Changeset 5612 for branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles
- Timestamp:
- 2015-07-20T11:11:11+02:00 (9 years ago)
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- branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles
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branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Biblio/Biblio.bib
r4560 r5612 271 271 volume = {326}, 272 272 pages = {677--684} 273 } 274 275 @ARTICLE{Beckmann2003, 276 author = {A. Beckmann and H. Goosse}, 277 title = {A parameterization of ice shelf-ocean interaction for climate models}, 278 journal = OM 279 year = {2003} 280 volume = {5} 281 pages = {157--170} 273 282 } 274 283 -
branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Chapters/Chap_DIA.tex
r5213 r5612 74 74 The second functionality targets output performance when running in parallel (\key{mpp\_mpi}). Iomput provides the possibility to specify N dedicated I/O processes (in addition to the NEMO processes) to collect and write the outputs. With an appropriate choice of N by the user, the bottleneck associated with the writing of the output files can be greatly reduced. 75 75 76 In version 3.6, the iom\_put interface depends on an external code called \href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS/branchs/xios-1.0}{XIOS-1.0} . This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to create a single output file and therefore to bypass the rebuilding phase. Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to an HDF5 library that has been correctly compiled (i.e. with the configure option $--$enable-parallel). Note that the files created by iomput through XIOS are incompatible with NetCDF3. All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3.76 In version 3.6, the iom\_put interface depends on an external code called \href{https://forge.ipsl.jussieu.fr/ioserver/browser/XIOS/branchs/xios-1.0}{XIOS-1.0} (use of revision 618 or higher is required). This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to create a single output file and therefore to bypass the rebuilding phase. Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to an HDF5 library that has been correctly compiled (i.e. with the configure option $--$enable-parallel). Note that the files created by iomput through XIOS are incompatible with NetCDF3. All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3. 77 77 78 78 Even if not using the parallel I/O functionality of NetCDF4, using N dedicated I/O servers, where N is typically much less than the number of NEMO processors, will reduce the number of output files created. This can greatly reduce the post-processing burden usually associated with using large numbers of NEMO processors. Note that for smaller configurations, the rebuilding phase can be avoided, even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server. … … 546 546 547 547 \subsection{XML reference tables} 548 \label{IOM_xmlref} 548 549 549 550 (1) Simple computation: directly define the computation when refering to the variable in the file definition. … … 979 980 \end{longtable} 980 981 982 \subsection{CF metadata standard compliance} 983 984 Output from the XIOS-1.0 IO server is compliant with \href{http://cfconventions.org/Data/cf-conventions/cf-conventions-1.5/build/cf-conventions.html}{version 1.5} of the CF metadata standard. Therefore while a user may wish to add their own metadata to the output files (as demonstrated in example 4 of section \ref{IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard. 985 986 Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by the namelist parameter \np{ln\_cfmeta} in the \ngn{namrun} namelist. This must be set to true if these metadata are to be included in the output files. 981 987 982 988 -
branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Chapters/Chap_DOM.tex
r4147 r5612 493 493 $z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). This option can be used with full step 494 494 bathymetry or $s$-coordinate (hybrid and partial step coordinates have not 495 yet been tested in NEMO v2.3). 495 yet been tested in NEMO v2.3). If using $z$-coordinate with partial step bathymetry 496 (\np{ln\_zps}~=~true), ocean cavity beneath ice shelves can be open (\np{ln\_isfcav}~=~true). 496 497 497 498 Contrary to the horizontal grid, the vertical grid is computed in the code and no -
branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Chapters/Chap_DYN.tex
r4759 r5612 627 627 \eqref{Eq_dynhpg_zco_surf} - \eqref{Eq_dynhpg_zco}, and $z_T$ is the depth of 628 628 the $T$-point evaluated from the sum of the vertical scale factors at the $w$-point 629 ($e_{3w}$). 629 ($e_{3w}$). 630 631 $\bullet$ Traditional coding with adaptation for ice shelf cavities (\np{ln\_dynhpg\_isf}=true). 632 This scheme need the activation of ice shelf cavities (\np{ln\_isfcav}=true). 630 633 631 634 $\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np{ln\_dynhpg\_prj}=true) -
branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Chapters/Chap_MISC.tex
r4147 r5612 141 141 computational domain is laid out on local processor memories following a 2D 142 142 horizontal splitting. % (see {\S}IV.2-c) ref to the section to be updated 143 144 \subsection{Simple subsetting of input files via netCDF attributes} 145 146 The extended grids for use with the under-shelf ice cavities will result in redundant rows 147 around Antarctica if the ice cavities are not active. A simple mechanism for subsetting 148 input files associated with the extended domains has been implemented to avoid the need to 149 maintain different sets of input fields for use with or without active ice cavities. The 150 existing 'zoom' options are overly complex for this task and marked for deletion anyway. 151 This alternative subsetting operates for the j-direction only and works by optionally 152 looking for and using a global file attribute (named: \np{open\_ocean\_jstart}) to 153 determine the starting j-row for input. The use of this option is best explained with an 154 example: Consider an ORCA1 configuration using the extended grid bathymetry and coordinate 155 files: 156 \vspace{-10pt} 157 \begin{alltt} 158 \tiny 159 \begin{verbatim} 160 eORCA1_bathymetry_v2.nc 161 eORCA1_coordinates.nc 162 \end{verbatim} 163 \end{alltt} 164 \noindent These files define a horizontal domain of 362x332. Assuming the first row with 165 open ocean wet points in the non-isf bathymetry for this set is row 42 (Fortran indexing) 166 then the formally correct setting for \np{open\_ocean\_jstart} is 41. Using this value as the 167 first row to be read will result in a 362x292 domain which is the same size as the original 168 ORCA1 domain. Thus the extended coordinates and bathymetry files can be used with all the 169 original input files for ORCA1 if the ice cavities are not active (\np{ln\_isfcav = 170 .false.}). Full instructions for achieving this are: 171 172 \noindent Add the new attribute to any input files requiring a j-row offset, i.e: 173 \vspace{-10pt} 174 \begin{alltt} 175 \tiny 176 \begin{verbatim} 177 ncatted -a open_ocean_jstart,global,a,d,41 eORCA1_coordinates.nc 178 ncatted -a open_ocean_jstart,global,a,d,41 eORCA1_bathymetry_v2.nc 179 \end{verbatim} 180 \end{alltt} 181 182 \noindent Add the logical switch to \ngn{namcfg} in the configuration namelist and set true: 183 %--------------------------------------------namcfg-------------------------------------------------------- 184 \namdisplay{namcfg_orca1} 185 %-------------------------------------------------------------------------------------------------------------- 186 187 \noindent Note the j-size of the global domain is the (extended j-size minus 188 \np{open\_ocean\_jstart} + 1 ) and this must match the size of all datasets other than 189 bathymetry and coordinates currently. However the option can be extended to any global, 2D 190 and 3D, netcdf, input field by adding the: 191 \vspace{-10pt} 192 \begin{alltt} 193 \tiny 194 \begin{verbatim} 195 lrowattr=ln_use_jattr 196 \end{verbatim} 197 \end{alltt} 198 optional argument to the appropriate \np{iom\_get} call and the \np{open\_ocean\_jstart} attribute to the corresponding input files. It remains the users responsibility to set \np{jpjdta} and \np{jpjglo} values in the \np{namelist\_cfg} file according to their needs. 143 199 144 200 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> -
branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Chapters/Chap_SBC.tex
r4661 r5612 1 1 % ================================================================ 2 % Chapter � Surface Boundary Condition (SBC, I CB)3 % ================================================================ 4 \chapter{Surface Boundary Condition (SBC, I CB) }2 % Chapter � Surface Boundary Condition (SBC, ISF, ICB) 3 % ================================================================ 4 \chapter{Surface Boundary Condition (SBC, ISF, ICB) } 5 5 \label{SBC} 6 6 \minitoc … … 48 48 below ice-covered areas (using observed ice-cover or a sea-ice model) 49 49 (\np{nn\_ice}~=~0,1, 2 or 3); the addition of river runoffs as surface freshwater 50 fluxes or lateral inflow (\np{ln\_rnf}~=~true); the addition of a freshwater flux adjustment 51 in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2); the 50 fluxes or lateral inflow (\np{ln\_rnf}~=~true); the addition of isf melting as lateral inflow (parameterisation) 51 (\np{nn\_isf}~=~2 or 3 and \np{ln\_isfcav}~=~false) or as surface flux at the land-ice ocean interface 52 (\np{nn\_isf}~=~1 or 4 and \np{ln\_isfcav}~=~true); 53 the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2); the 52 54 transformation of the solar radiation (if provided as daily mean) into a diurnal 53 55 cycle (\np{ln\_dm2dc}~=~true); and a neutral drag coefficient can be read from an external wave … … 60 62 Finally, the different options that further modify the fluxes applied to the ocean are discussed. 61 63 One of these is modification by icebergs (see \S\ref{ICB_icebergs}), which act as drifting sources of fresh water. 64 Another example of modification is that due to the ice shelf melting/freezing (see \S\ref{SBC_isf}), 65 which provides additional sources of fresh water. 62 66 63 67 … … 686 690 air temperature, sea-surface temperature, cloud cover and relative humidity. 687 691 Sensible heat and latent heat fluxes are computed by classical 688 bulk formulae parameteri zed according to \citet{Kondo1975}.692 bulk formulae parameterised according to \citet{Kondo1975}. 689 693 Details on the bulk formulae used can be found in \citet{Maggiore_al_PCE98} and \citet{Castellari_al_JMS1998}. 690 694 … … 826 830 \Pi-g\delta = (1+k-h) \Pi_{A}(\lambda,\phi) 827 831 \end{equation} 828 with $k$ a number of Love estimated to 0.6 which paramet rized the astronomical tidal land,829 and $h$ a number of Love to 0.3 which paramet rized the parametrization due to the astronomical tidal land.832 with $k$ a number of Love estimated to 0.6 which parameterised the astronomical tidal land, 833 and $h$ a number of Love to 0.3 which parameterised the parameterisation due to the astronomical tidal land. 830 834 831 835 % ================================================================ … … 945 949 946 950 %} 947 948 951 % ================================================================ 952 % Ice shelf melting 953 % ================================================================ 954 \section [Ice shelf melting (\textit{sbcisf})] 955 {Ice shelf melting (\mdl{sbcisf})} 956 \label{SBC_isf} 957 %------------------------------------------namsbc_isf---------------------------------------------------- 958 \namdisplay{namsbc_isf} 959 %-------------------------------------------------------------------------------------------------------- 960 Namelist variable in \ngn{namsbc}, \np{nn\_isf}, control the kind of ice shelf representation used. 961 \begin{description} 962 \item[\np{nn\_isf}~=~1] 963 The ice shelf cavity is represented. The fwf and heat flux are computed. 964 Full description, sensitivity and validation in preparation. 965 966 \item[\np{nn\_isf}~=~2] 967 A parameterisation of isf is used. The ice shelf cavity is not represented. 968 The fwf is distributed along the ice shelf edge between the depth of the average grounding line (GL) 969 (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}~=~3). 970 Furthermore the fwf is computed using the \citet{Beckmann2003} parameterisation of isf melting. 971 The effective melting length (\np{sn\_Leff\_isf}) is read from a file. 972 973 \item[\np{nn\_isf}~=~3] 974 A simple parameterisation of isf is used. The ice shelf cavity is not represented. 975 The fwf (\np{sn\_rnfisf}) is distributed along the ice shelf edge between the depth of the average grounding line (GL) 976 (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}). 977 Full description, sensitivity and validation in preparation. 978 979 \item[\np{nn\_isf}~=~4] 980 The ice shelf cavity is represented. However, the fwf (\np{sn\_fwfisf}) and heat flux (\np{sn\_qisf}) are 981 not computed but specified from file. 982 \end{description} 983 984 \np{nn\_isf}~=~1 and \np{nn\_isf}~=~2 compute a melt rate based on the water masse properties, ocean velocities and depth. 985 This flux is thus highly dependent of the model resolution (horizontal and vertical), realism of the water masse onto the shelf ... 986 987 \np{nn\_isf}~=~3 and \np{nn\_isf}~=~4 read the melt rate and heat flux from a file. You have total control of the fwf scenario. 988 989 This can be usefull if the water masses on the shelf are not realistic or the resolution (horizontal/vertical) are too 990 coarse to have realistic melting or for sensitivity studies where you want to control your input. 991 Full description, sensitivity and validation in preparation. 992 993 There is 2 ways to apply the fwf to NEMO. The first possibility (\np{ln\_divisf}~=~false) applied the fwf 994 and heat flux directly on the salinity and temperature tendancy. The second possibility (\np{ln\_divisf}~=~true) 995 apply the fwf as for the runoff fwf (see \S\ref{SBC_rnf}). The mass/volume addition due to the ice shelf melting is, 996 at each relevant depth level, added to the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div} 997 (called from \mdl{divcur}). 998 % 949 999 % ================================================================ 950 1000 % Handling of icebergs -
branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Chapters/Chap_ZDF.tex
r4147 r5612 830 830 % Bottom Friction 831 831 % ================================================================ 832 \section [Bottom Friction (\textit{zdfbfr})] {Bottom Friction (\mdl{zdfbfr} module)}832 \section [Bottom and top Friction (\textit{zdfbfr})] {Bottom Friction (\mdl{zdfbfr} module)} 833 833 \label{ZDF_bfr} 834 834 … … 837 837 %-------------------------------------------------------------------------------------------------------------- 838 838 839 Options are defined through the \ngn{nambfr} namelist variables. 839 Options to define the top and bottom friction are defined through the \ngn{nambfr} namelist variables. 840 The top friction is activated only if the ice shelf cavities are opened (\np{ln\_isfcav}~=~true). 841 As the friction processes at the top and bottom are the represented similarly, only the bottom friction is described in detail. 842 840 843 Both the surface momentum flux (wind stress) and the bottom momentum 841 844 flux (bottom friction) enter the equations as a condition on the vertical -
branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Namelist/nambfr
r4147 r5612 5 5 ! = 2 : nonlinear friction 6 6 rn_bfri1 = 4.e-4 ! bottom drag coefficient (linear case) 7 rn_bfri2 = 1.e-3 ! bottom drag coefficient (non linear case) 7 rn_bfri2 = 1.e-3 ! bottom drag coefficient (non linear case). Minimum coeft if ln_loglayer=T 8 rn_bfri2_max = 1.e-1 ! max. bottom drag coefficient (non linear case and ln_loglayer=T) 8 9 rn_bfeb2 = 2.5e-3 ! bottom turbulent kinetic energy background (m2/s2) 9 rn_bfrz0 = 3.e-3 ! bottom roughness for loglayer bfr coeff10 rn_bfrz0 = 3.e-3 ! bottom roughness [m] if ln_loglayer=T 10 11 ln_bfr2d = .false. ! horizontal variation of the bottom friction coef (read a 2D mask file ) 11 12 rn_bfrien = 50. ! local multiplying factor of bfr (ln_bfr2d=T) 13 rn_tfri1 = 4.e-4 ! top drag coefficient (linear case) 14 rn_tfri2 = 2.5e-3 ! top drag coefficient (non linear case). Minimum coeft if ln_loglayer=T 15 rn_tfri2_max = 1.e-1 ! max. top drag coefficient (non linear case and ln_loglayer=T) 16 rn_tfeb2 = 0.0 ! top turbulent kinetic energy background (m2/s2) 17 rn_tfrz0 = 3.e-3 ! top roughness [m] if ln_loglayer=T 18 ln_tfr2d = .false. ! horizontal variation of the top friction coef (read a 2D mask file ) 19 rn_tfrien = 50. ! local multiplying factor of tfr (ln_tfr2d=T) 20 12 21 ln_bfrimp = .true. ! implicit bottom friction (requires ln_zdfexp = .false. if true) 22 ln_loglayer = .false. ! logarithmic formulation (non linear case) 13 23 / -
branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Namelist/namdyn_hpg
r4147 r5612 5 5 ln_hpg_zps = .true. ! z-coordinate - partial steps (interpolation) 6 6 ln_hpg_sco = .false. ! s-coordinate (standard jacobian formulation) 7 ln_hpg_isf = .false. ! s-coordinate (sco ) adapted to ice shelf cavity 7 8 ln_hpg_djc = .false. ! s-coordinate (Density Jacobian with Cubic polynomial) 8 9 ln_hpg_prj = .false. ! s-coordinate (Pressure Jacobian scheme) -
branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Namelist/namsbc
r4230 r5612 19 19 ln_dm2dc = .false. ! daily mean to diurnal cycle on short wave 20 20 ln_rnf = .true. ! runoffs (T => fill namsbc_rnf) 21 nn_isf = 0 ! ice shelf melting/freezing (/=0 => fill namsbc_isf) 22 ! 0 =no isf 1 = presence of ISF 23 ! 2 = bg03 parametrisation 3 = rnf file for isf 24 ! 4 = ISF fwf specified 25 ! option 1 and 4 need ln_isfcav = .true. (domzgr) 21 26 ln_ssr = .true. ! Sea Surface Restoring on T and/or S (T => fill namsbc_ssr) 22 27 nn_fwb = 3 ! FreshWater Budget: =0 unchecked -
branches/UKMO/dev_r5518_CICE_coupling_GSI7/DOC/TexFiles/Namelist/namzgr
r3294 r5612 5 5 ln_zps = .true. ! z-coordinate - partial steps (T/F) 6 6 ln_sco = .false. ! s- or hybrid z-s-coordinate (T/F) 7 ln_isfcav = .false. ! ice shelf cavity (T/F) 7 8 /
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