Changeset 10530
 Timestamp:
 20190116T12:18:17+01:00 (18 months ago)
 Location:
 NEMO/trunk/doc
 Files:

 3 edited
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NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.bib
r10499 r10530 2807 2807 } 2808 2808 2809 @Article{Mathiot2017, 2810 AUTHOR = {Mathiot, P. and Jenkins, A. and Harris, C. and Madec, G.}, 2811 TITLE = {Explicit representation and parametrised impacts of under ice shelf seas in the ${z}^{\ast}$ coordinate ocean model NEMO 3.6}, 2812 JOURNAL = {Geoscientific Model Development}, 2813 VOLUME = {10}, 2814 YEAR = {2017}, 2815 NUMBER = {7}, 2816 PAGES = {28492874}, 2817 URL = {https://www.geoscimodeldev.net/10/2849/2017/}, 2818 DOI = {10.5194/gmd1028492017} 2819 } 2820 2809 2821 @ARTICLE{McDougall1987, 2810 2822 author = {T. J. McDougall}, 
NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex
r10481 r10530 391 391 392 392 Options are defined through the \ngn{nambdy} \ngn{nambdy\_dta} namelist variables. 393 The BDY module is the core implementation of open boundary conditions for regional configurations. 394 It implements the Flow Relaxation Scheme algorithm for temperature, salinity, velocities and ice fields, and 395 the Flather radiation condition for the depthmean transports. 393 The BDY module is the core implementation of open boundary conditions for regional configurations on 394 temperature, salinity, barotropic and baroclinic velocities, as well as ice concentration, ice and snow thicknesses). 395 396 The BDY module was modelled on the OBC module (see NEMO 3.4) and shares many features and 397 a similar coding structure \citep{Chanut2005}. 396 398 The specification of the location of the open boundary is completely flexible and 397 399 allows for example the open boundary to follow an isobath or other irregular contour. 398 399 The BDY module was modelled on the OBC module (see NEMO 3.4) and shares many features and 400 a similar coding structure \citep{Chanut2005}. 401 402 Boundary data files used with earlier versions of NEMO may need to be reordered to work with this version. 400 Boundary data files used with versions of NEMO prior to Version 3.4 may need to be reordered to work with this version. 403 401 See the section on the Input Boundary Data Files for details. 404 402 … … 407 405 \label{subsec:BDY_namelist} 408 406 409 The BDY module is activated by setting \np{ln\_bdy} to true.407 The BDY module is activated by setting \np{ln\_bdy}\forcode{ = .true.} . 410 408 It is possible to define more than one boundary ``set'' and apply different boundary conditions to each set. 411 409 The number of boundary sets is defined by \np{nb\_bdy}. 412 410 Each boundary set may be defined as a set of straight line segments in a namelist 413 411 (\np{ln\_coords\_file}\forcode{ = .false.}) or read in from a file (\np{ln\_coords\_file}\forcode{ = .true.}). 414 If the set is defined in a namelist, then the namelists nambdy\_indexmust be included separately, one for each set.412 If the set is defined in a namelist, then the namelists \ngn{nambdy\_index} must be included separately, one for each set. 415 413 If the set is defined by a file, then a ``\ifile{coordinates.bdy}'' file must be provided. 416 414 The coordinates.bdy file is analagous to the usual NEMO ``\ifile{coordinates}'' file. … … 420 418 421 419 For each boundary set a boundary condition has to be chosen for the barotropic solution 422 (``u2d'':seasurface height and barotropic velocities), for the baroclinic velocities (``u3d''), and423 for the active tracers \footnote{The BDY module does not deal with passive tracers at this version} (``tra'') .420 (``u2d'':seasurface height and barotropic velocities), for the baroclinic velocities (``u3d''), 421 for the active tracers \footnote{The BDY module does not deal with passive tracers at this version} (``tra''), and seaice (``ice''). 424 422 For each set of variables there is a choice of algorithm and a choice for the data, 425 eg. for the active tracers the algorithm is set by \np{ nn\_tra} and the choice of data is set by \np{nn\_tra\_dta}.423 eg. for the active tracers the algorithm is set by \np{cn\_tra} and the choice of data is set by \np{nn\_tra\_dta}.\\ 426 424 427 425 The choice of algorithm is currently as follows: 428 426 429 \begin{ itemize}430 \item[ 0.] No boundary condition applied.427 \begin{description} 428 \item[\forcode{'none'}:] No boundary condition applied. 431 429 So the solution will ``see'' the land points around the edge of the edge of the domain. 432 \item[1.] Flow Relaxation Scheme (FRS) available for all variables. 433 \item[2.] Flather radiation scheme for the barotropic variables. 434 The Flather scheme is not compatible with the filtered free surface 435 ({\it dynspg\_ts}). 436 \end{itemize} 430 \item[\forcode{'specified'}:] Specified boundary condition applied (only available for baroclinic velocity and tracer variables). 431 \item[\forcode{'neumann'}:] Value at the boundary are duplicated (No gradient). Only available for baroclinic velocity and tracer variables. 432 \item[\forcode{'frs'}:] Flow Relaxation Scheme (FRS) available for all variables. 433 \item[\forcode{'Orlanski'}:] Orlanski radiation scheme (fully oblique) for barotropic, baroclinic and tracer variables. 434 \item[\forcode{'Orlanski_npo'}:] Orlanski radiation scheme for barotropic, baroclinic and tracer variables. 435 \item[\forcode{'flather'}:] Flather radiation scheme for the barotropic variables only. 436 \end{description} 437 437 438 438 The main choice for the boundary data is to use initial conditions as boundary data 439 439 (\np{nn\_tra\_dta}\forcode{ = 0}) or to use external data from a file (\np{nn\_tra\_dta}\forcode{ = 1}). 440 In case the 3d velocity data contain the total velocity (ie, baroclinic and barotropic velocity), 441 the bdy code can derived baroclinic and barotropic velocities by setting \np{ln\_full\_vel}\forcode{ = .true. } 440 442 For the barotropic solution there is also the option to use tidal harmonic forcing either by 441 itself or in addition to other external data. 442 443 If external boundary data is required then the nambdy\_dta namelist must be defined. 444 One nambdy\_dta namelist is required for each boundary set in the order in which 443 itself (\np{nn\_dyn2d\_dta}\forcode{ = 2}) or in addition to other external data (\np{nn\_dyn2d\_dta}\forcode{ = 3}).\\ 444 Seaice salinity, temperature and age data at the boundary are constant and defined repectively by \np{rn\_ice\_sal}, \np{rn\_ice\_tem} and \np{rn\_ice\_age}. 445 446 If external boundary data is required then the \ngn{nambdy\_dta} namelist must be defined. 447 One \ngn{nambdy\_dta} namelist is required for each boundary set in the order in which 445 448 the boundary sets are defined in nambdy. 446 In the example given, two boundary sets have been defined and so there are two nambdy\_dta namelists. 449 In the example given, two boundary sets have been defined. The first one is reading data file in the \ngn{nambdy\_dta} namelist shown above 450 and the second one is using data from intial condition (no namelist bloc needed). 447 451 The boundary data is read in using the fldread module, 448 so the nambdy\_dtanamelist is in the format required for fldread.452 so the \ngn{nambdy\_dta} namelist is in the format required for fldread. 449 453 For each variable required, the filename, the frequency of the files and 450 454 the frequency of the data in the files is given. 451 Also whether or not timeinterpolation is required and whether the data is climatological (timecyclic) data. 452 Note that onthefly spatial interpolation of boundary data is not available at this version. 455 Also whether or not timeinterpolation is required and whether the data is climatological (timecyclic) data.\\ 456 457 There is currently an option to vertically interpolate the open boundary data onto the native grid at runtime. 458 If \np{nn\_bdy\_jpk} $< 1$, it is assumed that the lateral boundary data are already on the native grid. 459 However, if \np{nn\_bdy\_jpk} is set to the number of vertical levels present in the boundary data, 460 a bilinear interpolation onto the native grid will be triggered at runtime. 461 For this to be successful the additional variables: $gdept$, $gdepu$, $gdepv$, $e3t$, $e3u$ and $e3v$, are required to be present in the lateral boundary files. 462 These correspond to the depths and scale factors of the input data, 463 the latter used to make any adjustment to the velocity fields due to differences in the total water depths between the two vertical grids.\\ 453 464 454 465 In the example namelists given, two boundary sets are defined. 455 466 The first set is defined via a file and applies FRS conditions to temperature and salinity and 456 Flather conditions to the barotropic variables. 467 Flather conditions to the barotropic variables. No condition specified for the baroclinic velocity and seaice. 457 468 External data is provided in daily files (from a largescale model). 458 469 Tidal harmonic forcing is also used. 459 470 The second set is defined in a namelist. 460 FRS conditions are applied on temperature and salinity and climatological data is read from externalfiles.471 FRS conditions are applied on temperature and salinity and climatological data is read from initial condition files. 461 472 462 473 % … … 521 532 522 533 % 534 \subsection{Orlanski radiation scheme} 535 \label{subsec:BDY_orlanski_scheme} 536 537 The Orlanski scheme is based on the algorithm described by \citep{Marchesiello2001}, hereafter MMS. 538 539 The adaptive Orlanski condition solves a wave plus relaxation equation at the boundary: 540 \begin{equation} 541 \frac{\partial\phi}{\partial t} + c_x \frac{\partial\phi}{\partial x} + c_y \frac{\partial\phi}{\partial y} = 542 \frac{1}{\tau}(\phi  \phi^{ext}) 543 \label{eq:wave_continuous} 544 \end{equation} 545 546 where $\phi$ is the model field, $x$ and $y$ refer to the normal and tangential directions to the boundary respectively, and the phase 547 velocities are diagnosed from the model fields as: 548 549 \begin{equation} \label{eq:cx} 550 c_x = \frac{\partial\phi}{\partial t}\frac{\partial\phi / \partial x}{(\partial\phi /\partial x)^2 + (\partial\phi /\partial y)^2} 551 \end{equation} 552 \begin{equation} 553 \label{eq:cy} 554 c_y = \frac{\partial\phi}{\partial t}\frac{\partial\phi / \partial y}{(\partial\phi /\partial x)^2 + (\partial\phi /\partial y)^2} 555 \end{equation} 556 557 (As noted by MMS, this is a circular diagnosis of the phase speeds which only makes sense on a discrete grid). 558 Equation (\autoref{eq:wave_continuous}) is defined adaptively depending on the sign of the phase velocity normal to the boundary $c_x$. 559 For $c_x$ outward, we have 560 561 \begin{equation} 562 \tau = \tau_{out} 563 \end{equation} 564 565 For $c_x$ inward, the radiation equation is not applied: 566 567 \begin{equation} 568 \tau = \tau_{in}\,\,\,;\,\,\, c_x = c_y = 0 569 \label{eq:tau_in} 570 \end{equation} 571 572 Generally the relaxation time scale at inward propagation points \np{(rn\_time\_dmp}) is set much shorter than the time scale at outward propagation 573 points (\np{rn\_time\_dmp\_out}) so that the solution is constrained more strongly by the external data at inward propagation points. 574 See \autoref{subsec:BDY_relaxation} for detailed on the spatial shape of the scaling.\\ 575 The ``normal propagation of oblique radiation'' or NPO approximation (called \forcode{'orlanski_npo'}) involves assuming 576 that $c_y$ is zero in equation (\autoref{eq:wave_continuous}), but including 577 this term in the denominator of equation (\autoref{eq:cx}). Both versions of the scheme are options in BDY. Equations 578 (\autoref{eq:wave_continuous})  (\autoref{eq:tau_in}) correspond to equations (13)  (15) and (2)  (3) in MMS.\\ 579 580 % 581 \subsection{Relaxation at the boundary} 582 \label{subsec:BDY_relaxation} 583 584 In addition to a specific boundary condition specified as \np{cn\_tra} and \np{cn\_dyn3d}, relaxation on baroclinic velocities and tracers variables are available. 585 It is control by the namelist parameter \np{ln\_tra\_dmp} and \np{ln\_dyn3d\_dmp} for each boundary set. 586 587 The relaxation time scale value (\np{rn\_time\_dmp} and \np{rn\_time\_dmp\_out}, $\tau$) are defined at the boundaries itself. 588 This time scale ($\alpha$) is weighted by the distance ($d$) from the boundary over \np{nn\_rimwidth} cells ($N$): 589 590 \[ 591 \alpha = \frac{1}{\tau}(\frac{N+1d}{N})^2, \quad d=1,N 592 \] 593 594 The same scaling is applied in the Orlanski damping. 595 596 % 523 597 \subsection{Boundary geometry} 524 598 \label{subsec:BDY_geometry} … … 536 610 by reading in a ``\ifile{coordinates.bdy}'' file. 537 611 The nambdy\_index namelist defines a series of straightline segments for north, east, south and west boundaries. 612 One nambdy\_index namelist bloc is needed for each boundary condition defined by indexes. 538 613 For the northern boundary, \np{nbdysegn} gives the number of segments, 539 614 \np{jpjnob} gives the $j$ index for each segment and \np{jpindt} and 540 615 \np{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries. 541 616 These segments define a list of $T$ grid points along the outermost row of the boundary ($nbr\,=\, 1$). 542 The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if $nn\_rimwidth\,>\,1$.617 The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np{nn\_rimwidth}\forcode{ > 1}. 543 618 544 619 The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file. … … 581 656 The 3D fields also have a depth dimension. 582 657 583 AtVersion 3.4 there are new restrictions on the order in which the boundary points are defined658 From Version 3.4 there are new restrictions on the order in which the boundary points are defined 584 659 (and therefore restrictions on the order of the data in the file). 585 660 In particular: … … 593 668 \end{enumerate} 594 669 595 These restrictions mean that data files used with previous versions of the model may not work with version 3.4. 596 A\fortran utility {\it bdy\_reorder} exists in the TOOLS directory which 597 will reorder the data in old BDY data files. 670 These restrictions mean that data files used with versions of the 671 model prior to Version 3.4 may not work with Version 3.4 onwards. 672 A \fortran utility {\it bdy\_reorder} exists in the TOOLS directory which 673 will reorder the data in old BDY data files. 598 674 599 675 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> … … 626 702 applied to all boundaries at once. 627 703 628 \newpage629 704 % 630 705 \subsection{Tidal harmonic forcing} … … 636 711 % 637 712 638 Options are defined through the \ngn{nambdy\_tide} namelist variables. 639 To be written.... 713 Options are defined through the \ngn{nambdy\_tide} namelist variables 714 for reading in the complex harmonic amplitudes of elevation (ssh) and barotropic velocity (u,v). 715 716 The tidal harmonic data can be specified in 2 ways.\\ 717 First it can be specified on a 2D grid covering the entire model domain in which case the user should set \np{ln\_bdytide\_2ddta }\forcode{ = .true.}. 718 In this case the model assumes that the real and imaginary parts are split. 719 The variable naming convention is \textit{constituent\_name\_z1} for real SSH and \textit{constituent\_name\_z2} for imaginary SSH. 720 The available \textit{constituent\_names} in NEMO are defined in \rou{SBC/tide.h90} 721 Likewise for $u$ and $v$ data. File name is assumed to be \np{filtide}\ifile{\_grid\_T} for the elevation component 722 and \np{filtide}\ifile{\_grid\_U} for the u barotropic velocity and \np{filtide}\ifile{\_grid\_V} for the v barotropic velocity.\\ 723 Otherwise, the tidal data must be specified along bdy segments. 724 In this case each constituent has its own file name and the real part is assumed to be z1 and the imaginary part z2 for SSH. 725 Similarly u1, u2 and v1, v2 for velocities. Input file name convention (for elevation of the M2 tidal component) is \np{filtide}\ifile{M2\_grid\_T}. 726 Similar logic applies for other components and u and v barotropic velocities.\\ 727 728 The data may also be in complex conjugate form. If that is the case then the user should set \np{ln\_bdytide\_conj}\forcode{ = .true. } 729 so the model correctly interprets the data. The default case assumes it is not in complex conjugate form. 730 731 Note the barotropic velocities are assumed to be on the model native grid and must be rotated as appropriate from the source grid upon which they are extracted from. 732 To do so convert to U, V amplitude and phase into tidal ellipses. Add the grid rotation to ellipse inclination and convert back. Be careful about conventions 733 of direction of rotation, e.g. anticlockwise or clockwise. 640 734 641 735 \biblio 
NEMO/trunk/doc/namelists/nambdy
r10445 r10530 3 3 ! 4 4 ln_bdy = .false. ! Use unstructured open boundaries 5 nb_bdy = 0! number of open boundary sets6 ln_coords_file = .true. ! =T : read bdy coordinates from file5 nb_bdy = 2 ! number of open boundary sets 6 ln_coords_file = .true. , .false. ! =T : read bdy coordinates from file 7 7 cn_coords_file = 'coordinates.bdy.nc' ! bdy coordinates files 8 8 ln_mask_file = .false. ! =T : read mask from file 9 cn_mask_file = '' 10 cn_dyn2d = ' none' !11 nn_dyn2d_dta = 0! = 0, bdy data are equal to the initial state9 cn_mask_file = '' ! name of mask file (if ln_mask_file=.TRUE.) 10 cn_dyn2d = 'flather', 'none' ! 11 nn_dyn2d_dta = 3 , 0 ! = 0, bdy data are equal to the initial state 12 12 ! ! = 1, bdy data are read in 'bdydata .nc' files 13 13 ! ! = 2, use tidal harmonic forcing data from files 14 14 ! ! = 3, use external data AND tidal harmonic forcing 15 cn_dyn3d = 'none' !16 nn_dyn3d_dta = 0 15 cn_dyn3d = 'none' , 'none' 16 nn_dyn3d_dta = 0 , 0 ! = 0, bdy data are equal to the initial state 17 17 ! ! = 1, bdy data are read in 'bdydata .nc' files 18 cn_tra = ' none' !19 nn_tra_dta = 0! = 0, bdy data are equal to the initial state18 cn_tra = 'frs' , 'frs' 19 nn_tra_dta = 1 , 0 ! = 0, bdy data are equal to the initial state 20 20 ! ! = 1, bdy data are read in 'bdydata .nc' files 21 cn_ice = 'none' !22 nn_ice_dta = 0 21 cn_ice = 'none' , 'none' 22 nn_ice_dta = 0, 0 ! = 0, bdy data are equal to the initial state 23 23 ! ! = 1, bdy data are read in 'bdydata .nc' files 24 rn_ice_tem = 270. 25 rn_ice_sal = 10. 26 rn_ice_age = 30. 24 rn_ice_tem = 270., 270. ! si3 only: arbitrary temperature of incoming sea ice 25 rn_ice_sal = 10. , 10. ! si3 only:  salinity  26 rn_ice_age = 30. , 30. ! si3 only:  age  27 27 ! 28 ln_tra_dmp =.false. 29 ln_dyn3d_dmp =.false. 30 rn_time_dmp = 1. 31 rn_time_dmp_out = 1. 32 nn_rimwidth = 10 28 ln_tra_dmp =.false., .false. ! open boudaries conditions for tracers 29 ln_dyn3d_dmp =.false., .false. ! open boundary condition for baroclinic velocities 30 rn_time_dmp = 1., 1. ! Damping time scale in days 31 rn_time_dmp_out = 1., 1. ! Outflow damping time scale 32 nn_rimwidth = 10, 5 ! width of the relaxation zone 33 33 ln_vol = .false. ! total volume correction (see nn_volctl parameter) 34 34 nn_volctl = 1 ! = 0, the total water flux across open boundaries is zero 35 35 nb_jpk_bdy = 1 ! number of levels in the bdy data (set < 0 if consistent with planned run) 36 36 / 37 ! 38 &nambdy_index ! index definition of bdy 39 ! 40 ctypebdy = 'S' 41 nbdyind = 2 42 nbdybeg = 2 43 nbdyend = 273 44 /
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