged history files being written for a 5 year simulation.

+

To run the compliance test:

+
cp configuration/scripts/tests/QC/cice.t-test.py .
+./cice.t-test.py /path/to/baseline/history /path/to/test/history
+
+
+

The script will produce output similar to:

+
+
+
INFO:__main__:Number of files: 1825
+
INFO:__main__:Two-Stage Test Passed
+
INFO:__main__:Quadratic Skill Test Passed for Northern Hemisphere
+
INFO:__main__:Quadratic Skill Test Passed for Southern Hemisphere
+
INFO:__main__:
+
INFO:__main__:Quality Control Test PASSED
+
+
+

Additionally, the exit code from the test (echo $?) will be 0 if the test passed, +and 1 if the test failed.

+

Implementation notes: 1) Provide a pass/fail on each of the confidence +intervals, 2) Facilitate output of a bitmap for each test so that +locations of failures can be identified.

diff --git a/cice_4_index.html b/cice_4_index.html index 4081a606e..22505b320 100644 --- a/cice_4_index.html +++ b/cice_4_index.html @@ -1661,7 +1661,7 @@

4.1. Comprehensive Alphabetical Indexkstrength -\(\bullet\) ice stength formulation (1= [57], 0 = [26]) +\(\bullet\) ice stength formulation (1= [61], 0 = [26]) 1   diff --git a/searchindex.js b/searchindex.js index 16489f87b..22d74533d 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ 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Introduction - CICE5","2. Science Guide","3. User Guide","4. Index of primary variables and parameters","CICE Documentation","5. References"],titleterms:{"case":2,"new":1,Adding:2,Ice:1,Useful:4,acknowledg:0,addit:2,aerosol:1,age:1,albedo:2,alphabet:3,anoth:2,approach:1,appropri:2,area:1,atmospher:1,balanc:1,baselin:2,bio:2,biogeochemistri:1,block:2,boundari:2,brine:1,bug:2,chang:1,choos:2,cice5:0,cice:[0,2,4],climat:1,code:2,coeffici:1,column:2,compar:2,complianc:2,compon:1,comprehens:3,condit:2,configur:2,content:4,copyright:0,coupl:[1,2],data:[0,2],dataset:2,debug:2,departur:1,depend:1,detail:[0,2],diagnost:2,directori:2,document:4,domain:2,dynam:1,exampl:2,exchang:1,execut:2,field:[1,2],file:2,forc:[0,1,2],format:2,gener:2,get:0,grid:2,growth:1,guid:[0,1,2],head:[],height:1,hint:2,histori:2,horizont:1,ice:1,implement:2,index:3,individu:2,initi:2,integr:1,intern:1,interpret:2,introduct:0,known:2,local:2,locat:1,major:0,mask:2,mechan:1,melt:1,method:[],model:[0,1,2],modif:2,momentum:1,more:0,namelist:2,numer:2,ocean:1,onlin:0,option:2,other:1,output:2,pair:2,paramet:3,parameter:2,perform:2,pond:1,practic:2,primari:3,procedur:2,prolifer:2,quadrat:2,quick:0,quickstart:2,reconstruct:1,redistribut:1,refer:5,resourc:0,restart:2,revis:1,run:[0,2],scienc:1,script:2,sea:1,setup:2,skill:2,slow:2,space:1,stage:2,start:0,state:1,step:2,stress:1,structur:2,subprocess:2,suit:2,surfac:1,tabl:[1,2,4],temperatur:1,test:2,thermodynam:1,thick:[1,2],thing:2,time:2,timer:2,tool:4,tracer:[1,2],transport:1,triangl:1,tripol:2,troubleshoot:2,two:2,updat:[0,1],user:2,variabl:[1,3]}}) \ No newline at end of file From dc521fc85a0f5460a340d8e98b26b25a349018ff Mon Sep 17 00:00:00 2001 From: David Bailey Date: Sat, 2 Dec 2017 08:03:09 -0700 Subject: [PATCH 6/6] Update testing documents. --- _sources/cice_3_user_guide.rst.txt | 37 ------------------------------ cice_3_user_guide.html | 35 ---------------------------- searchindex.js | 2 +- 3 files changed, 1 insertion(+), 73 deletions(-) diff --git a/_sources/cice_3_user_guide.rst.txt b/_sources/cice_3_user_guide.rst.txt index 12a8be696..81e867c03 100644 --- a/_sources/cice_3_user_guide.rst.txt +++ b/_sources/cice_3_user_guide.rst.txt @@ -2262,43 +2262,6 @@ hemispheres, and must exceed a critical value nominally set to test and the Two-Stage test described in the previous section are provided in :cite:`Hunke2018`. -In applying equations :eq:`t-distribution` through :eq:`short-means`, -we are accounting for the fact, however imperfectly, that a -:math:`t`-test should be a comparison of the means from two series of -independent samples. The typical affect of applying these equations to -sea ice model output is that :math:`n' \ll n`. For that reason, we need -a lengthy time series to narrow the range of acceptable values -in :eq:`t-crit`. There is little point in using more frequent output -from CICE than daily instantaneous values, since this would have little -impact on decreasing :math:`r_1` in :eq:`lag-1-auto-correlation`. - -Using these equations, a standard procedure in testing for -science-changing answers in CICE and Icepack is as follows: First, make -every attempt to obtain bit-for-bit reproducibility in the model code. -Once all available software-testing options have been exhausted, and the -source of the bit-for-bit test failure has been pinpointed, proceed with -the :math:`t`-test documented above if the expectation is that code -alterations should not be science-changing. -Equations :eq:`t-distribution` through :eq:`short-means` are -implemented in the reverse order from which they are presented here, and -applied individually to daily samples of :math:`h`, :math:`c`, :math:`u` -and :math:`v` from 5-year time series at every model grid point: i) -Calculate :math:`\bar{x}_{1:n-1}`, :math:`\bar{x}_{2:n}`, and -:math:`\bar{x}` in :eq:`short-means` for simulations :math:`a` and -:math:`b`; ii) Compute :eq:`lag-1-auto-correlation`, -:eq:`effective-sample-size` and :eq:`unbiased-sigma`, in that order, -for each simulation :math:`a` and :math:`b`, and finally; iii) Determine -whether the null hypothesis is true at each model grid point in -:eq:`t-crit` using equation :eq:`t-distribution` and a lookup -:math:`t`-distribution table. Should :math:`H_0` be confirmed at each -grid point, and for each variable :math:`h`, :math:`c`, :math:`u` and -:math:`v`, this test contributes to evidence that changes to CICE and -Icepack code are unlikely to alter scientific results. To guard against -the possibility of a Type II error, the test should be performed for -several different confidence intervals, nominally set at 68, 80 and 95%, -the first and last of these values corresponding to :math:`\sigma` and -:math:`2\sigma` tests. - *************************** Practical Testing Procedure *************************** diff --git a/cice_3_user_guide.html b/cice_3_user_guide.html index ac3abe050..b1a770081 100644 --- a/cice_3_user_guide.html +++ b/cice_3_user_guide.html @@ -2133,41 +2133,6 @@

3.6.4.6. Additional Details\(S_{crit}=0.99\) to pass the test. Practical illustrations of this test and the Two-Stage test described in the previous section are provided in [38].

-

In applying equations (1) through (4), -we are accounting for the fact, however imperfectly, that a -\(t\)-test should be a comparison of the means from two series of -independent samples. The typical affect of applying these equations to -sea ice model output is that \(n' \ll n\). For that reason, we need -a lengthy time series to narrow the range of acceptable values -in t-crit. There is little point in using more frequent output -from CICE than daily instantaneous values, since this would have little -impact on decreasing \(r_1\) in lag-1-auto-correlation.

-

Using these equations, a standard procedure in testing for -science-changing answers in CICE and Icepack is as follows: First, make -every attempt to obtain bit-for-bit reproducibility in the model code. -Once all available software-testing options have been exhausted, and the -source of the bit-for-bit test failure has been pinpointed, proceed with -the \(t\)-test documented above if the expectation is that code -alterations should not be science-changing. -Equations (1) through (4) are -implemented in the reverse order from which they are presented here, and -applied individually to daily samples of \(h\), \(c\), \(u\) -and \(v\) from 5-year time series at every model grid point: i) -Calculate \(\bar{x}_{1:n-1}\), \(\bar{x}_{2:n}\), and -\(\bar{x}\) in (4) for simulations \(a\) and -\(b\); ii) Compute lag-1-auto-correlation, -effective-sample-size and unbiased-sigma, in that order, -for each simulation \(a\) and \(b\), and finally; iii) Determine -whether the null hypothesis is true at each model grid point in -t-crit using equation (1) and a lookup -\(t\)-distribution table. Should \(H_0\) be confirmed at each -grid point, and for each variable \(h\), \(c\), \(u\) and -\(v\), this test contributes to evidence that changes to CICE and -Icepack code are unlikely to alter scientific results. To guard against -the possibility of a Type II error, the test should be performed for -several different confidence intervals, nominally set at 68, 80 and 95%, -the first and last of these values corresponding to \(\sigma\) and -\(2\sigma\) tests.

3.6.5.3. Practical Testing Procedure

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