/home/cermak/venv/esmg/bin/doxygen Doxyfile_rtd_dox Searching for include files... Searching for files in directory /home/cermak/src/MOM6/src/framework Searching for files in directory /home/cermak/src/MOM6/config_src/dynamic_symmetric Searching for example files... Searching for files in directory /home/cermak/src/MOM6/src Searching for files in directory /home/cermak/src/MOM6/src/ALE Searching for files in directory /home/cermak/src/MOM6/src/core Searching for files in directory /home/cermak/src/MOM6/src/diagnostics Searching for files in directory /home/cermak/src/MOM6/src/equation_of_state Searching for files in directory /home/cermak/src/MOM6/src/equation_of_state/TEOS10 Searching for files in directory /home/cermak/src/MOM6/src/framework Searching for files in directory /home/cermak/src/MOM6/src/ice_shelf Searching for files in directory /home/cermak/src/MOM6/src/initialization Searching for files in directory /home/cermak/src/MOM6/src/ocean_data_assim Searching for files in directory /home/cermak/src/MOM6/src/parameterizations Searching for files in directory /home/cermak/src/MOM6/src/parameterizations/lateral Searching for files in directory /home/cermak/src/MOM6/src/parameterizations/vertical Searching for files in directory /home/cermak/src/MOM6/src/tracer Searching for files in directory /home/cermak/src/MOM6/src/user Searching for images... Searching for files in directory /home/cermak/src/MOM6/docs/images Searching for files in directory /home/cermak/src/MOM6/src Searching for files in directory /home/cermak/src/MOM6/src/ALE Searching for files in directory /home/cermak/src/MOM6/src/core Searching for files in directory /home/cermak/src/MOM6/src/diagnostics Searching for files in directory /home/cermak/src/MOM6/src/equation_of_state Searching for files in directory /home/cermak/src/MOM6/src/equation_of_state/TEOS10 Searching for files in directory /home/cermak/src/MOM6/src/framework Searching for files in directory /home/cermak/src/MOM6/src/ice_shelf Searching for files in directory /home/cermak/src/MOM6/src/initialization Searching for files in directory /home/cermak/src/MOM6/src/ocean_data_assim Searching for files in directory /home/cermak/src/MOM6/src/parameterizations Searching for files in directory /home/cermak/src/MOM6/src/parameterizations/lateral Searching for files in directory /home/cermak/src/MOM6/src/parameterizations/vertical Searching for files in directory /home/cermak/src/MOM6/src/tracer Searching for files in directory /home/cermak/src/MOM6/src/user Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching for files in directory /home/cermak/src/MOM6/src/equation_of_state/TEOS10 Searching INPUT for files to process... Searching for files in directory /home/cermak/src/MOM6/src Searching for files in directory /home/cermak/src/MOM6/src/ALE Searching for files in directory /home/cermak/src/MOM6/src/core Searching for files in directory /home/cermak/src/MOM6/src/diagnostics Searching for files in directory /home/cermak/src/MOM6/src/equation_of_state Searching for files in directory /home/cermak/src/MOM6/src/equation_of_state/TEOS10 Searching for files in directory /home/cermak/src/MOM6/src/framework Searching for files in directory /home/cermak/src/MOM6/src/ice_shelf Searching for files in directory /home/cermak/src/MOM6/src/initialization Searching for files in directory /home/cermak/src/MOM6/src/ocean_data_assim Searching for files in directory /home/cermak/src/MOM6/src/parameterizations Searching for files in directory /home/cermak/src/MOM6/src/parameterizations/lateral Searching for files in directory /home/cermak/src/MOM6/src/parameterizations/vertical Searching for files in directory /home/cermak/src/MOM6/src/tracer Searching for files in directory /home/cermak/src/MOM6/src/user Searching for files in directory /home/cermak/src/MOM6/config_src/solo_driver Searching for files in directory /home/cermak/src/MOM6/config_src/dynamic_symmetric Searching for files in directory /home/cermak/src/MOM6/config_src/external Searching for files in directory /home/cermak/src/MOM6/config_src/external/GFDL_ocean_BGC Searching for files in directory /home/cermak/src/MOM6/config_src/external/ODA_hooks Searching for files in directory /home/cermak/src/MOM6/config_src/coupled_driver Reading and parsing tag files Parsing files Preprocessing /home/cermak/src/MOM6/src/ALE/_ALE.dox... Parsing file /home/cermak/src/MOM6/src/ALE/_ALE.dox... Preprocessing /home/cermak/src/MOM6/src/ALE/_ALE_timestep.dox... Parsing file /home/cermak/src/MOM6/src/ALE/_ALE_timestep.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Baroclinic_Momentum.dox... Parsing file /home/cermak/src/MOM6/src/core/_Baroclinic_Momentum.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Barotropic_Baroclinic_Coupling.dox... Parsing file /home/cermak/src/MOM6/src/core/_Barotropic_Baroclinic_Coupling.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Barotropic_Momentum.dox... Parsing file /home/cermak/src/MOM6/src/core/_Barotropic_Momentum.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Discrete_Coriolis.dox... Parsing file /home/cermak/src/MOM6/src/core/_Discrete_Coriolis.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Discrete_grids.dox... Parsing file /home/cermak/src/MOM6/src/core/_Discrete_grids.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Discrete_OBC.dox... Parsing file /home/cermak/src/MOM6/src/core/_Discrete_OBC.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Discrete_PG.dox... Parsing file /home/cermak/src/MOM6/src/core/_Discrete_PG.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Energetic_consistancy.dox... Parsing file /home/cermak/src/MOM6/src/core/_Energetic_consistancy.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Finite_difference.dox... Parsing file /home/cermak/src/MOM6/src/core/_Finite_difference.dox... Preprocessing /home/cermak/src/MOM6/src/core/_General_coordinate.dox... Parsing file /home/cermak/src/MOM6/src/core/_General_coordinate.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Governing.dox... Parsing file /home/cermak/src/MOM6/src/core/_Governing.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Notation.dox... Parsing file /home/cermak/src/MOM6/src/core/_Notation.dox... Preprocessing /home/cermak/src/MOM6/src/core/_PPM.dox... Parsing file /home/cermak/src/MOM6/src/core/_PPM.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Sea_ice.dox... Parsing file /home/cermak/src/MOM6/src/core/_Sea_ice.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Solar_radiation.dox... Parsing file /home/cermak/src/MOM6/src/core/_Solar_radiation.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Specifics.dox... Parsing file /home/cermak/src/MOM6/src/core/_Specifics.dox... Preprocessing /home/cermak/src/MOM6/src/core/_Time_Filter.dox... Parsing file /home/cermak/src/MOM6/src/core/_Time_Filter.dox... Preprocessing /home/cermak/src/MOM6/src/equation_of_state/_Equation_of_State.dox... Parsing file /home/cermak/src/MOM6/src/equation_of_state/_Equation_of_State.dox... Preprocessing /home/cermak/src/MOM6/src/framework/_Diagnostics.dox... Parsing file /home/cermak/src/MOM6/src/framework/_Diagnostics.dox... Preprocessing /home/cermak/src/MOM6/src/framework/_Domain_decomposition.dox... Parsing file /home/cermak/src/MOM6/src/framework/_Domain_decomposition.dox... Preprocessing /home/cermak/src/MOM6/src/framework/_Global_grids.dox... Parsing file /home/cermak/src/MOM6/src/framework/_Global_grids.dox... Preprocessing /home/cermak/src/MOM6/src/framework/_Horizontal_indexing.dox... Parsing file /home/cermak/src/MOM6/src/framework/_Horizontal_indexing.dox... Preprocessing /home/cermak/src/MOM6/src/framework/_Parallel_IO.dox... Parsing file /home/cermak/src/MOM6/src/framework/_Parallel_IO.dox... Preprocessing /home/cermak/src/MOM6/src/framework/_Regional_grids.dox... Parsing file /home/cermak/src/MOM6/src/framework/_Regional_grids.dox... Preprocessing /home/cermak/src/MOM6/src/framework/_Runtime_parameter_system.dox... Parsing file /home/cermak/src/MOM6/src/framework/_Runtime_parameter_system.dox... Preprocessing /home/cermak/src/MOM6/src/framework/_Testing.dox... Parsing file /home/cermak/src/MOM6/src/framework/_Testing.dox... Preprocessing /home/cermak/src/MOM6/src/framework/_Vertical_grids.dox... Parsing file /home/cermak/src/MOM6/src/framework/_Vertical_grids.dox... Preprocessing /home/cermak/src/MOM6/src/parameterizations/vertical/_CVMix_KPP.dox... Parsing file /home/cermak/src/MOM6/src/parameterizations/vertical/_CVMix_KPP.dox... Preprocessing /home/cermak/src/MOM6/src/tracer/_Advection.dox... Parsing file /home/cermak/src/MOM6/src/tracer/_Advection.dox... Preprocessing /home/cermak/src/MOM6/src/tracer/_Discrete_tracer.dox... Parsing file /home/cermak/src/MOM6/src/tracer/_Discrete_tracer.dox... Preprocessing /home/cermak/src/MOM6/src/tracer/_Horizontal_diffusion.dox... Parsing file /home/cermak/src/MOM6/src/tracer/_Horizontal_diffusion.dox... Preprocessing /home/cermak/src/MOM6/src/tracer/_Passive_tracer.dox... Parsing file /home/cermak/src/MOM6/src/tracer/_Passive_tracer.dox... Preprocessing /home/cermak/src/MOM6/src/tracer/_Tracer_fluxes.dox... Parsing file /home/cermak/src/MOM6/src/tracer/_Tracer_fluxes.dox... Preprocessing /home/cermak/src/MOM6/src/tracer/_Tracer_timestep.dox... Parsing file /home/cermak/src/MOM6/src/tracer/_Tracer_timestep.dox... Preprocessing /home/cermak/src/MOM6/src/tracer/_Tracer_Transport.dox... Parsing file /home/cermak/src/MOM6/src/tracer/_Tracer_Transport.dox... Preprocessing /home/cermak/src/MOM6/src/tracer/_Vertical_diffusion.dox... Parsing file /home/cermak/src/MOM6/src/tracer/_Vertical_diffusion.dox... Preprocessing /home/cermak/src/MOM6/src/core/MOM.F90... Parsing file /home/cermak/src/MOM6/src/core/MOM.F90... Preprocessing /home/cermak/src/MOM6/src/ALE/MOM_ALE.F90... Parsing file /home/cermak/src/MOM6/src/ALE/MOM_ALE.F90... Preprocessing /home/cermak/src/MOM6/src/equation_of_state/MOM_EOS.F90... Parsing file /home/cermak/src/MOM6/src/equation_of_state/MOM_EOS.F90... Preprocessing /home/cermak/src/MOM6/src/framework/MOM_unit_scaling.F90... Parsing file /home/cermak/src/MOM6/src/framework/MOM_unit_scaling.F90... Preprocessing /home/cermak/src/MOM6/src/ice_shelf/MOM_ice_shelf.F90... Parsing file /home/cermak/src/MOM6/src/ice_shelf/MOM_ice_shelf.F90... Preprocessing /home/cermak/src/MOM6/src/parameterizations/lateral/MOM_MEKE.F90... Parsing file /home/cermak/src/MOM6/src/parameterizations/lateral/MOM_MEKE.F90... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Associating documentation with classes... Computing nesting relations for classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Freeing entry tree Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Distributing member group documentation. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Computing dependencies between directories... Generating citations page... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Parsing code for file /home/cermak/src/MOM6/src/ALE/_ALE.dox... Parsing code for file /home/cermak/src/MOM6/src/ALE/_ALE_timestep.dox... Generating code for file /home/cermak/src/MOM6/src/ALE/MOM_ALE.F90... Parsing code for file /home/cermak/src/MOM6/src/core/_Baroclinic_Momentum.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Barotropic_Baroclinic_Coupling.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Barotropic_Momentum.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Discrete_Coriolis.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Discrete_grids.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Discrete_OBC.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Discrete_PG.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Energetic_consistancy.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Finite_difference.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_General_coordinate.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Governing.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Notation.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_PPM.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Sea_ice.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Solar_radiation.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Specifics.dox... Parsing code for file /home/cermak/src/MOM6/src/core/_Time_Filter.dox... Generating code for file /home/cermak/src/MOM6/src/core/MOM.F90... Parsing code for file /home/cermak/src/MOM6/src/equation_of_state/_Equation_of_State.dox... Generating code for file /home/cermak/src/MOM6/src/equation_of_state/MOM_EOS.F90... Parsing code for file /home/cermak/src/MOM6/src/framework/_Diagnostics.dox... Parsing code for file /home/cermak/src/MOM6/src/framework/_Domain_decomposition.dox... Parsing code for file /home/cermak/src/MOM6/src/framework/_Global_grids.dox... Parsing code for file /home/cermak/src/MOM6/src/framework/_Horizontal_indexing.dox... Parsing code for file /home/cermak/src/MOM6/src/framework/_Parallel_IO.dox... Parsing code for file /home/cermak/src/MOM6/src/framework/_Regional_grids.dox... Parsing code for file /home/cermak/src/MOM6/src/framework/_Runtime_parameter_system.dox... Parsing code for file /home/cermak/src/MOM6/src/framework/_Testing.dox... Parsing code for file /home/cermak/src/MOM6/src/framework/_Vertical_grids.dox... Generating code for file /home/cermak/src/MOM6/src/framework/MOM_unit_scaling.F90... Generating code for file /home/cermak/src/MOM6/src/ice_shelf/MOM_ice_shelf.F90... Generating code for file /home/cermak/src/MOM6/src/parameterizations/lateral/MOM_MEKE.F90... Parsing code for file /home/cermak/src/MOM6/src/parameterizations/vertical/_CVMix_KPP.dox... Parsing code for file /home/cermak/src/MOM6/src/tracer/_Advection.dox... Parsing code for file /home/cermak/src/MOM6/src/tracer/_Discrete_tracer.dox... Parsing code for file /home/cermak/src/MOM6/src/tracer/_Horizontal_diffusion.dox... Parsing code for file /home/cermak/src/MOM6/src/tracer/_Passive_tracer.dox... Parsing code for file /home/cermak/src/MOM6/src/tracer/_Tracer_fluxes.dox... Parsing code for file /home/cermak/src/MOM6/src/tracer/_Tracer_timestep.dox... Parsing code for file /home/cermak/src/MOM6/src/tracer/_Tracer_Transport.dox... Parsing code for file /home/cermak/src/MOM6/src/tracer/_Vertical_diffusion.dox... Generating file documentation... Generating docs for file /home/cermak/src/MOM6/src/ALE/_ALE.dox... Generating docs for file /home/cermak/src/MOM6/src/ALE/_ALE_timestep.dox... Generating docs for file /home/cermak/src/MOM6/src/ALE/MOM_ALE.F90... Generating docs for file /home/cermak/src/MOM6/src/core/_Baroclinic_Momentum.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Barotropic_Baroclinic_Coupling.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Barotropic_Momentum.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Discrete_Coriolis.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Discrete_grids.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Discrete_OBC.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Discrete_PG.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Energetic_consistancy.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Finite_difference.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_General_coordinate.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Governing.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Notation.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_PPM.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Sea_ice.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Solar_radiation.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Specifics.dox... Generating docs for file /home/cermak/src/MOM6/src/core/_Time_Filter.dox... Generating docs for file /home/cermak/src/MOM6/src/core/MOM.F90... Generating docs for file /home/cermak/src/MOM6/src/equation_of_state/_Equation_of_State.dox... Generating docs for file /home/cermak/src/MOM6/src/equation_of_state/MOM_EOS.F90... Generating docs for file /home/cermak/src/MOM6/src/framework/_Diagnostics.dox... Generating docs for file /home/cermak/src/MOM6/src/framework/_Domain_decomposition.dox... Generating docs for file /home/cermak/src/MOM6/src/framework/_Global_grids.dox... Generating docs for file /home/cermak/src/MOM6/src/framework/_Horizontal_indexing.dox... Generating docs for file /home/cermak/src/MOM6/src/framework/_Parallel_IO.dox... Generating docs for file /home/cermak/src/MOM6/src/framework/_Regional_grids.dox... Generating docs for file /home/cermak/src/MOM6/src/framework/_Runtime_parameter_system.dox... Generating docs for file /home/cermak/src/MOM6/src/framework/_Testing.dox... Generating docs for file /home/cermak/src/MOM6/src/framework/_Vertical_grids.dox... Generating docs for file /home/cermak/src/MOM6/src/framework/MOM_unit_scaling.F90... Generating docs for file /home/cermak/src/MOM6/src/ice_shelf/MOM_ice_shelf.F90... Generating docs for file /home/cermak/src/MOM6/src/parameterizations/lateral/MOM_MEKE.F90... Generating docs for file /home/cermak/src/MOM6/src/parameterizations/vertical/_CVMix_KPP.dox... Generating docs for file /home/cermak/src/MOM6/src/tracer/_Advection.dox... Generating docs for file /home/cermak/src/MOM6/src/tracer/_Discrete_tracer.dox... Generating docs for file /home/cermak/src/MOM6/src/tracer/_Horizontal_diffusion.dox... Generating docs for file /home/cermak/src/MOM6/src/tracer/_Passive_tracer.dox... Generating docs for file /home/cermak/src/MOM6/src/tracer/_Tracer_fluxes.dox... Generating docs for file /home/cermak/src/MOM6/src/tracer/_Tracer_timestep.dox... Generating docs for file /home/cermak/src/MOM6/src/tracer/_Tracer_Transport.dox... Generating docs for file /home/cermak/src/MOM6/src/tracer/_Vertical_diffusion.dox... Generating page documentation... Generating docs for page ALE... Generating docs for page ALE_Timestep... Generating docs for page Baroclinic_Momentum_Equations... Generating docs for page Barotropic_Baroclinic_Coupling... Generating docs for page Barotropic_Momentum_Equations... Generating docs for page Discrete_Coriolis... Generating docs for page Discrete_Grids... Generating docs for page Discrete_OBC... Generating docs for page Discrete_PG... Generating docs for page Energetic_Consistency... Generating docs for page Finite_Difference_Operators... Generating docs for page General_Coordinate... Generating docs for page Governing_Equations... Generating docs for page Notation... Generating docs for page PPM... Generating docs for page Sea_Ice... Generating docs for page Solar_Radiation... Generating docs for page Specifics... Generating docs for page Time_Filtering... Generating docs for page Equation_of_State... Generating docs for page Diagnostics... Generating docs for page Domain_Decomposition... Generating docs for page Global_Grids... Generating docs for page Horizontal_Indexing... Generating docs for page Parallel_IO... Generating docs for page Regional_Grids... Generating docs for page Runtime_Parameter_System... Generating docs for page Testing... Generating docs for page Vertical_Grids... Generating docs for page CVMix_KPP... Generating docs for page Tracer_Advection... Generating docs for page Discrete_Tracer... Generating docs for page Horizontal_Diffusion... Generating docs for page Passive_Tracers... Generating docs for page Tracer_Fluxes... Generating docs for page Tracer_Timestep... Generating docs for page Tracer_Transport_Equations... Generating docs for page Vertical_Diffusion... Generating docs for page citelist... Generating group documentation... Generating class documentation... Generating namespace index... Generating docs for namespace mom Generating docs for compound mom::mom_control_struct... Generating docs for compound mom::mom_diag_ids... Generating docs for namespace mom_ale Generating docs for compound mom_ale::ale_cs... Generating docs for namespace mom_eos Generating docs for compound mom_eos::calculate_compress... Generating docs for compound mom_eos::calculate_density... Generating docs for compound mom_eos::calculate_density_derivs... Generating docs for compound mom_eos::calculate_density_second_derivs... Generating docs for compound mom_eos::calculate_spec_vol... Generating docs for compound mom_eos::calculate_specific_vol_derivs... Generating docs for compound mom_eos::calculate_tfreeze... Generating docs for compound mom_eos::eos_type... Generating docs for namespace mom_ice_shelf Generating docs for compound mom_ice_shelf::ice_shelf_cs... Generating docs for namespace mom_meke Generating docs for compound mom_meke::meke_cs... Generating docs for namespace mom_unit_scaling Generating docs for compound mom_unit_scaling::unit_scale_type... Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Generating XML output... Generating XML output for class mom_ale::ale_cs Generating XML output for class mom_eos::calculate_compress Generating XML output for class mom_eos::calculate_density Generating XML output for class mom_eos::calculate_density_derivs Generating XML output for class mom_eos::calculate_density_second_derivs Generating XML output for class mom_eos::calculate_spec_vol Generating XML output for class mom_eos::calculate_specific_vol_derivs Generating XML output for class mom_eos::calculate_tfreeze Generating XML output for class mom_eos::eos_type Generating XML output for class mom_ice_shelf::ice_shelf_cs Generating XML output for class mom_meke::meke_cs Generating XML output for class mom::mom_control_struct Generating XML output for class mom::mom_diag_ids Generating XML output for class mom_unit_scaling::unit_scale_type Generating XML output for namespace mom Generating XML output for namespace mom_ale Generating XML output for namespace mom_eos Generating XML output for namespace mom_ice_shelf Generating XML output for namespace mom_meke Generating XML output for namespace mom_unit_scaling Generating XML output for file _ALE.dox Generating XML output for file _ALE_timestep.dox Generating XML output for file MOM_ALE.F90 Generating XML output for file _Baroclinic_Momentum.dox Generating XML output for file _Barotropic_Baroclinic_Coupling.dox Generating XML output for file _Barotropic_Momentum.dox Generating XML output for file _Discrete_Coriolis.dox Generating XML output for file _Discrete_grids.dox Generating XML output for file _Discrete_OBC.dox Generating XML output for file _Discrete_PG.dox Generating XML output for file _Energetic_consistancy.dox Generating XML output for file _Finite_difference.dox Generating XML output for file _General_coordinate.dox Generating XML output for file _Governing.dox Generating XML output for file _Notation.dox Generating XML output for file _PPM.dox Generating XML output for file _Sea_ice.dox Generating XML output for file _Solar_radiation.dox Generating XML output for file _Specifics.dox Generating XML output for file _Time_Filter.dox Generating XML output for file MOM.F90 Generating XML output for file _Equation_of_State.dox Generating XML output for file MOM_EOS.F90 Generating XML output for file _Diagnostics.dox Generating XML output for file _Domain_decomposition.dox Generating XML output for file _Global_grids.dox Generating XML output for file _Horizontal_indexing.dox Generating XML output for file _Parallel_IO.dox Generating XML output for file _Regional_grids.dox Generating XML output for file _Runtime_parameter_system.dox Generating XML output for file _Testing.dox Generating XML output for file _Vertical_grids.dox Generating XML output for file MOM_unit_scaling.F90 Generating XML output for file MOM_ice_shelf.F90 Generating XML output for file MOM_MEKE.F90 Generating XML output for file _CVMix_KPP.dox Generating XML output for file _Advection.dox Generating XML output for file _Discrete_tracer.dox Generating XML output for file _Horizontal_diffusion.dox Generating XML output for file _Passive_tracer.dox Generating XML output for file _Tracer_fluxes.dox Generating XML output for file _Tracer_timestep.dox Generating XML output for file _Tracer_Transport.dox Generating XML output for file _Vertical_diffusion.dox Generating XML output for page ALE Generating XML output for page ALE_Timestep Generating XML output for page Baroclinic_Momentum_Equations Generating XML output for page Barotropic_Baroclinic_Coupling Generating XML output for page Barotropic_Momentum_Equations Generating XML output for page Discrete_Coriolis Generating XML output for page Discrete_Grids Generating XML output for page Discrete_OBC Generating XML output for page Discrete_PG Generating XML output for page Energetic_Consistency Generating XML output for page Finite_Difference_Operators Generating XML output for page General_Coordinate Generating XML output for page Governing_Equations Generating XML output for page Notation Generating XML output for page PPM Generating XML output for page Sea_Ice Generating XML output for page Solar_Radiation Generating XML output for page Specifics Generating XML output for page Time_Filtering Generating XML output for page Equation_of_State Generating XML output for page Diagnostics Generating XML output for page Domain_Decomposition Generating XML output for page Global_Grids Generating XML output for page Horizontal_Indexing Generating XML output for page Parallel_IO Generating XML output for page Regional_Grids Generating XML output for page Runtime_Parameter_System Generating XML output for page Testing Generating XML output for page Vertical_Grids Generating XML output for page CVMix_KPP Generating XML output for page Tracer_Advection Generating XML output for page Discrete_Tracer Generating XML output for page Horizontal_Diffusion Generating XML output for page Passive_Tracers Generating XML output for page Tracer_Fluxes Generating XML output for page Tracer_Timestep Generating XML output for page Tracer_Transport_Equations Generating XML output for page Vertical_Diffusion Generating XML output for page citelist Generate XML output for dir /home/cermak/src/MOM6/src/ALE/ Generate XML output for dir /home/cermak/src/MOM6/src/core/ Generate XML output for dir /home/cermak/src/MOM6/src/equation_of_state/ Generate XML output for dir /home/cermak/src/MOM6/src/framework/ Generate XML output for dir /home/cermak/src/MOM6/src/ice_shelf/ Generate XML output for dir /home/cermak/src/MOM6/src/parameterizations/lateral/ Generate XML output for dir /home/cermak/src/MOM6/src/parameterizations/ Generate XML output for dir /home/cermak/src/MOM6/src/ lookup cache used 776/65536 hits=5732 misses=903 finished... # Make sure we are in nonstopmode for generating the pdf by patching the Makefile # Older doxygen versions doe not have LATEX_CMD grep -q "pdflatex refman" _build/doxygen_latex/Makefile && sed -i.bak 's/pdflatex 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] Chapter 1. (./ALE.tex Package natbib Warning: Citation `adcroft2006' on page 1 undefined on input lin e 3. 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[28 <./PG_loop.png>] LaTeX Warning: Reference `eq:PG_vert' on page 29 undefined on input line 33. LaTeX Warning: Reference `eq:PG_loop' on page 29 undefined on input line 35. ) [29] [30] Chapter 10. (./Energetic_Consistency.tex) [31] [32] Chapter 11. (./Finite_Difference_Operators.tex) [33] [34] Chapter 12. (./General_Coordinate.tex Package natbib Warning: Citation `bleck2002' on page 35 undefined on input line 11. LaTeX Warning: Reference `eq:h-horz-momentum' on page 35 undefined on input lin e 15. Package natbib Warning: Citation `adcroft2008' on page 35 undefined on input li ne 15. Package natbib Warning: Citation `white2008' on page 35 undefined on input line 15. Package natbib Warning: Citation `white2009' on page 35 undefined on input line 15. ) [35] [36] Chapter 13. (./Governing_Equations.tex Package natbib Warning: Citation `wright1997' on page 37 undefined on input lin e 7. [37]) [38] Chapter 14. (./Notation.tex) [39] [40] Chapter 15. 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(./Horizontal_Indexing.tex Underfull \vbox (badness 10000) has occurred while \output is active [63] [64] Underfull \vbox (badness 10000) has occurred while \output is active [65 <./Hor izontal_NE_indexing_nonsym.png>] Underfull \hbox (badness 10000) in paragraph at lines 55--56 []\T1/pcr/m/n/10 real, dimension(HI%isd[]:HI%ied, HI%jsd[]:HI%jed, GV%ke) []:[] : h !$\OML/cmm/m/it/10 <$ \T1/pcr/m/n/10 Layer Overfull \hbox (21.53372pt too wide) in paragraph at lines 60--61 []\T1/pcr/m/n/10 real, dimension(HI%IsdB[]:HI%IedB, HI%jsd[]:HI%jed) []:[]: Du !$\OML/cmm/m/it/10 <$ \T1/pcr/m/n/10 Depth at u-points [66 <./Horizontal_NE_indexing_sym.png>] Underfull \hbox (badness 10000) in paragraph at lines 61--62 []\T1/pcr/m/n/10 real, dimension(HI%IsdB[]:HI%IedB, HI%jsd[]:HI%jed, GV%ke) []: []: h !$\OML/cmm/m/it/10 <$ \T1/pcr/m/n/10 Zonal Overfull \hbox (21.53372pt too wide) in paragraph at lines 66--67 []\T1/pcr/m/n/10 real, dimension(HI%isd[]:HI%ied, HI%JsdB[]:HI%JedB) []:[]: Dv !$\OML/cmm/m/it/10 <$ \T1/pcr/m/n/10 Depth at v-points Underfull \hbox (badness 10000) in paragraph at lines 67--68 []\T1/pcr/m/n/10 real, dimension(HI%isd[]:HI%ied, HI%JsdB[]:HI%JedB, GV%ke) []: []: h !$\OML/cmm/m/it/10 <$ \T1/pcr/m/n/10 Zonal Underfull \hbox (badness 10000) in paragraph at lines 72--73 []\T1/pcr/m/n/10 real, dimension(HI%IsdB[]:HI%IedB, HI%JsdB[]:HI%JedB) []:[]: D q !$\OML/cmm/m/it/10 <$ \T1/pcr/m/n/10 Depth at Underfull \hbox (badness 10000) in paragraph at lines 73--74 []\T1/pcr/m/n/10 real, dimension(HI%IsdB[]:HI%IedB, HI%JsdB[]:HI%JedB, GV%ke) [ ]:[]: vort !$\OML/cmm/m/it/10 <$ ) [67] [68] Chapter 25. (./Parallel_IO.tex) [69] [70] Chapter 26. (./Regional_Grids.tex) [71] [72] Chapter 27. (./Runtime_Parameter_System.tex [73] [74]) [75] [76] Chapter 28. (./Testing.tex Underfull \hbox (badness 10000) detected at line 12 [][][] [77] [78 <./consortium.png>] Underfull \hbox (badness 10000) detected at line 73 [][][] [79]) [80 <./Rotated_indices.png>] Chapter 29. (./Vertical_Grids.tex) [81] [82] Chapter 30. (./CVMix_KPP.tex Package natbib Warning: Citation `large1994' on page 83 undefined on input line 1. Package natbib Warning: Citation `large1994' on page 83 undefined on input line 4. Underfull \hbox (badness 10000) detected at line 10 [][][] ) [83] [84] Chapter 31. (./Tracer_Advection.tex Package natbib Warning: Citation `easter1993' on page 85 undefined on input lin e 3. Package natbib Warning: Citation `colella1984' on page 85 undefined on input li ne 3. Package natbib Warning: Citation `huynh1997' on page 85 undefined on input line 3. Package natbib Warning: Citation `lin1994' on page 85 undefined on input line 7 . ) [85] [86] Chapter 32. (./Discrete_Tracer.tex) [87] [88] Chapter 33. (./Horizontal_Diffusion.tex Package natbib Warning: Citation `shao2019-in-review' on page 89 undefined on i nput line 17. [89 <./eddy_fluxes.png>] [90 <./shao0.png>] [91 <./shao1.png>] [92 <./shao2.png >] [93 <./shao3.png>] Underfull \vbox (badness 10000) has occurred while \output is active [94 <./sha o4.png>] Underfull \vbox (badness 10000) has occurred while \output is active [95 <./sha o5.png>] Underfull \vbox (badness 10000) has occurred while \output is active [96 <./sbl 1.png>]) [97 <./sbl2.png>] [98] Chapter 34. (./Passive_Tracers.tex) [99] [100] Chapter 35. (./Tracer_Fluxes.tex) [101] [102] Chapter 36. (./Tracer_Timestep.tex) [103] [104] Chapter 37. (./Tracer_Transport_Equations.tex [105 <./PPM_1d.png>] Package natbib Warning: Citation `easter1993' on page 106 undefined on input li ne 52. Package natbib Warning: Citation `durran2010' on page 106 undefined on input li ne 52. Package natbib Warning: Citation `russell1981' on page 106 undefined on input l ine 52. [106]) [107] [108] Chapter 38. (./Vertical_Diffusion.tex) [109] [110] Chapter 39. (./namespaces.tex LaTeX Warning: Reference `namespacemom' on page 111 undefined on input line 3. LaTeX Warning: Reference `namespacemom__ale' on page 111 undefined on input lin e 4. LaTeX Warning: Reference `namespacemom__eos' on page 111 undefined on input lin e 5. LaTeX Warning: Reference `namespacemom__ice__shelf' on page 111 undefined on in put line 6. LaTeX Warning: Reference `namespacemom__meke' on page 111 undefined on input li ne 7. LaTeX Warning: Reference `namespacemom__unit__scaling' on page 111 undefined on input line 8. ) [111] [112] Chapter 40. (./annotated.tex LaTeX Warning: Reference `structmom__ale_1_1ale__cs' on page 113 undefined on i nput line 3. LaTeX Warning: Reference `interfacemom__eos_1_1calculate__compress' on page 113 undefined on input line 4. LaTeX Warning: Reference `interfacemom__eos_1_1calculate__density' on page 113 undefined on input line 5. LaTeX Warning: Reference `interfacemom__eos_1_1calculate__density__derivs' on p age 113 undefined on input line 6. LaTeX Warning: Reference `interfacemom__eos_1_1calculate__density__second__deri vs' on page 113 undefined on input line 7. LaTeX Warning: Reference `interfacemom__eos_1_1calculate__spec__vol' on page 11 3 undefined on input line 8. LaTeX Warning: Reference `interfacemom__eos_1_1calculate__specific__vol__derivs ' on page 113 undefined on input line 9. LaTeX Warning: Reference `interfacemom__eos_1_1calculate__tfreeze' on page 113 undefined on input line 10. LaTeX Warning: Reference `structmom__eos_1_1eos__type' on page 113 undefined on input line 11. LaTeX Warning: Reference `structmom__ice__shelf_1_1ice__shelf__cs' on page 113 undefined on input line 12. LaTeX Warning: Reference `structmom__meke_1_1meke__cs' on page 113 undefined on input line 13. LaTeX Warning: Reference `structmom_1_1mom__control__struct' on page 113 undefi ned on input line 14. LaTeX Warning: Reference `structmom_1_1mom__diag__ids' on page 113 undefined on input line 15. LaTeX Warning: Reference `structmom__unit__scaling_1_1unit__scale__type' on pag e 113 undefined on input line 16. ) [113] [114] Chapter 41. (./files.tex LaTeX Warning: Reference `MOM__ALE_8F90' on page 115 undefined on input line 3. LaTeX Warning: Reference `MOM_8F90' on page 115 undefined on input line 4. LaTeX Warning: Reference `MOM__EOS_8F90' on page 115 undefined on input line 5. LaTeX Warning: Reference `MOM__unit__scaling_8F90' on page 115 undefined on inp ut line 6. LaTeX Warning: Reference `MOM__ice__shelf_8F90' on page 115 undefined on input line 7. LaTeX Warning: Reference `MOM__MEKE_8F90' on page 115 undefined on input line 8 . ) [115] [116] Chapter 42. (./namespacemom.tex [117] [118] Underfull \hbox (badness 10000) detected at line 104 [][][] [119] [120] [121] [122] [123] [124] Package longtable Warning: Column widths have changed (longtable) in table 42.1 on input line 305. Overfull \hbox (15.15555pt too wide) in paragraph at lines 316--317 []\T1/pcr/m/n/7 02964 []type[](thermo_var_ptrs), []intent(in)[] :: tv[] !< A structure pointing to various thermodynamic[] [125] Package longtable Warning: Column widths have changed (longtable) in table 42.2 on input line 372. Overfull \hbox (15.15555pt too wide) in paragraph at lines 394--394 []\T1/pcr/m/n/7 03019 []type[](unit_scale_type), []pointer[] :: us => null( ) []!< structure containing various unit conversion factors[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 401--401 []\T1/pcr/m/n/7 03026 []real[] :: dh[] !< Thickness of a laye r within the mixed layer [Z ~> m] or [H ~> m or kg m-2][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 408--409 []\T1/pcr/m/n/7 03032 [] !! calculation of properti es of the uppermost ocean [nondim] or [Z H-1 ~> 1 or[] [126] Underfull \vbox (badness 10000) has occurred while \output is active [127] Underfull \vbox (badness 10000) has occurred while \output is active [128] Underfull \vbox (badness 10000) has occurred while \output is active [129] Underfull \vbox (badness 10000) has occurred while \output is active [130] Package longtable Warning: Column widths have changed (longtable) in table 42.3 on input line 807. [131] Package longtable Warning: Column widths have changed (longtable) in table 42.4 on input line 891. [132] Package longtable Warning: Column widths have changed (longtable) in table 42.5 on input line 936. [133] Package longtable Warning: Column widths have changed (longtable) in table 42.6 on input line 994. Overfull \hbox (19.35555pt too wide) in paragraph at lines 1016--1016 []\T1/pcr/m/n/7 01613 [] !! model is not being started from a restart file[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1017--1018 []\T1/pcr/m/n/7 01614 []logical[], []optional[], []intent(out)[] :: offline_tracer_mode[] !< True is returned if tracers are being[] [134] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1059--1060 []\T1/pcr/m/n/7 01653 []real[], []dimension(:,:)[], []allocatable[], []target [] :: frac_shelf_h []! fraction of total area occupied by ice shelf[] Underfull \vbox (badness 10000) has occurred while \output is active [135] Underfull \vbox (badness 10000) has occurred while \output is active [136] Underfull \vbox (badness 10000) has occurred while \output is active [137] Underfull \vbox (badness 10000) has occurred while \output is active [138] Underfull \vbox (badness 10000) has occurred while \output is active [139] Underfull \vbox (badness 10000) has occurred while \output is active [140] Underfull \vbox (badness 10000) has occurred while \output is active [141] Underfull \vbox (badness 10000) has occurred while \output is active [142] Underfull \vbox (badness 10000) has occurred while \output is active [143] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1879--1879 []\T1/pcr/m/n/7 02471 []call []calltree_waypoint([]"Calling adjustGridForIn tegrity() to remap initial conditions (initialize_MOM)"[])[] Underfull \vbox (badness 10000) has occurred while \output is active [144] Underfull \vbox (badness 10000) has occurred while \output is active [145] Underfull \vbox (badness 10000) has occurred while \output is active [146] [147] Package longtable Warning: Column widths have changed (longtable) in table 42.7 on input line 2194. [148] Package longtable Warning: Column widths have changed (longtable) in table 42.8 on input line 2258. Underfull \hbox (badness 10000) detected at line 2259 [][][] Package longtable Warning: Column widths have changed (longtable) in table 42.9 on input line 2303. [149] Package longtable Warning: Column widths have changed (longtable) in table 42.10 on input line 2372. [150] [151] Package longtable Warning: Column widths have changed (longtable) in table 42.11 on input line 2467. [152] Package longtable Warning: Column widths have changed (longtable) in table 42.12 on input line 2580. Underfull \hbox (badness 922) in paragraph at lines 2587--2588 \T1/phv/m/n/10 _[]ocean[][], [][]id[]_[]clock[]_[]other[][], [][]id[]_[]clock[] _[]pass[][], [][]mom[]_[]state[]_[]is[]_[]synchronized()[][], [][]step[]_[]mom[ ]_[]dynamics()[][], [][]step[]_[]mom[]_[] Overfull \hbox (15.15555pt too wide) in paragraph at lines 2591--2591 []\T1/pcr/m/n/7 00422 []type[](mech_forcing), []target[], []intent(inout)[] : : forces_in[] !< A structure with the driving mechanical forces[][] [153] Underfull \vbox (badness 10000) has occurred while \output is active [154] Underfull \vbox (badness 10000) has occurred while \output is active [155] Underfull \vbox (badness 10000) has occurred while \output is active [156] Underfull \vbox (badness 10000) has occurred while \output is active [157] Underfull \vbox (badness 10000) has occurred while \output is active [158] [159] Package longtable Warning: Column widths have changed (longtable) in table 42.13 on input line 3142. Overfull \hbox (15.15555pt too wide) in paragraph at lines 3168--3168 []\T1/pcr/m/n/7 00957 [] !! bo ttom boundary layer properties will apply [T ~> s],[][] [160] Underfull \vbox (badness 10000) has occurred while \output is active [161] [162] Package longtable Warning: Column widths have changed (longtable) in table 42.14 on input line 3376. Overfull \hbox (15.15555pt too wide) in paragraph at lines 3405--3405 []\T1/pcr/m/n/7 01226 []type[](time_type), []intent(in)[] :: time _end_thermo[] !< End of averaging interval for thermo diags[][] [163] Underfull \vbox (badness 10000) has occurred while \output is active [164] [165] Package longtable Warning: Column widths have changed (longtable) in table 42.15 on input line 3602. Overfull \hbox (19.35555pt too wide) in paragraph at lines 3622--3623 []\T1/pcr/m/n/7 01137 []intent(in)[] :: h[] !< layer thicknesses after the transports [H ~> m or kg[] [166] Package longtable Warning: Column widths have changed (longtable) in table 42.16 on input line 3718. [167] Underfull \vbox (badness 10000) has occurred while \output is active [168] Underfull \vbox (badness 10000) has occurred while \output is active [169] [170] [171] [172] [173] [174]) (./namespacemom__ale.tex [175] [176] [177] Package longtable Warning: Column widths have changed (longtable) in table 42.17 on input line 98. Package longtable Warning: Column widths have changed (longtable) in table 42.18 on input line 141. Overfull \hbox (15.15555pt too wide) in paragraph at lines 152--152 []\T1/pcr/m/n/7 00620 []type[](thermo_var_ptrs), []intent(i nout)[] :: tv[] !< Thermodynamical variable structure[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 153--153 []\T1/pcr/m/n/7 00621 []real[], []dimension(SZI_(G),SZJ_(G), SZK_(GV))[], []i ntent(inout)[] :: h[] !< Current 3D grid obtained after the[][] [178] Package longtable Warning: Column widths have changed (longtable) in table 42.19 on input line 202. [179] Package longtable Warning: Column widths have changed (longtable) in table 42.20 on input line 232. Package longtable Warning: Column widths have changed (longtable) in table 42.21 on input line 259. Package longtable Warning: Column widths have changed (longtable) in table 42.22 on input line 295. Overfull \vbox (44.87186pt too high) has occurred while \output is active [180] [181] Package longtable Warning: Column widths have changed (longtable) in table 42.23 on input line 437. [182] Package longtable Warning: Column widths have changed (longtable) in table 42.24 on input line 486. [183] Package longtable Warning: Column widths have changed (longtable) in table 42.25 on input line 542. Overfull \hbox (19.35555pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/7 00327 []real[], []dimension(SZIB_(G),SZJ_(G),SZK_(GV))[], []i ntent(inout)[] :: u[] !< Zonal velocity field [L T-1 ~> m s-1][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 559--560 []\T1/pcr/m/n/7 00328 []real[], []dimension(SZI_(G),SZJB_(G),SZK_(GV))[], []i ntent(inout)[] :: v[] !< Meridional velocity field [L T-1 ~> m[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 572--573 []\T1/pcr/m/n/7 00338 []real[], []dimension(SZI_(G),SZJ_(G),SZK_(GV))[] :: h_ new []! New 3D grid obtained after last time step [H ~> m or[] [184] Package longtable Warning: Column widths have changed (longtable) in table 42.26 on input line 666. Overfull \vbox (43.59442pt too high) has occurred while \output is active [185] Overfull \hbox (19.35555pt too wide) in paragraph at lines 689--690 []\T1/pcr/m/n/7 00420 []real[], []dimension(SZI_(G),SZJ_(G),SZK_(GV))[] :: h_ new []! New 3D grid obtained after last time step [H ~> m or[] [186] Package longtable Warning: Column widths have changed (longtable) in table 42.27 on input line 762. Overfull \hbox (19.35555pt too wide) in paragraph at lines 773--773 []\T1/pcr/m/n/7 00463 []type[](ale_cs), []poi nter[] :: cs[] !< Regridding parameters and options[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 777--777 []\T1/pcr/m/n/7 00467 []type[](thermo_var_ptrs), []int ent(inout)[] :: tv[] !< Thermodynamic variable structure[][] [187] Underfull \hbox (badness 10000) in paragraph at lines 852--853 | \T1/pcr/m/n/8 real, dimension( g %isd[]: g %ied, g %jsd[]: g %jed, gv %ke), intent(inout) \T1/pcr/m/sl/8 h[]_[] Package longtable Warning: Column widths have changed (longtable) in table 42.28 on input line 876. Overfull \hbox (19.35555pt too wide) in paragraph at lines 893--893 []\T1/pcr/m/n/7 00550 [] !! last time step [H ~> m or kg-2][][] [188] Package longtable Warning: Column widths have changed (longtable) in table 42.29 on input line 958. Underfull \vbox (badness 10000) has occurred while \output is active [189] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1000--1000 []\T1/pcr/m/n/7 01070 slp(k) = plm_slope_wa(h(i,j,k-1), h(i,j,k), h(i,j,k +1), h_neglect, q(i,j,k-1), q(i,j,k), q(i,j,k+1))[] [190] Package longtable Warning: Column widths have changed (longtable) in table 42.30 on input line 1050. Overfull \hbox (19.35555pt too wide) in paragraph at lines 1088--1088 []\T1/pcr/m/n/7 00281 cs%id_vert_remap_h_tendency = register_diag_field([]'oc ean_model'[],[]'vert_remap_h_tendency'[],diag%axestl,time,[] Underfull \hbox (badness 10000) in paragraph at lines 1098--1099 | \T1/pcr/m/n/8 real, dimension( g %isd[]: g %ied, g %jsd[]: g %jed, gv %ke+1) , intent(inout), [191] [192] Package longtable Warning: Column widths have changed (longtable) in table 42.31 on input line 1132. Overfull \hbox (15.15555pt too wide) in paragraph at lines 1157--1158 []\T1/pcr/m/n/7 00674 []real[], []optional[], []intent(in)[] :: d t[] !< Model timestep to provide a timescale for regridding[] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1168--1168 []\T1/pcr/m/n/7 00684 []real[], []dimension(SZI_(G),SZJ_(G),SZK_(GV))[] :: h_loc, h_orig []! A working copy of layer thicknesses[][] [193] Package longtable Warning: Column widths have changed (longtable) in table 42.32 on input line 1235. [194] Package longtable Warning: Column widths have changed (longtable) in table 42.33 on input line 1281. Overfull \hbox (15.15555pt too wide) in paragraph at lines 1317--1318 []\T1/pcr/m/n/7 00963 [] !! use more robust forms of the same[] [195] Package longtable Warning: Column widths have changed (longtable) in table 42.34 on input line 1380. [196] Package longtable Warning: Column widths have changed (longtable) in table 42.35 on input line 1421. 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Overfull \hbox (19.35555pt too wide) in paragraph at lines 1601--1601 []\T1/pcr/m/n/7 00749 []type[](verticalgrid_type), []intent (in)[] :: gv[] !< Ocean vertical grid structure[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1604--1604 []\T1/pcr/m/n/7 00752 []real[], []dimension(SZI_(G),SZJ_(G),SZK_(GV))[], []in tent(in)[] :: h_new[] !< Thickness of destination grid[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1609--1609 []\T1/pcr/m/n/7 00757 []optional[], []intent (in)[] :: dxinterface[] !< Change in interface position[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1617--1617 []\T1/pcr/m/n/7 00764 []real[], []optional[], []in tent(in)[] :: dt[] !< time step for diagnostics [T ~> s][][] [199] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1637--1637 []\T1/pcr/m/n/7 00784 []! If remap_uv_using_old_alg is .true. and u or v is r equested, then we must have dxInterface. Otherwise,[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1639--1639 []\T1/pcr/m/n/7 00786 []if[] ( .not. []present[](dxinterface) .and. (cs_ale%r emap_uv_using_old_alg .and. ([]present[](u) .or. []present[](v)))[] Underfull \vbox (badness 10000) has occurred while \output is active [200] Underfull \vbox (badness 10000) has occurred while \output is active [201] Package longtable Warning: Column widths have changed (longtable) in table 42.39 on input line 1825. [202] Package longtable Warning: Column widths have changed (longtable) in table 42.40 on input line 1889. [203]) (./namespacemom__eos.tex [204] [205] [206] [207] Package longtable Warning: Column widths have changed (longtable) in table 42.41 on input line 185. [208] [209] Package longtable Warning: Column widths have changed (longtable) in table 42.42 on input line 317. Overfull \hbox (15.15555pt too wide) in paragraph at lines 336--336 []\T1/pcr/m/n/7 01196 []intent(in)[] :: p_b[] !< Press ure at the bottom of the layer [R L2 T-2 ~> Pa] or [Pa][][] [210] Overfull \hbox (19.35555pt too wide) in paragraph at lines 365--366 []\T1/pcr/m/n/7 01225 []real[] :: pres_scale []! A unit conversion factor from the rescaled units of pressure to Pa [Pa T2 R-1 L-2[] [211] Package longtable Warning: Column widths have changed (longtable) in table 42.43 on input line 420. Overfull \hbox (15.15555pt too wide) in paragraph at lines 447--448 []\T1/pcr/m/n/7 00586 []real[] :: spv_scale []! A factor to convert specific volume from m3 kg-1 to the desired units [kg m-3 R-1 ~>[] [212] Package longtable Warning: Column widths have changed (longtable) in table 42.44 on input line 512. Overfull \hbox (19.35555pt too wide) in paragraph at lines 526--526 []\T1/pcr/m/n/7 01043 []real[], []dimension(:)[], []intent(inout)[] :: dsv_dt [] !< The partial derivative of specific volume with potential[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 528--528 []\T1/pcr/m/n/7 01045 []real[], []dimension(:)[], []intent(inout)[] :: dsv_ds [] !< The partial derivative of specific volume with salinity[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 535--535 []\T1/pcr/m/n/7 01051 [] !! volu me in combination with scaling given by US [various][][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 539--540 []\T1/pcr/m/n/7 01055 []real[] :: spv_scale []! A factor to convert specific volume from m3 kg-1 to the desired units [kg R-1 m-3 ~>[] [213] Package longtable Warning: Column widths have changed (longtable) in table 42.45 on input line 595. Overfull \hbox (15.15555pt too wide) in paragraph at lines 617--618 []\T1/pcr/m/n/7 00544 []real[] :: spv_scale []! A factor to convert specific volume from m3 kg-1 to the desired units [kg R-1 m-3 ~>[] [214] Package longtable Warning: Column widths have changed (longtable) in table 42.46 on input line 669. [215] Package longtable Warning: Column widths have changed (longtable) in table 42.47 on input line 753. [216] Package longtable Warning: Column widths have changed (longtable) in table 42.48 on input line 811. Overfull \hbox (15.15555pt too wide) in paragraph at lines 826--826 []\T1/pcr/m/n/7 00363 []real[], []dimension(:)[], []intent(inout)[] :: rho [] !< Density (in-situ if pressure is local) [R ~> kg m-3][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 831--831 []\T1/pcr/m/n/7 00368 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] [217] Package longtable Warning: Column widths have changed (longtable) in table 42.49 on input line 903. [218] Overfull \hbox (19.35555pt too wide) in paragraph at lines 921--922 []\T1/pcr/m/n/7 00266 []real[], []dimension(:)[], []intent(inout)[] :: rho[] !< Density (in-situ if pressure is local) [kg m-3] or [R ~>[] [219] Package longtable Warning: Column widths have changed (longtable) in table 42.50 on input line 984. Overfull \hbox (19.35555pt too wide) in paragraph at lines 1006--1006 []\T1/pcr/m/n/7 00761 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1007--1007 []\T1/pcr/m/n/7 00762 [] !! in combination with scaling given by US [various][][] [220] Package longtable Warning: Column widths have changed (longtable) in table 42.51 on input line 1070. [221] Package longtable Warning: Column widths have changed (longtable) in table 42.52 on input line 1153. [222] Package longtable Warning: Column widths have changed (longtable) in table 42.53 on input line 1230. [223] Package longtable Warning: Column widths have changed (longtable) in table 42.54 on input line 1316. [224] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1346--1346 []\T1/pcr/m/n/7 00860 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] [225] Package longtable Warning: Column widths have changed (longtable) in table 42.55 on input line 1442. [226] [227] Package longtable Warning: Column widths have changed (longtable) in table 42.56 on input line 1540. Overfull \hbox (19.35555pt too wide) in paragraph at lines 1564--1564 []\T1/pcr/m/n/7 00495 [] !! volu me in combination with scaling given by US [various][][] [228] Package longtable Warning: Column widths have changed (longtable) in table 42.57 on input line 1626. [229] Package longtable Warning: Column widths have changed (longtable) in table 42.58 on input line 1723. [230] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1742--1742 []\T1/pcr/m/n/7 00423 []real[], []dimension(:)[], []intent(inout)[] :: rho [] !< Density (in-situ if pressure is local) [R ~> kg m-3][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1747--1747 []\T1/pcr/m/n/7 00428 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] [231] Package longtable Warning: Column widths have changed (longtable) in table 42.59 on input line 1838. [232] Package longtable Warning: Column widths have changed (longtable) in table 42.60 on input line 1933. [233] Package longtable Warning: Column widths have changed (longtable) in table 42.61 on input line 2019. Overfull \vbox (25.39507pt too high) has occurred while \output is active [234] Package longtable Warning: Column widths have changed (longtable) in table 42.62 on input line 2099. Overfull \vbox (19.90533pt too high) has occurred while \output is active [235] Package longtable Warning: Column widths have changed (longtable) in table 42.63 on input line 2162. [236] Package longtable Warning: Column widths have changed (longtable) in table 42.64 on input line 2217. [237] Package longtable Warning: Column widths have changed (longtable) in table 42.65 on input line 2248. Underfull \hbox (badness 10000) detected at line 2249 [][][] Package longtable Warning: Column widths have changed (longtable) in table 42.66 on input line 2286. [238] Package longtable Warning: Column widths have changed (longtable) in table 42.67 on input line 2315. [239] Package longtable Warning: Column widths have changed (longtable) in table 42.68 on input line 2469. [240] Overfull \hbox (15.15555pt too wide) in paragraph at lines 2477--2477 []\T1/pcr/m/n/7 01459 []integer[], []optional[], []intent(in)[] :: form_of_eo s[] !< A coded integer indicating the equation of state to use.[][] Package longtable Warning: Column widths have changed (longtable) in table 42.69 on input line 2520. [241] Underfull \hbox (badness 10000) detected at line 2542 [][][] Package longtable Warning: Column widths have changed (longtable) in table 42.70 on input line 2557. Overfull \hbox (15.15555pt too wide) in paragraph at lines 2571--2571 []\T1/pcr/m/n/7 01511 []real[], []intent(in)[] :: drho_ds[] !< Partial derivative of density with salinity [kg m-3 ppt-1][][] [242] Package longtable Warning: Column widths have changed (longtable) in table 42.71 on input line 2622. Overfull \hbox (19.35555pt too wide) in paragraph at lines 2630--2630 []\T1/pcr/m/n/7 01575 []integer[], []optional[], []intent(out)[] :: form_of_e os[] !< A coded integer indicating the equation of state to use.[][] [243] Package longtable Warning: Column widths have changed (longtable) in table 42.72 on input line 2673. Overfull \hbox (15.15555pt too wide) in paragraph at lines 2754--2754 []\T1/pcr/m/n/7 00143 []character*(10), parameter :: EOS_LINEAR_STRING = "LINEA R" !< A string for specifying the equation of state[][] [244] Underfull \hbox (badness 10000) in paragraph at lines 2772--2773 []\T1/phv/m/n/10 Referenced by [][]calculate[]_[]compress[]_[]array()[][], [][] calculate[]_[]density[]_[]array()[][], [][]calculate[]_[]density[]_[]derivs[]_[ ]array()[][], Overfull \hbox (15.15555pt too wide) in paragraph at lines 2798--2798 []\T1/pcr/m/n/7 00147 []character*(10), parameter :: EOS_NEMO_STRING = "NEMO" !< A string for specifying the equation of state[][] Underfull \hbox (badness 10000) in paragraph at lines 2816--2817 []\T1/phv/m/n/10 Referenced by [][]calculate[]_[]compress[]_[]array()[][], [][] calculate[]_[]density[]_[]array()[][], [][]calculate[]_[]density[]_[]derivs[]_[ ]array()[][], Underfull \hbox (badness 2334) in paragraph at lines 2816--2817 \T1/phv/m/n/10 _[]density[]_[]second[]_[]derivs[]_[]scalar()[][], [][]calculate []_[]spec[]_[]vol[]_[]array()[][], [][]calculate[]_[]spec[]_[]vol[]_[]derivs[]_ []array()[][], [][]calculate[]_[] [245] Overfull \hbox (15.15555pt too wide) in paragraph at lines 2842--2842 []\T1/pcr/m/n/7 00146 []character*(10), parameter :: EOS_TEOS10_STRING = "TEOS1 0" !< A string for specifying the equation of state[][] Underfull \hbox (badness 10000) in paragraph at lines 2860--2861 []\T1/phv/m/n/10 Referenced by [][]calculate[]_[]compress[]_[]array()[][], [][] calculate[]_[]density[]_[]array()[][], [][]calculate[]_[]density[]_[]derivs[]_[ ]array()[][], Overfull \hbox (15.15555pt too wide) in paragraph at lines 2886--2886 []\T1/pcr/m/n/7 00144 []character*(10), parameter :: EOS_UNESCO_STRING = "UNESC O" !< A string for specifying the equation of state[][] [246] Overfull \hbox (15.15555pt too wide) in paragraph at lines 2930--2930 []\T1/pcr/m/n/7 00145 []character*(10), parameter :: EOS_WRIGHT_STRING = "WRIGH T" !< A string for specifying the equation of state[][] [247] Overfull \hbox (19.35555pt too wide) in paragraph at lines 2997--2998 []\T1/pcr/m/n/7 00153 []character*(10), parameter :: TFREEZE_LINEAR_STRING = "L INEAR" !< A string for specifying the freezing point[] [248] Overfull \hbox (19.35555pt too wide) in paragraph at lines 3086--3087 []\T1/pcr/m/n/7 00156 []character*(10), parameter :: TFREEZE_TEOS10_STRING = "T EOS10" !< A string for specifying the freezing point[] ) (./namespacemom__ice__shelf.tex [249] [250] [251] Package longtable Warning: Column widths have changed (longtable) in table 42.73 on input line 98. [252] Overfull \hbox (15.15555pt too wide) in paragraph at lines 196--196 []\T1/pcr/m/n/7 00965 fluxes%lprec(i,j) = frac_shelf*iss%water_flux(i, j)*cs%flux_factor + frac_open * fluxes%lprec(i,j)[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 205--206 []\T1/pcr/m/n/7 00974 []! The salt flux should be mostly from sea ice, so p erhaps none should be intercepted and this should be[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 208--208 []\T1/pcr/m/n/7 00976 fluxes%salt_flux(i,j) = frac_shelf * iss%salt_flux( i,j)*cs%flux_factor + frac_open * fluxes%salt_flux[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 213--213 []\T1/pcr/m/n/7 00980 []call []hchksum(iss%water_flux, []"water_flux add sh elf fluxes"[], g%HI, haloshift=0, scale=us%RZ_T_to_kg_m2s)[] Underfull \vbox (badness 10000) has occurred while \output is active [253] Overfull \hbox (19.35555pt too wide) in paragraph at lines 241--241 []\T1/pcr/m/n/7 01008 last_mass_shelf(i,j) = us%kg_m3_to_R*us%m_to_Z * last_mass_shelf(i,j) []! Rescale after time_interp[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 288--288 []\T1/pcr/m/n/7 01054 balancing_flux = ( us%kg_m2s_to_RZ_T*global_area_in tegral(iss%water_flux, g, scale=us%RZ_T_to_kg_m2s,[] [254] Package longtable Warning: Column widths have changed (longtable) in table 42.74 on input line 337. [255] Package longtable Warning: Column widths have changed (longtable) in table 42.75 on input line 445. [256] Package longtable Warning: Column widths have changed (longtable) in table 42.76 on input line 509. [257] Package longtable Warning: Column widths have changed (longtable) in table 42.77 on input line 578. Package longtable Warning: Column widths have changed (longtable) in table 42.78 on input line 618. Overfull \vbox (48.24297pt too high) has occurred while \output is active [258] Package longtable Warning: Column widths have changed (longtable) in table 42.79 on input line 675. Overfull \hbox (19.35555pt too wide) in paragraph at lines 686--686 []\T1/pcr/m/n/7 01084 []type[](param_file_type), []intent(in)[] :: param_file[] !< A structure to parse for run-time parameters[][] [259] Overfull \hbox (15.15555pt too wide) in paragraph at lines 693--693 []\T1/pcr/m/n/7 01089 []type[](forcing), []optional[], []intent(inout)[] :: fluxes[] !< A structure containing pointers to any possible[][] Underfull \vbox (badness 10000) has occurred while \output is active [260] Underfull \vbox (badness 10000) has occurred while \output is active [261] Underfull \vbox (badness 10000) has occurred while \output is active [262] Underfull \vbox (badness 10000) has occurred while \output is active [263] Underfull \vbox (badness 10000) has occurred while \output is active [264] Underfull \vbox (badness 10000) has occurred while \output is active [265] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1215--1215 []\T1/pcr/m/n/7 01611 cs%id_thermal_driving = register_diag_field([]'ocean_mo del'[], []'thermal_driving'[], cs%diag%axesT1, cs%Time, &[] Package longtable Warning: Column widths have changed (longtable) in table 42.80 on input line 1266. [266] [267] Package longtable Warning: Column widths have changed (longtable) in table 42.81 on input line 1379. [268] Underfull \vbox (badness 10000) has occurred while \output is active [269] Underfull \vbox (badness 10000) has occurred while \output is active [270] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1627--1627 []\T1/pcr/m/n/7 00431 []call []mom_error(fatal, []"Impossible con ditions found in 3-equation skin salinity calculation."[])[] Underfull \vbox (badness 10000) has occurred while \output is active [271] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1746--1746 []\T1/pcr/m/n/7 00550 []!other options: dTi/dz linear through shelf , with draft in [Z ~> m], KTI in [Z2 T-1 ~> m2 s-1][][] Underfull \vbox (badness 10000) has occurred while \output is active [272] Underfull \vbox (badness 10000) has occurred while \output is active [273] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1898--1898 []\T1/pcr/m/n/7 00701 []if[] (cs%id_thermal_driving > 0) []call []post_data(c s%id_thermal_driving, (sfc_state%sst-iss%tfreeze), cs%diag[] Package longtable Warning: Column widths have changed (longtable) in table 42.82 on input line 1945. Overfull \vbox (14.26237pt too high) has occurred while \output is active [274] [275] Package longtable Warning: Column widths have changed (longtable) in table 42.83 on input line 2042. [276]) (./namespacemom__meke.tex [277] [278] [279] Underfull \hbox (badness 1616) in paragraph at lines 89--89 []\T1/phv/m/n/10 In the non-lin-ear drag limit, where $\OML/cmm/m/it/10 U[] >> []\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 U[]; \OMS/cmsy/m/n/10 j\OML/cmm/m/it/10 u\O MS/cmsy/m/n/10 j[]\OML/cmm/m/it/10 ; C[]^^U\OT1/cmr/m/n/10 )$\T1/phv/m/n/10 , t he equi-lib-rium be-comes $[] \OMS/cmsy/m/n/10 ^^Y Overfull \vbox (82.47147pt too high) has occurred while \output is active [280] Package longtable Warning: Column widths have changed (longtable) in table 42.86 on input line 165. [281] Package longtable Warning: Column widths have changed (longtable) in table 42.87 on input line 264. [282] Package longtable Warning: Column widths have changed (longtable) in table 42.88 on input line 319. [283] Underfull \vbox (badness 10000) has occurred while \output is active [284] [285] Package longtable Warning: Column widths have changed (longtable) in table 42.89 on input line 510. Package longtable Warning: Column widths have changed (longtable) in table 42.90 on input line 576. [286] [287] Underfull \vbox (badness 10000) has occurred while \output is active [288] Underfull \vbox (badness 10000) has occurred while \output is active [289] Underfull \vbox (badness 10000) has occurred while \output is active [290] Overfull \hbox (18.19756pt too wide) in paragraph at lines 947--948 | \T1/pcr/m/n/8 real, dimension( g %isd[]: g %ied, g %jsd[]: g %jed), intent(o ut) \T1/pcr/m/sl/8 Lmix[]Scale \T1/pcr/m/n/8 ) [private] Package longtable Warning: Column widths have changed (longtable) in table 42.91 on input line 977. Overfull \vbox (14.84415pt too high) has occurred while \output is active [291] [292] Package longtable Warning: Column widths have changed (longtable) in table 42.92 on input line 1097. [293] [294] Package longtable Warning: Column widths have changed (longtable) in table 42.93 on input line 1212. Overfull \hbox (15.15555pt too wide) in paragraph at lines 1233--1233 []\T1/pcr/m/n/7 00120 []real[], []intent( in)[] :: dt[] !< Model(baroclinic) time-step [T ~> s].[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1235--1236 []\T1/pcr/m/n/7 00122 []real[], []dimension(SZIB_(G),SZJ_(G),SZK_(G))[], []in tent(in)[] :: hu[] !< Accumlated zonal mass flux [H L2 ~> m3[] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1237--1238 []\T1/pcr/m/n/7 00123 []real[], []dimension(SZI_(G),SZJB_(G),SZK_(G))[], []in tent(in)[] :: hv[] !< Accumlated meridional mass flux [H L2[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1251--1251 []\T1/pcr/m/n/7 00136 del4meke, & []! Time-integrated MEKE tendency ari sing from the biharmonic of MEKE [L2 T-2 ~> m2 s-2].[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1260--1261 []\T1/pcr/m/n/7 00144 []! In one place, MEKE_uflux is used as temporary work space with units of [L2 T-2 ~> m2[] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1269--1270 []\T1/pcr/m/n/7 00151 []! In one place, MEKE_vflux is used as temporary work space with units of [L2 T-2 ~> m2[] [295] Underfull \vbox (badness 10000) has occurred while \output is active [296] Underfull \vbox (badness 10000) has occurred while \output is active [297] Underfull \vbox (badness 10000) has occurred while \output is active [298] Underfull \vbox (badness 10000) has occurred while \output is active [299] Underfull \vbox (badness 10000) has occurred while \output is active [300]) (./namespacemom__unit__scaling.tex [301] Package longtable Warning: Column widths have changed (longtable) in table 42.94 on input line 42. Package longtable Warning: Column widths have changed (longtable) in table 42.95 on input line 76. [302] Package longtable Warning: Column widths have changed (longtable) in table 42.96 on input line 104. [303]) [304] Chapter 43. (./structmom__ale_1_1ale__cs.tex [305] [306] [307] [308] [309] Overfull \hbox (15.15555pt too wide) in paragraph at lines 405--405 []\T1/pcr/m/n/7 00076 []logical[] :: remap_after_initialization[] !< Indicate s whether to regrid/remap after initializing the state.[][] [310]) (./interfacemom__eos_1_1calculate__compress.tex [311] [312] Package longtable Warning: Column widths have changed (longtable) in table 43.1 on input line 53. [313] Package longtable Warning: Column widths have changed (longtable) in table 43.2 on input line 129. ) (./interfacemom__eos_1_1calculate__density.tex [314] Package longtable Warning: Column widths have changed (longtable) in table 43.3 on input line 61. Overfull \vbox (45.34691pt too high) has occurred while \output is active [315] Overfull \hbox (15.15555pt too wide) in paragraph at lines 72--72 []\T1/pcr/m/n/7 00363 []real[], []dimension(:)[], []intent(inout)[] :: rho [] !< Density (in-situ if pressure is local) [R ~> kg m-3][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 77--77 []\T1/pcr/m/n/7 00368 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] [316] Package longtable Warning: Column widths have changed (longtable) in table 43.4 on input line 149. Overfull \hbox (19.35555pt too wide) in paragraph at lines 159--160 []\T1/pcr/m/n/7 00266 []real[], []dimension(:)[], []intent(inout)[] :: rho[] !< Density (in-situ if pressure is local) [kg m-3] or [R ~>[] [317] [318] Package longtable Warning: Column widths have changed (longtable) in table 43.5 on input line 220. [319] Package longtable Warning: Column widths have changed (longtable) in table 43.6 on input line 300. Overfull \hbox (15.15555pt too wide) in paragraph at lines 315--315 []\T1/pcr/m/n/7 00423 []real[], []dimension(:)[], []intent(inout)[] :: rho [] !< Density (in-situ if pressure is local) [R ~> kg m-3][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 320--320 []\T1/pcr/m/n/7 00428 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] [320] Package longtable Warning: Column widths have changed (longtable) in table 43.7 on input line 411. Overfull \vbox (18.74098pt too high) has occurred while \output is active [321] [322] Package longtable Warning: Column widths have changed (longtable) in table 43.8 on input line 502. ) (./interfacemom__eos_1_1calculate__density__derivs.tex [323] Package longtable Warning: Column widths have changed (longtable) in table 43.9 on input line 55. Overfull \vbox (20.21097pt too high) has occurred while \output is active [324] Overfull \hbox (19.35555pt too wide) in paragraph at lines 73--73 []\T1/pcr/m/n/7 00761 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 74--74 []\T1/pcr/m/n/7 00762 [] !! in combination with scaling given by US [various][][] Package longtable Warning: Column widths have changed (longtable) in table 43.10 on input line 137. [325] [326] Package longtable Warning: Column widths have changed (longtable) in table 43.11 on input line 212. ) (./interfacemom__eos_1_1calculate__density__second__derivs.tex [327] Package longtable Warning: Column widths have changed (longtable) in table 43.12 on input line 61. [328] Overfull \hbox (19.35555pt too wide) in paragraph at lines 87--87 []\T1/pcr/m/n/7 00860 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] [329] Package longtable Warning: Column widths have changed (longtable) in table 43.13 on input line 183. [330]) (./interfacemom__eos_1_1calculate__spec__vol.tex [331] Package longtable Warning: Column widths have changed (longtable) in table 43.14 on input line 55. Overfull \hbox (15.15555pt too wide) in paragraph at lines 78--79 []\T1/pcr/m/n/7 00586 []real[] :: spv_scale []! A factor to convert specific volume from m3 kg-1 to the desired units [kg m-3 R-1 ~>[] [332] Package longtable Warning: Column widths have changed (longtable) in table 43.15 on input line 141. [333] Overfull \hbox (15.15555pt too wide) in paragraph at lines 159--160 []\T1/pcr/m/n/7 00544 []real[] :: spv_scale []! A factor to convert specific volume from m3 kg-1 to the desired units [kg R-1 m-3 ~>[] Package longtable Warning: Column widths have changed (longtable) in table 43.16 on input line 213. Underfull \vbox (badness 10000) has occurred while \output is active [334] Overfull \hbox (19.35555pt too wide) in paragraph at lines 229--229 []\T1/pcr/m/n/7 00495 [] !! volu me in combination with scaling given by US [various][][] ) (./interfacemom__eos_1_1calculate__specific__vol__derivs.tex [335] Package longtable Warning: Column widths have changed (longtable) in table 43.17 on input line 53. Overfull \hbox (19.35555pt too wide) in paragraph at lines 63--63 []\T1/pcr/m/n/7 01043 []real[], []dimension(:)[], []intent(inout)[] :: dsv_dt [] !< The partial derivative of specific volume with potential[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 65--65 []\T1/pcr/m/n/7 01045 []real[], []dimension(:)[], []intent(inout)[] :: dsv_ds [] !< The partial derivative of specific volume with salinity[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 72--72 []\T1/pcr/m/n/7 01051 [] !! volu me in combination with scaling given by US [various][][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 76--77 []\T1/pcr/m/n/7 01055 []real[] :: spv_scale []! A factor to convert specific volume from m3 kg-1 to the desired units [kg R-1 m-3 ~>[] [336] Package longtable Warning: Column widths have changed (longtable) in table 43.18 on input line 134. [337]) (./interfacemom__eos_1_1calculate__tfreeze.tex [338] Package longtable Warning: Column widths have changed (longtable) in table 43.19 on input line 51. [339] Package longtable Warning: Column widths have changed (longtable) in table 43.20 on input line 127. ) (./structmom__eos_1_1eos__type.tex [340] [341] [342] Overfull \hbox (19.35555pt too wide) in paragraph at lines 211--211 []\T1/pcr/m/n/7 00128 []real[] :: kg_m3_to_r = 1.[] !< A constant that trans lates kilograms per meter cubed to the units of density.[][] [343] Overfull \hbox (19.35555pt too wide) in paragraph at lines 265--265 []\T1/pcr/m/n/7 00129 []real[] :: r_to_kg_m3 = 1.[] !< A constant that trans lates the units of density to kilograms per meter cubed.[][] [344]) (./structmom__ice__shelf_1_1ice__shelf__cs.tex [345] [346] [347] [348] [349] [350] [351] Overfull \hbox (15.15555pt too wide) in paragraph at lines 445--446 []\T1/pcr/m/n/7 00159 []real[] :: dtfr_ds[] !< Partial derivative of freezing temperature with salinity [degC[] [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [363] [364] [365]) (./structmom__meke_1_1meke__cs.tex [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] [376] [377] [378] [379] [380] [381] [382] [383] [384]) (./structmom_1_1mom__control__struct.tex [385] [386] [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399] [400] [401] [402] [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415]) (./structmom_1_1mom__diag__ids.tex [416] [417]) (./structmom__unit__scaling_1_1unit__scale__type.tex [418] [419] [420] [421] [422] [423] [424] [425] [426]) [427] [428] Chapter 44. (./__ALE_8dox.tex) (./__ALE__timestep_8dox.tex) (./MOM__ALE_8F90.tex Underfull \hbox (badness 10000) in paragraph at lines 3--4 [429] [430]) (./MOM__ALE_8F90_source.tex [431] Overfull \hbox (15.15555pt too wide) in paragraph at lines 80--80 [][][]\T1/pcr/m/n/7 00076[][] []logical[] :: remap_after_initialization[] !< Indicates whether to regrid/remap after initializing the state.[][] Underfull \vbox (badness 10000) has occurred while \output is active [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] Overfull \hbox (19.35555pt too wide) in paragraph at lines 285--285 []\T1/pcr/m/n/7 00281 cs%id_vert_remap_h_tendency = register_diag_field([]'oc ean_model'[],[]'vert_remap_h_tendency'[],diag%axestl,time,[] Underfull \vbox (badness 10000) has occurred while \output is active [434] Overfull \hbox (19.35555pt too wide) in paragraph at lines 334--334 []\T1/pcr/m/n/7 00327 []real[], []dimension(SZIB_(G),SZJ_(G),SZK_(GV))[], []i ntent(inout)[] :: u[] !< Zonal velocity field [L T-1 ~> m s-1][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 335--336 []\T1/pcr/m/n/7 00328 []real[], []dimension(SZI_(G),SZJB_(G),SZK_(GV))[], []i ntent(inout)[] :: v[] !< Meridional velocity field [L T-1 ~> m[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 349--350 []\T1/pcr/m/n/7 00338 []real[], []dimension(SZI_(G),SZJ_(G),SZK_(GV))[] :: h_ new []! New 3D grid obtained after last time step [H ~> m or[] Underfull \vbox (badness 10000) has occurred while \output is active [435] Overfull \hbox (19.35555pt too wide) in paragraph at lines 434--435 []\T1/pcr/m/n/7 00420 []real[], []dimension(SZI_(G),SZJ_(G),SZK_(GV))[] :: h_ new []! New 3D grid obtained after last time step [H ~> m or[] Overfull \hbox (15.15555pt too wide) in paragraph at lines 474--474 []\T1/pcr/m/n/7 00459 []!> Regrid/remap stored fields used for offline tracer i ntegrations. These input fields are assumed to have[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 475--475 []\T1/pcr/m/n/7 00460 []!! the same layer thicknesses at the end of the last of fline interval (which should be a Zstar grid). This[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 483--483 []\T1/pcr/m/n/7 00467 []type[](thermo_var_ptrs), []int ent(inout)[] :: tv[] !< Thermodynamic variable structure[][] Underfull \vbox (badness 10000) has occurred while \output is active [436] Overfull \hbox (19.35555pt too wide) in paragraph at lines 569--569 []\T1/pcr/m/n/7 00550 [] !! last time step [H ~> m or kg-2][][] Underfull \vbox (badness 10000) has occurred while \output is active [437] Overfull \hbox (15.15555pt too wide) in paragraph at lines 642--642 []\T1/pcr/m/n/7 00620 []type[](thermo_var_ptrs), []intent(i nout)[] :: tv[] !< Thermodynamical variable structure[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 643--643 []\T1/pcr/m/n/7 00621 []real[], []dimension(SZI_(G),SZJ_(G), SZK_(GV))[], []i ntent(inout)[] :: h[] !< Current 3D grid obtained after the[][] Underfull \vbox (badness 10000) has occurred while \output is active [438] Overfull \hbox (15.15555pt too wide) in paragraph at lines 697--698 []\T1/pcr/m/n/7 00674 []real[], []optional[], []intent(in)[] :: d t[] !< Model timestep to provide a timescale for regridding[] Overfull \hbox (15.15555pt too wide) in paragraph at lines 708--708 []\T1/pcr/m/n/7 00684 []real[], []dimension(SZI_(G),SZJ_(G),SZK_(GV))[] :: h_loc, h_orig []! A working copy of layer thicknesses[][] Underfull \vbox (badness 10000) has occurred while \output is active [439] Overfull \hbox (19.35555pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/7 00749 []type[](verticalgrid_type), []intent (in)[] :: GV[] !< Ocean vertical grid structure[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 777--777 []\T1/pcr/m/n/7 00752 []real[], []dimension(SZI_(G),SZJ_(G),SZK_(GV))[], []in tent(in)[] :: h_new[] !< Thickness of destination grid[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 782--782 []\T1/pcr/m/n/7 00757 []optional[], []intent (in)[] :: dxInterface[] !< Change in interface position[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 790--790 []\T1/pcr/m/n/7 00764 []real[], []optional[], []in tent(in)[] :: dt[] !< time step for diagnostics [T ~> s][][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 810--810 []\T1/pcr/m/n/7 00784 []! If remap_uv_using_old_alg is .true. and u or v is r equested, then we must have dxInterface. Otherwise,[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 812--812 []\T1/pcr/m/n/7 00786 []if[] ( .not. []present[](dxinterface) .and. (cs_ale%r emap_uv_using_old_alg .and. ([]present[](u) .or. []present[](v)))[] Underfull \vbox (badness 10000) has occurred while \output is active [440] Underfull \vbox (badness 10000) has occurred while \output is active [441] Overfull \hbox (15.15555pt too wide) in paragraph at lines 998--999 []\T1/pcr/m/n/7 00963 [] !! use more robust forms of the same[] Underfull \vbox (badness 10000) has occurred while \output is active [442] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1106--1106 []\T1/pcr/m/n/7 01070 slp(k) = plm_slope_wa(h(i,j,k-1), h(i,j,k), h(i,j,k +1), h_neglect, q(i,j,k-1), q(i,j,k), q(i,j,k+1))[] Underfull \vbox (badness 10000) has occurred while \output is active [443] Underfull \vbox (badness 10000) has occurred while \output is active [444] Underfull \vbox (badness 10000) has occurred while \output is active [445]) (./__Baroclinic__Momentum_8dox.tex) (./__Barotropic__Baroclinic__Coupling_8dox.tex) (./__Barotropic__Momentum_8dox.tex) (./__Discrete__Coriolis_8dox.tex) (./__Discrete__grids_8dox.tex [446]) (./__Discrete__OBC_8dox.tex) (./__Discrete__PG_8dox.tex) (./__Energetic__consistancy_8dox.tex) (./__Finite__difference_8dox.tex) (./__General__coordinate_8dox.tex) (./__Governing_8dox.tex) (./__Notation_8dox.tex) (./__PPM_8dox.tex) (./__Sea__ice_8dox.tex) (./__Solar__radiation_8dox.tex) (./__Specifics_8dox.tex ) (./__Time__Filter_8dox.tex) (./MOM_8F90.tex Underfull \hbox (badness 10000) in paragraph at lines 3--4 [447] [448]) (./MOM_8F90_source.tex [449] Overfull \hbox (15.15555pt too wide) in paragraph at lines 67--67 []\T1/pcr/m/n/7 00060 []use []mom_diabatic_driver[], only[] : diabatic, d iabatic_driver_init, diabatic_cs, extract_diabatic_member[] [450] Underfull \vbox (badness 10000) has occurred while \output is active [451] Underfull \vbox (badness 10000) has occurred while \output is active [452] Underfull \vbox (badness 10000) has occurred while \output is active [453] Underfull \vbox (badness 10000) has occurred while \output is active [454] Overfull \hbox (15.15555pt too wide) in paragraph at lines 438--438 [][][]\T1/pcr/m/n/7 00422[][] []type[](mech_forcing), []target[], []intent(in out)[] :: forces_in[] !< A structure with the driving mechanical forces[][] Underfull \vbox (badness 10000) has occurred while \output is active [455] Underfull \vbox (badness 10000) has occurred while \output is active [456] Underfull \vbox (badness 10000) has occurred while \output is active [457] Underfull \vbox (badness 10000) has occurred while \output is active [458] Underfull \vbox (badness 10000) has occurred while \output is active [459] Underfull \vbox (badness 10000) has occurred while \output is active [460] Overfull \hbox (15.15555pt too wide) in paragraph at lines 978--978 []\T1/pcr/m/n/7 00957 [] !! bo ttom boundary layer properties will apply [T ~> s],[][] Underfull \vbox (badness 10000) has occurred while \output is active [461] Underfull \vbox (badness 10000) has occurred while \output is active [462] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1161--1162 []\T1/pcr/m/n/7 01137 []intent(in)[] :: h[] !< layer thicknesses after the transports [H ~> m or kg[] Underfull \vbox (badness 10000) has occurred while \output is active [463] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1258--1258 []\T1/pcr/m/n/7 01226 []type[](time_type), []intent(in)[] :: Time _end_thermo[] !< End of averaging interval for thermo diags[][] Underfull \vbox (badness 10000) has occurred while \output is active [464] Underfull \vbox (badness 10000) has occurred while \output is active [465] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1437--1437 []\T1/pcr/m/n/7 01402 []!! the work is very preliminary. Some more detail about this capability along with some of the subroutines[][] Underfull \vbox (badness 10000) has occurred while \output is active [466] Underfull \vbox (badness 10000) has occurred while \output is active [467] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1655--1655 []\T1/pcr/m/n/7 01613 [] !! model is not being started from a restart file[][] Underfull \vbox (badness 10000) has occurred while \output is active [468] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1656--1657 []\T1/pcr/m/n/7 01614 []logical[], []optional[], []intent(out)[] :: offline_tracer_mode[] !< True is returned if tracers are being[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1698--1699 []\T1/pcr/m/n/7 01653 []real[], []dimension(:,:)[], []allocatable[], []target [] :: frac_shelf_h []! fraction of total area occupied by ice shelf[] Underfull \vbox (badness 10000) has occurred while \output is active [469] Underfull \vbox (badness 10000) has occurred while \output is active [470] Underfull \vbox (badness 10000) has occurred while \output is active [471] Underfull \vbox (badness 10000) has occurred while \output is active [472] Underfull \vbox (badness 10000) has occurred while \output is active [473] Underfull \vbox (badness 10000) has occurred while \output is active [474] Underfull \vbox (badness 10000) has occurred while \output is active [475] Underfull \vbox (badness 10000) has occurred while \output is active [476] Underfull \vbox (badness 10000) has occurred while \output is active [477] Overfull \hbox (19.35555pt too wide) in paragraph at lines 2518--2518 []\T1/pcr/m/n/7 02471 []call []calltree_waypoint([]"Calling adjustGridForIn tegrity() to remap initial conditions (initialize_MOM)"[])[] Underfull \vbox (badness 10000) has occurred while \output is active [478] Underfull \vbox (badness 10000) has occurred while \output is active [479] Underfull \vbox (badness 10000) has occurred while \output is active [480] Underfull \vbox (badness 10000) has occurred while \output is active [481] Underfull \vbox (badness 10000) has occurred while \output is active [482] Underfull \vbox (badness 10000) has occurred while \output is active [483] Overfull \hbox (15.15555pt too wide) in paragraph at lines 3021--3022 [][][]\T1/pcr/m/n/7 02964[][] []type[](thermo_var_ptrs), []intent (in)[] :: tv[] !< A structure pointing to various thermodynamic[] Underfull \vbox (badness 10000) has occurred while \output is active [484] Overfull \hbox (15.15555pt too wide) in paragraph at lines 3077--3077 []\T1/pcr/m/n/7 03019 []type[](unit_scale_type), []pointer[] :: US => null( ) []!< structure containing various unit conversion factors[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 3084--3084 []\T1/pcr/m/n/7 03026 []real[] :: dh[] !< Thickness of a laye r within the mixed layer [Z ~> m] or [H ~> m or kg m-2][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 3091--3092 []\T1/pcr/m/n/7 03032 [] !! calculation of properti es of the uppermost ocean [nondim] or [Z H-1 ~> 1 or[] Underfull \vbox (badness 10000) has occurred while \output is active [485] Underfull \vbox (badness 10000) has occurred while \output is active [486] Underfull \vbox (badness 10000) has occurred while \output is active [487] Underfull \vbox (badness 10000) has occurred while \output is active [488] Underfull \vbox (badness 10000) has occurred while \output is active [489] Underfull \vbox (badness 10000) has occurred while \output is active [490] Underfull \vbox (badness 10000) has occurred while \output is active [491] Underfull \vbox (badness 10000) has occurred while \output is active [492] Underfull \vbox (badness 10000) has occurred while \output is active [493] Underfull \vbox (badness 10000) has occurred while \output is active [494]) (./__Equation__of__State_8dox.tex) (./MOM__EOS_8F90.tex Underfull \hbox (badness 10000) in paragraph at lines 3--5 [495] [496] [497] [498]) (./MOM__EOS_8F90_source.tex [499] Overfull \hbox (19.35555pt too wide) in paragraph at lines 140--140 [][][]\T1/pcr/m/n/7 00128[][] []real[] :: kg_m3_to_r = 1.[] !< A constant th at translates kilograms per meter cubed to the units of density.[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 141--141 [][][]\T1/pcr/m/n/7 00129[][] []real[] :: r_to_kg_m3 = 1.[] !< A constant th at translates the units of density to kilograms per meter cubed.[][] Underfull \vbox (badness 10000) has occurred while \output is active [500] Underfull \vbox (badness 10000) has occurred while \output is active [501] Overfull \hbox (19.35555pt too wide) in paragraph at lines 296--297 []\T1/pcr/m/n/7 00266 []real[], []dimension(:)[], []intent(inout)[] :: rho[] !< Density (in-situ if pressure is local) [kg m-3] or [R ~>[] Underfull \vbox (badness 10000) has occurred while \output is active [502] Overfull \hbox (15.15555pt too wide) in paragraph at lines 400--400 []\T1/pcr/m/n/7 00363 []real[], []dimension(:)[], []intent(inout)[] :: rho [] !< Density (in-situ if pressure is local) [R ~> kg m-3][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 405--405 []\T1/pcr/m/n/7 00368 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] Underfull \vbox (badness 10000) has occurred while \output is active [503] Overfull \hbox (15.15555pt too wide) in paragraph at lines 466--466 []\T1/pcr/m/n/7 00423 []real[], []dimension(:)[], []intent(inout)[] :: rho [] !< Density (in-situ if pressure is local) [R ~> kg m-3][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 471--471 []\T1/pcr/m/n/7 00428 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] Underfull \vbox (badness 10000) has occurred while \output is active [504] Overfull \hbox (19.35555pt too wide) in paragraph at lines 540--540 []\T1/pcr/m/n/7 00495 [] !! volu me in combination with scaling given by US [various][][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 589--590 []\T1/pcr/m/n/7 00544 []real[] :: spv_scale []! A factor to convert specific volume from m3 kg-1 to the desired units [kg R-1 m-3 ~>[] Underfull \vbox (badness 10000) has occurred while \output is active [505] Overfull \hbox (15.15555pt too wide) in paragraph at lines 633--634 []\T1/pcr/m/n/7 00586 []real[] :: spv_scale []! A factor to convert specific volume from m3 kg-1 to the desired units [kg m-3 R-1 ~>[] Underfull \vbox (badness 10000) has occurred while \output is active [506] Underfull \vbox (badness 10000) has occurred while \output is active [507] Overfull \hbox (19.35555pt too wide) in paragraph at lines 815--815 []\T1/pcr/m/n/7 00761 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 816--816 []\T1/pcr/m/n/7 00762 [] !! in combination with scaling given by US [various][][] Underfull \vbox (badness 10000) has occurred while \output is active [508] Overfull \hbox (19.35555pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/7 00860 []real[], []optional[], []intent(in)[] :: scale[] !< A multiplicative factor by which to scale density[][] Underfull \vbox (badness 10000) has occurred while \output is active [509] Underfull \vbox (badness 10000) has occurred while \output is active [510] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1106--1106 []\T1/pcr/m/n/7 01043 []real[], []dimension(:)[], []intent(inout)[] :: dSV_dT [] !< The partial derivative of specific volume with potential[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1108--1108 []\T1/pcr/m/n/7 01045 []real[], []dimension(:)[], []intent(inout)[] :: dSV_dS [] !< The partial derivative of specific volume with salinity[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1115--1115 []\T1/pcr/m/n/7 01051 [] !! volu me in combination with scaling given by US [various][][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1119--1120 []\T1/pcr/m/n/7 01055 []real[] :: spv_scale []! A factor to convert specific volume from m3 kg-1 to the desired units [kg R-1 m-3 ~>[] Underfull \vbox (badness 10000) has occurred while \output is active [511] Underfull \vbox (badness 10000) has occurred while \output is active [512] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1263--1263 []\T1/pcr/m/n/7 01196 []intent(in)[] :: p_b[] !< Press ure at the bottom of the layer [R L2 T-2 ~> Pa] or [Pa][][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1292--1293 []\T1/pcr/m/n/7 01225 []real[] :: pres_scale []! A unit conversion factor from the rescaled units of pressure to Pa [Pa T2 R-1 L-2[] Underfull \vbox (badness 10000) has occurred while \output is active [513] Underfull \vbox (badness 10000) has occurred while \output is active [514] Underfull \vbox (badness 10000) has occurred while \output is active [515] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1529--1529 []\T1/pcr/m/n/7 01459 []integer[], []optional[], []intent(in)[] :: form_of_EO S[] !< A coded integer indicating the equation of state to use.[][] Underfull \vbox (badness 10000) has occurred while \output is active [516] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1582--1582 []\T1/pcr/m/n/7 01511 []real[], []intent(in)[] :: dRho_dS[] !< Partial derivative of density with salinity [kg m-3 ppt-1][][] Underfull \vbox (badness 10000) has occurred while \output is active [517] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1648--1648 []\T1/pcr/m/n/7 01575 []integer[], []optional[], []intent(out)[] :: form_of_E OS[] !< A coded integer indicating the equation of state to use.[][] ) (./__Diagnostics_8dox.tex) (./__Domain__decomposition_8dox.tex Underfull \hbox (badness 2343) in paragraph at lines 1--1 []\T1/phv/bc/n/14.4 /home/cermak/src/[]M[]O[]M6/src/framework/[]_[][]Domain[]_[ ]decomposition.dox File Ref-er- ) (./__Global__grids_8dox.tex) (./__Horizontal__indexing_8dox.tex) (./__Parallel__IO_8dox.tex) (./__Regional__grids_8dox.tex) (./__Runtime__parameter__system_8dox.tex Underfull \hbox (badness 10000) in paragraph at lines 1--1 []\T1/phv/bc/n/14.4 /home/cermak/src/[]M[]O[]M6/src/framework/[]_[][]Runtime[]_ []parameter[]_[]system.dox File ) (./__Testing_8dox.tex) (./__Vertical__grids_8dox.tex) (./MOM__unit__scaling_8F90.tex Underfull \hbox (badness 10000) in paragraph at lines 3--4 [518]) (./MOM__unit__scaling_8F90_source.tex [519] Underfull \vbox (badness 10000) has occurred while \output is active [520]) (./MOM__ice__shelf_8F90.tex Underfull \hbox (badness 10000) in paragraph at lines 3--5 Underfull \vbox (badness 10000) has occurred while \output is active [521] [522]) (./MOM__ice__shelf_8F90_source.tex [523] Underfull \vbox (badness 10000) has occurred while \output is active [524] Overfull \hbox (15.15555pt too wide) in paragraph at lines 168--169 [][][]\T1/pcr/m/n/7 00159[][] []real[] :: dtfr_ds[] !< Partial derivative of freezing temperature with salinity [degC[] Underfull \vbox (badness 10000) has occurred while \output is active [525] Underfull \vbox (badness 10000) has occurred while \output is active [526] Underfull \vbox (badness 10000) has occurred while \output is active [527] Overfull \hbox (19.35555pt too wide) in paragraph at lines 443--443 []\T1/pcr/m/n/7 00431 []call []mom_error(fatal, []"Impossible con ditions found in 3-equation skin salinity calculation."[])[] Underfull \vbox (badness 10000) has occurred while \output is active [528] Overfull \hbox (15.15555pt too wide) in paragraph at lines 563--563 []\T1/pcr/m/n/7 00550 []!other options: dTi/dz linear through shelf , with draft in [Z ~> m], KTI in [Z2 T-1 ~> m2 s-1][][] Underfull \vbox (badness 10000) has occurred while \output is active [529] Underfull \vbox (badness 10000) has occurred while \output is active [530] Overfull \hbox (19.35555pt too wide) in paragraph at lines 717--717 []\T1/pcr/m/n/7 00701 []if[] (cs%id_thermal_driving > 0) []call []post_data(c s%id_thermal_driving, (sfc_state%sst-iss%tfreeze), cs%diag[] Underfull \vbox (badness 10000) has occurred while \output is active [531] Underfull \vbox (badness 10000) has occurred while \output is active [532] Underfull \vbox (badness 10000) has occurred while \output is active [533] Overfull \hbox (15.15555pt too wide) in paragraph at lines 987--987 []\T1/pcr/m/n/7 00965 fluxes%lprec(i,j) = frac_shelf*iss%water_flux(i, j)*cs%flux_factor + frac_open * fluxes%lprec(i,j)[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 996--997 []\T1/pcr/m/n/7 00974 []! The salt flux should be mostly from sea ice, so p erhaps none should be intercepted and this should be[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 999--999 []\T1/pcr/m/n/7 00976 fluxes%salt_flux(i,j) = frac_shelf * iss%salt_flux( i,j)*cs%flux_factor + frac_open * fluxes%salt_flux[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1004--1004 []\T1/pcr/m/n/7 00980 []call []hchksum(iss%water_flux, []"water_flux add sh elf fluxes"[], g%HI, haloshift=0, scale=us%RZ_T_to_kg_m2s)[] Underfull \vbox (badness 10000) has occurred while \output is active [534] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1032--1032 []\T1/pcr/m/n/7 01008 last_mass_shelf(i,j) = us%kg_m3_to_R*us%m_to_Z * last_mass_shelf(i,j) []! Rescale after time_interp[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1079--1079 []\T1/pcr/m/n/7 01054 balancing_flux = ( us%kg_m2s_to_RZ_T*global_area_in tegral(iss%water_flux, g, scale=us%RZ_T_to_kg_m2s,[] Underfull \vbox (badness 10000) has occurred while \output is active [535] Overfull \hbox (19.35555pt too wide) in paragraph at lines 1111--1111 [][][]\T1/pcr/m/n/7 01084[][] []type[](param_file_type), []intent(in)[ ] :: param_file[] !< A structure to parse for run-time parameters[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1119--1119 []\T1/pcr/m/n/7 01089 []type[](forcing), []optional[], []intent(inout)[] :: fluxes[] !< A structure containing pointers to any possible[][] Underfull \vbox (badness 10000) has occurred while \output is active [536] Underfull \vbox (badness 10000) has occurred while \output is active [537] Underfull \vbox (badness 10000) has occurred while \output is active [538] Underfull \vbox (badness 10000) has occurred while \output is active [539] Underfull \vbox (badness 10000) has occurred while \output is active [540] Underfull \vbox (badness 10000) has occurred while \output is active [541] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1641--1641 []\T1/pcr/m/n/7 01611 cs%id_thermal_driving = register_diag_field([]'ocean_mo del'[], []'thermal_driving'[], cs%diag%axesT1, cs%Time, &[] Underfull \vbox (badness 10000) has occurred while \output is active [542] Underfull \vbox (badness 10000) has occurred while \output is active [543] Underfull \vbox (badness 10000) has occurred while \output is active [544] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1915--1916 []\T1/pcr/m/n/7 01884 []!! - CURRENTLY: initializes mass_shelf as well, bu t this is unnecessary, as mass_shelf is initialized[] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1951--1952 []\T1/pcr/m/n/7 01915 []!! and ocean model intercomparison projects: MISMIP v. 3 (MISMIP+), ISOMIP v. 2 (ISOMIP+) and MISOMIP v. 1[] ) (./MOM__MEKE_8F90.tex Underfull \hbox (badness 10000) in paragraph at lines 3--5 Underfull \vbox (badness 1412) has occurred while \output is active [545]) (./MOM__MEKE_8F90_source.tex [546] [547] Overfull \hbox (15.15555pt too wide) in paragraph at lines 130--130 []\T1/pcr/m/n/7 00120 []real[], []intent( in)[] :: dt[] !< Model(baroclinic) time-step [T ~> s].[][] Overfull \hbox (19.35555pt too wide) in paragraph at lines 132--133 []\T1/pcr/m/n/7 00122 []real[], []dimension(SZIB_(G),SZJ_(G),SZK_(G))[], []in tent(in)[] :: hu[] !< Accumlated zonal mass flux [H L2 ~> m3[] Overfull \hbox (15.15555pt too wide) in paragraph at lines 134--135 []\T1/pcr/m/n/7 00123 []real[], []dimension(SZI_(G),SZJB_(G),SZK_(G))[], []in tent(in)[] :: hv[] !< Accumlated meridional mass flux [H L2[] Overfull \hbox (19.35555pt too wide) in paragraph at lines 148--148 []\T1/pcr/m/n/7 00136 del4meke, & []! Time-integrated MEKE tendency ari sing from the biharmonic of MEKE [L2 T-2 ~> m2 s-2].[][] Overfull \hbox (15.15555pt too wide) in paragraph at lines 157--158 []\T1/pcr/m/n/7 00144 []! In one place, MEKE_uflux is used as temporary work space with units of [L2 T-2 ~> m2[] Overfull \hbox (15.15555pt too wide) in paragraph at lines 166--167 []\T1/pcr/m/n/7 00151 []! In one place, MEKE_vflux is used as temporary work space with units of [L2 T-2 ~> m2[] Underfull \vbox (badness 10000) has occurred while \output is active [548] Underfull \vbox (badness 10000) has occurred while \output is active [549] Underfull \vbox (badness 10000) has occurred while \output is active [550] Underfull \vbox (badness 10000) has occurred while \output is active [551] Underfull \vbox (badness 10000) has occurred while \output is active [552] Underfull \vbox (badness 10000) has occurred while \output is active [553] Underfull \vbox (badness 10000) has occurred while \output is active [554] Underfull \vbox (badness 10000) has occurred while \output is active [555] Underfull \vbox (badness 10000) has occurred while \output is active [556] Underfull \vbox (badness 10000) has occurred while \output is active [557] Underfull \vbox (badness 10000) has occurred while \output is active [558] Underfull \vbox (badness 10000) has occurred while \output is active [559] Underfull \vbox (badness 10000) has occurred while \output is active [560] Underfull \vbox (badness 10000) has occurred while \output is active [561] Underfull \vbox (badness 10000) has occurred while \output is active [562] Underfull \vbox (badness 10000) has occurred while \output is active [563] Underfull \vbox (badness 10000) has occurred while \output is active [564] Underfull \vbox (badness 10000) has occurred while \output is active [565] Overfull \hbox (15.15555pt too wide) in paragraph at lines 1696--1697 []\T1/pcr/m/n/7 01673 []!! Marshall, D. P., and A. J. Adcroft, 2010: Parameteri zation of ocean eddies: Potential vorticity mixing,[] ) (./__CVMix__KPP_8dox.tex) (./__Advection_8dox.tex) (./__Discrete__tracer_8dox.tex) (./__Horizontal__diffusion_8dox.tex) (./__Passive__tracer_8dox.tex) (./__Tracer__fluxes_8dox.tex) (./__Tracer__timestep_8dox.tex) (./__Tracer__Transport_8dox.tex) (./__Vertical__diffusion_8dox.tex) [566] [567] No file refman.bbl. [568] No file refman.ind. Package natbib Warning: There were undefined citations. Package longtable Warning: Table widths have changed. Rerun LaTeX. ! LaTeX Error: \begin{equation*} on input line 3 ended by \end{document}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.393 \end{document} (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (\end occurred inside a group at level 1) ### semi simple group (level 1) entered at line 3 (\begingroup) ### bottom level (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (572 pages, 3955594 bytes). Transcript written on refman.log. make[1]: *** [Makefile:6: refman.pdf] Error 1 make[1]: Leaving directory '/home/cermak/src/MOM6/docs/_build/doxygen_latex' make: *** [Makefile:219: nortd_latex] Error 2