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Changeset 7492 for branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS – NEMO

Ignore:
Timestamp:
2016-12-13T17:45:59+01:00 (7 years ago)
Author:
timgraham
Message:

Final merge of head of v3.6 STABLE branch into this branch

Location:
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS
Files:
1 deleted
16 edited
2 copied

Legend:

Unmodified
Added
Removed

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/NESTING/agulhas

    r7491 r7492  
    4141    N  = 31 
    4242    ldbletanh   = .FALSE. 
    43     ppa2        = 0.0 
     43    pa2         = 0.0 
    4444    ppkth2      = 0.0 
    4545    ppacr2      = 0.0 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/NESTING/src/agrif_types.f90

    r7491 r7492  
    7676  NAMELIST /nesting/imin,imax,jmin,jmax,rho,rhot,bathy_update,updated_parent_file       
    7777  ! 
    78   NAMELIST /vertical_grid/ppkth,ppacr,ppdzmin,pphmax,psur,pa0,pa1,N,ldbletanh,ppa2,ppkth2,ppacr2 
     78  NAMELIST /vertical_grid/ppkth,ppacr,ppdzmin,pphmax,psur,pa0,pa1,N,ldbletanh,pa2,ppkth2,ppacr2 
    7979  !  
    8080  NAMELIST /partial_cells/partial_steps,parent_bathy_meter,parent_batmet_name,e3zps_min,e3zps_rat       

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/REBUILD_NEMO/icb_combrest.py

    r7491 r7492  
    169169    sys.exit(15) 
    170170  fo = Dataset(pathout, 'w') 
    171   for dim in ['x','y','c']: 
     171  for dim in ['x','y','c','k']: 
    172172    indim = fi.dimensions[dim] 
    173173    fo.createDimension(dim, len(indim)) 
    174   for var in ['calving','calving_hflx','stored_ice','stored_heat']: 
     174  for var in ['kount','calving','calving_hflx','stored_ice','stored_heat']: 
    175175    invar = fi.variables[var] 
    176176    fo.createVariable(var, invar.datatype, invar.dimensions) 
    177177    fo.variables[var][:] = invar[:] 
    178     fo.variables[var].long_name = invar.long_name 
    179     fo.variables[var].units = invar.units 
    180     os.remove(pathout.replace('.nc','_WORK.nc')) 
     178    if "long_name" in invar.ncattrs(): 
     179        fo.variables[var].long_name = invar.long_name 
     180    if "units" in invar.ncattrs(): 
     181        fo.variables[var].units = invar.units 
     182  os.remove(pathout.replace('.nc','_WORK.nc')) 
    181183# 
    182184add_k = 1 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/README

    r7491 r7492  
    1 This is a first release of SIREN. 
    21 
    3 To create SIREN documentation, go to ./src and run doxygen  
     2To create SIREN documentation, run doxygen in TOOLS/SIREN directory 
    43(http://www.stack.nl/~dimitri/doxygen/index.html version 1.8.3.1 or upper) 
    54then 
    6    open ../doc/index.html  
     5   open ./TOOLS/SIREN/doc/html/index.html in your web browser  
    76or  
    8    run ../doc/latex/gmake and open refman.pdf  
    9  
    10  
    11 templates of namelists could be find in templates directory. 
    12 read documentation for more information. 
    13  
    14  1- program to create coordinate file : 
    15  
    16    ./create_coord create_coord.nam 
    17  
    18  
    19  Variables are extracted from the input coordinates coarse grid and 
    20  interpolated to create fine coordinates files. 
    21  
    22  2- program to create bathymetry file: 
    23  
    24  ./create_bathy create_bathy.nam 
    25  
    26  Bathymetry could be extracted from fine grid Bathymetry file, or 
    27  interpolated from coarse grid Bathymetry file. 
    28  
    29  3- program to merge bathymetry file at boundaries : 
    30  
    31  ./merge_bathy merge_bathy.nam 
    32  
    33  Coarse grid Bathymetry is interpolated on fine grid. 
    34  Then fine Bathymetry and refined coarse bathymetry are merged at 
    35  boundaries. 
    36  
    37  4- program to create restart file : 
    38  
    39  ./create_restart create_restart.nam 
    40  
    41  Variables are read from restart file, or standard output. 
    42  Then theses variables are interpolated on fine grid. 
    43  Finally table are split over new decomposition. 
    44  
    45  5- program to create boundary files (OBC) : 
    46  
    47  ./create_boundary create_boundary.nam 
    48  
    49  Variables are read from standard output. 
    50  Then theses variables are interpolated on fine grid boundaries. 
     7   run ./TOOLS/SIREN/doc/latex/gmake and open ./TOOLS/SIREN/doc/latex/refman.pdf  

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/boundary.f90

    r7491 r7492  
    15291529   !> @author J.Paul  
    15301530   !> @date November, 2013 - Initial Version  
    1531    !  
     1531   !> @date June, 2016 
     1532   !> - Bug fix: take into account that boundaries are compute on T point, 
     1533   !>   but expressed on U,V point 
     1534   !> 
    15321535   !> @param[inout] td_bdy boundary structure  
    15331536   !> @param[in] td_var    variable structure  
    … …  
    15521555      il_max(jp_west )=td_var%t_dim(2)%i_len 
    15531556  
    1554       il_maxindex(jp_north)=td_var%t_dim(2)%i_len-ip_ghost 
     1557      ! index expressed on U,V point, move on T point. 
     1558      il_maxindex(jp_north)=td_var%t_dim(2)%i_len-ip_ghost+1 
    15551559      il_maxindex(jp_south)=td_var%t_dim(2)%i_len-ip_ghost 
    1556       il_maxindex(jp_east )=td_var%t_dim(1)%i_len-ip_ghost 
     1560      il_maxindex(jp_east )=td_var%t_dim(1)%i_len-ip_ghost+1 
    15571561      il_maxindex(jp_west )=td_var%t_dim(1)%i_len-ip_ghost 
    15581562 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/1_install.md

    r7491 r7492  
    2020  <b> 
    2121  - @ref index 
    22   - @ref md_docsrc_2_quickstart 
    23   - @ref md_docsrc_3_support_bug 
    24   - @ref md_docsrc_4_codingRules 
    25   - @ref md_docsrc_5_changeLog 
     22  - @ref md_src_docsrc_2_quickstart 
     23  - @ref md_src_docsrc_3_support_bug 
     24  - @ref md_src_docsrc_4_codingRules 
     25  - @ref md_src_docsrc_5_changeLog 
    2626  - @ref todo 
    2727  </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md

    r7491 r7492  
    3535Here after we briefly describe how to use each programs, 
    3636and so how to create your own regional configuration. 
    37 @note A set of GLORYS files (global reanalysis on *ORCA025* 
    38 grid), as well as examples of namelists are available in dods repository.<br/> 
    39 You could create and forced a first release of your own regional configuration, 
    40 with those files.  
     37@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=1658ec1aaeda2878f2b3915ed140af37). 
     38 
    4139<!-- ######################################################################  --> 
    4240# Create coordinates file # {#coord} 
    … …  
    121119example: ORCA05</dd> 
    122120</dl> 
    123 @sa For more information see @ref md_docsrc_6_perio 
     121@sa For more information see @ref md_src_docsrc_6_perio 
    124122</dd> 
    125123</dl> 
    … …  
    442440Finally, this **namout** sub-namelist defines the output files.<br/> 
    443441Here we ask for output on 81 processors, with *restart_out.nc* as file "basename".<br/> 
    444 So SIREN computes the optimal layout for 81 porcessors 
     442So SIREN computes the optimal layout for 81 processors 
    445443available,<br/> 
    446 and split restart on output files named *restart_out_num.nc*, where *num* is the porc number. 
     444and split restart on output files named *restart_out_num.nc*, where *num* is the proc number. 
    447445 
    448446@note SIREN could also create the other fields you may need for 
    … …  
    592590   <b> 
    593591   - @ref index 
    594    - @ref md_docsrc_1_install 
    595    - @ref md_docsrc_2_quickstart 
    596    - @ref md_docsrc_3_support_bug 
    597    - @ref md_docsrc_4_codingRules 
    598    - @ref md_docsrc_5_changeLog 
     592   - @ref md_src_docsrc_1_install 
     593   - @ref md_src_docsrc_2_quickstart 
     594   - @ref md_src_docsrc_3_support_bug 
     595   - @ref md_src_docsrc_4_codingRules 
     596   - @ref md_src_docsrc_5_changeLog 
    599597   - @ref todo 
    600598   </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/3_support_bug.md

    r7491 r7492  
    2020   <b> 
    2121   - @ref index 
    22    - @ref md_docsrc_1_install 
    23    - @ref md_docsrc_2_quickstart 
    24    - @ref md_docsrc_3_support_bug 
    25    - @ref md_docsrc_4_codingRules 
    26    - @ref md_docsrc_5_changeLog 
     22   - @ref md_src_docsrc_1_install 
     23   - @ref md_src_docsrc_2_quickstart 
     24   - @ref md_src_docsrc_3_support_bug 
     25   - @ref md_src_docsrc_4_codingRules 
     26   - @ref md_src_docsrc_5_changeLog 
    2727   - @ref todo 
    2828   </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/4_codingRules.md

    r7491 r7492  
    1515_GET_COMMAND_ARGUMENT_.<br/> 
    1616There exist no equivalent for those Fortran 03 intrinsec functions in Fortran 
    17 95.<br/> At least none convenient for compilers tested (see @ref md_docsrc_1_install).  
     1795.<br/> At least none convenient for compilers tested (see @ref md_src_docsrc_1_install).  
    1818 
    1919#  Free Form Source {#free} 
    … …  
    9393   <b> 
    9494   - @ref index 
    95    - @ref md_docsrc_1_install 
    96    - @ref md_docsrc_2_quickstart 
    97    - @ref md_docsrc_3_support_bug 
    98    - @ref md_docsrc_5_changeLog 
     95   - @ref md_src_docsrc_1_install 
     96   - @ref md_src_docsrc_2_quickstart 
     97   - @ref md_src_docsrc_3_support_bug 
     98   - @ref md_src_docsrc_5_changeLog 
    9999   - @ref todo 
    100100   </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/5_changeLog.md

    r7491 r7492  
    33@tableofcontents 
    44 
    5 # Release $Revision$ 
    6 Initial release (2016-03-17) 
     5# Release 2016-11-28 
    76 
    87## Changes 
    98## New Features 
    109## Bug fixes 
     10 - boundary.f90: take into account that boundaries are compute on T point, but expressed on U,V point 
     11 - iom_cdf.f90: define type cdf4 as cdf 
     12 
     13release (2016-07-01) 
     14 
     15## Changes 
     16## New Features 
     17## Bug fixes 
     18 - correct check of boundary indices 
     19 
     20# Release 
     21Initial release (2016-04-11) 
    1122 
    1223 <HR> 
    1324   <b> 
    1425   - @ref index 
    15    - @ref md_docsrc_1_install 
    16    - @ref md_docsrc_2_quickstart 
    17    - @ref md_docsrc_3_support_bug 
    18    - @ref md_docsrc_4_codingRules 
     26   - @ref md_src_docsrc_1_install 
     27   - @ref md_src_docsrc_2_quickstart 
     28   - @ref md_src_docsrc_3_support_bug 
     29   - @ref md_src_docsrc_4_codingRules 
    1930   - @ref todo 
    2031   </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/6_perio.md

    r7491 r7492  
    66<dd>ghost cells (solid walls) are imposed at all model boundaries.</dd>  
    77@image html perio0_20.png  
    8 @image latex perio0_20.png 
     8@latexonly 
     9\begin{center} 
     10\includegraphics{perio0_20.png} 
     11\end{center} 
     12@endlatexonly 
    913<dt>cyclic east-west boundary (in_perio=1)</dt> 
    1014<dd>first and last rows are closed, whilst the first column is set to the value of the last-but-one column and the last column to the value of the second one.</dd>   
    1115@image html perio1_20.png  
    12 @image latex perio1_20.png 
     16@latexonly 
     17\begin{center} 
     18\includegraphics{perio1_20.png} 
     19\end{center} 
     20@endlatexonly 
    1321<dt>symmetric boundary condition across the equator. (in_perio=2)</dt> 
    1422<dd>last row, and first and last columns are closed. </dd>  
    1523@image html perio2_20.png  
    16 @image latex perio2_20.png 
     24@latexonly 
     25\begin{center} 
     26\includegraphics{perio2_20.png} 
     27\end{center} 
     28@endlatexonly 
    1729<dt>North fold boundary with a T -point pivot (in_perio=3)</dt> 
    1830<dd>first row, and first and last columns are closed. </dd>  
    1931@image html perio3_20.png  
    20 @image latex perio3_20.png 
     32@latexonly 
     33\begin{center} 
     34\includegraphics{perio3_20.png} 
     35\end{center} 
     36@endlatexonly 
    2137<dt>North fold boundary with a T -point pivot and cyclic east-west boundary (in_perio=4)</dt> 
    2238<dd>first row is closed. The first column is set to the value of the last-but-one column and the last column to the value of the second one. </dd>  
    2339@image html perio4_20.png  
    24 @image latex perio4_20.png 
     40@latexonly 
     41\begin{center} 
     42\includegraphics{perio4_20.png} 
     43\end{center} 
     44@endlatexonly 
    2545<dt>North fold boundary with a F -point pivot (in_perio=5)</dt> 
    2646<dd>first row, and first and last columns are closed. </dd>  
    2747@image html perio5_20.png  
    28 @image latex perio5_20.png 
     48@latexonly 
     49\begin{center} 
     50\includegraphics{perio5_20.png} 
     51\end{center} 
     52@endlatexonly 
    2953<dt>North fold boundary with a F -point pivot and cyclic east-west boundary (in_perio=6)</dt> 
    3054<dd>first row is closed. The first column is set to the value of the last-but-one column and the last column to the value of the second one.</dd>  
    3155@image html perio6_20.png  
    32 @image latex perio6_20.png 
     56@image html perio5_20.png  
     57@latexonly 
     58\begin{center} 
     59\includegraphics{perio6_20.png} 
     60\end{center} 
     61@endlatexonly 
    3362</dl> 
    3463@sa For more information about NEMO periodicity, see _Model Boundary Condition_ chapter in [NEMO documentation](http://www.nemo-ocean.eu/About-NEMO/Reference-manuals)) 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/main.dox

    r7491 r7492  
    22 @mainpage About  
    33 
    4  SIREN is a software to create regional configuration with [NEMO](http://www.nemo-ocean.eu).<br/>  
    5  Actually SIREN create input files needed for a basic NEMO configuration.<br/> 
     4 SIREN is a software to set up regional configuration with [NEMO](http://www.nemo-ocean.eu).<br/>  
     5 Actually SIREN creates the input files you need to run a NEMO regional configuration.<br/> 
     6  
     7 SIREN allows you to create your own regional configuration embedded in a wider one.<br/> 
    68 
    7  SIREN allows you to create your own regional configuration embedded in a wider one.<br/> 
    8  In order to help you, a set of GLORYS files (global reanalysis on ORCA025 grid), as well as examples 
    9  of namelists are available in dods repository. 
     9 To know how to install SIREN see @ref md_src_docsrc_1_install. 
    1010 
    11  @note This software was created, and is maintain by the Configuration Manager Working Group, composed 
    12  of NEMO system team members. 
    13   
    14  To know how to install SIREN see @ref md_docsrc_1_install. 
    15  
    16  You could find a tutorial for a quick start with SIREN in @ref md_docsrc_2_quickstart.<br/> 
     11 You could find a tutorial for a quick start with SIREN in @ref md_src_docsrc_2_quickstart.<br/> 
    1712 For more information about how to use each component of SIREN 
    1813 - see create_coord.f90 to create fine grid coordinate file 
    … …  
    2419<HR> 
    2520   <b> 
    26    - @ref md_docsrc_1_install 
    27    - @ref md_docsrc_2_quickstart 
    28    - @ref md_docsrc_3_support_bug 
    29    - @ref md_docsrc_4_codingRules 
    30    - @ref md_docsrc_5_changeLog 
     21   - @ref md_src_docsrc_1_install 
     22   - @ref md_src_docsrc_2_quickstart 
     23   - @ref md_src_docsrc_3_support_bug 
     24   - @ref md_src_docsrc_4_codingRules 
     25   - @ref md_src_docsrc_5_changeLog 
    3126   - @ref todo 
    3227   </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/file.f90

    r7491 r7492  
    495495         END SELECT 
    496496      ELSE 
     497         CALL logger_debug("FILE INIT: look for file type "//TRIM(file_init%c_name)) 
    497498         file_init%c_type=TRIM(file_get_type(cd_file)) 
    498499      ENDIF 
    … …  
    572573         CASE('.nc','.cdf') 
    573574            CALL logger_debug(" FILE GET TYPE: file "//TRIM(cd_file)//" is cdf") 
     575            ! Warning : type could be change to cdf4 when opening file. 
    574576            file_get_type='cdf' 
    575577         CASE('.dimg') 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/grid.f90

    r7491 r7492  
    13411341         il_dim(:)=td_var%t_dim(:)%i_len 
    13421342 
    1343          CALL logger_debug("GRID GET PERIO: use varibale "//TRIM(td_var%c_name)) 
     1343         CALL logger_debug("GRID GET PERIO: use variable "//TRIM(td_var%c_name)) 
    13441344         CALL logger_debug("GRID GET PERIO: fill value "//TRIM(fct_str(td_var%d_fill))) 
    13451345         CALL logger_debug("GRID GET PERIO: first value "//TRIM(fct_str(td_var%d_value(1,1,1,1)))) 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/iom.f90

    r7491 r7492  
    174174         CASE('cdf') 
    175175            CALL iom_cdf_open(td_file) 
     176         !CASE('cdf4') 
    176177         CASE('dimg') 
    177178            CALL iom_rstdimg_open(td_file) 
    … …  
    240241            CALL iom_rstdimg_close(td_file) 
    241242         CASE DEFAULT 
     243            CALL logger_debug( "IOM CLOSE: type "//TRIM(td_file%c_type)) 
    242244            CALL logger_error( "IOM CLOSE: can't close file "//& 
    243245            &               TRIM(td_file%c_name)//": type unknown " ) 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/iom_cdf.f90

    r7491 r7492  
    340340            td_file%c_type='cdf' 
    341341         CASE(nf90_format_netcdf4, nf90_format_netcdf4_classic) 
    342             td_file%c_type='cdf4' 
     342            td_file%c_type='cdf' 
     343            !td_file%c_type='cdf4' 
    343344      END SELECT 
     345      CALL logger_debug("IOM CDF GET INFO: type "//TRIM(td_file%c_type))  
    344346 
    345347      ! record header infos 
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