Changes between Version 33 and Version 34 of Users/SetupNewConfiguration
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- 2018-07-13T19:10:09+02:00 (6 years ago)
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Users/SetupNewConfiguration
v33 v34 1 {{{#!rst 2 3 ============================== 4 Setting up a new configuration 5 ============================== 6 7 Last edition: :code-block:`Wikinfo:changed_ts` by :code-block:`Wikinfo:changed_by` 8 9 .. contents:: Table of contents 10 11 ----------------------------- 12 Starting from an existing one 13 ----------------------------- 14 15 There are three options for creating new configurations based on an existing one: 16 17 Option 1: Duplicate an existing configuration 18 ============================================= 19 20 Create and compile a new configuration duplicating a reference configuration (ORCA_LIM3 21 in the following example) 22 23 .. code-block:: bash 24 25 makenemo –n 'ORCA_LIM3_MYCONFIG' -r ORCA_LIM3 26 27 Option 2: Duplicate with differences 28 ==================================== 29 30 Create and compile a new configuration based on a reference configuration (ORCA_LIM3 in 1 = Setting up a new configuration 2 3 [[PageOutline]] 4 [[BR]] 5 [[BR]] 6 [[BR]] 7 [[BR]] 8 [[BR]] 9 [[BR]] 10 [[BR]] 11 [[BR]] 12 [[BR]] 13 [[BR]] 14 [[BR]] 15 Last edition on '''[[Wikinfo(changed_ts)]]''' by '''[[Wikinfo(changed_by)]]''' 16 17 18 == Starting from an existing configuration 19 20 21 There are three options to build a new configuration from an existing one: 22 23 === Option 1: Duplicate an existing configuration 24 25 The NEMO so-called Reference Configurations [wiki:Users/ReferenceConfigurations list available here] cover a number of major features for NEMO setup (global, regional, 1D, using embeded zoom with AGRIF...) 26 27 One can create a new configuration by duplicating one of the reference configurations (ORCA2_LIM3_PISCES in the following example) 28 29 30 {{{ 31 makenemo –n 'ORCA2_LIM3_PISCES_MINE' -r ORCA2_LIM3_PISCES 32 }}} 33 34 35 === Option 2: Duplicate with differences 36 37 Create and compile a new configuration based on a reference configuration (ORCA2_LIM3_PISCES in 31 38 the following example) but with different pre-processor options. For this either add 32 39 (add_key) or remove (del_key) keys as required; e.g. 33 40 34 .. code-block:: bash 35 36 makenemo –n 'ORCA2_LIM3_MYCONFIG' -r ORCA2_LIM3 del_key 'key_iomput' add_key 'key_xios' 37 38 Option 3: Use the SIREN tools to subset an existing model 39 ========================================================= 41 42 {{{ 43 makenemo –n 'ORCA2_LIM3_PISCES_MINE' -r ORCA2_LIM3_PISCES del_key 'key_iomput' add_key 'key_xios' 44 }}} 45 46 === Option 3: Use the SIREN tools to subset an existing model 47 40 48 41 49 Define a regional configuration which is a sub- or super-set of an existing … … 50 58 configuration. As a basic demonstrator, a set of GLORYS files (GLObal ReanalYSis on the 51 59 ORCA025 grid), as well as examples of namelists are available 52 :trac:`[http://prodn.idris.fr/thredds/catalog/ipsl_public/rron463/catalog.html?dataset=DatasetScanipsl_public/rron463/INPUT_SIREN.tar here]`.53 54 :trac:`[/doxygen/index.html SIREN documentation]` 55 56 Any questions or comments regarding the use of SIREN should be posted in the corresponding57 :trac:`forum:2 forum`.58 59 --------------------------------------- 60 Creating a completely new configuration61 --------------------------------------- 60 [http://prodn.idris.fr/thredds/catalog/ipsl_public/rron463/catalog.html?dataset=DatasetScanipsl_public/rron463/INPUT_SIREN.tar here]`. 61 62 [/doxygen/index.html SIREN documentation] 63 64 Any questions or comments regarding the use of SIREN should be 65 [forum:2 posted in the corresponding forum]. 66 67 68 == Creating a completely new configuration 69 62 70 63 71 From NEMO version 4.0 there are two ways to build configurations from scratch. The … … 67 75 simple geometries and formulae. 68 76 69 Option 1: Create and use a domain configuration file70 ==================================================== 71 72 **1** Even whenstarting from scratch it is advisable to create the directory structure to77 === Option 1: Create and use a domain configuration file 78 79 This method is used by each of the reference configurations, so that [wiki:Users/ReferenceConfigurations downloading their input files linked to their description can help] 80 Although starting from scratch it is advisable to create the directory structure to 73 81 house your new configuration by duplicating the closest reference configuration to your 74 target application. For example, If your application requires both ocean and ice 75 components then run 76 77 .. code-block:: bash 78 79 makenemo –n 'MY_NEW_CONFIG' -r ORCA_LIM3 82 target application. For example, If your application requires both ocean ice and passive tracers, then use the ORCA2_LIM3_PISCES as template, and execute following command to build your MY_NEW_CONFIG configuration: 83 84 {{{ 85 makenemo –n 'MY_NEW_CONFIG' -r ORCA2_LIM3_PISCES 86 }}} 80 87 81 88 where ``'MY_NEW_CONFIG'`` can be substituted with a suitably descriptive name for your new 82 configuration. The purpose of this step is simply to create and populate the appropriate WORK, 89 configuration. 90 91 The purpose of this step is simply to create and populate the appropriate WORK, 83 92 MY_SRC and EXP00 subdirectories for your new configuration. Other choices for the base reference 84 93 configuration might be … … 86 95 * GYRE - If your target application is ocean-only 87 96 * AMM12 - If your target application is regional with open boundaries 88 * ORCA2_LIM_PISCES - If your target application requires ocean, sea-ice and passive tracers 89 90 **2** All the domain information for your new configuration will be contained within a netcdf 97 98 All the domain information for your new configuration will be contained within a netcdf 91 99 file called ``domain_cfg.nc`` which you will need to create and place in the 92 100 93 .. code-block:: bash 94 101 {{{ 95 102 NEMOGCM/CONFIG/'MY_NEW_CONFIG'/EXP00 96 103 }}} 97 104 sub-directory. Firstly though, ensure that your configuration is set to use such a file by 98 c onfirming that99 100 .. code-block:: fortran 101 105 checking that 106 107 108 {{{ 102 109 ln_read_cfg = .true. 103 110 }}} 104 111 in 105 106 .. code-block:: bash 107 112 {{{ 108 113 NEMOGCM/CONFIG/'MY_NEW_CONFIG'/EXP00/namelist_cfg 109 110 **3**Create the domain_cfg.nc file which must contain the following fields111 112 .. code-block:: cpp 113 114 }}} 115 ==== Create the domain_cfg.nc file which must contain the following fields 116 117 118 {{{ 114 119 int ORCA, ORCA_index /* configuration name, configuration resolution */ 115 120 int jpiglo, jpjglo, jpkglo /* global domain sizes */ … … 128 133 int bottom_level, top_level /* last wet T-points, 1st wet T-points (for ice shelf cavities) */ 129 134 130 135 }}} 131 136 There are two options for creating a domain_cfg.nc file: 132 137 … … 139 144 for details. 140 145 141 Option 2: Copy and modify user-defined configuration modules 142 ============================================================ 143 144 This method is intended for configuring easily defined idealised configurations which are 146 === Option 2: Adapt the usr_def configuration module of NEMO for you own purposes 147 148 This method is intended for configuring easily simple/idealised configurations which are 145 149 often used as demonstrators or for process evaluation and comparison. This method can be 146 150 used whenever the domain geometry has a simple mathematical description and the ocean 147 initial state and boundary forcing is described analytically. From version 4.0, the NEMO 148 release includes a ``TEST_CASES`` subdirectory of the reference ``CONFIG`` directory which 149 includes several examples and will, over time, include further user-contributed examples. 150 These will not necessarily be fully supported but should provide a source of raw material 151 and ideas for constructing your own examples. 152 153 For now, consider the case of starting a completely new ocean-only test case based on the 151 initial state and boundary forcing is described analytically. 152 As a start, consider the case of starting a completely new ocean-only test case based on the 154 153 LOCK_EXCHANGE example. [Note: we probably need an even more basic example than this with 155 154 only one namelist and minimal changes to the usrdef modules] … … 157 156 Firstly, construct the directory structure, starting in the ``CONFIG`` directory: 158 157 159 .. code-block:: bash 160 158 159 {{{ 161 160 ./makenemo -a TEST_CASES -n 'MY_NEW_TEST' -r LOCK_EXCHANGE 162 161 }}} 163 162 where the ``-a`` option has been used to locate the new configuration in the 164 163 ``TEST_CASES`` subdirectory (it is recommended practice to keep full configurations and … … 166 165 the following files and directories: 167 166 168 .. code-block:: bash 169 167 168 {{{ 170 169 TEST_CASES/'MY_NEW_TEST': 171 170 BLD MY_SRC cpp_MY_NEW_TEST.fcm … … 182 181 usrdef_hgr.F90 usrdef_nam.F90 usrdef_zgr.F90 183 182 usrdef_istate.F90 usrdef_sbc.F90 zdfini.F90 184 183 }}} 185 184 The key to setting up an idealised configuration lies in adapting a small set of short fortran90 186 185 modules which should be dropped into the MY_SRC directory. Here the LOCK_EXCHANGE example is using 187 186 5 such routines but the full set that is availablein the ``NEMO/OPA_SRC/USR`` directory is: 188 187 189 .. code-block:: bash 190 188 189 {{{ 191 190 ../NEMO/OPA_SRC/USR: 192 191 usrdef_closea.F90 usrdef_istate.F90 usrdef_zgr.F90 193 192 usrdef_fmask.F90 usrdef_nam.F90 194 193 usrdef_hgr.F90 usrdef_sbc.F90 194 }}} 195 195 196 196 Before discussing these in more detail it is worth noting the various namelist controls … … 202 202 activated whenever: 203 203 204 .. code-block:: fortran 205 204 205 {{{ 206 206 ln_read_cfg = .false. 207 207 }}} 208 208 in any configuration's ``namelist_cfg`` file. This setting also activates the reading of 209 209 an optional ``nam_usrdef`` namelist which can be used to supply configuration specific … … 212 212 Another explicit control is available in the ``namsbc`` namelist which activates the 213 213 use of analytical forcing. With 214 215 .. code-block:: fortran 216 214 {{{ 217 215 ln_usr = .true. 218 216 }}} 219 217 Other usrdef modules are activated by less explicit means. For example, code in 220 218 ``usrdef_istate.F90`` is used to define initial temperature and salinity fields if 221 222 .. code-block:: fortran 223 219 {{{ 224 220 ln_tsd_init = .false. 225 221 }}} 226 222 in the ``namtsd`` namelist. The remaining modules, namely 227 228 .. code-block:: bash 229 223 {{{ 230 224 usrdef_closea.F90 usrdef_fmask.F90 231 225 }}} 232 226 are specific to ORCA configurations and set local variations of some specific 233 227 fields for the various resolutions of the global models. They do not need to be … … 251 245 the initial state and the surface boundary conditions for your new configuration. 252 246 253 In summary, the base set of modules is:247 To summarize, the base set of modules is: 254 248 255 249 * usrdef_hgr.F90 : define horizontal grid … … 265 259 * usrdef_fmask.F90 : only used in ORCA CONFIGURATIONS for alteration of f-point land/ocean mask in some straits 266 260 * usrdef_closea.F90 : only used in ORCA CONFIGURATIONS for specific treatments associated with closed seas 267 }}} 261 262 From version 4.0, the NEMO 263 release includes a ``test`` subdirectory 264 containing available and up to date test cases build by the community . 265 These will not be fully supported as is NEMO reference but should provide a source of raw material.
