source: NEMO/branches/UKMO/NEMO_4.0_GO8_package_text_diagnostics/src/TOP/README.rst @ 10947

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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
131.. literalinclude:: ../../namelists/namtrc
132
133.. literalinclude:: ../../namelists/namtrc_dta
134
135.. literalinclude:: ../../namelists/namtrc_adv
136
137.. literalinclude:: ../../namelists/namtrc_ldf
138
139.. literalinclude:: ../../namelists/namtrc_rad
140
141.. literalinclude:: ../../namelists/namtrc_snk
142
143.. literalinclude:: ../../namelists/namtrc_dmp
144
145.. literalinclude:: ../../namelists/namtrc_ice
146
147.. literalinclude:: ../../namelists/namtrc_trd
148
149.. literalinclude:: ../../namelists/namtrc_bc
150
151.. literalinclude:: ../../namelists/namtrc_bdy
152
153.. literalinclude:: ../../namelists/namage
154
155Two main types of data structure are used within TOP interface to initialize tracer properties (1) and
156to provide related initial and boundary conditions (2).
157
158**1. TOP tracers initialization**: sn_tracer (namtrc)
159
160Beside providing name and metadata for tracers,
161here are also defined the use of initial ({{{sn_tracer%llinit}}}) and
162boundary ({{{sn_tracer%llsbc, sn_tracer%llcbc, sn_tracer%llobc}}}) conditions.
163
164In the following, an example of the full structure definition is given for two idealized tracers both with
165initial conditions given, while the first has only surface boundary forcing and
166the second both surface and coastal forcings:
167
168.. code-block:: fortran
169
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.
173
174As tracers in BGC models are increasingly growing,
175the same structure can be written also in a more compact and readable way:
176
177.. code-block:: fortran
178
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.
187
188The data structure is internally initialized by code with dummy names and
189all 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)
192
193The 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
196Input fields are prescribed within namtrc_dta (with sn_trcdta structure),
197while Boundary Conditions are applied to the model by means of namtrc_bc,
198with dedicated structure fields for surface (sn_trcsbc), riverine (sn_trccbc), and
199lateral open (sn_trcobc) boundaries.
200
201The following example illustrates the data structure in the case of initial condition for
202a single tracer contained in the file named tracer_1_data.nc (.nc is implicitly assumed in namelist filename),
203with a doubled initial value, and located in the usr/work/model/inputdata/ folder:
204
205.. code-block:: fortran
206
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
213Note 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
216namelist_trc
217------------
218
219Here 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
229``MY_TRC`` interface for coupling external BGC models
230=====================================================
231
232The generalized interface is pivoted on MY_TRC module that contains template files to build the coupling between
233NEMO and any external BGC model.
234
235The call to MY_TRC is activated by setting ``ln_my_trc = .true.`` (in namtrc)
236
237The following 6 fortran files are available in MY_TRC with the specific purposes here described.
238
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.
269
270Coupling an external BGC model using NEMO framework
271===================================================
272
273The coupling with an external BGC model through the NEMO compilation framework can be achieved in
274different ways according to the degree of coding complexity of the Biogeochemical model, like e.g.,
275the whole code is made only by one file or it has multiple modules and interfaces spread across several subfolders.
276
277Beside the 6 core files of MY_TRC module, let’s assume an external BGC model named *MYBGC* and constituted by
278a rather essential coding structure, likely few Fortran files.
279The new coupled configuration name is *NEMO_MYBGC*.
280
281The best solution is to have all files (the modified ``MY_TRC`` routines and the BGC model ones) placed in
282a unique folder with root ``MYBGCPATH`` and to use the makenemo external readdressing of ``MY_SRC`` folder.
283
284The coupled configuration listed in ``work_cfgs.txt`` will look like
285
286::
287
288   NEMO_MYBGC OPA_SRC TOP_SRC
289
290and the related ``cpp_MYBGC.fcm`` content will be
291
292.. code-block:: perl
293
294   bld::tool::fppkeys  key_iomput key_mpp_mpi key_top
295
296the compilation with ``makenemo`` will be executed through the following syntax
297
298.. code-block:: console
299
300   $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>'
301
302The 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
305The 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]),
307requires some additional features.
308
309As before, let’s assume a coupled configuration name *NEMO_MYBGC*,
310but in this case MYBGC model root becomes ``<MYBGCPATH>`` that contains 4 different subfolders for
311biogeochemistry, named ``initialization``, ``pelagic``, and ``benthic``, and
312a separate one named ``nemo_coupling`` including the modified ``MY_SRC`` routines.
313The latter folder containing the modified NEMO coupling interface will be still linked using
314the makenemo “-e” option.
315
316In order to include the BGC model subfolders in the compilation of NEMO code,
317it 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
319
320.. code-block:: perl
321
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
331
332where *MYBGC_MACROS* is the space delimited list of macros used in *MYBGC* model for
333selecting/excluding specific parts of the code.
334The BGC model code will be preprocessed in the configuration ``BLD`` folder as for NEMO,
335but with an independent path, like ``NEMO_MYBGC/BLD/MYBGC/<subforlders>``.
336
337The compilation will be performed similarly to in the previous case with the following
338
339.. code-block:: console
340
341   $ makenemo -n 'NEMO_MYBGC' -m '<arch_my_machine>' -j 8 -e '<MYBGCPATH>/nemo_coupling'
342
343Note that, the additional lines specific for the BGC model source and build paths can be written into
344a 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
351This 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,
354as the same files already exists in NEMO and they are overridden only with the readdressing of MY_SRC contents to
355avoid compilation conflicts due to duplicate routines.
356
357All modifications illustrated above, can be easily implemented using shell or python scripting to
358edit the NEMO configuration CPP.fcm file and to create the BGC model specific FCM compilation file with code paths.
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