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1***************
2Oceanic tracers
3***************
4
5.. contents::
6   :local:
7
8TOP (Tracers in the Ocean Paradigm) is the NEMO hardwired interface toward biogeochemical models and
9provide the physical constraints/boundaries for oceanic tracers.
10It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules.
11
12This component of the NEMO framework allows one to exploit available modules (see below) and
13further develop a range of applications, spanning from the implementation of a dye passive tracer to
14evaluate dispersion processes (by means of MY_TRC), track water masses age (AGE module),
15assess the ocean interior penetration of persistent chemical compounds (e.g., gases like CFC or even PCBs),
16up to the full set of equations involving marine biogeochemical cycles.
17
18Structure
19=========
20
21TOP interface has the following location in the source code ``./src/MBG/`` and
22the following modules are available:
23
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
44The usage of TOP is activated i) by including in the configuration definition  the component ``MBG`` and
45ii) 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"]).
47
48As an example, the user can refer to already available configurations in the code,
49``GYRE_PISCES`` being the NEMO biogeochemical demonstrator and
50``GYRE_BFM`` to see the required configuration elements to couple with an external biogeochemical model
51(see also Section 4) .
52
53Note that, since version 4.0, TOP interface core functionalities are activated by means of logical keys and
54all submodules preprocessing macros from previous versions were removed.
55
56Here below the list of preprocessing keys that applies to the TOP interface (beside ``key_top``):
57
58``key_iomput``
59   use XIOS I/O
60
61``key_agrif``
62   enable AGRIF coupling
63
64``key_trdtrc`` & ``key_trdmxl_trc``
65   trend computation for tracers
66
67Synthetic Workflow
68==================
69
70A synthetic description of the TOP interface workflow is given below to summarize the steps involved in
71the computation of biogeochemical and physical trends and their time integration and outputs,
72by reporting also the principal Fortran subroutine herein involved.
73
74**Model initialization (OPA_SRC/nemogcm.F90)**
75
76call 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
92call 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
117
118Namelists walkthrough
119=====================
120
121namelist_top
122------------
123
124Here below are listed the features/options of the TOP interface accessible through the namelist_top_ref and
125modifiable by means of namelist_top_cfg (as for NEMO physical ones).
126
127Note that ## is used to refer to a number in an array field.
128
129.. literalinclude:: ../../namelists/namtrc_run
130   :language: fortran
131
132.. literalinclude:: ../../namelists/namtrc
133   :language: fortran
134
135.. literalinclude:: ../../namelists/namtrc_dta
136   :language: fortran
137
138.. literalinclude:: ../../namelists/namtrc_adv
139   :language: fortran
140
141.. literalinclude:: ../../namelists/namtrc_ldf
142   :language: fortran
143
144.. literalinclude:: ../../namelists/namtrc_rad
145   :language: fortran
146
147.. literalinclude:: ../../namelists/namtrc_snk
148   :language: fortran
149
150.. literalinclude:: ../../namelists/namtrc_dmp
151   :language: fortran
152
153.. literalinclude:: ../../namelists/namtrc_ice
154   :language: fortran
155
156.. literalinclude:: ../../namelists/namtrc_trd
157   :language: fortran
158
159.. literalinclude:: ../../namelists/namtrc_bc
160   :language: fortran
161
162.. literalinclude:: ../../namelists/namtrc_bdy
163   :language: fortran
164
165.. literalinclude:: ../../namelists/namage
166   :language: fortran
167
168Two main types of data structure are used within TOP interface to initialize tracer properties (1) and
169to provide related initial and boundary conditions (2).
170
171**1. TOP tracers initialization**: sn_tracer (namtrc)
172
173Beside providing name and metadata for tracers,
174here are also defined the use of initial ({{{sn_tracer%llinit}}}) and
175boundary ({{{sn_tracer%llsbc, sn_tracer%llcbc, sn_tracer%llobc}}}) conditions.
176
177In the following, an example of the full structure definition is given for two idealized tracers both with
178initial conditions given, while the first has only surface boundary forcing and
179the second both surface and coastal forcings:
180
181.. code-block:: fortran
182
183   !             !    name   !           title of the field            !   units    ! initial data ! sbc   !   cbc  !   obc  !
184   sn_tracer(1)  = 'TRC1'    , 'Tracer 1 Concentration                ',   ' - '    ,  .true.      , .true., .false., .true.
185   sn_tracer(2)  = 'TRC2 '   , 'Tracer 2 Concentration                ',   ' - '    ,  .true.      , .true., .true. , .false.
186
187As tracers in BGC models are increasingly growing,
188the same structure can be written also in a more compact and readable way:
189
190.. code-block:: fortran
191
192   !             !    name   !           title of the field            !   units    ! initial data !
193   sn_tracer(1)  = 'TRC1'    , 'Tracer 1 Concentration                ',   ' - '    ,   .true.
194   sn_tracer(2)  = 'TRC2 '   , 'Tracer 2 Concentration                ',   ' - '    ,   .true.
195   ! sbc
196   sn_tracer(1)%llsbc = .true.
197   sn_tracer(2)%llsbc = .true.
198   ! cbc
199   sn_tracer(2)%llcbc = .true.
200
201The data structure is internally initialized by code with dummy names and
202all initialization/forcing logical fields set to .false. .
203
204**2. Structures to read input initial and boundary conditions**: namtrc_dta (sn_trcdta), namtrc_bc (sn_trcsbc/sn_trccbc/sn_trcobc)
205
206The overall data structure (Fortran type) is based on the general one defined for NEMO core in the SBC component
207(see details in User Manual SBC Chapter on Input Data specification).
208
209Input fields are prescribed within namtrc_dta (with sn_trcdta structure),
210while Boundary Conditions are applied to the model by means of namtrc_bc,
211with dedicated structure fields for surface (sn_trcsbc), riverine (sn_trccbc), and
212lateral open (sn_trcobc) boundaries.
213
214The following example illustrates the data structure in the case of initial condition for
215a single tracer contained in the file named tracer_1_data.nc (.nc is implicitly assumed in namelist filename),
216with a doubled initial value, and located in the usr/work/model/inputdata/ folder:
217
218.. code-block:: fortran
219
220   !               !  file name             ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
221   !               !                        !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
222     sn_trcdta(1)  = 'tracer_1_data'        ,        -12        ,  'TRC1'   ,    .false.   , .true. , 'yearly'  , ''       , ''       , ''
223     rf_trfac(1) = 2.0
224     cn_dir = “usr/work/model/inputdata/”
225
226Note that, the Lateral Open Boundaries conditions are applied on the segments defined for the physical core of NEMO
227(see BDY description in the User Manual).
228
229namelist_trc
230------------
231
232Here below the description of namelist_trc_ref used to handle Carbon tracers modules, namely CFC and C14.
233
234|||| &'''namcfc'''     !   CFC ||
235
236|||| &'''namc14_typ'''     !  C14 - type of C14 tracer, default values of C14/C and pco2 ||
237
238|||| &'''namc14_sbc'''     !  C14 - surface BC ||
239
240|||| &'''namc14_fcg'''     !  files & dates ||
241
242``MY_TRC`` interface for coupling external BGC models
243=====================================================
244
245The generalized interface is pivoted on MY_TRC module that contains template files to build the coupling between
246NEMO and any external BGC model.
247
248The call to MY_TRC is activated by setting ``ln_my_trc = .true.`` (in namtrc)
249
250The following 6 fortran files are available in MY_TRC with the specific purposes here described.
251
252``par_my_trc.F90``
253   This module allows to define additional arrays and public variables to be used within the MY_TRC interface
254
255``trcini_my_trc.F90``
256   Here are initialized user defined namelists and the call to the external BGC model initialization procedures to
257   populate general tracer array (trn and trb). Here are also likely to be defined suport arrays related to
258   system metrics that could be needed by the BGC model.
259
260``trcnam_my_trc.F90``
261   This routine is called at the beginning of trcini_my_trc and should contain the initialization of
262   additional namelists for the BGC model or user-defined code.
263
264``trcsms_my_trc.F90``
265   The routine performs the call to Boundary Conditions and its main purpose is to
266   contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model.
267   Be aware that lateral boundary conditions are applied in trcnxt routine.
268   IMPORTANT: the routines to compute the light penetration along the water column and
269   the tracer vertical sinking should be defined/called in here, as generalized modules are still missing in
270   the code.
271
272``trcice_my_trc.F90``
273   Here it is possible to prescribe the tracers concentrations in the seaice that will be used as
274   boundary conditions when ice melting occurs (nn_ice_tr =1 in namtrc_ice).
275   See e.g. the correspondent PISCES subroutine.
276
277``trcwri_my_trc.F90``
278   This routine performs the output of the model tracers (only those defined in namtrc) using IOM module
279   (see Manual Chapter “Output and Diagnostics”).
280   It is possible to place here the output of additional variables produced by the model,
281   if not done elsewhere in the code, using the call to iom_put.
282
283Coupling an external BGC model using NEMO framework
284===================================================
285
286The coupling with an external BGC model through the NEMO compilation framework can be achieved in
287different ways according to the degree of coding complexity of the Biogeochemical model, like e.g.,
288the whole code is made only by one file or it has multiple modules and interfaces spread across several subfolders.
289
290Beside the 6 core files of MY_TRC module, let’s assume an external BGC model named *MYBGC* and constituted by
291a rather essential coding structure, likely few Fortran files.
292The new coupled configuration name is *NEMO_MYBGC*.
293
294The best solution is to have all files (the modified ``MY_TRC`` routines and the BGC model ones) placed in
295a unique folder with root ``MYBGCPATH`` and to use the makenemo external readdressing of ``MY_SRC`` folder.
296
297The coupled configuration listed in ``work_cfgs.txt`` will look like
298
299::
300
301   NEMO_MYBGC OPA_SRC TOP_SRC
302
303and the related ``cpp_MYBGC.fcm`` content will be
304
305.. code-block:: perl
306
307   bld::tool::fppkeys  key_iomput key_mpp_mpi key_top
308
309the compilation with ``makenemo`` will be executed through the following syntax
310
311.. code-block:: console
312
313   $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>'
314
315The makenemo feature “-e” was introduced to readdress at compilation time the standard MY_SRC folder
316(usually found in NEMO configurations) with a user defined external one.
317
318The compilation of more articulated BGC model code & infrastructure, like in the case of BFM
319([http://www.bfm-community.eu/publications/bfmnemomanual_r1.0_201508.pdf BFM-NEMO coupling manual]),
320requires some additional features.
321
322As before, let’s assume a coupled configuration name *NEMO_MYBGC*,
323but in this case MYBGC model root becomes ``<MYBGCPATH>`` that contains 4 different subfolders for
324biogeochemistry, named ``initialization``, ``pelagic``, and ``benthic``, and
325a separate one named ``nemo_coupling`` including the modified ``MY_SRC`` routines.
326The latter folder containing the modified NEMO coupling interface will be still linked using
327the makenemo “-e” option.
328
329In order to include the BGC model subfolders in the compilation of NEMO code,
330it will be necessary to extend the configuration ``cpp_NEMO_MYBGC.fcm`` file to include the specific paths of
331``MYBGC`` folders, as in the following example
332
333.. code-block:: perl
334
335   bld::tool::fppkeys  key_iomput key_mpp_mpi key_top
336
337   src::MYBGC::initialization         <MYBGCPATH>/initialization
338   src::MYBGC::pelagic                <MYBGCPATH>/pelagic
339   src::MYBGC::benthic                <MYBGCPATH>/benthic
340
341   bld::pp::MYBGC      1
342   bld::tool::fppflags::MYBGC   %FPPFLAGS
343   bld::tool::fppkeys           %bld::tool::fppkeys MYBGC_MACROS
344
345where *MYBGC_MACROS* is the space delimited list of macros used in *MYBGC* model for
346selecting/excluding specific parts of the code.
347The BGC model code will be preprocessed in the configuration ``BLD`` folder as for NEMO,
348but with an independent path, like ``NEMO_MYBGC/BLD/MYBGC/<subforlders>``.
349
350The compilation will be performed similarly to in the previous case with the following
351
352.. code-block:: console
353
354   $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>/nemo_coupling'
355
356Note that, the additional lines specific for the BGC model source and build paths can be written into
357a separate file, e.g. named ``MYBGC.fcm``, and then simply included in the ``cpp_NEMO_MYBGC.fcm`` as follow
358
359.. code-block:: perl
360
361   bld::tool::fppkeys  key_zdftke key_dynspg_ts key_iomput key_mpp_mpi key_top
362   inc <MYBGCPATH>/MYBGC.fcm
363
364This will enable a more portable compilation structure for all MYBGC related configurations.
365
366**Important**: the coupling interface contained in nemo_coupling cannot be added using the FCM syntax,
367as the same files already exists in NEMO and they are overridden only with the readdressing of MY_SRC contents to
368avoid compilation conflicts due to duplicate routines.
369
370All modifications illustrated above, can be easily implemented using shell or python scripting to
371edit the NEMO configuration CPP.fcm file and to create the BGC model specific FCM compilation file with code paths.
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