Changeset 7235 for branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md
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- 2016-11-16T11:40:55+01:00 (7 years ago)
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branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md
r7025 r7235 16 16 This break may cause inconsistency between forcing fields at boundary and regional fields. 17 17 </li> 18 <li>create_meshmask.f90 to create meshmask file(s) which contain(s) all the ocean domain informations.</li>18 <li>create_meshmask.f90 to create meshmask or domain_cfg file(s) which contain(s) all the ocean domain informations.</li> 19 19 <li>create_restart.f90 to create initial state file from coarse grid restart 20 20 or standard outputs. … … 36 36 Here after we briefly describe how to use each programs, 37 37 and so how to create your own regional configuration. 38 @note As demonstrator for a first start a set of GLORYS files (global reanalysis on *ORCA025* grid), as well as examples of namelists are available [here](https://cloud.mercator-ocean.fr/public.php?service=files&t= 877fb1b6e4f589340fc0df1ea6a53228).38 @note As demonstrator for a first start a set of GLORYS files (global reanalysis on *ORCA025* grid), as well as examples of namelists are available [here](https://cloud.mercator-ocean.fr/public.php?service=files&t=f2a19864f95f1944a51851479b627e2e). 39 39 40 40 <!-- ###################################################################### --> … … 60 60 &namcfg 61 61 cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 62 cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 62 63 / 63 64 … … 91 92 empty, as done here.<br/> This will create a log file named *create_coord.log* 92 93 93 The **namcfg** sub-namelist defines where found SIREN configuration file .<br/>94 Thisconfiguration file defines standard name, default interpolation method,94 The **namcfg** sub-namelist defines where found SIREN configuration files.<br/> 95 - The variable configuration file defines standard name, default interpolation method, 95 96 axis,... to be used for some known variables.<br/> 96 97 Obviously, you could add other variables to those already list, in this file. 97 98 @note You could find the generic version of *variable.cfg* in the directory *NEMOGCM/TOOLS/SIREN/cfg*. 98 - The dimension configuration file defines dimensions allowed. 99 100 @note You could find the generic version of those configuration files in the directory *NEMOGCM/TOOLS/SIREN/cfg*. 99 101 100 102 The **namcrs** sub-namelist set parameters of the wide 101 coordinates file, <br/>as path to find it, and NEMO periodicity of the wide grid.<br/>103 coordinates file, as path to find it, and NEMO periodicity of the wide grid.<br/> 102 104 103 105 @note the NEMO periodicity could be choose between 0 to 6: … … 219 221 &namcfg 220 222 cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 223 cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 221 224 / 222 225 … … 253 256 coordinates file.<br/> 254 257 @note in all SIREN namelist: <br/> 255 0referred to the coarse/wide grid.<br/>256 1referred to the fine grid.258 **0** referred to the coarse/wide grid.<br/> 259 **1** referred to the fine grid. 257 260 258 261 In the same way, the **namfin** sub-namelist set parameters of the fine 259 262 coordinates file.<br/> 260 263 @note in this namelist example, there is no need to set the variable *in_perio1* to define the NEMO 261 periodicity of the fine grid. <br/> Indeed, if this variable is not inform, SIREN tries to read it in the attributes of the file.<br/>262 So if you created the fine coordinates with SIREN, you do not have to264 periodicity of the fine grid. Indeed, if this variable is not inform, SIREN tries to read it 265 in the global attributes of the file. So if you created the fine coordinates with SIREN, you do not have to 263 266 fill it. In other case, you should add it to the namelist. 264 267 … … 300 303 # Merge bathymetry file # {#merge} 301 304 302 The Bathymetry you build differsfrom the wider one.<br/>305 The Bathymetry you build, may differ from the wider one.<br/> 303 306 To avoid issue with boundaries forcing fields, you should merge fine and coarse Bathymetry on boundaries.<br/> 304 307 SIREN allows you to do this.<br/> … … 316 319 &namcfg 317 320 cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 321 cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 318 322 / 319 323 … … 352 356 353 357 The **nambdy** sub-namelist defines the subdomain boundaries.<br/> 354 By default SIREN tries to create boundaries for each side. Boundary exist if there is at least one sea point on the second row of each side.<br/> 355 So you could let this namelist empty. 356 358 By default SIREN tries to create boundaries for each side. Boundary exist if there is at least one sea point on the second row of each side. So you could let this namelist empty. 357 359 @sa For more information about boundaries, see @ref boundary 358 360 … … 366 368 367 369 368 Depending on the vertical grid you choose to use, NEMO may not see the bathymetry as you defined it just before. To get the ocean domain informations as seen by NEMO, SIREN allows you to create the meshmask file(s) which contain(s) all those informations. 369 370 To create this new meshmask file(s), you have to run : 370 Depending on the vertical grid you choose to use, NEMO may not see the bathymetry exactly as you defined it just before. To get the ocean domain informations as seen by NEMO, SIREN allows you to create the meshmask file(s) which contain(s) all those informations.<br/> 371 Morevoer SIREN allows you to create the *domain_cfg* file which is the new input file for NEMO (release 3.7 and upper).<br/> 372 373 To create the meshmask file(s), you have to run : 371 374 ~~~~~~~~~~~~~~~~~~ 372 375 ./SIREN/create_meshmask.exe create_meshmask.nam … … 384 387 &namcfg 385 388 cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 389 cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 386 390 / 387 391 … … 427 431 / 428 432 429 &namcla430 /431 432 433 &namlbc 433 434 / … … 437 438 438 439 &namgrd 439 /440 441 &namzoom442 440 / 443 441 … … 454 452 Mainly SIREN need Bathymetry to create meshmask. 455 453 Here we also read coordinates directly on a file. 456 @note here again you could add the *in_perio* parameter if need be i.e. if your 457 Bathymetry was not created by SIREN.<br/> 458 @note By default SIREN suppress closed sea/lake from the ORCA domain. 454 @note 455 1. here again you could add the *in_perio* parameter if need be i.e. if your 456 Bathymetry was not created by SIREN. 457 2. by default SIREN suppress closed sea/lake from the ORCA domain. 458 459 459 460 460 The **namhgr** sub-namelist defines the horizontal grid. … … 470 470 The **namzgr** sub-namelist allows to choose the type of vertical grid (z-coordinate full steps, partial steps, sigma or hybrid coordinates) and the number of level. 471 471 472 The **namdmin** sub-namelist d fines the minimum ocean depth. It could be defines in meter (>0) or in number of level (<0).473 474 The **namzco** sub-namelist defines respectivelyparameters to compute z-coordinate vertical grid (**needed for all type of vertical grid**)472 The **namdmin** sub-namelist defines the minimum ocean depth. It could be defines in meter (>0) or in number of level (<0). 473 474 The **namzco** sub-namelist defines parameters to compute z-coordinate vertical grid (**needed for all type of vertical grid**) 475 475 <!-- By default, those parameters are defined the same way than in GLORYS (i.e. 75 vertical levels).<br/> --> 476 476 … … 479 479 The **namsco** sub-namelist defines extra parameters needed to define sigma or hybrid coordinates (not needed here). 480 480 481 The **namcla** sub-namelist defines cross land advection for exchanges through some straits only used for ORCA2 (see namgrd). 481 <!--The **namcla** sub-namelist defines cross land advection for exchanges through some straits only used for ORCA2 (see namgrd).--> 482 482 483 483 The **namlbc** sub-namelist defines lateral boundary conditions at the coast. It is needed to modify the fmask. … … 485 485 The **namwd** sub-namelist defines the wetting and drying parameters if activated (see namzgr sub-namelist) 486 486 487 The **namgrd** and **namzoom** sub-namelists define grid configuration. Those namelist only activated local correction.487 The **namgrd** sub-namelist allows to use configuration 1D or to choose vertical scale factors (e3.=dk or old definition). 488 488 489 489 Finally, this **namout** sub-namelist defines the number output file(s).<br/> 490 @note To create the domain_cfg file, you should put **in_msh=0**. 490 491 491 492 @sa For more information about how to create meshmask, see create_meshmask.f90 … … 498 499 time step). Or you could start from "partial" information about ocean state (Temperature and Salinity for example). 499 500 500 S irenallows you to create both of those initial state.<br/>501 SIREN allows you to create both of those initial state.<br/> 501 502 To create the initial state, you have to run:<br/> 502 503 ~~~~~~~~~~~~~~~~~~ … … 505 506 506 507 Here after is an example of namelist for *create_restart.exe*.<br/> 507 In this example, you create an initial state split on 81 "processors", and named restar _out.nc.<br/>508 In this example, you create an initial state split on 81 "processors", and named restart_out.nc.<br/> 508 509 The initial state is composed of temperature and salinity refined from an extraction of GLORYS fields. 509 510 ~~~~~~~~~~~~~~~~~~ … … 513 514 &namcfg 514 515 cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 516 cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 515 517 / 516 518 … … 612 614 &namcfg 613 615 cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 616 cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 614 617 / 615 618
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