Ignore:
Timestamp:
2019-11-22T17:15:18+01:00 (15 months ago)
Author:
acc
Message:

Branch 2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles. Merge in trunk changes up to 11943 in preparation for end of year merge

Location:
NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/src/TOP
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  • NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/src/TOP/README.rst

    r10549 r11954  
    33*************** 
    44 
     5.. todo:: 
     6 
     7 
     8 
    59.. contents:: 
    6    :local: 
    7  
    8 TOP (Tracers in the Ocean Paradigm) is the NEMO hardwired interface toward biogeochemical models and 
    9 provide the physical constraints/boundaries for oceanic tracers. 
    10 It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules. 
     10   :local: 
     11 
     12TOP (Tracers in the Ocean Paradigm) is the NEMO hardwired interface toward 
     13biogeochemical models and provide the physical constraints/boundaries for oceanic tracers. 
     14It consists of a modular framework to handle multiple ocean tracers, 
     15including also a variety of built-in modules. 
    1116 
    1217This component of the NEMO framework allows one to exploit available modules (see below) and 
    1318further develop a range of applications, spanning from the implementation of a dye passive tracer to 
    1419evaluate dispersion processes (by means of MY_TRC), track water masses age (AGE module), 
    15 assess the ocean interior penetration of persistent chemical compounds (e.g., gases like CFC or even PCBs), 
    16 up to the full set of equations involving marine biogeochemical cycles. 
     20assess the ocean interior penetration of persistent chemical compounds 
     21(e.g., gases like CFC or even PCBs), up to the full set of equations involving 
     22marine biogeochemical cycles. 
    1723 
    1824Structure 
    1925========= 
    2026 
    21 TOP interface has the following location in the source code ``./src/MBG/`` and 
     27TOP interface has the following location in the source code :file:`./src/TOP` and 
    2228the following modules are available: 
    2329 
    24 ``TRP`` 
    25    Interface to NEMO physical core for computing tracers transport 
    26  
    27 ``CFC`` 
    28    Inert carbon tracers (CFC11,CFC12,SF6) 
    29  
    30 ``C14`` 
    31    Radiocarbon passive tracer 
    32  
    33 ``AGE`` 
    34    Water age tracking 
    35  
    36 ``MY_TRC`` 
    37    Template for creation of new modules and external BGC models coupling 
    38  
    39 ``PISCES`` 
    40    Built in BGC model. 
    41    See [https://www.geosci-model-dev.net/8/2465/2015/gmd-8-2465-2015-discussion.html Aumont et al. (2015)] for 
    42    a throughout description. | 
    43  
    44 The usage of TOP is activated i) by including in the configuration definition  the component ``MBG`` and 
    45 ii) by adding the macro ``key_top`` in the configuration CPP file 
    46 (see for more details [http://forge.ipsl.jussieu.fr/nemo/wiki/Users "Learn more about the model"]). 
     30:file:`TRP` 
     31   Interface to NEMO physical core for computing tracers transport 
     32 
     33:file:`CFC` 
     34   Inert carbon tracers (CFC11,CFC12,SF6) 
     35 
     36:file:`C14` 
     37   Radiocarbon passive tracer 
     38 
     39:file:`AGE` 
     40   Water age tracking 
     41 
     42:file:`MY_TRC` 
     43   Template for creation of new modules and external BGC models coupling 
     44 
     45:file:`PISCES` 
     46   Built in BGC model. See :cite:`gmd-8-2465-2015` for a throughout description. 
     47 
     48The usage of TOP is activated 
     49*i)* by including in the configuration definition the component ``TOP`` and 
     50*ii)* by adding the macro ``key_top`` in the configuration CPP file 
     51(see for more details :forge:`"Learn more about the model" <wiki/Users>`). 
    4752 
    4853As an example, the user can refer to already available configurations in the code, 
     
    5156(see also Section 4) . 
    5257 
    53 Note that, since version 4.0, TOP interface core functionalities are activated by means of logical keys and 
     58Note that, since version 4.0, 
     59TOP interface core functionalities are activated by means of logical keys and 
    5460all submodules preprocessing macros from previous versions were removed. 
    5561 
     
    5763 
    5864``key_iomput`` 
    59    use XIOS I/O 
     65   use XIOS I/O 
    6066 
    6167``key_agrif`` 
    62    enable AGRIF coupling 
     68   enable AGRIF coupling 
    6369 
    6470``key_trdtrc`` & ``key_trdmxl_trc`` 
    65    trend computation for tracers 
     71   trend computation for tracers 
    6672 
    6773Synthetic Workflow 
    6874================== 
    6975 
    70 A synthetic description of the TOP interface workflow is given below to summarize the steps involved in 
    71 the computation of biogeochemical and physical trends and their time integration and outputs, 
     76A synthetic description of the TOP interface workflow is given below to 
     77summarize the steps involved in the computation of biogeochemical and physical trends and 
     78their time integration and outputs, 
    7279by reporting also the principal Fortran subroutine herein involved. 
    7380 
    74 **Model initialization (OPA_SRC/nemogcm.F90)** 
    75  
    76 call to trc_init (trcini.F90) 
    77  
    78   ↳ call trc_nam (trcnam.F90) to initialize TOP tracers and run setting 
    79  
    80   ↳ call trc_ini_sms, to initialize each submodule 
    81  
    82   ↳ call trc_ini_trp, to initialize transport for tracers 
    83  
    84   ↳ call trc_ice_ini, to initialize tracers in seaice 
    85  
    86   ↳ call trc_ini_state, read passive tracers from a restart or input data 
    87  
    88   ↳ call trc_sub_ini, setup substepping if {{{nn_dttrc /= 1}}} 
    89  
    90 **Time marching procedure (OPA_SRC/stp.F90)** 
    91  
    92 call to trc_stp.F90 (trcstp.F90) 
    93  
    94   ↳ call trc_sub_stp, averaging physical variables for sub-stepping 
    95  
    96   ↳ call trc_wri, call XIOS for output of data 
    97  
    98   ↳ call trc_sms, compute BGC trends for each submodule 
    99  
    100     ↳ call trc_sms_my_trc, includes also surface and coastal BCs trends 
    101  
    102   ↳ call trc_trp (TRP/trctrp.F90), compute physical trends 
    103  
    104     ↳ call trc_sbc, get trend due to surface concentration/dilution 
    105  
    106     ↳ call trc_adv, compute tracers advection 
    107  
    108     ↳ call to trc_ldf, compute tracers lateral diffusion 
    109  
    110     ↳ call to trc_zdf, vertical mixing and after tracer fields 
    111  
    112     ↳ call to trc_nxt, tracer fields at next time step. Lateral Boundary Conditions are solved in here. 
    113  
    114     ↳ call to trc_rad, Correct artificial negative concentrations 
    115  
    116   ↳ call trc_rst_wri, output tracers restart files 
     81Model initialization (:file:`./src/OCE/nemogcm.F90`) 
     82---------------------------------------------------- 
     83 
     84Call to ``trc_init`` subroutine (:file:`./src/TOP/trcini.F90`) to initialize TOP. 
     85 
     86.. literalinclude:: ../../../src/TOP/trcini.F90 
     87   :language:        fortran 
     88   :lines:           41-86 
     89   :emphasize-lines: 21,30-32,38-40 
     90   :caption:         ``trc_init`` subroutine 
     91 
     92Time marching procedure (:file:`./src/OCE/step.F90`) 
     93---------------------------------------------------- 
     94 
     95Call to ``trc_stp`` subroutine (:file:`./src/TOP/trcstp.F90`) to compute/update passive tracers. 
     96 
     97.. literalinclude:: ../../../src/TOP/trcstp.F90 
     98   :language:        fortran 
     99   :lines:           46-125 
     100   :emphasize-lines: 42,55-57 
     101   :caption:         ``trc_stp`` subroutine 
     102 
     103BGC trends computation for each submodule (:file:`./src/TOP/trcsms.F90`) 
     104------------------------------------------------------------------------ 
     105 
     106.. literalinclude:: ../../../src/TOP/trcsms.F90 
     107   :language:        fortran 
     108   :lines:           21 
     109   :caption:         :file:`trcsms` snippet 
     110 
     111Physical trends computation (:file:`./src/TOP/TRP/trctrp.F90`) 
     112-------------------------------------------------------------- 
     113 
     114.. literalinclude:: ../../../src/TOP/TRP/trctrp.F90 
     115   :language:        fortran 
     116   :lines:           46-95 
     117   :emphasize-lines: 17,21,29,33-35 
     118   :caption:         ``trc_trp`` subroutine 
    117119 
    118120Namelists walkthrough 
    119121===================== 
    120122 
    121 namelist_top 
    122 ------------ 
    123  
    124 Here below are listed the features/options of the TOP interface accessible through the namelist_top_ref and 
    125 modifiable by means of namelist_top_cfg (as for NEMO physical ones). 
    126  
    127 Note that ## is used to refer to a number in an array field. 
     123:file:`namelist_top` 
     124-------------------- 
     125 
     126Here below are listed the features/options of the TOP interface accessible through 
     127the :file:`namelist_top_ref` and modifiable by means of :file:`namelist_top_cfg` 
     128(as for NEMO physical ones). 
     129 
     130Note that ``##`` is used to refer to a number in an array field. 
    128131 
    129132.. literalinclude:: ../../namelists/namtrc_run 
     133   :language: fortran 
    130134 
    131135.. literalinclude:: ../../namelists/namtrc 
     136   :language: fortran 
    132137 
    133138.. literalinclude:: ../../namelists/namtrc_dta 
     139   :language: fortran 
    134140 
    135141.. literalinclude:: ../../namelists/namtrc_adv 
     142   :language: fortran 
    136143 
    137144.. literalinclude:: ../../namelists/namtrc_ldf 
     145   :language: fortran 
    138146 
    139147.. literalinclude:: ../../namelists/namtrc_rad 
     148   :language: fortran 
    140149 
    141150.. literalinclude:: ../../namelists/namtrc_snk 
     151   :language: fortran 
    142152 
    143153.. literalinclude:: ../../namelists/namtrc_dmp 
     154   :language: fortran 
    144155 
    145156.. literalinclude:: ../../namelists/namtrc_ice 
     157   :language: fortran 
    146158 
    147159.. literalinclude:: ../../namelists/namtrc_trd 
     160   :language: fortran 
    148161 
    149162.. literalinclude:: ../../namelists/namtrc_bc 
     163   :language: fortran 
    150164 
    151165.. literalinclude:: ../../namelists/namtrc_bdy 
     166   :language: fortran 
    152167 
    153168.. literalinclude:: ../../namelists/namage 
    154  
    155 Two main types of data structure are used within TOP interface to initialize tracer properties (1) and 
     169   :language: fortran 
     170 
     171Two main types of data structure are used within TOP interface 
     172to initialize tracer properties (1) and 
    156173to provide related initial and boundary conditions (2). 
    157174 
    158 **1. TOP tracers initialization**: sn_tracer (namtrc) 
     1751. TOP tracers initialization: ``sn_tracer`` (``&namtrc``) 
     176^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    159177 
    160178Beside providing name and metadata for tracers, 
    161 here are also defined the use of initial ({{{sn_tracer%llinit}}}) and 
    162 boundary ({{{sn_tracer%llsbc, sn_tracer%llcbc, sn_tracer%llobc}}}) conditions. 
    163  
    164 In the following, an example of the full structure definition is given for two idealized tracers both with 
    165 initial conditions given, while the first has only surface boundary forcing and 
     179here are also defined the use of initial (``sn_tracer%llinit``) and 
     180boundary (``sn_tracer%llsbc, sn_tracer%llcbc, sn_tracer%llobc``) conditions. 
     181 
     182In the following, an example of the full structure definition is given for 
     183two idealized tracers both with initial conditions given, 
     184while the first has only surface boundary forcing and 
    166185the second both surface and coastal forcings: 
    167186 
    168187.. code-block:: fortran 
    169188 
    170    !             !    name   !           title of the field            !   units    ! initial data ! sbc   !   cbc  !   obc  ! 
    171    sn_tracer(1)  = 'TRC1'    , 'Tracer 1 Concentration                ',   ' - '    ,  .true.      , .true., .false., .true. 
    172    sn_tracer(2)  = 'TRC2 '   , 'Tracer 2 Concentration                ',   ' - '    ,  .true.      , .true., .true. , .false. 
     189   !             !    name   !           title of the field            !   units    ! initial data ! sbc   !   cbc  !   obc  ! 
     190   sn_tracer(1)  = 'TRC1'    , 'Tracer 1 Concentration                ',   ' - '    ,  .true.      , .true., .false., .true. 
     191   sn_tracer(2)  = 'TRC2 '   , 'Tracer 2 Concentration                ',   ' - '    ,  .true.      , .true., .true. , .false. 
    173192 
    174193As tracers in BGC models are increasingly growing, 
     
    177196.. code-block:: fortran 
    178197 
    179    !             !    name   !           title of the field            !   units    ! initial data ! 
    180    sn_tracer(1)  = 'TRC1'    , 'Tracer 1 Concentration                ',   ' - '    ,   .true. 
    181    sn_tracer(2)  = 'TRC2 '   , 'Tracer 2 Concentration                ',   ' - '    ,   .true. 
    182    ! sbc 
    183    sn_tracer(1)%llsbc = .true. 
    184    sn_tracer(2)%llsbc = .true. 
    185    ! cbc 
    186    sn_tracer(2)%llcbc = .true. 
     198   !             !    name   !           title of the field            !   units    ! initial data ! 
     199   sn_tracer(1)  = 'TRC1'    , 'Tracer 1 Concentration                ',   ' - '    ,   .true. 
     200   sn_tracer(2)  = 'TRC2 '   , 'Tracer 2 Concentration                ',   ' - '    ,   .true. 
     201   ! sbc 
     202   sn_tracer(1)%llsbc = .true. 
     203   sn_tracer(2)%llsbc = .true. 
     204   ! cbc 
     205   sn_tracer(2)%llcbc = .true. 
    187206 
    188207The data structure is internally initialized by code with dummy names and 
    189 all initialization/forcing logical fields set to .false. . 
    190  
    191 **2. Structures to read input initial and boundary conditions**: namtrc_dta (sn_trcdta), namtrc_bc (sn_trcsbc/sn_trccbc/sn_trcobc) 
     208all initialization/forcing logical fields set to ``.false.`` . 
     209 
     2102. Structures to read input initial and boundary conditions: ``&namtrc_dta`` (``sn_trcdta``), ``&namtrc_bc`` (``sn_trcsbc`` / ``sn_trccbc`` / ``sn_trcobc``) 
     211^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    192212 
    193213The overall data structure (Fortran type) is based on the general one defined for NEMO core in the SBC component 
    194 (see details in User Manual SBC Chapter on Input Data specification). 
    195  
    196 Input fields are prescribed within namtrc_dta (with sn_trcdta structure), 
    197 while Boundary Conditions are applied to the model by means of namtrc_bc, 
    198 with dedicated structure fields for surface (sn_trcsbc), riverine (sn_trccbc), and 
    199 lateral open (sn_trcobc) boundaries. 
     214(see details in ``SBC`` Chapter of :doc:`Reference Manual <cite>` on Input Data specification). 
     215 
     216Input fields are prescribed within ``&namtrc_dta`` (with ``sn_trcdta`` structure), 
     217while Boundary Conditions are applied to the model by means of ``&namtrc_bc``, 
     218with dedicated structure fields for surface (``sn_trcsbc``), riverine (``sn_trccbc``), and 
     219lateral open (``sn_trcobc``) boundaries. 
    200220 
    201221The following example illustrates the data structure in the case of initial condition for 
    202 a single tracer contained in the file named tracer_1_data.nc (.nc is implicitly assumed in namelist filename), 
    203 with a doubled initial value, and located in the usr/work/model/inputdata/ folder: 
     222a single tracer contained in the file named :file:`tracer_1_data.nc` 
     223(``.nc`` is implicitly assumed in namelist filename), 
     224with a doubled initial value, and located in the :file:`usr/work/model/inputdata` folder: 
    204225 
    205226.. code-block:: fortran 
    206227 
    207    !               !  file name             ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    208    !               !                        !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    209      sn_trcdta(1)  = 'tracer_1_data'        ,        -12        ,  'TRC1'   ,    .false.   , .true. , 'yearly'  , ''       , ''       , '' 
    210      rf_trfac(1) = 2.0 
    211      cn_dir = “usr/work/model/inputdata/” 
    212  
    213 Note that, the Lateral Open Boundaries conditions are applied on the segments defined for the physical core of NEMO 
    214 (see BDY description in the User Manual). 
    215  
    216 namelist_trc 
    217 ------------ 
    218  
    219 Here below the description of namelist_trc_ref used to handle Carbon tracers modules, namely CFC and C14. 
    220  
    221 |||| &'''namcfc'''     !   CFC || 
    222  
    223 |||| &'''namc14_typ'''     !  C14 - type of C14 tracer, default values of C14/C and pco2 || 
    224  
    225 |||| &'''namc14_sbc'''     !  C14 - surface BC || 
    226  
    227 |||| &'''namc14_fcg'''     !  files & dates || 
     228   !               !  file name             ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
     229   !               !                        !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
     230     sn_trcdta(1)  = 'tracer_1_data'        ,        -12        ,  'TRC1'   ,    .false.   , .true. , 'yearly'  , ''       , ''       , '' 
     231     rf_trfac(1) = 2.0 
     232     cn_dir = 'usr/work/model/inputdata/' 
     233 
     234Note that, the Lateral Open Boundaries conditions are applied on 
     235the segments defined for the physical core of NEMO 
     236(see ``BDY`` description in the :doc:`Reference Manual <cite>`). 
     237 
     238:file:`namelist_trc` 
     239-------------------- 
     240 
     241Here below the description of :file:`namelist_trc_ref` used to handle Carbon tracers modules, 
     242namely CFC and C14. 
     243 
     244.. literalinclude:: ../../../cfgs/SHARED/namelist_trc_ref 
     245   :language: fortran 
     246   :lines: 7,17,26,34 
     247   :caption: :file:`namelist_trc_ref` snippet 
    228248 
    229249``MY_TRC`` interface for coupling external BGC models 
    230250===================================================== 
    231251 
    232 The generalized interface is pivoted on MY_TRC module that contains template files to build the coupling between 
     252The generalized interface is pivoted on MY_TRC module that contains template files to 
     253build the coupling between 
    233254NEMO and any external BGC model. 
    234255 
    235 The call to MY_TRC is activated by setting ``ln_my_trc = .true.`` (in namtrc) 
     256The call to MY_TRC is activated by setting ``ln_my_trc = .true.`` (in ``&namtrc``) 
    236257 
    237258The following 6 fortran files are available in MY_TRC with the specific purposes here described. 
    238259 
    239 ``par_my_trc.F90`` 
    240    This module allows to define additional arrays and public variables to be used within the MY_TRC interface 
    241  
    242 ``trcini_my_trc.F90`` 
    243    Here are initialized user defined namelists and the call to the external BGC model initialization procedures to 
    244    populate general tracer array (trn and trb). Here are also likely to be defined suport arrays related to 
    245    system metrics that could be needed by the BGC model. 
    246  
    247 ``trcnam_my_trc.F90`` 
    248    This routine is called at the beginning of trcini_my_trc and should contain the initialization of 
    249    additional namelists for the BGC model or user-defined code. 
    250  
    251 ``trcsms_my_trc.F90`` 
    252    The routine performs the call to Boundary Conditions and its main purpose is to 
    253    contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model. 
    254    Be aware that lateral boundary conditions are applied in trcnxt routine. 
    255    IMPORTANT: the routines to compute the light penetration along the water column and 
    256    the tracer vertical sinking should be defined/called in here, as generalized modules are still missing in 
    257    the code. 
    258  
    259 ``trcice_my_trc.F90`` 
    260    Here it is possible to prescribe the tracers concentrations in the seaice that will be used as 
    261    boundary conditions when ice melting occurs (nn_ice_tr =1 in namtrc_ice). 
    262    See e.g. the correspondent PISCES subroutine. 
    263  
    264 ``trcwri_my_trc.F90`` 
    265    This routine performs the output of the model tracers (only those defined in namtrc) using IOM module 
    266    (see Manual Chapter “Output and Diagnostics”). 
    267    It is possible to place here the output of additional variables produced by the model, 
    268    if not done elsewhere in the code, using the call to iom_put. 
     260:file:`par_my_trc.F90` 
     261   This module allows to define additional arrays and public variables to 
     262   be used within the MY_TRC interface 
     263 
     264:file:`trcini_my_trc.F90` 
     265   Here are initialized user defined namelists and 
     266   the call to the external BGC model initialization procedures to populate general tracer array 
     267   (``trn`` and ``trb``). 
     268   Here are also likely to be defined support arrays related to system metrics that 
     269   could be needed by the BGC model. 
     270 
     271:file:`trcnam_my_trc.F90` 
     272   This routine is called at the beginning of ``trcini_my_trc`` and 
     273   should contain the initialization of additional namelists for the BGC model or user-defined code. 
     274 
     275:file:`trcsms_my_trc.F90` 
     276   The routine performs the call to Boundary Conditions and its main purpose is to 
     277   contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model. 
     278   Be aware that lateral boundary conditions are applied in trcnxt routine. 
     279 
     280   .. warning:: 
     281      The routines to compute the light penetration along the water column and 
     282      the tracer vertical sinking should be defined/called in here, 
     283      as generalized modules are still missing in the code. 
     284 
     285:file:`trcice_my_trc.F90` 
     286   Here it is possible to prescribe the tracers concentrations in the sea-ice that 
     287   will be used as boundary conditions when ice melting occurs (``nn_ice_tr = 1`` in ``&namtrc_ice``). 
     288   See e.g. the correspondent PISCES subroutine. 
     289 
     290:file:`trcwri_my_trc.F90` 
     291   This routine performs the output of the model tracers (only those defined in ``&namtrc``) using 
     292   IOM module (see chapter “Output and Diagnostics” in the :doc:`Reference Manual <cite>`). 
     293   It is possible to place here the output of additional variables produced by the model, 
     294   if not done elsewhere in the code, using the call to ``iom_put``. 
    269295 
    270296Coupling an external BGC model using NEMO framework 
     
    273299The coupling with an external BGC model through the NEMO compilation framework can be achieved in 
    274300different ways according to the degree of coding complexity of the Biogeochemical model, like e.g., 
    275 the whole code is made only by one file or it has multiple modules and interfaces spread across several subfolders. 
    276  
    277 Beside the 6 core files of MY_TRC module, let’s assume an external BGC model named *MYBGC* and constituted by 
    278 a rather essential coding structure, likely few Fortran files. 
     301the whole code is made only by one file or 
     302it has multiple modules and interfaces spread across several subfolders. 
     303 
     304Beside the 6 core files of MY_TRC module, let’s assume an external BGC model named *MYBGC* and 
     305constituted by a rather essential coding structure, likely few Fortran files. 
    279306The new coupled configuration name is *NEMO_MYBGC*. 
    280307 
    281 The best solution is to have all files (the modified ``MY_TRC`` routines and the BGC model ones) placed in 
    282 a unique folder with root ``MYBGCPATH`` and to use the makenemo external readdressing of ``MY_SRC`` folder. 
    283  
    284 The coupled configuration listed in ``work_cfgs.txt`` will look like 
     308The best solution is to have all files (the modified ``MY_TRC`` routines and the BGC model ones) 
     309placed in a unique folder with root ``MYBGCPATH`` and 
     310to use the makenemo external readdressing of ``MY_SRC`` folder. 
     311 
     312The coupled configuration listed in :file:`work_cfgs.txt` will look like 
    285313 
    286314:: 
    287315 
    288    NEMO_MYBGC OPA_SRC TOP_SRC 
     316   NEMO_MYBGC OCE TOP 
    289317 
    290318and the related ``cpp_MYBGC.fcm`` content will be 
     
    292320.. code-block:: perl 
    293321 
    294    bld::tool::fppkeys key_iomput key_mpp_mpi key_top 
    295  
    296 the compilation with ``makenemo`` will be executed through the following syntax 
     322   bld::tool::fppkeys key_iomput key_mpp_mpi key_top 
     323 
     324the compilation with :file:`makenemo` will be executed through the following syntax 
    297325 
    298326.. code-block:: console 
    299327 
    300    $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>' 
    301  
    302 The makenemo feature “-e” was introduced to readdress at compilation time the standard MY_SRC folder 
    303 (usually found in NEMO configurations) with a user defined external one. 
    304  
    305 The compilation of more articulated BGC model code & infrastructure, like in the case of BFM 
    306 ([http://www.bfm-community.eu/publications/bfmnemomanual_r1.0_201508.pdf BFM-NEMO coupling manual]), 
    307 requires some additional features. 
     328   $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>' 
     329 
     330The makenemo feature ``-e`` was introduced to 
     331readdress at compilation time the standard MY_SRC folder (usually found in NEMO configurations) with 
     332a user defined external one. 
     333 
     334The compilation of more articulated BGC model code & infrastructure, 
     335like in the case of BFM (|BFM man|_), requires some additional features. 
    308336 
    309337As before, let’s assume a coupled configuration name *NEMO_MYBGC*, 
    310 but in this case MYBGC model root becomes ``<MYBGCPATH>`` that contains 4 different subfolders for 
    311 biogeochemistry, named ``initialization``, ``pelagic``, and ``benthic``, and 
    312 a separate one named ``nemo_coupling`` including the modified ``MY_SRC`` routines. 
     338but in this case MYBGC model root becomes :file:`MYBGC` path that 
     339contains 4 different subfolders for biogeochemistry, 
     340named :file:`initialization`, :file:`pelagic`, and :file:`benthic`, 
     341and a separate one named :file:`nemo_coupling` including the modified `MY_SRC` routines. 
    313342The latter folder containing the modified NEMO coupling interface will be still linked using 
    314 the makenemo “-e” option. 
     343the makenemo ``-e`` option. 
    315344 
    316345In order to include the BGC model subfolders in the compilation of NEMO code, 
    317 it will be necessary to extend the configuration ``cpp_NEMO_MYBGC.fcm`` file to include the specific paths of 
    318 ``MYBGC`` folders, as in the following example 
     346it will be necessary to extend the configuration :file:`cpp_NEMO_MYBGC.fcm` file to include the specific paths of :file:`MYBGC` folders, as in the following example 
    319347 
    320348.. code-block:: perl 
    321349 
    322    bld::tool::fppkeys  key_iomput key_mpp_mpi key_top 
    323     
    324    src::MYBGC::initialization         <MYBGCPATH>/initialization 
    325    src::MYBGC::pelagic                <MYBGCPATH>/pelagic 
    326    src::MYBGC::benthic                <MYBGCPATH>/benthic 
    327     
    328    bld::pp::MYBGC      1 
    329    bld::tool::fppflags::MYBGC   %FPPFLAGS 
    330    bld::tool::fppkeys           %bld::tool::fppkeys MYBGC_MACROS 
     350   bld::tool::fppkeys  key_iomput key_mpp_mpi key_top 
     351 
     352   src::MYBGC::initialization         <MYBGCPATH>/initialization 
     353   src::MYBGC::pelagic                <MYBGCPATH>/pelagic 
     354   src::MYBGC::benthic                <MYBGCPATH>/benthic 
     355 
     356   bld::pp::MYBGC      1 
     357   bld::tool::fppflags::MYBGC   %FPPFLAGS 
     358   bld::tool::fppkeys           %bld::tool::fppkeys MYBGC_MACROS 
    331359 
    332360where *MYBGC_MACROS* is the space delimited list of macros used in *MYBGC* model for 
    333361selecting/excluding specific parts of the code. 
    334 The BGC model code will be preprocessed in the configuration ``BLD`` folder as for NEMO, 
    335 but with an independent path, like ``NEMO_MYBGC/BLD/MYBGC/<subforlders>``. 
     362The BGC model code will be preprocessed in the configuration :file:`BLD` folder as for NEMO, 
     363but with an independent path, like :file:`NEMO_MYBGC/BLD/MYBGC/<subforlders>`. 
    336364 
    337365The compilation will be performed similarly to in the previous case with the following 
     
    339367.. code-block:: console 
    340368 
    341    $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>/nemo_coupling' 
    342  
    343 Note that, the additional lines specific for the BGC model source and build paths can be written into 
    344 a separate file, e.g. named ``MYBGC.fcm``, and then simply included in the ``cpp_NEMO_MYBGC.fcm`` as follow 
    345  
    346 .. code-block:: perl 
    347  
    348    bld::tool::fppkeys  key_zdftke key_dynspg_ts key_iomput key_mpp_mpi key_top 
    349    inc <MYBGCPATH>/MYBGC.fcm 
    350  
    351 This will enable a more portable compilation structure for all MYBGC related configurations. 
    352  
    353 **Important**: the coupling interface contained in nemo_coupling cannot be added using the FCM syntax, 
    354 as the same files already exists in NEMO and they are overridden only with the readdressing of MY_SRC contents to 
    355 avoid compilation conflicts due to duplicate routines. 
    356  
    357 All modifications illustrated above, can be easily implemented using shell or python scripting to 
    358 edit the NEMO configuration CPP.fcm file and to create the BGC model specific FCM compilation file with code paths. 
     369   $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>/nemo_coupling' 
     370 
     371.. note:: 
     372   The additional lines specific for the BGC model source and build paths can be written into 
     373   a separate file, e.g. named :file:`MYBGC.fcm`, 
     374   and then simply included in the :file:`cpp_NEMO_MYBGC.fcm` as follow 
     375 
     376   .. code-block:: perl 
     377 
     378      bld::tool::fppkeys  key_zdftke key_dynspg_ts key_iomput key_mpp_mpi key_top 
     379      inc <MYBGCPATH>/MYBGC.fcm 
     380 
     381   This will enable a more portable compilation structure for all MYBGC related configurations. 
     382 
     383.. warning:: 
     384   The coupling interface contained in :file:`nemo_coupling` cannot be added using the FCM syntax, 
     385   as the same files already exists in NEMO and they are overridden only with 
     386   the readdressing of MY_SRC contents to avoid compilation conflicts due to duplicate routines. 
     387 
     388All modifications illustrated above, can be easily implemented using shell or python scripting 
     389to edit the NEMO configuration :file:`CPP.fcm` file and 
     390to create the BGC model specific FCM compilation file with code paths. 
     391 
     392.. |BFM man| replace:: BFM-NEMO coupling manual 
  • NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/src/TOP/trcbdy.F90

    r11536 r11954  
    9595         END DO 
    9696         IF( ANY(llsend1) .OR. ANY(llrecv1) ) THEN   ! if need to send/recv in at least one direction 
    97             CALL lbc_lnk( 'bdytra', tsa, 'T',  1., kfillmode=jpfillnothing ,lsend=llsend1, lrecv=llrecv1 ) 
     97            CALL lbc_lnk( 'trcbdy', tra, 'T',  1., kfillmode=jpfillnothing ,lsend=llsend1, lrecv=llrecv1 ) 
    9898         END IF 
    9999         ! 
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