| Nallreduction_inter_io_mod | All reduction, which does a reduce and then broadcasts the data to all IO servers |
| Narithmetic_operator_mod | The arithmetic operator which allows the user to define arithmetic formulas based on fields and constants which are then executed BDMAS style. This works by parsing the text forumula into an execution tree which is walked in order to perform the final result. Building the tree is the potentially expensive aspect of this, so built trees are cached as it is likely that the equation will be run many times. Currently this is expressed in terms of scalars, and it will operate on all elements of the data |
| Nbroadcast_inter_io_mod | Broadcast inter IO communication which sends a value from one IO server to all others. This tracks field name and timestep and only issues one call (and one results call to completion) for that combination |
| Nbuoyancy_mod | Calculates buoyancy terms for the SW field |
| Ncasim_mod | Implimentation of CASIM microphysics |
| Ncasim_monc_dgs_space | |
| Ncasim_profile_dgs_mod | Dummy stub when not compiling with CASIM microphysics |
| Ncfltest_mod | This contains the CFL test. It will perform the local advective CFL and Galilean transfromation calculations, compute the global values of these, then check the cfl criterion and determine an absolute new dtm. Depending upon the maximum and increment values this is then smoothed into a new dtm value. The value of dtm is physically set to this new value at the start of the next timestep |
| Ncheckpointer_common_mod | Common checkpoint functionality which is used by reader and writers to NetCDF checkpoints |
| Ncheckpointer_mod | Checkpointing NetCDF functionality |
| Ncheckpointer_read_checkpoint_mod | Will read in a NetCDF checkpoint file and initialise the model state_mod based upon this |
| Ncheckpointer_write_checkpoint_mod | Writes out model state_mod to a checkpoint NetCDF file |
| Nclearsourceterms_mod | Clears the source terms at the start of a timestep to then be populated by items in the dynamics group |
| Ncollections_mod | Collection data structures |
| Ncommunication_types_mod | Contains the types used for communication, holding the state of communications and supporting activities. These are held in a separate module to allow for dependencies from multiple areas of the code base which might otherwise result in circular dependencies if they lived in a specific module of functionality |
| Nconditional_diagnostics_column_mod | Conditionally averaged diagnostics, Part 1 of 2 |
| Nconditional_diagnostics_whole_mod | Conditionally averaged diagnostics, Part 2 of 2 |
| Nconfiguration_checkpoint_netcdf_parser_mod | Loads in the configuration stored in a NetCDF checkpoint file for the model to start from |
| Nconfiguration_file_parser_mod | Parses a configuration file and loads the contents into the options database which can then be interogated by components in the model |
| Nconfiguration_parser_mod | Parses the XML configuration file to produce the io configuration description which contains the data layout specification and rules for handling received data |
| Nconversions_mod | Conversion between common inbuilt FORTRAN data types |
| Ncoriolis_mod | This calculates the coriolis and mean pressure gradient terms which impact su and sv fields |
| Ndamping_mod | Damping applied to the W field at some point to stop stuff flying up and off |
| Ndata_utils_mod | Contains functionality for managing and extracting data from the raw data dumps that the IO server receives from a MONC process during model dumping |
| Ndatadefn_mod | Contains common definitions for the data and datatypes used by MONC |
| Ndebugger_mod | General purpose debugger. By changing the priority and other logic we can plug it in whereever we want in the run to dump out information |
| Ndecomposition_mod | Parallel decomposition to determine the grid points and data columns that are located on this process |
| Ndef_mcc_profiles | |
| Ndef_merge_atm | |
| Ndef_socrates_derived_fields | |
| Ndef_socrates_options | |
| Ndef_tvd_diagnostic_terms | |
| Ndiagnostic_federator_mod | This diagnostics federator will take in data fields sent from a MONC, perform operators on these as required by the diagnostics definition to produce diagnostic instantaneous fields which are then sent along to anything interested in them |
| Ndiagnostics_3d_mod | Derive 3-D diagnostic fields which are available in current_state |
| Ndiffusion_mod | Diffusion on the TH and Q fields |
| Ndiverr_mod | Calculates the local divergence error |
| Ndummy_netcdf_mod | |
| Nfftsolver_mod | Pressure solver which uses a tridiagonal algorithm operating on the pressure terms in Fourier space. It uses the pencil FFT module for 3D FFTs in pencil decomposition. These use FFTW for the actual FFT kernel |
| Nfftw_mod | Wrapper around the FFTW3 bindings. This will privatise by default all of FFTW3 apart from the calls that we explicitly need in our pencil solver |
| Nfieldcoarsener_operator_mod | Coarsens a field by selecting data with a specific period in any number of dimensions |
| Nfieldslicer_operator_mod | Slices a field based upon the selected dimension and index |
| Nflux_budget_mod | Flux budget component which produces diagnostic data for the flux aspects of the model |
| Nforcing_mod | Forcing, both subsidence and large scale |
| Nforthread_ciface_mod | |
| Nforthread_data | |
| Nforthread_mod | |
| Nforthread_types | |
| Nget_and_test_socrates_options_mod | |
| Nglobal_callback_inter_io_mod | Global callback inter IO, which registers the callback with identifiers and then the procedure is actually called in a thread once all other IO servers have issued a matching call |
| Ngridmanager_mod | Manages the grid based upon the model state_mod |
| Ngrids_mod | Functionality to support the different types of grid and abstraction between global grids and local ones after decomposition |
| Nhalo_communication_mod | Provides the mechanism for halo swapping. This module contains the functionality required to determine what messages get sent where, pack data up en mass, send and receive from neighbouring processes and unpack into the appropriate data locations. There is also some functionality to help local copying of data to corresponding locations. The idea is that the caller will determine the policy (i.e. exactly what fields are to be communicated) through procedure arguments and this mechanism can be used again and again. It implements bulk sending of all field data in one large message to reduce communication overhead |
| Nhaloswapper_mod | Performs halo swapping. In the parallel case this is between neighbouring processes and in the serial case it still needs to wrap the halos around for the boundary conditions. This module determines the policy of halo swapping (i.e. the fields to communicate) and the halo communication module is used to provide the actual mechanism |
| Ninstantaneous_time_manipulation_mod | Performs instantaneous time manipulation and only returns a value if the output frequency determines one should be |
| Ninter_io_specifics_mod | Inter IO server communication specific functionality. This manages all of the communication that might happen between different IO servers |
| Ninterpolation_mod | |
| Nio_server_client_mod | This defines some constants and procedures that are useful to the IO server and clients that call it. By using the contents then the client can guarantee consistency against what the server expects |
| Nio_server_mod | The main IO server functionality which handles waiting for commands and data both of which are delt with. The lower level details of the communication, configuration parsing etc are all held elsewhere. The server can be thought of similar to a bus, with command and data channels. The command gives context to what is on the data channel and not all commands require data (such as deregistration of MONC process) |
| Nio_server_state_reader_mod | Reads the IO server state that was stored in a NetCDF checkpoint file |
| Nio_server_state_writer_mod | The IO server state module which will write out the current state of the IO server to a NetCDF file |
| Niobridge_mod | Bridge between MONC and the IO server, this registers the current MONC process, will issue data dumps and deregister MONCs when the model run is completed |
| Niterativesolver_mod | This is the iterative pressure solver and uses a Jacobi preconditioned BiCGStab which we implement here |
| Nkidreader_mod | Component to set up the model based upon a KiD model configuration |
| Nlateral_bcs_mod | Applies lateral boundary conditions. Note that these boundary conditions only make sense if bi-periodicity is switched off in the the halo swapping and solver. The FFT solver should have bi-periodic conditions |
| Nlocalreduce_operator_mod | Performs a local reduction, reducing a local array into a single scalar value |
| Nlogging_mod | Logging utility |
| Nlowerbc_mod | This sets the lower boundary conditions for theta and the q variables |
| Nlw_control_default_mod | |
| Nlw_control_mod | |
| Nlw_rad_input_mod | |
| Nlwrad_exponential_mod | Simple exponential scheme to calculate the longwave radiation associated with cloud. The scheme is based on the methods used in GASS intercomparison cases, e.g. DYCOMS, ISDAC |
| Nmaths_mod | |
| Nmcclatchey_profiles | |
| Nmeanprofiles_mod | Calculates the mean profiles of prognostic variables which are then used in smoothing and other areas |
| Nmerge_atm_data | |
| Nmissing_data_mod | |
| Nmodelsynopsis_mod | Displays information about the current state_mod of the model run |
| Nmonc_component_mod | Interfaces and types that MONC components must specify |
| Nmonc_mod | Main core entry point to the rest of the model, this is called by the program main |
| Nmphys_radar_mod | |
| Nmpi_communication_mod | Abstraction layer around MPI, this issues and marshals the lower level communication details |
| Nnaming_conventions_mod | |
| Nnetcdf_filetype_writer_mod | The NetCDF file type writer which performs actual writing of NetCDF files to the parallel filesystem. These are opened by all IO servers and all IO servers can participate as variables might be located across the different IO processes |
| Nnetcdf_misc_mod | NetCDF misc functionality which can be shared between modules that work with NetCDF files |
| Nnone_time_manipulation_mod | Performs no time manipulation and returns the value, basically a no-op |
| Noperator_mod | Operator federator which manages the different operators which are available. Operators take in any number of scalar reals and output a single scalar real |
| Noptionsdatabase_mod | Manages the options database. Contains administration functions and deduce runtime options from the command line |
| Nparkind1 | |
| Npdf_analysis_mod | Calculates fields related to distributions of data on full-domain horizontal 2d slices |
| Npencil_fft_mod | This Pencil FFT performs 3D forward and backwards FFTs using pencil decomposition. It uses FFTW for the actual FFT kernel and this module contains all the data decomposition around this. There is no FFT required in Z, so this performs FFTs in Y and X (in that order forward and reversed backwards.) The data decomposition is the complex aspect, there is the concept of forward and backwards transformations. Forward transformations will go from pencil Z to Y to X and the backwards transformations undo these, so go from X to Y to Z. Note that we use quite a lot of buffer space here, this could be cut down if Y=X dimensions so some optimisation on memory could be done there in that case |
| Npetsc_solver_mod | PETSc solver component to call out to PETSc for solving the Poisson equation for pressure |
| Npressuresource_mod | Calculates the gradient of the source flow fields (SU, SV, SW.) This is based upon the P field values already set for the divergence error in the diverr component. Note that some communication is required, as a process needs to know the x and y -1 values, which are held on the -1 neighbour in that dimension. These are computed here and sent to neighbour +1, the recvs from a process to neighbour -1 are also registered here and the handles are waited upon the the results combined into P in the solver. If the neighbour is local in any dimension then it is just a local memory copy |
| Nprofile_diagnostics_mod | |
| Nprognostics_mod | Contains prognostic field definitions and functions |
| Npstep_mod | Stepping of the pressure field. Completes the time-stepping of the velocity fields by adding the pressure term (dp/dx_i). In addition, ensures that l_zu and l_zv satisfy the Galilean-transformed boundary condition. This does not do the flow field _p terms which are only needed for diagnostics, nore does it do field halo swapping which is again only needed for diagnostics |
| Npwadvection_mod | Piacsek-Williams advection scheme |
| Nq_indices_mod | This manages the Q variables and specifically the mapping between names and the index that they are stored at |
| Nrad_ctl_mod | |
| Nrandomnoise_mod | Add random noise into the fields |
| Nreduction_inter_io_mod | Reduction inter IO action which will perform reductions between IO servers. This is not as trivial as calling the MPI function as it is nondeterministic when messages will arrive and hence when one reduction on a process and a reduction on another should be called |
| Nreductionlocation_operator_mod | |
| Nregistry_mod | MONC component registry |
| Nsaturation_mod | Saturation physics functionality which is used throughout the code |
| Nsax_xml_parser_mod | A SAX parser for XML files. This is used to parse the description of the data and rules. Being a SAX parser it works in a callback fashion, as these often do, and will call the start and end subroutines along with tag details. It still requires some additional stability work to handle ill formatted XML and error checking |
| Nscalar_diagnostics_mod | |
| Nscience_constants_mod | Scientific constant values used throughout simulations. Each has a default value and this can be overridden by the configuration supplied by the user |
| Nset_consistent_lowbc_mod | This component sets the source term for the lowest level (Level 1) so that, depending on surface consitionm, there is consistent lower boundary condition |
| Nsetfluxlook_mod | |
| Nsimplecloud_mod | A very simple saturation adjustment scheme without any microphysics |
| Nsimplesetup_mod | |
| Nsmagorinsky_mod | Calculates the Smagorinsky eddy viscosity and diffusivity at l_w-points |
| Nsocrates_couple_mod | This module sets up the logicals and parameters for the edward-slingo code from the UM. It also calls the shortwave and longwave ES code and outputs the heating rates and fluxes |
| Nsolar_position_angle_mod | |
| Nstate_mod | The model state which represents the current state of a run |
| Nstencil_mod | Performs the interpolation between the primal and dual grids via a stencil approach. For performance reasons, for each field we store the entirety of the y dimension and the number of x slices required by the stencil. Therefore a new interpolation is simply the calculation of one point and reuse of existing computed points (unless this is the first x or y.) The applicable interpolation stenciled data is copied out, with :,1,1 being the central point, minus and plus in each y and x dimension as determined by the stencil size. This is done so that the stencil size can easily be different for each flow field and this is the case with u (where we need u-2 in the X.) |
| Nstepfields_mod | Does the field stepping Stepping is called at the end of processing a column and steps the x-2 column |
| Nsteppingdirection_mod | Determines the current stepping direction, which can be either forward or centred. This is mainly for field stepping, which is u, v, w fields but also scalars as well which is th and q |
| Nstring_utils_mod | String utility functionality that is commonly used throughout MONC |
| Nsubgrid_profile_diagnostics_mod | |
| Nsw_control_default_mod | |
| Nsw_control_mod | |
| Nsw_rad_input_mod | |
| Nswapsmooth_mod | Does the swapping and smoothing which is called for each column as part of the pressure-terms group of components Note that this does not currently implement smoothing for mean profiles |
| Nterminationcheck_mod | This component will check for termination conditions at stages of the model run and terminate that specific stage if the parameters have been met |
| Ntest_checkpointer_mod | |
| Ntest_collections_mod | |
| Ntest_communication_types_mod | |
| Ntest_configuration_file_parser_mod | |
| Ntest_conversions_mod | |
| Ntest_grid_mod | |
| Ntest_halo_communication_mod | |
| Ntest_interpolation_mod | |
| Ntest_logging_mod | |
| Ntest_maths_mod | |
| Ntest_monc_component_mod | |
| Ntest_monc_mod | |
| Ntest_naming_conventions_mod | |
| Ntest_optionsdatabase_mod | |
| Ntest_prognostic_mod | |
| Ntest_q_indices_mod | |
| Ntest_registry_mod | |
| Ntest_saturation_mod | |
| Ntest_science_constants_mod | |
| Ntest_stencil_mod | |
| Ntest_terminationcheck_mod | |
| Nthadvection_mod | Specific theta advection, which involves the vertical advection of reference state and advection of mean baroclinicity |
| Nthreadpool_mod | This is a thread pool and the single management "main" thread will spawn out free threads in the pool to perform specific work. If there are no free threads then it will block until one becomes available. It uses ForThreads, which is a wrapper around pthreads. The thread pool works by creating a number of threads and then passing the work to these threads, rather than creating a new thread for each piece of work |
| Ntimeaveraged_time_manipulation_mod | Performs time averaged, time manipulation and only returns a value if the output frequency determines one should be |
| Ntimestepper_mod | Performs the actual time stepping over groups of components. Each group can be the whole (which is one call per component per timestep) or column, which calls components for each column of the timestep. Groups are executed sequentially in the order that they have been configured (which is already set up in the registry) |
| Ntvdadvection_mod | Implements TVD advection for prognostic fields |
| Nultimateflux_mod | Calculates the effective face values for advection using Leonard's ultimate quickest scheme with first multi-dimension limiter and gradient terms added to the quickest scheme |
| Nviscosity_mod | Computes the viscosity dynamics for the U,V,W source terms |
| Nwriter_federator_mod | This federates over the writing of diagnostic and prognostic data to the file system. It also manages the time manipulation of fields and groups |
| Nwriter_field_manager_mod | The writer field manager will manage aspects of the fields being provided to the writer federator. There are two major aspects to this, firstly extraction of fields from the data sent directly from MONC and then passed on if these fields are needed. Secondly, this will queue up the data to ensure that it is sent to the writer federator in strict order and that only one piece of a fields data is in the writer federator at any one time |
| Nwriter_types_mod | Writer types which are shared across writing functionality. Also includes serialisation functionality for these types |
| Nyomhook | |
