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Changeset 7235 – NEMO

Changeset 7235


Ignore:
Timestamp:
2016-11-16T11:40:55+01:00 (8 years ago)
Author:
jpaul
Message:

see ticket #1781

Location:
branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN
Files:
1 added
15 edited

Legend:

Unmodified
Added
Removed

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/README

    r7025 r7235  
    55   open ./TOOLS/SIREN/doc/html/index.html in your web browser 
    66or  
    7    run ./TOOLS/SIREN/doc/latex/gmake and open ./TOOLS/SIREN/doc/latex/refman.pdf  
     7   run gmake in ./TOOLS/SIREN/doc/latex directory and open ./TOOLS/SIREN/doc/latex/refman.pdf  

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/cfg/dummy.cfg

    r6393 r7235  
    11&namdum 
    2    cn_dumvar="" 
     2   cn_dumvar="orca_lon", "orca_lat", "time_instant", "time_centered" 
    33   cn_dumdim="" 
    44   cn_dumatt="history" 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/create_bathy.f90

    r7153 r7235  
    4646!>       - cn_varcfg : variable configuration file  
    4747!> (see ./SIREN/cfg/variable.cfg) 
    48 !>       - cn_dimcfg : dimension configuration file. define dimension allowed to 
    49 !> be used (see ./SIREN/cfg/dimension.cfg). 
     48!>       - cn_dimcfg : dimension configuration file. defines dimension allowed 
     49!> (see ./SIREN/cfg/dimension.cfg). 
    5050!>       - cn_dumcfg : useless (dummy) configuration file, for useless  
    5151!> dimension or variable (see ./SIREN/cfg/dummy.cfg). 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/create_boundary.F90

    r7153 r7235  
    5252!>       - cn_varcfg : variable configuration file 
    5353!> (see ./SIREN/cfg/variable.cfg) 
    54 !>       - cn_dimcfg : dimension configuration file. define dimension allowed to 
    55 !> be used (see ./SIREN/cfg/dimension.cfg). 
     54!>       - cn_dimcfg : dimension configuration file. define dimensions allowed 
     55!> (see ./SIREN/cfg/dimension.cfg). 
    5656!>       - cn_dumcfg : useless (dummy) configuration file, for useless  
    5757!> dimension or variable (see ./SIREN/cfg/dummy.cfg). 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/create_coord.f90

    r7153 r7235  
    4444!>       - cn_varcfg : variable configuration file  
    4545!> (see ./SIREN/cfg/variable.cfg) 
    46 !>       - cn_dimcfg : dimension configuration file. define dimension allowed to 
    47 !> be used (see ./SIREN/cfg/dimension.cfg). 
     46!>       - cn_dimcfg : dimension configuration file. define dimensions allowed  
     47!> (see ./SIREN/cfg/dimension.cfg). 
    4848!>       - cn_dumcfg : useless (dummy) configuration file, for useless  
    4949!> dimension or variable (see ./SIREN/cfg/dummy.cfg). 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/create_meshmask.f90

    r7233 r7235  
    4646!>       - partial step namelist (namzps) 
    4747!>       - sigma or hybrid namelist (namsco) 
    48 !       - cross land advection namelist (namcla) 
    4948!>       - lateral boundary condition namelist (namlbc) 
    5049!>       - wetting and dryong namelist (namwd) 
    5150!>       - grid namelist (namgrd) 
    52 !       - zoom namelist (namzoom) 
    5351!>       - output namelist (namout) 
    5452!> 
    … …  
    6159!>    * _config namelist (namcfg)_:<br/> 
    6260!>       - cn_varcfg : variable configuration file 
    63 !> (see ./SIREN/cfg/variable.cfg) 
     61!> (see ./SIREN/cfg/variable.cfg). 
     62!>       - cn_dimcfg : dimension configuration file. define dimensions allowed 
     63!> (see ./SIREN/cfg/dimension.cfg). 
    6464!>       - cn_dumcfg : useless (dummy) configuration file, for useless  
    6565!> dimension or variable (see ./SIREN/cfg/dummy.cfg). 
    … …  
    142142!>          - dn_zb_b      : Offset for Zb 
    143143!> 
    144 !    * _cross land advection namelist (namcla)_:<br/> 
    145 !       - in_cla : =1 cross land advection for exchanges through some straits (only for ORCA2) 
    146 ! 
    147144!>    * _lateral boundary condition namelist (namlbc)_:<br/> 
    148145!>       - rn_shlat : lateral boundary conditions at the coast (modify fmask) 
    … …  
    160157!>     
    161158!>    * _grid namelist (namgrd)_:<br/> 
    162 !       - cn_cfg    : name of the configuration 
    163159!>       - in_cfg    : inverse resolution of the configuration (1/4° => 4) 
    164160!>       - ln_bench  : GYRE (in_mshhgr = 5 ) used as Benchmark.<br/> 
    165161!>                     => forced the resolution to be about 100 km 
    166 !       - ln_zoom   : use zoom (namzoom) 
    167162!>       - ln_c1d    : use configuration 1D 
    168163!>       - ln_e3_dep : vertical scale factors =T: e3.=dk[depth] =F: old definition 
    169 ! 
    170 !    * _zoom namelist (namzoom)_:<br/> 
    171 !       - cn_cfz       : name of the zoom of configuration 
    172 !       - in_izoom     : left bottom i-indices of the zoom in data domain indices 
    173 !       - in_jzoom     : left bottom j-indices of the zoom in data domain indices 
    174 !       - ln_zoom_s    : South zoom type flag 
    175 !       - ln_zoom_e    : East  zoom type flag 
    176 !       - ln_zoom_w    : West  zoom type flag 
    177 !       - ln_zoom_n    : North zoom type flag 
    178 ! 
    179164!>    * _output namelist (namout)_:<br/> 
    180165!>       - cn_domcfg    : output file name 
    … …  
    185170!> 
    186171!>    @note 
    187 !>        if     in_msh == 0  : write '<b>domain_cfg.nc</b>' file 
    188 !>        MOD(in_msh, 3) = 1  :       '<b>mesh_mask.nc</b>' file 
    189 !>                       = 2  :       '<b>mesh.nc</b>' and '<b>mask.nc</b>' files 
    190 !>                       = 0  :       '<b>mesh_hgr.nc</b>', '<b>mesh_zgr.nc</b>' and '<b>mask.nc</b>' files 
    191 !> 
     172!>        - if         in_msh = 0  : write '**domain_cfg.nc**' file. 
     173!>        - if MOD(in_msh, 3) = 1  : write '<b>mesh_mask.nc</b>' file. 
     174!>        - if MOD(in_msh, 3) = 2  : write '<b>mesh.nc</b>' and '<b>mask.nc</b>' files. 
     175!>        - if MOD(in_msh, 3) = 0  : write '<b>mesh_hgr.nc</b>', '<b>mesh_zgr.nc</b>' and '<b>mask.nc</b>' files.<br/> 
    192176!>        For huge size domain, use option 2 or 3 depending on your vertical coordinate. 
    193 !> 
    194 !>        if     in_msh <= 3: write full 3D arrays for e3[tuvw] and gdep[tuvw] 
    195 !>        if 3 < in_msh <= 6: write full 3D arrays for e3[tuvw] and 2D arrays  
     177!>        - if     in_msh <= 3: write full 3D arrays for e3[tuvw] and gdep[tuvw] 
     178!>        - if 3 < in_msh <= 6: write full 3D arrays for e3[tuvw] and 2D arrays  
    196179!>                            corresponding to the depth of the bottom t- and w-points 
    197 !>        if 6 < in_msh <= 9: write 2D arrays corresponding to the depth and the 
     180!>        - if 6 < in_msh <= 9: write 2D arrays corresponding to the depth and the 
    198181!>                            thickness (e3[tw]_ps) of the bottom points 
    199182!> 
    … …  
    321304 
    322305   ! namlbc 
    323    REAL(sp)          :: rn_shlat    = -100. !2. 
     306   REAL(sp)          :: rn_shlat    = 2. 
    324307 
    325308   ! namout 
    … …  
    12771260CONTAINS 
    12781261   !------------------------------------------------------------------- 
    1279    !> @brief This subroutine compute land/ocean mask arrays at tracer points, hori- 
    1280    !>      zontal velocity points (u & v), vorticity points (f) and baro- 
    1281    !>      tropic stream function  points (b).  
     1262   !> @brief This subroutine compute land/ocean mask arrays at tracer points,  
     1263   !>      horizontal velocity points (u & v), vorticity points (f) and  
     1264   !>      barotropic stream function  points (b).  
    12821265   !> 
    12831266   !> @details 
    12841267   !> 
    1285    !> ** Method  :   The ocean/land mask is computed from the basin bathy- 
    1286    !>      metry in level (mbathy) which is defined or read in dommba. 
    1287    !>      mbathy equals 0 over continental T-point  
    1288    !>      and the number of ocean level over the ocean. 
     1268   !> ** Method  :   The ocean/land mask is computed from the basin bathymetry in level (mbathy) which is defined or read in dommba. 
     1269   !>      mbathy equals 0 over continental T-point and the number of ocean level over the ocean. 
    12891270   !> 
    12901271   !>      At a given position (ji,jj,jk) the ocean/land mask is given by: 
    1291    !>      t-point : 0. IF mbathy( ji ,jj) =< 0 
    1292    !>                1. IF mbathy( ji ,jj) >= jk 
    1293    !>      u-point : 0. IF mbathy( ji ,jj)  or mbathy(ji+1, jj ) =< 0 
    1294    !>                1. IF mbathy( ji ,jj) and mbathy(ji+1, jj ) >= jk. 
    1295    !>      v-point : 0. IF mbathy( ji ,jj)  or mbathy( ji ,jj+1) =< 0 
    1296    !>                1. IF mbathy( ji ,jj) and mbathy( ji ,jj+1) >= jk. 
    1297    !>      f-point : 0. IF mbathy( ji ,jj)  or mbathy( ji ,jj+1) 
    1298    !>                   or mbathy(ji+1,jj)  or mbathy(ji+1,jj+1) =< 0 
    1299    !>                1. IF mbathy( ji ,jj) and mbathy( ji ,jj+1) 
    1300    !>                  and mbathy(ji+1,jj) and mbathy(ji+1,jj+1) >= jk. 
    1301    !>      b-point : the same definition as for f-point of the first ocean 
     1272   !>      - t-point :  
     1273   !>             - 0. IF mbathy( ji ,jj) =< 0 
     1274   !>             - 1. IF mbathy( ji ,jj) >= jk 
     1275   !>      - u-point :  
     1276   !>             - 0. IF mbathy( ji ,jj)  or mbathy(ji+1, jj ) =< 0 
     1277   !>             - 1. IF mbathy( ji ,jj) and mbathy(ji+1, jj ) >= jk. 
     1278   !>      - v-point :  
     1279   !>             - 0. IF mbathy( ji ,jj)  or mbathy( ji ,jj+1) =< 0 
     1280   !>             - 1. IF mbathy( ji ,jj) and mbathy( ji ,jj+1) >= jk. 
     1281   !>      - f-point :  
     1282   !>             - 0. IF mbathy( ji ,jj)  or mbathy( ji ,jj+1) or mbathy(ji+1,jj)  or mbathy(ji+1,jj+1) =< 0 
     1283   !>             - 1. IF mbathy( ji ,jj) and mbathy( ji ,jj+1) and mbathy(ji+1,jj) and mbathy(ji+1,jj+1) >= jk. 
     1284   !>      - b-point : the same definition as for f-point of the first ocean 
    13021285   !>                level (surface level) but with 0 along coastlines. 
    1303    !>      tmask_i : interior ocean mask at t-point, i.e. excluding duplicated 
     1286   !>      - tmask_i : interior ocean mask at t-point, i.e. excluding duplicated 
    13041287   !>                rows/lines due to cyclic or North Fold boundaries as well 
    13051288   !>                as MPP halos. 
    13061289   !> 
    1307    !>   @WARNING do not set the lateral friction through the value of fmask along 
     1290   !> @warning do not set the lateral friction through the value of fmask along 
    13081291   !>      the coast and topography.  
    13091292   !> 
    1310    !>      N.B. If nperio not equal to 0, the land/ocean mask arrays 
     1293   !> @note If nperio not equal to 0, the land/ocean mask arrays 
    13111294   !>      are defined with the proper value at lateral domain boundaries, 
    13121295   !>      but bmask. indeed, bmask defined the domain over which the 
    … …  
    13221305   !>        - bmask is  set to 0 on the open boundaries. 
    13231306   !> 
    1324    !> ** Action :   tmask    : land/ocean mask at t-point (=0. or 1.) 
    1325    !>               umask    : land/ocean mask at u-point (=0. or 1.) 
    1326    !>               vmask    : land/ocean mask at v-point (=0. or 1.) 
    1327    !>               fmask    : land/ocean mask at f-point (=0. or 1.) 
    1328    !>               bmask    : land/ocean mask at barotropic stream 
    1329    !>                          function point (=0. or 1.) and set to 0 along lateral boundaries 
    1330    !>               tmask_i  : interior ocean mask 
     1307   !> ** Action :    
     1308   !>       - tmask    : land/ocean mask at t-point (=0. or 1.) 
     1309   !>       - umask    : land/ocean mask at u-point (=0. or 1.) 
     1310   !>       - vmask    : land/ocean mask at v-point (=0. or 1.) 
     1311   !>       - fmask    : land/ocean mask at f-point (=0. or 1.) 
     1312   !>       - bmask    : land/ocean mask at barotropic stream 
     1313   !>                  function point (=0. or 1.) and set to 0 along lateral boundaries 
     1314   !>       - tmask_i  : interior ocean mask 
    13311315   !> 
    13321316   !> @author J.Paul 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/create_restart.f90

    r7153 r7235  
    4848!>       - cn_varcfg : variable configuration file 
    4949!> (see ./SIREN/cfg/variable.cfg) 
    50 !>       - cn_dimcfg : dimension configuration file. define dimension allowed to 
    51 !> be used (see ./SIREN/cfg/dimension.cfg). 
     50!>       - cn_dimcfg : dimension configuration file. define dimensions allowed 
     51!> (see ./SIREN/cfg/dimension.cfg). 
    5252!>       - cn_dumcfg : useless (dummy) configuration file, for useless  
    5353!> dimension or variable (see ./SIREN/cfg/dummy.cfg). 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md

    r7025 r7235  
    1616 This break may cause inconsistency between forcing fields  at boundary and regional fields. 
    1717 </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> 
    1919 <li>create_restart.f90 to create initial state file from coarse grid restart 
    2020 or standard outputs. 
    … …  
    3636Here after we briefly describe how to use each programs, 
    3737and 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). 
    3939 
    4040<!-- ######################################################################  --> 
    … …  
    6060&namcfg 
    6161   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     62   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    6263/ 
    6364 
    … …  
    9192empty, as done here.<br/> This will create a log file named *create_coord.log* 
    9293 
    93 The **namcfg** sub-namelist defines where found SIREN configuration file.<br/> 
    94 This configuration file defines standard name, default interpolation method, 
     94The **namcfg** sub-namelist defines where found SIREN configuration files.<br/> 
     95- The variable configuration file defines standard name, default interpolation method, 
    9596axis,... to be used for some known variables.<br/> 
    9697Obviously, 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*. 
    99101 
    100102The **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/> 
     103coordinates file, as path to find it, and NEMO periodicity of the wide grid.<br/> 
    102104 
    103105@note the NEMO periodicity could be choose between 0 to 6: 
    … …  
    219221&namcfg 
    220222   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     223   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    221224/ 
    222225 
    … …  
    253256coordinates file.<br/> 
    254257@note in all SIREN namelist: <br/> 
    255 0 referred to the coarse/wide grid.<br/> 
    256 1 referred to the fine grid. 
     258**0** referred to the coarse/wide grid.<br/> 
     259**1** referred to the fine grid. 
    257260 
    258261In the same way, the **namfin** sub-namelist  set parameters of the fine 
    259262coordinates file.<br/> 
    260263@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 to 
     264periodicity of the fine grid. Indeed, if this variable is not inform, SIREN tries to read it  
     265in the global attributes of the file. So if you created the fine coordinates with SIREN, you do not have to 
    263266fill it. In other case, you should add it to the namelist. 
    264267 
    … …  
    300303# Merge bathymetry file # {#merge} 
    301304 
    302 The Bathymetry you build differs from the wider one.<br/> 
     305The Bathymetry you build, may differ from the wider one.<br/> 
    303306To avoid issue with boundaries forcing fields, you should merge fine and coarse Bathymetry on boundaries.<br/> 
    304307SIREN allows you to do this.<br/> 
    … …  
    316319&namcfg 
    317320   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     321   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    318322/ 
    319323 
    … …  
    352356 
    353357The **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  
     358By 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. 
    357359@sa For more information about boundaries, see @ref boundary 
    358360 
    … …  
    366368 
    367369 
    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 : 
     370Depending 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/> 
     371Morevoer SIREN allows you to create the *domain_cfg* file which is the new input file for NEMO (release 3.7 and upper).<br/> 
     372 
     373To create the meshmask file(s), you have to run : 
    371374~~~~~~~~~~~~~~~~~~ 
    372375./SIREN/create_meshmask.exe create_meshmask.nam 
    … …  
    384387&namcfg 
    385388   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     389   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    386390/ 
    387391 
    … …  
    427431/ 
    428432 
    429 &namcla 
    430 / 
    431  
    432433&namlbc 
    433434/ 
    … …  
    437438 
    438439&namgrd 
    439 / 
    440  
    441 &namzoom 
    442440/ 
    443441 
    … …  
    454452Mainly SIREN need Bathymetry to create meshmask. 
    455453Here 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 
     456Bathymetry was not created by SIREN. 
     457 2. by default SIREN suppress closed sea/lake from the ORCA domain. 
     458 
    459459 
    460460The **namhgr** sub-namelist defines the horizontal grid. 
    … …  
    470470The **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. 
    471471 
    472 The **namdmin** sub-namelist dfines the minimum ocean depth. It could be defines in meter (>0) or in number of level (<0). 
    473  
    474 The **namzco** sub-namelist defines respectively parameters to compute z-coordinate vertical grid (**needed for all type of vertical grid**) 
     472The **namdmin** sub-namelist defines the minimum ocean depth. It could be defines in meter (>0) or in number of level (<0). 
     473 
     474The **namzco** sub-namelist defines parameters to compute z-coordinate vertical grid (**needed for all type of vertical grid**) 
    475475<!-- By default, those parameters are defined the same way than in GLORYS (i.e. 75 vertical levels).<br/> --> 
    476476 
    … …  
    479479The **namsco** sub-namelist defines extra parameters needed to define sigma or hybrid coordinates (not needed here). 
    480480 
    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).--> 
    482482 
    483483The **namlbc** sub-namelist defines lateral boundary conditions at the coast. It is needed to modify the fmask. 
    … …  
    485485The **namwd** sub-namelist defines the wetting and drying parameters if activated (see namzgr sub-namelist) 
    486486 
    487 The **namgrd** and **namzoom** sub-namelists define grid configuration. Those namelist only activated local correction. 
     487The **namgrd** sub-namelist allows to use configuration 1D or to choose vertical scale factors (e3.=dk or old definition). 
    488488 
    489489Finally, 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**. 
    490491 
    491492@sa For more information about how to create meshmask, see create_meshmask.f90 
    … …  
    498499time step). Or you could start from "partial" information about ocean state (Temperature and Salinity for example). 
    499500 
    500 Siren allows you to create both of those initial state.<br/> 
     501SIREN allows you to create both of those initial state.<br/> 
    501502To create the initial state, you have to run:<br/> 
    502503~~~~~~~~~~~~~~~~~~ 
    … …  
    505506 
    506507Here 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/> 
     508In this example, you create an initial state split on 81 "processors", and named restart_out.nc.<br/> 
    508509The initial state is composed of temperature and salinity refined from an extraction of GLORYS fields. 
    509510~~~~~~~~~~~~~~~~~~ 
    … …  
    513514&namcfg 
    514515   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     516   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    515517/ 
    516518 
    … …  
    612614&namcfg 
    613615   cn_varcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/variable.cfg" 
     616   cn_dimcfg = "PATH/NEMOGCM/TOOLS/SIREN/cfg/dimension.cfg" 
    614617/ 
    615618 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/docsrc/5_changeLog.md

    r7153 r7235  
    77## New Features 
    88- create_meshmask.f90 program to create meshmask from coordinates and bathymetry files. 
    9 - create_meshmask.f90 allows to write domain_cfg file 
     9- create_meshmask.f90 allows to write domain_cfg file. 
    1010- merge_bathy.f90: allow to choose the number of boundary point with coarse grid value. 
    1111- dimension.f90: dimension allowed read in configuration file. 
     12- variable.f90: allow to add scalar value. 
     13- create_meshmask.f90: choose vertical scale factors (e3.=dk[depth] or old definition). 
    1214## Changes 
    1315- create_coord.f90: allow to define sub domain with coarse grid indices or coordinates. 
    1416- grid.f90:grid__get_closest_str: add function to get closest grid point using coarse grid coordinates strucutre. 
    15 - iom_cdf.f90:iom_cdf__get_info: define cdf4 as cdf 
     17- iom_cdf.f90:iom_cdf__get_info: define cdf4 as cdf. 
    1618- variable.f90: add subroutine to clean global array of extra information, and define logical for variable to be used. 
    17 - create_coord.f90: dimension to be used select from configuration file 
    18 - create_bathy.f90: dimension to be used select from configuration file 
    19 - merge_bathy.f90: dimension to be used select from configuration file 
    20 - create_boundary.f90: dimension to be used select from configuration file 
    21 - create_restart.f90: dimension to be used select from configuration file 
     19- create_coord.f90: dimension to be used select from configuration file. 
     20- create_bathy.f90: dimension to be used select from configuration file. 
     21- merge_bathy.f90: dimension to be used select from configuration file. 
     22- create_boundary.f90: dimension to be used select from configuration file. 
     23- create_restart.f90: dimension to be used select from configuration file. 
    2224## Bug fixes 
    23 - boundary.f90:boundary_check: take into account that boundaries are compute on T point, but expressed on U,V point 
    24 - grid.f90:grid__get_closest_str: use max of zero and east-west overlap instead of east-west overlap 
     25- boundary.f90:boundary_check: take into account that boundaries are compute on T point, but expressed on U,V point. 
     26- grid.f90:grid__get_closest_str: use max of zero and east-west overlap instead of east-west overlap. 
     27- mpp.f90: compare index to td_lay number of proc instead of td_mpp (bug fix) . 
    2528 
    2629# Initial Release 2016-03-17 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/docsrc/main.dox

    r7025 r7235  
    1414 - see create_bathy.f90 to create fine grid bathymetry 
    1515 - see merge_bathy.f90 to merge fine grid bathymetry 
    16  - see create_meshmask.f90 to create mesh mask grid 
     16 - see create_meshmask.f90 to create mesh mask or domain_cfg file. 
    1717 - see create_restart.f90 to create initial state file, or other fields. 
    1818 - see create_boundary.F90 to create boundary condition 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/grid.f90

    r7153 r7235  
    17341734 
    17351735               IF( TRIM(td_var%c_stdname) == 'longitude' .OR. & 
    1736                  & SCAN(TRIM(td_var%c_longname), 'longitude') == 0 )THEN 
     1736                 & SCAN( TRIM(td_var%c_longname), 'longitude') == 0 )THEN 
    17371737                  WHERE( dl_value(:,:) > 180._dp .AND. & 
    17381738                  &      dl_value(:,:) /= td_var%d_fill )  

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/grid_hgr.f90

    r7233 r7235  
    1414!> 
    1515!> ** Method  :   The geographical position of the model grid-points is 
    16 !>      defined from analytical functions, fslam and fsphi, the deriva- 
    17 !>      tives of which gives the horizontal scale factors e1,e2. 
    18 !>      Defining two function fslam and fsphi and their derivatives in  
    19 !>      the two horizontal directions (fse1 and fse2), the model grid- 
    20 !>      point position and scale factors are given by: 
    21 !>         t-point:<br/> 
    22 !>      glamt(i,j) = fslam(i    ,j    )   e1t(i,j) = fse1(i    ,j    )<br/> 
    23 !>      gphit(i,j) = fsphi(i    ,j    )   e2t(i,j) = fse2(i    ,j    )<br/> 
    24 !>         u-point:<br/> 
    25 !>      glamu(i,j) = fslam(i+1/2,j    )   e1u(i,j) = fse1(i+1/2,j    )<br/> 
    26 !>      gphiu(i,j) = fsphi(i+1/2,j    )   e2u(i,j) = fse2(i+1/2,j    )<br/> 
    27 !>         v-point:<br/> 
    28 !>      glamv(i,j) = fslam(i    ,j+1/2)   e1v(i,j) = fse1(i    ,j+1/2)<br/> 
    29 !>      gphiv(i,j) = fsphi(i    ,j+1/2)   e2v(i,j) = fse2(i    ,j+1/2)<br/> 
    30 !>            f-point:<br/> 
    31 !>      glamf(i,j) = fslam(i+1/2,j+1/2)   e1f(i,j) = fse1(i+1/2,j+1/2)<br/> 
    32 !>      gphif(i,j) = fsphi(i+1/2,j+1/2)   e2f(i,j) = fse2(i+1/2,j+1/2)<br/> 
    33 !>      Where fse1 and fse2 are defined by:<br/> 
    34 !>         fse1(i,j) = ra * rad * SQRT( (cos(phi) di(fslam))**2 
    35 !>                                     +          di(fsphi) **2 )(i,j)<br/> 
    36 !>         fse2(i,j) = ra * rad * SQRT( (cos(phi) dj(fslam))**2 
    37 !>                                     +          dj(fsphi) **2 )(i,j)<br/> 
     16!>    defined from analytical functions, fslam and fsphi, the derivatives of which gives the horizontal scale factors e1,e2. 
     17!>    Defining two function fslam and fsphi and their derivatives in the two horizontal directions (fse1 and fse2),  
     18!>    the model grid-point position and scale factors are given by: 
     19!>    - t-point: 
     20!>       - glamt(i,j) = fslam(i    ,j    )   e1t(i,j) = fse1(i    ,j    ) 
     21!>       - gphit(i,j) = fsphi(i    ,j    )   e2t(i,j) = fse2(i    ,j    ) 
     22!>    - u-point: 
     23!>       - glamu(i,j) = fslam(i+1/2,j    )   e1u(i,j) = fse1(i+1/2,j    ) 
     24!>       - gphiu(i,j) = fsphi(i+1/2,j    )   e2u(i,j) = fse2(i+1/2,j    ) 
     25!>    - v-point: 
     26!>       - glamv(i,j) = fslam(i    ,j+1/2)   e1v(i,j) = fse1(i    ,j+1/2) 
     27!>       - gphiv(i,j) = fsphi(i    ,j+1/2)   e2v(i,j) = fse2(i    ,j+1/2) 
     28!>    - f-point: 
     29!>       - glamf(i,j) = fslam(i+1/2,j+1/2)   e1f(i,j) = fse1(i+1/2,j+1/2) 
     30!>       - gphif(i,j) = fsphi(i+1/2,j+1/2)   e2f(i,j) = fse2(i+1/2,j+1/2) 
    3831!> 
    39 !>        The coriolis factor is given at z-point by:<br/> 
    40 !>                     ff = 2.*omega*sin(gphif)      (in s-1)<br/> 
     32!>    Where fse1 and fse2 are defined by: 
     33!>       - fse1(i,j) = ra * rad * SQRT( (cos(phi) di(fslam))**2 
     34!>                                     +          di(fsphi) **2 )(i,j) 
     35!>       - fse2(i,j) = ra * rad * SQRT( (cos(phi) dj(fslam))**2 
     36!>                                     +          dj(fsphi) **2 )(i,j) 
     37!> 
     38!>    The coriolis factor is given at z-point by: 
     39!>        - ff = 2.*omega*sin(gphif)      (in s-1)<br/> 
    4140!> 
    4241!>        This routine is given as an example, it must be modified 
    … …  
    4645!>      second order accuracy schemes. 
    4746!> 
    48 !> N.B. If the domain is periodic, verify that scale factors are also 
     47!> @note If the domain is periodic, verify that scale factors are also 
    4948!>      periodic, and the coriolis term again. 
    5049!> 
    51 !> ** Action  : - define  glamt, glamu, glamv, glamf: longitude of t-,  
    52 !>                u-, v- and f-points (in degre) 
    53 !>              - define  gphit, gphiu, gphiv, gphit: latitude  of t-, 
    54 !>               u-, v-  and f-points (in degre) 
    55 !>        define e1t, e2t, e1u, e2u, e1v, e2v, e1f, e2f: horizontal 
    56 !>      scale factors (in meters) at t-, u-, v-, and f-points. 
    57 !>        define ff: coriolis factor at f-point 
     50!> ** Action  :  
     51!>    - define  glamt, glamu, glamv, glamf: longitude of t-, u-, v- and f-points (in degre) 
     52!>    - define  gphit, gphiu, gphiv, gphit: latitude  of t-, u-, v-  and f-points (in degre) 
     53!>    - define e1t, e2t, e1u, e2u, e1v, e2v, e1f, e2f: horizontal 
     54!>    - scale factors (in meters) at t-, u-, v-, and f-points. 
     55!>    - define ff: coriolis factor at f-point 
    5856!> 
    5957!> References :   Marti, Madec and Delecluse, 1992, JGR 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/grid_zgr.f90

    r7233 r7235  
    1212!>              vertical scale factors. 
    1313!> 
    14 !> ** Method  : - reference 1D vertical coordinate (gdep._1d, e3._1d) 
    15 !>              - read/set ocean depth and ocean levels (bathy, mbathy) 
    16 !>              - vertical coordinate (gdep., e3.) depending on the  
    17 !>                coordinate chosen : 
    18 !>                   ln_zco=T   z-coordinate    
    19 !>                   ln_zps=T   z-coordinate with partial steps 
    20 !>                   ln_zco=T   s-coordinate  
     14!> ** Method  :  
     15!>    - reference 1D vertical coordinate (gdep._1d, e3._1d) 
     16!>    - read/set ocean depth and ocean levels (bathy, mbathy) 
     17!>    - vertical coordinate (gdep., e3.) depending on the coordinate chosen : 
     18!>       - ln_zco=T   z-coordinate    
     19!>       - ln_zps=T   z-coordinate with partial steps 
     20!>       - ln_zco=T   s-coordinate  
    2121!> 
    2222!> ** Action  :   define gdep., e3., mbathy and bathy 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/merge_bathy.f90

    r7153 r7235  
    5151!>       - cn_varcfg : variable configuration file  
    5252!> (see ./SIREN/cfg/variable.cfg) 
    53 !>       - cn_dimcfg : dimension configuration file. define dimension allowed to 
    54 !> be used (see ./SIREN/cfg/dimension.cfg). 
     53!>       - cn_dimcfg : dimension configuration file. define dimensions allowed 
     54!> (see ./SIREN/cfg/dimension.cfg). 
    5555!>       - cn_dumcfg : useless (dummy) configuration file, for useless  
    5656!> dimension or variable (see ./SIREN/cfg/dummy.cfg). 

  • branches/2016/dev_r6999_CONFIGMAN_1/NEMOGCM/TOOLS/SIREN/src/variable.f90

    r7233 r7235  
    72437243   !> @brief 
    72447244   !> This subroutine read matrix value from character string in namelist 
    7245    !> and fill variable strucutre value. 
     7245   !> and fill variable structure value. 
    72467246   !> 
    72477247   !> @details 
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