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==<span class="alphabet">A</span>==
==<span class="alphabet">A</span>==


<section begin=ANA_BIOLOGY />;<span id="ANA_BIOLOGY"></span>'''ANA_BIOLOGY'''
<section begin=ANA_BIOLOGY />;<span id="ANA_BIOLOGY"></span>'''[[ANA_BIOLOGY]]'''
:Option to initialize any of the biological models with analytical expressions.
:Option to initialize any of the biological models with analytical expressions.
:'''related = ''' [[#BIOLOGY | BIOLOGY]]
:'''related = ''' [[BIOLOGY]]
:'''routine = ''' [[analytical.F]] (ana_biology)<section end=ANA_BIOLOGY />
:'''routine = ''' [[analytical.F]] (ana_biology)<section end=ANA_BIOLOGY />


;<span id="ANA_BPFLUX"></span>'''ANA_BPFLUX'''
<section begin=ANA_BPFLUX />;<span id="ANA_BPFLUX"></span>'''[[ANA_BPFLUX]]'''
:Option to set passive tracers bottom flux with analytical expressions (usually zero, no flux).
:Option to set passive tracers bottom flux with analytical expressions (usually zero, no flux).
:'''related = ''' [[#BIOLOGY | BIOLOGY]], [[#SEDIMENT | SEDIMENT]]
:'''related = ''' [[BIOLOGY]], [[SEDIMENT]]
:'''routine = ''' [[analytical.F]] (ana_bpflux)
:'''routine = ''' [[analytical.F]] (ana_bpflux)<section end=ANA_BPFLUX />


;<span id="ANA_SPFLUX"></span>'''ANA_SPFLUX'''
<section begin=ANA_SPFLUX />;<span id="ANA_SPFLUX"></span>'''[[ANA_SPFLUX]]'''
:Option to set passive tracers surface flux with analytical expressions (usually zero, no flux).
:Option to set passive tracers surface flux with analytical expressions (usually zero, no flux).
:'''related = ''' [[#BIOLOGY | BIOLOGY]], [[#SEDIMENT | SEDIMENT]]
:'''related = ''' [[BIOLOGY]], [[SEDIMENT]]
:'''routine = ''' [[analytical.F]] (ana_spflux)
:'''routine = ''' [[analytical.F]] (ana_spflux)<section end=ANA_SPFLUX />


==<span class="alphabet">B</span>==
==<span class="alphabet">B</span>==


;<span id="BIOLOGY"></span>'''BIOLOGY'''
<section begin=BIOLOGY />;<span id="BIOLOGY"></span>'''[[BIOLOGY]]'''
:Internal option defined when any of the biological models is activated.
:Internal option defined when any of the biological models is activated.
:'''related = ''' [[#BIO_FASHAM | BIO_FASHAM]], [[#ECOSIM | ECOSIM]], [[#NPZD_FRANKS | NPZD_FRANKS]], [[#NPZD_POWELL | NPZD_POWELL]]
:'''related = ''' [[BIO_FASHAM]], [[ECOSIM]], [[NPZD_FRANKS]], [[NPZD_POWELL]]
:'''routine = ''' [[biology.F]]
:'''routine = ''' [[biology.F]]<section end=BIOLOGY />


;<span id="BIO_FASHAM"></span>'''BIO_FASHAM'''
<section begin=BIO_FASHAM />;<span id="BIO_FASHAM"></span>'''[[BIO_FASHAM]]'''
:Option to activate Fasham-type, nitrogen-based biological model ([[Bibliography#FashamMJR_1990a |Fasham et al., 1990]]; [[Bibliography#FenellK_2006a | Fennel et al., 2006]])
:Option to activate Fasham-type, nitrogen-based biological model ([[Bibliography#FashamMJR_1990a |Fasham et al., 1990]]; [[Bibliography#FenellK_2006a | Fennel et al., 2006]])
:'''related = ''' [[#ANA_BIOLOGY | ANA_BIOLOGY]], [[#ANA_BPFLUX | ANA_BPFLUX]], [[#ANA_SPFLUX | ANA_SPFLUX]], [[#BIO_SEDIMENT | BIO_SEDIMENT]], [[#CARBON | CARBON]], [[#DENITRIFICATION | DENITRIFICATION]], [[#DIAGNOSTICS_BIO | DIAGNOSTICS_BIO]], [[#OXYGEN | OXYGEN]], [[#TALK_PROGNOSTIC | TALK_PROGNOSTIC]]
:'''related = ''' [[ANA_BIOLOGY]], [[ANA_BPFLUX]], [[ANA_SPFLUX]], [[BIO_SEDIMENT]], [[CARBON]], [[DENITRIFICATION]], [[DIAGNOSTICS_BIO]], [[OXYGEN]], [[TALK_PROGNOSTIC]]
:'''conflict = ''' [[#ECOSIM | ECOSIM]], [[#NPZD_FRANKS | NPZD_FRANKS]], [[#NPZD_POWELL | NPZD_POWELL]]
:'''conflict = ''' [[ECOSIM]], [[NPZD_FRANKS]], [[NPZD_POWELL]]
:'''routine = ''' [[fasham.h]], [[bioFasham.in]]
:'''routine = ''' [[fasham.h]], [[bioFasham.in]]<section end=BIO_FASHAM />


;<span id="BIO_SEDIMENT"></span>'''BIO_SEDIMENT'''
<section begin=BIO_SEDIMENT />;<span id="BIO_SEDIMENT"></span>'''[[BIO_SEDIMENT]]'''
:Option to restore fallen particulate material to the nutrient pool in Fasham-type model.
:Option to restore fallen particulate material to the nutrient pool in Fasham-type model.
:'''parent = ''' [[#BIO_FASHAM | BIO_FASHAM]]
:'''parent = ''' [[BIO_FASHAM]]
:'''routine = ''' [[fasham.h]]
:'''routine = ''' [[fasham.h]]<section end=BIO_SEDIMENT />


==<span class="alphabet">C</span>==
==<span class="alphabet">C</span>==


;<span id="CARBON"></span>'''CARBON'''
<section begin=CARBON />;<span id="CARBON"></span>'''[[CARBON]]'''
:Option to include carbon constituents in Fasham-type biological model. Currently, four carbon-based tracer are added to include large detritus ([[Variables#iLDeC|iLDeC]]), small detritus ([[Variables#iSDeC|iSDeC]]), total inorganic carbon ([[Variables#iTIC_|iTIC_]]), and total alkalinity ([[Variables#iTAlk|iTAlk]]).
:Option to include carbon constituents in Fasham-type biological model. Currently, four carbon-based tracer are added to include large detritus ([[Variables#iLDeC|iLDeC]]), small detritus ([[Variables#iSDeC|iSDeC]]), total inorganic carbon ([[Variables#iTIC_|iTIC_]]), and total alkalinity ([[Variables#iTAlk|iTAlk]]).
:'''parent = ''' [[#BIO_FASHAM | BIO_FASHAM]]
:'''parent = ''' [[BIO_FASHAM]]
:'''required = ''' [[#OXYGEN | OXYGEN]]
:'''required = ''' [[OXYGEN]]
:'''routine = ''' [[fasham.h]]
:'''routine = ''' [[fasham.h]]<section end=CARBON />


==<span class="alphabet">D</span>==
==<span class="alphabet">D</span>==


;<span id="DENITRIFICATION"></span>'''DENITRIFICATION'''
<section begin=DENITRIFICATION />;<span id="DENITRIFICATION"></span>'''[[DENITRIFICATION]]'''
:Option to include denitrification processes in Fasham-type biological model.
:Option to include denitrification processes in Fasham-type biological model.
:'''parent = ''' [[#BIO_FASHAM | BIO_FASHAM]]
:'''parent = ''' [[#BIO_FASHAM | BIO_FASHAM]]
:'''routine = ''' [[fasham.h]]
:'''routine = ''' [[fasham.h]]<section end=DENITRIFICATION />


;<span id="DIAGNOSTICS"></span>'''DIAGNOSTICS'''
<section begin=DIAGNOSTICS />;<span id="DIAGNOSTICS"></span>'''[[DIAGNOSTICS]]'''
:Internal option to compute and write balance term diagnostics for tracers and momentum.
:Internal option to compute and write balance term diagnostics for tracers and momentum.
:'''related = ''' [[#DIAGNOSTICS_BIO | DIAGNOSTICS_BIO]], [[#DIAGNOSTICS_TS | DIAGNOSTICS_TS]], [[#DIAGNOSTICS_UV | DIAGNOSTICS_UV]]
:'''related = ''' [[DIAGNOSTICS_BIO]], [[DIAGNOSTICS_TS]], [[DIAGNOSTICS_UV]]
:'''routine = ''' [[set_diags.F]], [[wrt_diags.F]]
:'''routine = ''' [[set_diags.F]], [[wrt_diags.F]]<section end=DIAGNOSTICS />


;<span id="DIAGNOSTICS_BIO"></span>'''DIAGNOSTICS_BIO'''
<section begin=DIAGNOSTICS_BIO />;<span id="DIAGNOSTICS_BIO"></span>'''[[DIAGNOSTICS_BIO]]'''
:Option to compute and write biological diagnostic terms in Fasham-type model.
:Option to compute and write biological diagnostic terms in Fasham-type model.
:'''parent = ''' [[#BIO_FASHAM | BIO_FASHAM]]
:'''parent = ''' [[BIO_FASHAM]]
:'''related = ''' [[#DIAGNOSTICS_TS | DIAGNOSTICS_TS]], [[#DIAGNOSTICS_UV | DIAGNOSTICS_UV]]
:'''related = ''' [[DIAGNOSTICS_TS]], [[DIAGNOSTICS_UV]]
:'''routine = ''' [[fasham.h]], [[wrt_diags.F]]
:'''routine = ''' [[fasham.h]], [[wrt_diags.F]]<section end=DIAGNOSTICS_BIO />


;<span id="DIAGNOSTICS_TS"></span>'''DIAGNOSTICS_TS'''
<section begin=DIAGNOSTICS_TS />;<span id="DIAGNOSTICS_TS"></span>'''[[DIAGNOSTICS_TS]]'''
:Option to compute and write diagnostic terms for tracer equations balances.
:Option to compute and write diagnostic terms for tracer equations balances.
:'''related = ''' [[#DIAGNOSTICS_BIO | DIAGNOSTICS_BIO]], [[#DIAGNOSTICS_UV | DIAGNOSTICS_UV]]
:'''related = ''' [[DIAGNOSTICS_BIO]], [[DIAGNOSTICS_UV]]
:'''routine = ''' [[set_diags.F]], [[step3d_t.F]], [[wrt_diags.F]]
:'''routine = ''' [[set_diags.F]], [[step3d_t.F]], [[wrt_diags.F]]<section end=DIAGNOSTICS_TS />


;<span id="DIAGNOSTICS_UV"></span>'''DIAGNOSTICS_UV'''
<section begin=DIAGNOSTICS_UV />;<span id="DIAGNOSTICS_UV"></span>'''[[DIAGNOSTICS_UV]]'''
:Option to compute and write diagnostic terms for momentum equations balances.
:Option to compute and write diagnostic terms for momentum equations balances.
:'''related = ''' [[#DIAGNOSTICS_BIO | DIAGNOSTICS_BIO]], [[#DIAGNOSTICS_TS | DIAGNOSTICS_TS]]
:'''related = ''' [[DIAGNOSTICS_BIO]], [[DIAGNOSTICS_TS]]
:'''routine = ''' [[set_diags.F]], [[step2d.F]], [[step3d_t.F]], [[wrt_diags.F]]
:'''routine = ''' [[set_diags.F]], [[step2d.F]], [[step3d_t.F]], [[wrt_diags.F]]<section end=DIAGNOSTICS_UV />


==<span class="alphabet">E</span>==
==<span class="alphabet">E</span>==


;<span id="ECOSIM"></span>'''ECOSIM'''
<section begin=ECOSIM />;<span id="ECOSIM"></span>'''[[ECOSIM]]'''
:Option to activate Bio-optical EcoSim ([[Bibliography#BissettWP_1999a |Bissett et al., 1999a,]] [[Bibliography#BissettWP_1999a |b]]) model.
:Option to activate Bio-optical EcoSim ([[Bibliography#BissettWP_1999a |Bissett et al., 1999a,]] [[Bibliography#BissettWP_1999a |b]]) model.
:'''related = ''' [[#ANA_BIOLOGY | ANA_BIOLOGY]], [[#ANA_BPFLUX | ANA_BPFLUX]], [[#ANA_SPFLUX | ANA_SP_FLUX]]
:'''related = ''' [[ANA_BIOLOGY]], [[ANA_BPFLUX]], [[ANA_SP_FLUX]]
:'''conflict = ''' [[#BIO_FASHAM | BIO_FASHAM]], [[#NPZD_FRANKS | NPZD_FRANKS]], [[#NPZD_POWELL | NPZD_POWELL]]
:'''conflict = ''' [[BIO_FASHAM]], [[NPZD_FRANKS]], [[NPZD_POWELL]]
:'''routine = ''' [[ecosim.h]], [[ecosim.in]]
:'''routine = ''' [[ecosim.h]], [[ecosim.in]]<section end=ECOSIM />


==<span class="alphabet">F</span>==
==<span class="alphabet">F</span>==
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==<span class="alphabet">G</span>==
==<span class="alphabet">G</span>==


<section begin=GLS_MIXING />
<section begin=GLS_MIXING />;<span id="GLS_MIXING"></span>'''[[GLS_MIXING]]'''
;<span id="GLS_MIXING"></span>'''[[GLS_MIXING]]'''
:Option to activate Generic Length Scale vertical mixing parameterization ([[Bibliography#WarnerJC_2005a|Warner et al., 2005]]).
:Option to activate ...
:'''related = ''' [[CANUTO_A]], [[CANUTO_B]]
:'''related = ''' [[#CANUTO_A | CANUTO_A]], [[#CANUTO_B | CANUTO_B]]
:'''conflict = ''' [[MY25_MIXING]], [[#LMD_MIXING]]
:'''conflict = ''' [[#MY25_MIXING | MY25_MIXING]], [[#LMD_MIXING | LMD_MIXING]]
:'''routine = ''' [[ gls_prestep.F]], [[ gls_corstep.F]], [[ocean.in]]<section end=GLS_MIXING />
:'''routine = ''' [[ gls_prestep.F]], [[ gls_corstep.F]], [[ocean.in]]
<section end=GLS_MIXING />


==<span class="alphabet">H</span>==
==<span class="alphabet">H</span>==
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==<span class="alphabet">N</span>==
==<span class="alphabet">N</span>==


;<span id="NPZD_FRANKS"></span>'''NPZ_FRANKS'''
<section begin=NPZ_FRANKS />;<span id="NPZD_FRANKS"></span>'''[[NPZ_FRANKS]]'''
:Option to activate [[Bibliography#FranksPJS_1986a | Franks et al. (1986)]] NPZD biological model.
:Option to activate [[Bibliography#FranksPJS_1986a | Franks et al. (1986)]] NPZD biological model.
:'''related = ''' [[#ANA_BIOLOGY | ANA_BIOLOGY]], [[#ANA_BPFLUX | ANA_BPFLUX]], [[#ANA_SPFLUX | ANA_SPFLUX]]
:'''related = ''' [[ANA_BIOLOGY]], [[ANA_BPFLUX]], [[ANA_SPFLUX]]
:'''conflict = ''' [[#BIO_FASHAM | BIO_FASHAM]], [[#ECOSIM | ECOSIM]], [[#NPZD_POWELL | NPZD_POWELL]]
:'''conflict = ''' [[BIO_FASHAM]], [[ECOSIM]], [[NPZD_POWELL]]
:'''routine = ''' [[npzd_Franks.h]], [[npzd_Franks.in]]
:'''routine = ''' [[npzd_Franks.h]], [[npzd_Franks.in]]<section end=NPZ_FRANKS />


;<span id="NPZD_POWELL"></span>'''NPZ_POWELL'''
<section begin=NPZ_POWELL />;<span id="NPZD_POWELL"></span>'''[[NPZ_POWELL]]'''
:Option to activate [[Bibliography#PowellTO_2006a | Powell et al. (1986)]] NPZD biological model.
:Option to activate [[Bibliography#PowellTO_2006a | Powell et al. (1986)]] NPZD biological model.
:'''related = ''' [[#ANA_BIOLOGY | ANA_BIOLOGY]], [[#ANA_BPFLUX | ANA_BPFLUX]], [[#ANA_SPFLUX | ANA_SPFLUX]]
:'''related = ''' [[ANA_BIOLOGY]], [[ANA_BPFLUX]], [[ANA_SPFLUX]]
:'''conflict = ''' [[#BIO_FASHAM | BIO_FASHAM]], [[#ECOSIM | ECOSIM]], [[#NPZD_FRANKS | NPZD_FRANKS]]
:'''conflict = ''' [[BIO_FASHAM]], [[ECOSIM]], [[NPZD_FRANKS]]
:'''routine = ''' [[npzd_Powell.h]], [[npzd_Powell.in]]
:'''routine = ''' [[npzd_Powell.h]], [[npzd_Powell.in]]<section end=NPZ_POWELL />


==<span class="alphabet">O</span>==
==<span class="alphabet">O</span>==


;<span id="OCMIP_OXYGEN_SC"></span>'''OCMIP_OXYGEN_SC'''
<section begin=OCMIP_OXYGEN_SC />;<span id="OCMIP_OXYGEN_SC"></span>'''[[OCMIP_OXYGEN_SC]]'''
:Option to use the [[Biblography#KeelingRF_1998a | Keeling et al. (1998)]] formulae for the Schmit number to model O<sub>2</sub> gas exchange. If deactivated, the formulation of [[Biblography#WanninkhofR_1992a | Wanninkhof (1992)]] is used instead.
:Option to use the [[Biblography#KeelingRF_1998a | Keeling et al. (1998)]] formulae for the Schmit number to model O<sub>2</sub> gas exchange. If deactivated, the formulation of [[Biblography#WanninkhofR_1992a | Wanninkhof (1992)]] is used instead.
:'''parent = ''' [[#BIO_FASHAM | BIO_FASHAM]]
:'''parent = ''' [[BIO_FASHAM]]
:'''required = ''' [[#OXYGEN | OXYGEN]]
:'''required = ''' [[OXYGEN]]
:'''routine = ''' [[fasham.h]]
:'''routine = ''' [[fasham.h]]<section end=OCMIP_OXYGEN_SC />


;<span id="OXYGEN"></span>'''OXYGEN'''
<section begin=OXYGEN />;<span id="OXYGEN"></span>'''[[OXYGEN]]'''
:Option to include oxygen dynamics in Fasham-type biological model. Currently, an additional tracer is added for dissolved oxygen concentration ([[Variables#iOxyg|iOxyg]]).
:Option to include oxygen dynamics in Fasham-type biological model. Currently, an additional tracer is added for dissolved oxygen concentration ([[Variables#iOxyg|iOxyg]]).
:'''parent = ''' [[#BIO_FASHAM | BIO_FASHAM]]
:'''parent = ''' [[BIO_FASHAM]]
:'''routine = ''' [[fasham.h]]
:'''routine = ''' [[fasham.h]]<section end=OXYGEN />


==<span class="alphabet">P</span>==
==<span class="alphabet">P</span>==
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==<span class="alphabet">S</span>==
==<span class="alphabet">S</span>==


;<span id="SOLVE3D"></span>'''SOLVE3D'''
<section begin=SOLVE3D />;<span id="SOLVE3D"></span>'''[[SOLVE3D]]'''
:Option to activate/deactivate 3D model configuration. If activated, ROMS solves 3D (baroclinic) primitive equations. If deactivated, ROMS solves vertically-integrated, shallow water (barotropic) equations.  
:Option to activate/deactivate 3D model configuration. If activated, ROMS solves 3D (baroclinic) primitive equations. If deactivated, ROMS solves vertically-integrated, shallow water (barotropic) equations.
:'''routine = ''' [[main2d.F]], [[main3d.F]]<section end=SOLVE3D />


==<span class="alphabet">T</span>==
==<span class="alphabet">T</span>==


;<span id="TALK_PROGNOSTIC"></span>'''TALK_PROGNOSTIC'''
<section begin=TALK_PROGNOSTIC />;<span id="TALK_PROGNOSTIC"></span>'''[[TALK_PROGNOSTIC]]'''
:Option to activate prognostic computation of alkalinity.
:Option to activate prognostic computation of alkalinity.
:'''parent = ''' [[#BIO_FASHAM | BIO_FASHAM]]
:'''parent = ''' [[BIO_FASHAM]]
:'''required = ''' [[#CARBON | CARBON]]
:'''required = ''' [[CARBON]]
:'''routine = ''' [[fasham.h]]
:'''routine = ''' [[fasham.h]]<section end=TALK_PROGNOSTIC />


==<span class="alphabet">U</span>==
==<span class="alphabet">U</span>==


;<span id="UV_ADV"></span>'''UV_ADV'''
<section begin=UV_ADV />;<span id="UV_ADV"></span>'''[[UV_ADV]]'''
:Option to activate/deactivate horizontal and vertical advection of momentum.  If no additional options are specified, the default is to discretize the horizontal momentum with a third-order upstream bias advection scheme with velocity dependent hyper-viscosity and the vertical momentum with a fourth-order, centered differences scheme. Since there is some implicit viscosity associated with the default discretization, the user may avoid adding an explicity vicosity to the solution to suppress excisive smoothing.
:Option to activate/deactivate horizontal and vertical advection of momentum.  If no additional options are specified, the default is to discretize the horizontal momentum with a third-order upstream bias advection scheme with velocity dependent hyper-viscosity and the vertical momentum with a fourth-order, centered differences scheme. Since there is some implicit viscosity associated with the default discretization, the user may avoid adding an explicity vicosity to the solution to suppress excisive smoothing.
:'''routine = ''' [[step2d.F]], [[rhs3d.F]]
:'''routine = ''' [[step2d.F]], [[rhs3d.F]]<section end=UV_ADV />


;<span id="UV_COR"></span>'''UV_COR'''
<section begin=UV_COR />;<span id="UV_COR"></span>'''[[UV_COR]]'''
:Option to activate/deactivate Coriolis acceleration term in momentum equations.
:Option to activate/deactivate Coriolis acceleration term in momentum equations.
:'''routine = ''' [[step2d.F]], [[rhs3d.F]]
:'''routine = ''' [[step2d.F]], [[rhs3d.F]]<section end=UV_COR />


;<span id="UV_C2ADVECTION"></span>'''UV_C2ADVECTION'''
<section begin=UV_C2ADVECTION />;<span id="UV_C2ADVECTION"></span>'''[[UV_C2ADVECTION]]'''
:Option to use second-order, centered, finite differences in advection of momentum.
:Option to use second-order, centered, finite differences in advection of momentum.
:'''parent = ''' [[#UV_ADV | UV_ADV]]
:'''parent = ''' [[UV_ADV]]
:'''conflit = ''' [[#UV_C4ADVECTION | UV_C4ADVECTION]]
:'''conflit = ''' [[UV_C4ADVECTION]]<section end=UV_C2ADVECTION />


;<span id="UV_C4ADVECTION"></span>'''UV_C4ADVECTION'''
<section begin=UV_C4ADVECTION />;<span id="UV_C4ADVECTION"></span>'''[[UV_C4ADVECTION]]'''
:Option to use fourth-order, centered, finite differences in advection of momentum.
:Option to use fourth-order, centered, finite differences in advection of momentum.
:'''parent = ''' [[#UV_ADV | UV_ADV]]
:'''parent = ''' [[UV_ADV]]
:'''conflit = ''' [[#UV_C2ADVECTION | UV_C2ADVECTION]]
:'''conflit = ''' [[UV_C2ADVECTION]]<section end=UV_C4ADVECTION />


;<span id="UV_SADVECTION"></span>'''UV_SADVECTION'''
<section begin=UV_SADVECTION />;<span id="UV_SADVECTION"></span>'''[[UV_SADVECTION]]'''
:Option to use conservative, parabolic splines discretization of momentum vertical advection. This scheme requires high vertical resolution so it is recommended to use this option in shallow, coastal applications.
:Option to use conservative, parabolic splines discretization of momentum vertical advection. This scheme requires high vertical resolution so it is recommended to use this option in shallow, coastal applications.
:'''parent = ''' [[#UV_ADV | UV_ADV]]
:'''parent = ''' [[UV_ADV]]
:'''conflit = ''' [[#UV_C2ADVECTION | UV_C2ADVECTION]], [[#UV_C4ADVECTION | UV_C4ADVECTION]]
:'''conflit = ''' [[UV_C2ADVECTION]], [[UV_C4ADVECTION]]<section end=UV_SADVECTION />


;<span id="UV_VIS2"></span>'''UV_VIS2'''
<section begin=UV_VIS2 />;<span id="UV_VIS2"></span>'''[[UV_VIS2]]'''
:Option to activate/deactivate horizontal, harmonic viscosity of momentum. The hamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor ([[Bibliography#WajsowiczRC_1993a |Wajsowicz, 1993]]).
:Option to activate/deactivate horizontal, harmonic viscosity of momentum. The hamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor ([[Bibliography#WajsowiczRC_1993a |Wajsowicz, 1993]]).
:'''parameter = ''' [[Variables#visc2 | visc2(ng)]], [[Variables#visc2_p | visc2_p(:,:)]], [[Variables#visc2_r | visc2_r(:,:)]]
:'''parameter = ''' [[Variables#visc2 | visc2(ng)]], [[Variables#visc2_p | visc2_p(:,:)]], [[Variables#visc2_r | visc2_r(:,:)]]
:'''required = ''' [[#MIX_S_UV | MIX_S_UV]], [[#MIX_GEO_UV | MIX_GEO_UV]]
:'''required = ''' [[MIX_S_UV]], [[MIX_GEO_UV]]
:'''related = ''' [[#VISC_GRID | VISC_GRID]]
:'''related = ''' [[VISC_GRID]]
:'''routine = ''' [[uv3dmix2_s.h]], [[uv3dmix2_geo.h]], [[uv3dmix.F]]
:'''routine = ''' [[uv3dmix2_s.h]], [[uv3dmix2_geo.h]], [[uv3dmix.F]]<section end=UV_VIS2 />


;<span id="UV_VIS4"></span>'''UV_VIS4'''
<section begin=UV_VIS4 />;<span id="UV_VIS4"></span>'''[[UV_VIS4]]'''
:Option to activate/deactivate horizontal, biharmonic viscosity of momentum. The bihamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor ([[Bibliography#WajsowiczRC_1993a |Wajsowicz, 1993]]).
:Option to activate/deactivate horizontal, biharmonic viscosity of momentum. The bihamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor ([[Bibliography#WajsowiczRC_1993a |Wajsowicz, 1993]]).
:'''parameter = ''' [[Variables#visc4 | visc4(ng)]], [[Variables#visc4_p | visc4_p(:,:)]], [[Variables#visc4_r | visc4_r(:,:)]]
:'''parameter = ''' [[Variables#visc4 | visc4(ng)]], [[Variables#visc4_p | visc4_p(:,:)]], [[Variables#visc4_r | visc4_r(:,:)]]
:'''required = ''' [[#MIX_S_UV | MIX_S_UV]], [[#MIX_GEO_UV | MIX_GEO_UV]]
:'''required = ''' [[MIX_S_UV]], [[MIX_GEO_UV]]
:'''related = ''' [[#VISC_GRID | VISC_GRID]]
:'''related = ''' [[VISC_GRID]]
:'''routine = ''' [[uv3dmix4_s.h]], [[uv3dmix4_geo.h]], [[uv3dmix.F]]
:'''routine = ''' [[uv3dmix4_s.h]], [[uv3dmix4_geo.h]], [[uv3dmix.F]]<section end=UV_VIS4 />


;<span id="UV_LOGDRAG"></span>'''UV_LOGDRAG'''
<section begin=UV_LOGDRAG />;<span id="UV_LOGDRAG"></span>'''[[UV_LOGDRAG]]'''
:Option to activate/deactivate logarithmic bottom friction of momentum.
:Option to activate/deactivate logarithmic bottom friction of momentum.
:'''parameter = ''' [[Variables#Zob | Zob(ng)]]
:'''parameter = ''' [[Variables#Zob | Zob(ng)]]
:'''required = ''' [[#SOLVE3D | SOLVE3D]]
:'''required = ''' [[SOLVE3D]]
:'''confict = ''' [[#BBL_MODEL | BBL_MODEL]], [[#UV_LDRAG | UV_LDRAG]], [[#UV_QDRAG | UV_QDRAG]]
:'''confict = ''' [[BBL_MODEL]], [[UV_LDRAG]], [[UV_QDRAG]]
:'''routine = ''' [[set_vbc.F]]
:'''routine = ''' [[set_vbc.F]]<section end=UV_LOGDRAG />


;<span id="UV_LDRAG"></span>'''UV_LDRAG'''
<section begin=UV_LDRAG />;<span id="UV_LDRAG"></span>'''[[UV_LDRAG]]'''
:Option to activate/deactivate linear bottom friction of momentum.
:Option to activate/deactivate linear bottom friction of momentum.
:'''parameter = ''' [[Variables#rdrg | rdrg(ng)]]
:'''parameter = ''' [[Variables#rdrg | rdrg(ng)]]
:'''confict = ''' [[#BBL_MODEL | BBL_MODEL]], [[#UV_LOGDRAG | UV_LOGDRAG]], [[#UV_QDRAG | UV_QDRAG]]
:'''confict = ''' [[BBL_MODEL]], [[UV_LOGDRAG]], [[UV_QDRAG]]
:'''routine = ''' [[set_vbc.F]]
:'''routine = ''' [[set_vbc.F]]<section end=UV_LDRAG />


;<span id="UV_PSOURCE"></span>'''UV_PSOURCE'''
<section begin=UV_PSOURCE />;<span id="UV_PSOURCE"></span>'''[[UV_PSOURCE]]'''
:Option to activate/deactivate point sources/sinks of momentum. This option is used to specify the mass transport in river runoff.
:Option to activate/deactivate point sources/sinks of momentum. This option is used to specify the mass transport in river runoff.
:'''parameter = ''' [[Variables#Dsrc | Dsrc(1:Nsrc)]], [[Variables#Qsrc | Qsrc(1:Nsrc,k)]]
:'''parameter = ''' [[Variables#Dsrc | Dsrc(1:Nsrc)]], [[Variables#Qsrc | Qsrc(1:Nsrc,k)]]
:'''related = ''' [[#ANA_PSOURCE | ANA_PSOURCE]], [[#TS_PSOURCE | TS_PSOURCE]]
:'''related = ''' [[ANA_PSOURCE]], [[TS_PSOURCE]]
:'''confict = ''' [[#BBL_MODEL | BBL_MODEL]], [[#UV_LOGDRAG | UV_LOGDRAG]], [[#UV_QDRAG | UV_QDRAG]]
:'''confict = ''' [[BBL_MODEL]], [[UV_LOGDRAG]], [[UV_QDRAG]]
:'''routine = ''' [[step2d.F]], [[step3d_uv.F]]
:'''routine = ''' [[step2d.F]], [[step3d_uv.F]]<section end=UV_PSOURCE />


;<span id="UV_QDRAG"></span>'''UV_QDRAG'''
<section begin=UV_QDRAG />;<span id="UV_QDRAG"></span>'''[[UV_QDRAG]]'''
:Option to activate/deactivate quadratic bottom friction of momentum.
:Option to activate/deactivate quadratic bottom friction of momentum.
:'''parameter = ''' [[Variables#rdrg2 | rdrg2(ng)]]
:'''parameter = ''' [[Variables#rdrg2 | rdrg2(ng)]]
:'''confict = ''' [[#BBL_MODEL | BBL_MODEL]], [[#UV_LDRAG | UV_LDRAG]], [[#UV_LOGDRAG | UV_LOGDRAG]]
:'''confict = ''' [[BBL_MODEL]], [[UV_LDRAG]], [[UV_LOGDRAG]]
:'''routine = ''' [[set_vbc.F]]
:'''routine = ''' [[set_vbc.F]]<section end=UV_QDRAG />


==<span class="alphabet">V</span>==
==<span class="alphabet">V</span>==

Revision as of 04:46, 23 November 2006

CPP Options

This wikipage includes all ROMS CPP options in alphabetic order. A single long page is built to facilitate printing. Each option has a unique anchor tag to facilitate linking from any wikipage. The following attributes have been identified to aid in the description of ROMS CPP options:

  • conflit: indicates mutually exclusive options.
  • parameter: important standard input parameter(s) or state array(s) associtated with the option.
  • parent: indicates association to a main option.
  • related: indicates other affiliated option(s) that may affect or not its scope.
  • required: indicates other dependent option(s) that must be activated.
  • routine: main files associated with the option.


Contents

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

ANA_BIOLOGY
Option to initialize any of the biological models with analytical expressions.
related = BIOLOGY
routine = analytical.F (ana_biology)
ANA_BPFLUX
Option to set passive tracers bottom flux with analytical expressions (usually zero, no flux).
related = BIOLOGY, SEDIMENT
routine = analytical.F (ana_bpflux)
ANA_SPFLUX
Option to set passive tracers surface flux with analytical expressions (usually zero, no flux).
related = BIOLOGY, SEDIMENT
routine = analytical.F (ana_spflux)

B

BIOLOGY
Internal option defined when any of the biological models is activated.
related = BIO_FASHAM, ECOSIM, NPZD_FRANKS, NPZD_POWELL
routine = biology.F
BIO_FASHAM
Option to activate Fasham-type, nitrogen-based biological model (Fasham et al., 1990; Fennel et al., 2006)
related = ANA_BIOLOGY, ANA_BPFLUX, ANA_SPFLUX, BIO_SEDIMENT, CARBON, DENITRIFICATION, DIAGNOSTICS_BIO, OXYGEN, TALK_PROGNOSTIC
conflict = ECOSIM, NPZD_FRANKS, NPZD_POWELL
routine = fasham.h, bioFasham.in
BIO_SEDIMENT
Option to restore fallen particulate material to the nutrient pool in Fasham-type model.
parent = BIO_FASHAM
routine = fasham.h

C

CARBON
Option to include carbon constituents in Fasham-type biological model. Currently, four carbon-based tracer are added to include large detritus (iLDeC), small detritus (iSDeC), total inorganic carbon (iTIC_), and total alkalinity (iTAlk).
parent = BIO_FASHAM
required = OXYGEN
routine = fasham.h

D

DENITRIFICATION
Option to include denitrification processes in Fasham-type biological model.
parent = BIO_FASHAM
routine = fasham.h
DIAGNOSTICS
Internal option to compute and write balance term diagnostics for tracers and momentum.
related = DIAGNOSTICS_BIO, DIAGNOSTICS_TS, DIAGNOSTICS_UV
routine = set_diags.F, wrt_diags.F
DIAGNOSTICS_BIO
Option to compute and write biological diagnostic terms in Fasham-type model.
parent = BIO_FASHAM
related = DIAGNOSTICS_TS, DIAGNOSTICS_UV
routine = fasham.h, wrt_diags.F
DIAGNOSTICS_TS
Option to compute and write diagnostic terms for tracer equations balances.
related = DIAGNOSTICS_BIO, DIAGNOSTICS_UV
routine = set_diags.F, step3d_t.F, wrt_diags.F
DIAGNOSTICS_UV
Option to compute and write diagnostic terms for momentum equations balances.
related = DIAGNOSTICS_BIO, DIAGNOSTICS_TS
routine = set_diags.F, step2d.F, step3d_t.F, wrt_diags.F

E

ECOSIM
Option to activate Bio-optical EcoSim (Bissett et al., 1999a, b) model.
related = ANA_BIOLOGY, ANA_BPFLUX, ANA_SP_FLUX
conflict = BIO_FASHAM, NPZD_FRANKS, NPZD_POWELL
routine = ecosim.h, ecosim.in

F

G

GLS_MIXING
Option to activate Generic Length Scale vertical mixing parameterization (Warner et al., 2005).
related = CANUTO_A, CANUTO_B
conflict = MY25_MIXING, #LMD_MIXING
routine = gls_prestep.F, gls_corstep.F, ocean.in

H

I

J

K

L

M

N

NPZ_FRANKS
Option to activate Franks et al. (1986) NPZD biological model.
related = ANA_BIOLOGY, ANA_BPFLUX, ANA_SPFLUX
conflict = BIO_FASHAM, ECOSIM, NPZD_POWELL
routine = npzd_Franks.h, npzd_Franks.in
NPZ_POWELL
Option to activate Powell et al. (1986) NPZD biological model.
related = ANA_BIOLOGY, ANA_BPFLUX, ANA_SPFLUX
conflict = BIO_FASHAM, ECOSIM, NPZD_FRANKS
routine = npzd_Powell.h, npzd_Powell.in

O

OCMIP_OXYGEN_SC
Option to use the Keeling et al. (1998) formulae for the Schmit number to model O2 gas exchange. If deactivated, the formulation of Wanninkhof (1992) is used instead.
parent = BIO_FASHAM
required = OXYGEN
routine = fasham.h
OXYGEN
Option to include oxygen dynamics in Fasham-type biological model. Currently, an additional tracer is added for dissolved oxygen concentration (iOxyg).
parent = BIO_FASHAM
routine = fasham.h

P

Q

R

S

SOLVE3D
Option to activate/deactivate 3D model configuration. If activated, ROMS solves 3D (baroclinic) primitive equations. If deactivated, ROMS solves vertically-integrated, shallow water (barotropic) equations.
routine = main2d.F, main3d.F

T

TALK_PROGNOSTIC
Option to activate prognostic computation of alkalinity.
parent = BIO_FASHAM
required = CARBON
routine = fasham.h

U

UV_ADV
Option to activate/deactivate horizontal and vertical advection of momentum. If no additional options are specified, the default is to discretize the horizontal momentum with a third-order upstream bias advection scheme with velocity dependent hyper-viscosity and the vertical momentum with a fourth-order, centered differences scheme. Since there is some implicit viscosity associated with the default discretization, the user may avoid adding an explicity vicosity to the solution to suppress excisive smoothing.
routine = step2d.F, rhs3d.F
UV_COR
Option to activate/deactivate Coriolis acceleration term in momentum equations.
routine = step2d.F, rhs3d.F
UV_C2ADVECTION
Option to use second-order, centered, finite differences in advection of momentum.
parent = UV_ADV
conflit = UV_C4ADVECTION
UV_C4ADVECTION
Option to use fourth-order, centered, finite differences in advection of momentum.
parent = UV_ADV
conflit = UV_C2ADVECTION
UV_SADVECTION
Option to use conservative, parabolic splines discretization of momentum vertical advection. This scheme requires high vertical resolution so it is recommended to use this option in shallow, coastal applications.
parent = UV_ADV
conflit = UV_C2ADVECTION, UV_C4ADVECTION
UV_VIS2
Option to activate/deactivate horizontal, harmonic viscosity of momentum. The hamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor (Wajsowicz, 1993).
parameter = visc2(ng), visc2_p(:,:), visc2_r(:,:)
required = MIX_S_UV, MIX_GEO_UV
related = VISC_GRID
routine = uv3dmix2_s.h, uv3dmix2_geo.h, uv3dmix.F
UV_VIS4
Option to activate/deactivate horizontal, biharmonic viscosity of momentum. The bihamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor (Wajsowicz, 1993).
parameter = visc4(ng), visc4_p(:,:), visc4_r(:,:)
required = MIX_S_UV, MIX_GEO_UV
related = VISC_GRID
routine = uv3dmix4_s.h, uv3dmix4_geo.h, uv3dmix.F
UV_LOGDRAG
Option to activate/deactivate logarithmic bottom friction of momentum.
parameter = Zob(ng)
required = SOLVE3D
confict = BBL_MODEL, UV_LDRAG, UV_QDRAG
routine = set_vbc.F
UV_LDRAG
Option to activate/deactivate linear bottom friction of momentum.
parameter = rdrg(ng)
confict = BBL_MODEL, UV_LOGDRAG, UV_QDRAG
routine = set_vbc.F
UV_PSOURCE
Option to activate/deactivate point sources/sinks of momentum. This option is used to specify the mass transport in river runoff.
parameter = Dsrc(1:Nsrc), Qsrc(1:Nsrc,k)
related = ANA_PSOURCE, TS_PSOURCE
confict = BBL_MODEL, UV_LOGDRAG, UV_QDRAG
routine = step2d.F, step3d_uv.F
UV_QDRAG
Option to activate/deactivate quadratic bottom friction of momentum.
parameter = rdrg2(ng)
confict = BBL_MODEL, UV_LDRAG, UV_LOGDRAG
routine = set_vbc.F

V

W

X

Y

Z

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