Changes between Version 10 and Version 11 of Users/Setup New Configuration/AGRIF-nesting-tool


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Timestamp:
2017-03-29T23:09:33+02:00 (3 years ago)
Author:
nicolasmartin
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  • Users/Setup New Configuration/AGRIF-nesting-tool

    v10 v11  
    11 
    2 === AGRIF nesting tools === 
    3 AGRIF is a package for the integration of adaptive mesh refinement (AMR) features within a multidimensional model written in Fortran and discretized on a structured grid. This nesting capability that allows resolution to be focused over a region of interest by introducing an additional grid has been added to NEMO. In the current implementation only horizontal refinement is available. This page aims to explain the way to run an embedded model by using the NEMO/AGRIF framework in a pre-defined configuration. In this way we are going to describe here how to provide the grid coordinates, the surface forcing and the initial conditions required by each child model. In order to become familiar with NEMO/AGRIF, you should read it even if you are going to create your own configuration. 
     2= AGRIF nesting tools 
    43 
    5 == Downloads : == 
     4[[PageOutline(2, ,inline)]] 
    65 
    7 Nesting tools source code : [https://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Users/SetupNewConfiguration/AGRIF-nesting-tool/Nesting_tools.tar Nesting_tools.tar] 430.00 kB 
     6Last edition: '''[[Wikinfo(changed_ts)]]''' by '''[[Wikinfo(changed_by)]]''' 
    87 
    9 documentation (pdf) : [https://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Users/SetupNewConfiguration/AGRIF-nesting-tool/doc_nesting_tools.pdf doc_nesting_tools.pdf] 3.07 MB 
     8AGRIF is a package for the integration of adaptive mesh refinement (AMR) features within a multidimensional model written in Fortran and discretized on a structured grid. This nesting capability that allows resolution to be focused over a region of interest by introducing an additional grid has been added to NEMO. In the current implementation only horizontal refinement is available. 
    109 
    11 NEMO User's meeting 2006 presentation (pdf ) : [https://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Users/SetupNewConfiguration/AGRIF-nesting-tool/AGRIF_talk.pdf AGRIF_talk.pdf] 2.14 MB 
     10This page aims to explain the way to run an embedded model by using the NEMO/AGRIF framework in a pre-defined configuration. In this way we are going to describe here how to provide the grid coordinates, the surface forcing and the initial conditions required by each child model. In order to become familiar with NEMO/AGRIF, you should read it even if you are going to create your own configuration. 
    1211 
    13 attached movie ITF (mpg): [https://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Users/SetupNewConfiguration/AGRIF-nesting-tool/film_lev1.mpg film_lev1.mpg] 6.93 MB 
     12== Downloads 
    1413 
     14Nesting tools source code : [[AttachmentNum(1)]] 
    1515 
     16documentation (pdf) : [[AttachmentNum(2, raw=true)]] 
    1617 
    17 == 1. Preparing the child model == 
     18NEMO User's meeting 2006 presentation (pdf ) : [[AttachmentNum(3, raw=true)]] 
    1819 
     20attached movie ITF (mpg): [[AttachmentNum(4)]] 
     21 
     22== Preparing the child model 
    1923 
    2024One of the features of the AGRIF package is its ability to deal with the use of fixed fine grids in the domain. Here are presented the various basic knowledges every user should have in order to define his child grid domain. 
    2125 
    22 =1.1 Refinement ratio= 
     26=== Refinement ratio 
    2327 
    2428In order to implement an embedded model user have to specify his space and time refinement ratio. Every integer number is allowed by AGRIF indeed even and odd refinement ratio in space as well as in time could be chosen. But user have to keep in mind that a too large value could imply numerical troubles, in this way a value between 2 and 5 seems to be an acceptable choice. Localization of fine grid points for odd and even refinement ratio are described in the figure below Concerning time refinement ratio, there is no specific criterion to determine its value but of course the selected value must prevent the model from blowing up. 
    2529 
    26 =1.2 Child Grid Position= 
     30=== Child Grid Position 
    2731 
    28 The nested grids are rectangular and are aligned with the parent (coarser) grid within they are nested. imin,imax,jmin and jmax refer to the positions of the child grid corners, in terms of its parent grid starting with the value 1 in each space direction. When the user chooses these positions, one has to take care that fine grid is contained in the parent grid. (imin,jmin) are the lower left corner position and (imax,jmax) are the upper right corner position. The indice of the first grid point inside the fine domain is given by the formulae:[[BR]] 
    29  
    30  
    31     - ibeg = imin+ptx-1 in x-direction 
    32     - jbeg = jmin+pty-1 in y-direction 
     32The nested grids are rectangular and are aligned with the parent (coarser) grid within they are nested. imin,imax,jmin and jmax refer to the positions of the child grid corners, in terms of its parent grid starting with the value 1 in each space direction. When the user chooses these positions, one has to take care that fine grid is contained in the parent grid. (imin,jmin) are the lower left corner position and (imax,jmax) are the upper right corner position. The indice of the first grid point inside the fine domain is given by the formulae: 
     33* ibeg = imin+ptx-1 in x-direction 
     34* jbeg = jmin+pty-1 in y-direction 
    3335 
    3436Where ptx and pty are indexes of the first fine grid point inside the domain, those values depend on the staggered variable. In the NEMO framework there is two ghost cells around fine grids so the ptx and pty values are the following :  
    35 ||point type||  ptx     ||pty ||                  
     37||point type||ptx       ||pty ||                  
    3638||T         ||3         || 3  || 
    3739||U         ||2         || 3  || 
     
    3941||F         ||2         || 2  || 
    4042 
    41  [[Image(AGRIF-Variable-Position.jpg)]] 
     43[[Image(AGRIF-Variable-Position.jpg)]] 
    4244 
    4345This is a quite important feature to know in order to properly choose integers imin,imax,jmin and jmax for your fine grid domain definition. Indeed the indice of the first coarse grid point inside child domain is (imin+2,jmin+2) and not (imin,jmin). To sum up, the configuration of a given AGRIF zoom on a coarse domain for a 1:3 refinement ratio is described here: 
     
    4547[[Image(AGRIF-Grid-Definition.jpg)]] 
    4648 
    47 Then in order to prepare a simulation, user must declare the fine grids characteristics in a file called AGRIF_FixedGrids.in which has to be in the directory where the code runs. For each fine grid and each space direction, a line indicates its position on its parent grid as well as its space and time refinement factors.[[BR]] 
     49Then in order to prepare a simulation, user must declare the fine grids characteristics in a file called `AGRIF_FixedGrids.in` which has to be in the directory where the code runs. For each fine grid and each space direction, a line indicates its position on its parent grid as well as its space and time refinement factors. 
    4850 
     51Typically a line contains those information in this order : `imin imax jmin jmax spacerefx spacerefy timeref` 
     52Let's consider an example with a root coarse grid (G0) which has two child grids (G1) and (G2), and G1 has one child grid (G3). Space and time refinement factors are equal to 3, in this case the `AGRIF_FixedGrids.in` file syntax is the following one :  
    4953 
    50 Typically a line contains those information in this order : imin imax jmin jmax spacerefx spacerefy timeref 
    51 Let's consider an example with a root coarse grid (G0) which has two child grids (G1) and (G2), and G1 has one child grid (G3). Space and time refinement factors are equal to 3, in this case the AGRIF_FixedGrids.in file syntax is the following one :  
    52  
    53 ||imin  ||imax  ||jmin  ||jmax  ||spacerefx     ||spacerefy     ||timeref||              
    54 ||2     ||      ||      ||      ||      ||      ||      ||(G0) has 2 child grids : (G1) and (G2)||       
    55 ||40    ||70    ||2     ||30    ||3     ||3     ||3     ||positions and refinement factors for (G1)|| 
    56 ||110   ||130   ||50    ||80    ||3     ||3     ||3     ||positions and refinement factors for (G2)|| 
    57 ||1     ||      ||      ||      ||      ||      ||      ||(G1) has 1 child grid (G3)|| 
    58 ||20    ||40    ||8     ||30    ||3     ||3     ||3     ||positions and refinement factors for (G3)|| 
    59 ||0     ||      ||      ||      ||      ||      ||      ||(G2) has no child grid|| 
    60 ||0     ||      ||      ||      ||      ||      ||      ||(G3) has no child grid || 
     54||imin  ||imax  ||jmin  ||jmax  ||spacerefx ||spacerefy ||timeref ||             
     55||2     ||      ||      ||      ||          ||          ||        ||(G0) has 2 child grids : (G1) and (G2)    || 
     56||40    ||70    ||2     ||30    ||3         ||3         ||3       ||positions and refinement factors for (G1) || 
     57||110   ||130   ||50    ||80    ||3         ||3         ||3       ||positions and refinement factors for (G2) || 
     58||1     ||      ||      ||      ||          ||          ||        ||(G1) has 1 child grid (G3)                || 
     59||20    ||40    ||8     ||30    ||3         ||3         ||3       ||positions and refinement factors for (G3) || 
     60||0     ||      ||      ||      ||          ||          ||        ||(G2) has no child grid                    || 
     61||0     ||      ||      ||      ||          ||          ||        ||(G3) has no child grid                    || 
    6162 
    6263[[Image(AGRIF-Hierarchy_medium.jpg​)]] 
    6364 
    64 =1.3 One-way vs Ywo-way nesting= 
     65=== One-way vs Ywo-way nesting 
    6566 
    66 Nested grid simulations can be produced using either 1-way nesting or 2-way nesting. Those options refer to how a coarse grid and the fine grid interact. In both the 1-way and 2-way simulation modes, the fine grid boundary conditions are interpolated from the coarse grid. In a 1-way nest, this is the only information exchange between the grids (coarse-to-fine). In the 2-way nest integration, the fine grid solution are used to update the coarse grid solution for coarse grid points that lie inside the fine grid (coarse-to-fine and fine-to-coarse). User can choose between those both kind of interactions by editing Agrif_OPA_Update.F90 file located in NESTING_SRC directory (as shown below). This file contains a cpp key called TWO_WAY if one puts "#define TWO_WAY", that means 2-way interactive grid nesting is selected at the opposite "#undef TWO_WAY" means 1-way nesting will be applied. 
     67Nested grid simulations can be produced using either 1-way nesting or 2-way nesting. Those options refer to how a coarse grid and the fine grid interact. In both the 1-way and 2-way simulation modes, the fine grid boundary conditions are interpolated from the coarse grid. In a 1-way nest, this is the only information exchange between the grids (coarse-to-fine). In the 2-way nest integration, the fine grid solution are used to update the coarse grid solution for coarse grid points that lie inside the fine grid (coarse-to-fine and fine-to-coarse). User can choose between those both kind of interactions by editing `Agrif_OPA_Update.F90` file located in `NESTING_SRC` directory (as shown below). This file contains a cpp key called `TWO_WAY` if one puts `#define TWO_WAY`, that means 2-way interactive grid nesting is selected at the opposite `#undef TWO_WAY` means 1-way nesting will be applied. 
    6768 
    6869[[Image(AGRIF_Organigrame.jpg​​)]] 
    6970 
     71=== Getting the lateral boundary conditions, winds and surface fluxes 
    7072 
     73This step makes use of NEMO/AGRIF Nesting tools package downloadable at the top of this page. Those tools are fully described in its attached documentation. 
    7174 
    72 ==2. Getting the lateral boundary conditions, winds and surface fluxes== 
     75Please refer to this file for a detailed approach of this package: 
    7376 
    74 This step makes use of NEMO/AGRIF Nesting tools package downloadable at the top of this page. Those tools are fully described in its attached documentation.[[BR]] 
     77Let's just consider the current chapter as a reminder of the functioning of nesting tools. 
    7578 
    76 Please refer to this file for a detailed approach of this package:[[BR]] 
    77  
    78  
    79 Let's just consider the current chapter as a reminder of the functioning of nesting tools.[[BR]] 
    80  
    81  
    82 The first stage consists in editing the Makefile corresponding to your architecture in src/ directory in order to properly mention the path to your netcdf library with F90 enabled.[[BR]] 
    83  
     79The first stage consists in editing the Makefile corresponding to your architecture in `src` directory in order to properly mention the path to your netcdf library with F90 enabled. 
    8480 
    8581{{{ 
    86  
    8782#elisha 
    8883 
     
    9287 
    9388The various architecture currently supported are :  
    94 || Architecture         ||Compiler|| 
    95 ||PC/Linux      ||ifort, pgf90, g95|| 
    96 ||Alpha Compaq ||       f95|| 
    97 ||IBM   ||xlf90|| 
    98 ||MacOS         ||g95|| 
     89||Architecture  ||Compiler          || 
     90||PC/Linux      ||ifort, pgf90, g95 || 
     91||Alpha Compaq  ||f95               || 
     92||IBM           ||xlf90             || 
     93||MacOS         ||g95               || 
    9994 
    100 hen once Makefile is properly edited, user can compile the code and check the result in bin/ directory. One should find five executables namely create_coordinates.exe, create_bathy.exe, create_data.exe , create_restart.exe (if needed) and create_restart_trc.exe (when using PISCES for instance). 
    101  
     95hen once Makefile is properly edited, user can compile the code and check the result in `bin` directory. One should find five executables namely `create_coordinates.exe create_bathy.exe create_data.exe create_restart.exe` (if needed) and `create_restart_trc.exe` (when using PISCES for instance). 
    10296 
    10397{{{ 
     
    108102}}} 
    109103 
    110 There is a sample namlist called agulhas to create forcing files for agulhas area. You may edit or copy this file to add your own forcing files, change the zoom area and adjust interpolation parameters. 
    111  
     104There is a sample namelist called agulhas to create forcing files for agulhas area. You may edit or copy this file to add your own forcing files, change the zoom area and adjust interpolation parameters. 
    112105 
    113106{{{ 
     
    122115 
    123116 
    124 This order must be kept because create_bathy.exe requires a coordinates file build by create_coordinates.exe in the same way create_data.exe makes use of a bathymetry file produced by create_bathy.exe.[[BR]] 
     117This order must be kept because `create_bathy.exe` requires a coordinates file build by `create_coordinates.exe` in the same way `create_data.exe` makes use of a bathymetry file produced by `create_bathy.exe`. 
    125118 
     119Both grid and bathymetry creation are needed to perform an AGRIF run. For fluxes (step 3), the user is free to use the nesting tools or online interpolation : 
    126120 
    127 Both grid and bathymetry creation are needed to perform an AGRIF run. For fluxes (step 3), the user is free to use the nesting tools or online interpolation :[[BR]] 
     121- when using the nesting tools, every forcing files needed for a traditional NEMO run (i.e. without AGRIF) have to be created for fine grids except specific files like runoff. 
    128122 
    129 - when using the nesting tools, every forcing files needed for a traditional NEMO run (i.e. without AGRIF) have to be created for fine grids except specific files like runoff.[[BR]] 
     123- when using online interpolation ,the child grid will use the coarse grid input files during the run, performing an interpolation on the fly (bilinear or bicubic), so we have to provide an weight file (see [/wiki/Users/SetupNewConfiguration/Weight-creator On the Fly Interpolation]) 
    130124 
    131 - when using online interpolation ,the child grid will use the coarse grid input files during the run, performing an interpolation on the fly (bilinear or bicubic), so we have to provide an weight file (see [https://forge.ipsl.jussieu.fr/nemo/wiki/Users/SetupNewConfiguration/Weight-creator On the Fly Interpolation])[[BR]] 
     125In case of a multiple nests configuration, one have to fill in `AGRIF_FixedGrids.in` in accordance with the prefix given by nesting tools code. Let's consider the example used in section 1.2, (G1) forcing files must be named with `1_` prefix, (G2) with `2_` and (G3) with `3_`. But if (G1) and (G2) definition lines are inverted, (G2) should correspond to `1_` prefix and (G1) to `2_`. When running nesting tools program if a whole set of `1_` prefix files is already present in `bin` directory the program will create by default `2_` prefix files. In the case of a number of level of zoom greater than 2, when considering level n one has just to fill in namelist file by replacing forcing files by those created at level n-1. 
    132126 
    133 In case of a multiple nests configuration, one have to fill in AGRIF_FixedGrids.in in accordance with the prefix given by nesting tools code. Let's consider the example used in section 1.2, (G1) forcing files must be named with '1_' prefix, (G2) with '2_' and (G3) with '3_'. But if (G1) and (G2) definition lines are inverted, (G2) should correspond to '1_' prefix and (G1) to '2_'. When running nesting tools program if a whole set of '1_' prefix files is already present in bin/ directory the program will create by default '2_' prefix files. In the case of a number of level of zoom greater than 2, when considering level n one has just to fill in namelist file by replacing forcing files by those created at level n-1.[[BR]] 
     127At this step, user should have filled in `AGRIF_FixedGrids.in` and build coordinates, bathymetry and forcing files for every grid mentioned in this file. 
    134128 
    135 At this step, user should have filled in AGRIF_FixedGrids.in and build coordinates, bathymetry and forcing files for every grid mentioned in this file. [[BR]] 
     129== Running the model 
    136130 
    137  
    138 == 3. Running the model== 
    139 =Input data : = 
    140 data needed to run with OPA are of two types : the namelists and the forcing files (already created thanks to nesting tools). Concerning namelists one need to provide one namelist by grid, the naming convention is the same than the one for forcing files.[[BR]] 
    141  
     131=== Input data 
     132data needed to run with OPA are of two types : the namelists and the forcing files (already created thanks to nesting tools). Concerning namelists one need to provide one namelist by grid, the naming convention is the same than the one for forcing files. 
    142133 
    143134{{{ 
    144135#elisha 
    145136 
    146  
    147137cp namelist 1_namelist 
    148138cp namelist_ice 1_namelist_ice  (if LIM is included in the configuration) 
    149139vi 1_namelist 
    150  
    151140}}} 
    152141 
    153142Then user should edit those namelists in order to modify the number and the duration of time steps in order that those number match the coarse grid values, taking into account refinement in time. Some other coefficients linked with the horizontal resolution of the grid can be tuned (mostly concerning diffusion and viscosity) indeed each grid has his own set of coefficients.  
    154143 
    155 || ||   Coarse Grid'namelist' || Fine Grid '1_namelist' 
    156 ||nitend||      52500   || 157500 || 
    157 ||rdt||         1800    || 600 || 
     144||       ||Coarse Grid `namelist` ||Fine Grid `1_namelist` || 
     145||nitend ||52500                  ||157500                || 
     146||rdt    ||1800                   ||600                    || 
    158147 
     148''Most important namelist variables to edit. Example for a 1:3 time refinement ratio'' 
    159149 
    160 ''Most important namelist variables to edit. Example for a 1:3 time refinement ratio''[[BR]] 
     150User has now to gather in a directory every forcing files, namelists as well as opa executable and `AGRIF_FixedGrids.in` file. The simulation is ready to be carried out. 
    161151 
    162 User has now to gather in a directory every forcing files, namelists as well as opa executable and AGRIF_FixedGrids.in file. The simulation is ready to be carried out.[[BR]] 
    163  
    164 When using online interpolation, the forcing part of 1_namelist will look like (here with core forcing):[[BR]] 
    165  
    166  
     152When using online interpolation, the forcing part of `1_namelist` will look like (here with core forcing): 
    167153     
    168154{{{ 
     
    182168}}} 
    183169 
     170And we need only a weight file called `1_bicubic_weights.nc` in the running directory, while core forcing files corresponds to the coarse grid input files. 
    184171 
    185 And we need only a weight file called 1_bicubic_weights.nc in the running directory, while core forcing files corresponds to the coarse grid input files.[[BR]] 
    186  
    187  
    188 =Output data :=  
     172=== Output data 
    189173output files are NetCDF or DIMG (key_dimgout activated) files giving the diagnostics at points T,U,V,W of the Arakawa C grid. For fine grids output files, the naming convention is exactly the same than the one mentioned above namely a different prefix for each grid of the hierarchy. The output files contain the both ghostcells, mentioned before, at the boundaries, so depending the visualization tool used, user can have the value zero at the boundaries of child grids. Note that the text file called ocean.ouput containing all the information printed during the run is also created for fine grids. 
    190174 
    191 ==Development Team== 
     175=== Development Team 
    192176 
     177||Organization      ||Name            ||Developments                                                                                    ||contact                 || 
     178||LMC/IMAG,Grenoble ||Laurent Debreu  ||MPI implementation,Numerical implementation,2 way grid nesting                                  ||Laurent.Debreu@imag.fr  || 
     179||LMC/IMAG,Grenoble ||Cyril Mazauric  ||Installation environment,Portability on various platforms,Test of performance,Computation issues||Cyril.Mazauric@imag.fr  || 
     180||LMC/IMAG,Grenoble ||Florian Lemarié ||Nesting tools,New AGRIF interpolation schemes (PPM/ENO),Numerical issues                        ||Florian.Lemarie@imag.fr || 
    193181 
    194 ||Organization  ||Name  ||Developments  ||contact|| 
    195 ||LMC/IMAG,Grenoble     ||Laurent Debreu        ||MPI implementation,Numerical implementation,2 way grid nesting ||     Laurent.Debreu@imag.fr|| 
    196 ||LMC/IMAG,Grenoble     ||Cyril Mazauric        ||Installation environment,Portability on various platforms,Test of performance,Computation issues||    Cyril.Mazauric@imag.fr|| 
    197 ||LMC/IMAG,Grenoble     ||Florian Lemarié       ||Nesting tools,New AGRIF interpolation schemes (PPM/ENO),Numerical issues      ||Florian.Lemarie@imag.fr|| 
    198  
    199 ==Support== 
    200  
     182=== Support 
    201183??? 
    202184 
     185=== Known Users 
     186||Organization           ||Name                                          ||Region of interest         ||Configuration          || 
     187||LEGI Grenoble FRANCE   ||Jean-Marc Molines                             ||Gulf of Mexico             ||NATL3/NATL4            || 
     188||CICESE Ensenada MEXICO ||Julio Scheinbob,Julio Candela, Julien Jouanno ||Gulf of Mexico             ||NATL3                  || 
     189||DFO St Johns CANADA    ||Andry Ratsimandresy,Fraser Davidson           ||Newfoundland, Labrador sea ||NOOFS based on ORCA025 || 
     190||LPO Brest              ||Virginie Thierry                              ||Bay of Biscay              ||NATL4                  || 
     191||NOCS Southampton       ||Steve Alderson                                ||                           ||                       ||         
     192||IFM-GEOMAR Kiel        ||Arne Biastoch                                 ||South Africa               ||ORCA025                || 
     193||Mercator OCean         || Jerome Chanut                                ||North Atlantic             ||CREG025, CREG12        || 
    203194 
    204 ==Known Users== 
    205  
    206 ||Organization  ||Name  ||Region of interest    ||configuration|| 
    207 ||LEGI Grenoble FRANCE  ||Jean-Marc Molines     ||Gulf of Mexico        ||NATL3/NATL4|| 
    208 ||CICESE Ensenada MEXICO        ||Julio Scheinbob,Julio Candela, Julien Jouanno||       Gulf of Mexico ||       NATL3|| 
    209 ||DFO St Johns CANADA   ||Andry Ratsimandresy,Fraser Davidson   ||Newfoundland, Labrador sea||  NOOFS based on ORCA025|| 
    210 ||LPO Brest     ||Virginie Thierry||    Bay of Biscay||         NATL4|| 
    211 ||NOCS Southampton      ||Steve Alderson        ||||||            
    212 ||IFM-GEOMAR Kiel       ||Arne Biastoch ||      South Africa || ORCA025|| 
    213 ||Mercator OCean || Jerome Chanut || North Atlantic || CREG025, CREG12 || 
    214  
    215  
    216 ==References :== 
    217   
    218   -[http://www-ljk.imag.fr/MOISE/AGRIF/ AGRIF ] web page - (Laurent Debreu, LMC-IMAG) 
    219  
    220   -Nesting Tool:[[BR]] 
    221  
    222  
    223     [http://www.croco-ocean.org/ CROCO] Matlab Toolbox - (Pierrick Penven, Patrick Marchesiello - IRD)[[BR]] 
    224  
    225     [http://oceans11.lanl.gov/trac/SCRIP SCRIP ] package - (Los Alamos National Laboratory)[[BR]] 
    226  
    227  
    228  
    229  
     195=== References 
     196 * [http://www-ljk.imag.fr/MOISE/AGRIF/ AGRIF ] web page - (Laurent Debreu, LMC-IMAG) 
     197 * Nesting Tool: 
     198   * [http://www.croco-ocean.org/ CROCO] Matlab Toolbox - (Pierrick Penven, Patrick Marchesiello - IRD) 
     199   * [http://oceans11.lanl.gov/trac/SCRIP SCRIP ] package - (Los Alamos National Laboratory)