Changes between Version 10 and Version 11 of Users/SetupNewConfiguration/AGRIF-nesting-tool
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- 2017-03-29T23:09:33+02:00 (7 years ago)
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Users/SetupNewConfiguration/AGRIF-nesting-tool
v10 v11 1 1 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 4 3 5 == Downloads : == 4 [[PageOutline(2, ,inline)]] 6 5 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 6 Last edition: '''[[Wikinfo(changed_ts)]]''' by '''[[Wikinfo(changed_by)]]''' 8 7 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 8 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. 10 9 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 10 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. 12 11 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 14 13 14 Nesting tools source code : [[AttachmentNum(1)]] 15 15 16 documentation (pdf) : [[AttachmentNum(2, raw=true)]] 16 17 17 == 1. Preparing the child model == 18 NEMO User's meeting 2006 presentation (pdf ) : [[AttachmentNum(3, raw=true)]] 18 19 20 attached movie ITF (mpg): [[AttachmentNum(4)]] 21 22 == Preparing the child model 19 23 20 24 One 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. 21 25 22 = 1.1 Refinement ratio=26 === Refinement ratio 23 27 24 28 In 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. 25 29 26 = 1.2 Child Grid Position=30 === Child Grid Position 27 31 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 32 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: 33 * ibeg = imin+ptx-1 in x-direction 34 * jbeg = jmin+pty-1 in y-direction 33 35 34 36 Where 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|| 37 ||point type||ptx ||pty || 36 38 ||T ||3 || 3 || 37 39 ||U ||2 || 3 || … … 39 41 ||F ||2 || 2 || 40 42 41 43 [[Image(AGRIF-Variable-Position.jpg)]] 42 44 43 45 This 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: … … 45 47 [[Image(AGRIF-Grid-Definition.jpg)]] 46 48 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]]49 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. 48 50 51 Typically a line contains those information in this order : `imin imax jmin jmax spacerefx spacerefy timeref` 52 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 : 49 53 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 || 61 62 62 63 [[Image(AGRIF-Hierarchy_medium.jpg)]] 63 64 64 = 1.3 One-way vs Ywo-way nesting=65 === One-way vs Ywo-way nesting 65 66 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.67 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. 67 68 68 69 [[Image(AGRIF_Organigrame.jpg)]] 69 70 71 === Getting the lateral boundary conditions, winds and surface fluxes 70 72 73 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. 71 74 72 ==2. Getting the lateral boundary conditions, winds and surface fluxes== 75 Please refer to this file for a detailed approach of this package: 73 76 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]] 77 Let's just consider the current chapter as a reminder of the functioning of nesting tools. 75 78 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 79 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. 84 80 85 81 {{{ 86 87 82 #elisha 88 83 … … 92 87 93 88 The 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 || 99 94 100 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 95 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). 102 96 103 97 {{{ … … 108 102 }}} 109 103 110 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. 111 104 There 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. 112 105 113 106 {{{ … … 122 115 123 116 124 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]]117 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`. 125 118 119 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 : 126 120 127 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. 128 122 129 - 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]) 130 124 131 - 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]] 125 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. 132 126 133 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]] 127 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. 134 128 135 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 136 130 137 138 == 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 132 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. 142 133 143 134 {{{ 144 135 #elisha 145 136 146 147 137 cp namelist 1_namelist 148 138 cp namelist_ice 1_namelist_ice (if LIM is included in the configuration) 149 139 vi 1_namelist 150 151 140 }}} 152 141 153 142 Then 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. 154 143 155 || || 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 || 158 147 148 ''Most important namelist variables to edit. Example for a 1:3 time refinement ratio'' 159 149 160 ''Most important namelist variables to edit. Example for a 1:3 time refinement ratio''[[BR]] 150 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. 161 151 162 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]] 165 166 152 When using online interpolation, the forcing part of `1_namelist` will look like (here with core forcing): 167 153 168 154 {{{ … … 182 168 }}} 183 169 170 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. 184 171 185 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 189 173 output 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. 190 174 191 == Development Team==175 === Development Team 192 176 177 ||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 || 193 181 194 ||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 201 183 ??? 202 184 185 === 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 || 203 194 204 ==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)
