Changeset 7492 for branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS
- Timestamp:
- 2016-12-13T17:45:59+01:00 (8 years ago)
- Location:
- branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS
- Files:
-
- 1 deleted
- 16 edited
- 2 copied
Legend:
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branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/NESTING/agulhas
r7491 r7492 41 41 N = 31 42 42 ldbletanh = .FALSE. 43 p pa2= 0.043 pa2 = 0.0 44 44 ppkth2 = 0.0 45 45 ppacr2 = 0.0 -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/NESTING/src/agrif_types.f90
r7491 r7492 76 76 NAMELIST /nesting/imin,imax,jmin,jmax,rho,rhot,bathy_update,updated_parent_file 77 77 ! 78 NAMELIST /vertical_grid/ppkth,ppacr,ppdzmin,pphmax,psur,pa0,pa1,N,ldbletanh,p pa2,ppkth2,ppacr278 NAMELIST /vertical_grid/ppkth,ppacr,ppdzmin,pphmax,psur,pa0,pa1,N,ldbletanh,pa2,ppkth2,ppacr2 79 79 ! 80 80 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 169 169 sys.exit(15) 170 170 fo = Dataset(pathout, 'w') 171 for dim in ['x','y','c' ]:171 for dim in ['x','y','c','k']: 172 172 indim = fi.dimensions[dim] 173 173 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']: 175 175 invar = fi.variables[var] 176 176 fo.createVariable(var, invar.datatype, invar.dimensions) 177 177 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')) 181 183 # 182 184 add_k = 1 -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/README
r7491 r7492 1 This is a first release of SIREN.2 1 3 To create SIREN documentation, go to ./src and run doxygen2 To create SIREN documentation, run doxygen in TOOLS/SIREN directory 4 3 (http://www.stack.nl/~dimitri/doxygen/index.html version 1.8.3.1 or upper) 5 4 then 6 open . ./doc/index.html5 open ./TOOLS/SIREN/doc/html/index.html in your web browser 7 6 or 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 1529 1529 !> @author J.Paul 1530 1530 !> @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 !> 1532 1535 !> @param[inout] td_bdy boundary structure 1533 1536 !> @param[in] td_var variable structure … … 1552 1555 il_max(jp_west )=td_var%t_dim(2)%i_len 1553 1556 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 1555 1559 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 1557 1561 il_maxindex(jp_west )=td_var%t_dim(1)%i_len-ip_ghost 1558 1562 -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/1_install.md
r7491 r7492 20 20 <b> 21 21 - @ref index 22 - @ref md_ docsrc_2_quickstart23 - @ref md_ docsrc_3_support_bug24 - @ref md_ docsrc_4_codingRules25 - @ref md_ docsrc_5_changeLog22 - @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 26 26 - @ref todo 27 27 </b> -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md
r7491 r7492 35 35 Here after we briefly describe how to use each programs, 36 36 and 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 41 39 <!-- ###################################################################### --> 42 40 # Create coordinates file # {#coord} … … 121 119 example: ORCA05</dd> 122 120 </dl> 123 @sa For more information see @ref md_ docsrc_6_perio121 @sa For more information see @ref md_src_docsrc_6_perio 124 122 </dd> 125 123 </dl> … … 442 440 Finally, this **namout** sub-namelist defines the output files.<br/> 443 441 Here we ask for output on 81 processors, with *restart_out.nc* as file "basename".<br/> 444 So SIREN computes the optimal layout for 81 p orcessors442 So SIREN computes the optimal layout for 81 processors 445 443 available,<br/> 446 and split restart on output files named *restart_out_num.nc*, where *num* is the p orc number.444 and split restart on output files named *restart_out_num.nc*, where *num* is the proc number. 447 445 448 446 @note SIREN could also create the other fields you may need for … … 592 590 <b> 593 591 - @ref index 594 - @ref md_ docsrc_1_install595 - @ref md_ docsrc_2_quickstart596 - @ref md_ docsrc_3_support_bug597 - @ref md_ docsrc_4_codingRules598 - @ref md_ docsrc_5_changeLog592 - @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 599 597 - @ref todo 600 598 </b> -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/3_support_bug.md
r7491 r7492 20 20 <b> 21 21 - @ref index 22 - @ref md_ docsrc_1_install23 - @ref md_ docsrc_2_quickstart24 - @ref md_ docsrc_3_support_bug25 - @ref md_ docsrc_4_codingRules26 - @ref md_ docsrc_5_changeLog22 - @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 27 27 - @ref todo 28 28 </b> -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/4_codingRules.md
r7491 r7492 15 15 _GET_COMMAND_ARGUMENT_.<br/> 16 16 There 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).17 95.<br/> At least none convenient for compilers tested (see @ref md_src_docsrc_1_install). 18 18 19 19 # Free Form Source {#free} … … 93 93 <b> 94 94 - @ref index 95 - @ref md_ docsrc_1_install96 - @ref md_ docsrc_2_quickstart97 - @ref md_ docsrc_3_support_bug98 - @ref md_ docsrc_5_changeLog95 - @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 99 99 - @ref todo 100 100 </b> -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/5_changeLog.md
r7491 r7492 3 3 @tableofcontents 4 4 5 # Release $Revision$ 6 Initial release (2016-03-17) 5 # Release 2016-11-28 7 6 8 7 ## Changes 9 8 ## New Features 10 9 ## 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 13 release (2016-07-01) 14 15 ## Changes 16 ## New Features 17 ## Bug fixes 18 - correct check of boundary indices 19 20 # Release 21 Initial release (2016-04-11) 11 22 12 23 <HR> 13 24 <b> 14 25 - @ref index 15 - @ref md_ docsrc_1_install16 - @ref md_ docsrc_2_quickstart17 - @ref md_ docsrc_3_support_bug18 - @ref md_ docsrc_4_codingRules26 - @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 19 30 - @ref todo 20 31 </b> -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/6_perio.md
r7491 r7492 6 6 <dd>ghost cells (solid walls) are imposed at all model boundaries.</dd> 7 7 @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 9 13 <dt>cyclic east-west boundary (in_perio=1)</dt> 10 14 <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> 11 15 @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 13 21 <dt>symmetric boundary condition across the equator. (in_perio=2)</dt> 14 22 <dd>last row, and first and last columns are closed. </dd> 15 23 @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 17 29 <dt>North fold boundary with a T -point pivot (in_perio=3)</dt> 18 30 <dd>first row, and first and last columns are closed. </dd> 19 31 @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 21 37 <dt>North fold boundary with a T -point pivot and cyclic east-west boundary (in_perio=4)</dt> 22 38 <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> 23 39 @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 25 45 <dt>North fold boundary with a F -point pivot (in_perio=5)</dt> 26 46 <dd>first row, and first and last columns are closed. </dd> 27 47 @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 29 53 <dt>North fold boundary with a F -point pivot and cyclic east-west boundary (in_perio=6)</dt> 30 54 <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> 31 55 @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 33 62 </dl> 34 63 @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 2 2 @mainpage About 3 3 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/> 6 8 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. 10 10 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/> 17 12 For more information about how to use each component of SIREN 18 13 - see create_coord.f90 to create fine grid coordinate file … … 24 19 <HR> 25 20 <b> 26 - @ref md_ docsrc_1_install27 - @ref md_ docsrc_2_quickstart28 - @ref md_ docsrc_3_support_bug29 - @ref md_ docsrc_4_codingRules30 - @ref md_ docsrc_5_changeLog21 - @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 31 26 - @ref todo 32 27 </b> -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/file.f90
r7491 r7492 495 495 END SELECT 496 496 ELSE 497 CALL logger_debug("FILE INIT: look for file type "//TRIM(file_init%c_name)) 497 498 file_init%c_type=TRIM(file_get_type(cd_file)) 498 499 ENDIF … … 572 573 CASE('.nc','.cdf') 573 574 CALL logger_debug(" FILE GET TYPE: file "//TRIM(cd_file)//" is cdf") 575 ! Warning : type could be change to cdf4 when opening file. 574 576 file_get_type='cdf' 575 577 CASE('.dimg') -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/grid.f90
r7491 r7492 1341 1341 il_dim(:)=td_var%t_dim(:)%i_len 1342 1342 1343 CALL logger_debug("GRID GET PERIO: use vari bale "//TRIM(td_var%c_name))1343 CALL logger_debug("GRID GET PERIO: use variable "//TRIM(td_var%c_name)) 1344 1344 CALL logger_debug("GRID GET PERIO: fill value "//TRIM(fct_str(td_var%d_fill))) 1345 1345 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 174 174 CASE('cdf') 175 175 CALL iom_cdf_open(td_file) 176 !CASE('cdf4') 176 177 CASE('dimg') 177 178 CALL iom_rstdimg_open(td_file) … … 240 241 CALL iom_rstdimg_close(td_file) 241 242 CASE DEFAULT 243 CALL logger_debug( "IOM CLOSE: type "//TRIM(td_file%c_type)) 242 244 CALL logger_error( "IOM CLOSE: can't close file "//& 243 245 & TRIM(td_file%c_name)//": type unknown " ) -
branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/iom_cdf.f90
r7491 r7492 340 340 td_file%c_type='cdf' 341 341 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' 343 344 END SELECT 345 CALL logger_debug("IOM CDF GET INFO: type "//TRIM(td_file%c_type)) 344 346 345 347 ! record header infos
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