Procedures

Expand every entry of the variables, groups or modules section into variable uses.

Check one variable against one stream and append it to uses.

Divide the aggregated data by a specified factor.

Initialise the aggregator by allocating the aggregated data array and its aggregation method. The values in the aggregated data array are reset according to the specified aggregation method.

Offset the aggregated data by a specified value.

Return the rank of the aggregator.

Scale the aggregated data by a specified factor.

Set the aggregation method for the aggregator by assigning the appropriate accumulation and reset procedures based on the specified method.

Return the shape of the aggregator.

Return a string identifier of the aggregator type (e.g., "int32", "real32", "real64").

Allocate phen derived type instance. Allocated arrays are initialised to zero.

set the following two backflow to set (see Bolker 199x)

Check if two integer arrays are equal.

Calculate the index corresponding to a given memory offset in a multi-dimensional array.

Calculate the memory offset corresponding to a given index in a multi-dimensional array.

Compute start and count for the p'th partition of an array of size n where p = 0, 1, ... , k - 1.

vh_js !!

Combine one catalogue entry with its binding.

Abort CABLE with an error message.

Model initialisation routine for the CABLE offline driver.

Model initialisation routine (CRU specific). TRENDY experiment using CRU-NCEP.

Model initialisation routine (default met specific).

Model initialisation routine (GSWP specific).

Model initialisation routine (PLUME specific). PLUME experiment setup using WATCH.

Model initialisation routine (site met specific). Site experiment, e.g. AmazonFace (spinup or transient run type).

Default implementation of the abort procedure for the base error handler.

Build an error message string.

Free the global error handler instance.

Implementation of the abort procedure for the MPI-aware error handler.

Set the global error handler instance.

Create a new decomposition for parallel I/O. This follows the degree of freedom approach for specifying I/O decompositions as described in Denis et al. (2011) [10.1177/1094342011428143].

Create a new netCDF file with the specified path and I/O type.

Module finalization procedure for the cable_netcdf_mod module.

Open an existing netCDF file with the specified path and I/O type.

Constructor for cable_output_binding_t.

Definitions of every variable in the built-in output catalogue.

Definitions of every variable in the catalogue given as YAML text.

Build the configuration from a parsed YAML document.

Read the configuration file file_name. Aborts, listing every problem, if it is invalid.

As cable_output_config_load, for a configuration held in a string.

Interfaces for procedures used by cable_output_impl.

Interfaces for procedures used by cable_output_impl.

Interfaces for procedures used by cable_output_impl.

Interfaces for procedures used by cable_output_impl.

Return the dimension name.

Return the dimension size.

Returns an output variable dimension. This function contains the definitions of all dimensions used to describe the in-memory data shapes of CABLE variables.

The grid type of the output files, from the output%grid setting and the grid type of the meteorological forcing.

Interface for associating a pointer array with the the appropriate reduction buffer, taking into account the output variable shape, type and reduction method.

Interfaces for procedures used by cable_output_impl.

Interfaces for procedures used by cable_output_impl.

Constructs the variable that writes a definition to the restart file: the working variable is written as it is, without aggregation or reduction, under its restart name.

Replace each {name} in template with the matching entry of values.

Constructor for cable_output_variable_t.

Constructs the use of a variable definition described by the arguments: the definition says what the variable is, the arguments say how it is written. The result owns its own copy of the aggregator, so one definition can be used in several streams.

Return the netCDF variable name, which defaults to field_name if not specified via netcdf_name.

Interfaces for procedures used by cable_output_impl.

The date elapsed_days after the given day of the given year, as YYYY-MM-DD.

Determines whether the current time step is the end of a period of the given frequency.

Position of frequency in cable_timing_frequencies, from finest (1) to coarsest, or 0 if it is not a known frequency.

Set the start year of the simulation. This is used for calculating monthly timing.

Parse the YAML file at file_name. Aborts if the file cannot be read or is not valid YAML.

Parse YAML held in a string. Aborts if the text is not valid YAML.

Computes the fraction of net photosynthate allocated to leaf, wood and froot using an allocation scheme modified from Pierre Friedlingstein.

revise turnover and NPP and dcplantdt to reflect above adjustments End of adjustments to avoid negative stores Ticket#108

vh_js!

vh_js !! vh_js !! vh_js

Carbon allocation algorithm implemented by Dan Qiu and YP Wang in 2011 based on Adam Wolf 1 and 2

CLN CHARACTER(LEN=99), INTENT(IN) :: fcnpspin vh_js !! CLN901 format(A99) WHERE (pop%pop_grid(:)%cmass_sum_old.gt.0.1 .and. pop%pop_grid(:)%cmass_sum.gt.0.1 ) casapool%Cplant(Iw,2) = casapool%Cplant(Iw,2)(1.0- min( POP%pop_grid(:)%cat_mortality/(POP%pop_grid(:)%cmass_sum_old),0.99)) casapool%Nplant(Iw,2) = casapool%Nplant(Iw,2)(1.0- min( POP%pop_grid(:)%cat_mortality/(POP%pop_grid(:)%cmass_sum_old),0.99)) ENDWHERE

The CF cell_methods attribute for a variable aggregated and reduced as given.

Report every key of the mapping node that is not in allowed.

Rule 1: no two variables in a stream share a NetCDF name. Rule 2: no two variables in a stream are numerically identical.

Stream numbers must be unique, and no two streams may write to the same file.

Reductions and frequencies must make sense for the variable being written.

Checks whether the value(s) of an output variable are within their specified range of physical values.

Calculates the extinction coefficients for black leaves. It returns:

This SUBROUTINE evaluates the value of the friction velocity $u_*$ as used during the iteration loop of the Monin-Obukhov (MO) similarity theory in define_canopy. $u_*$ is used when quantifying the stability parameter canopy%zetar in update_zetar, and when evaluating the resistance network components rt0 and rt1 in define_canopy. The friction velocity quantifies the magnitude of turbulent mixing that is occurring as well as the flux of momentum from the atmosphere to the land.

Compare reference values for quasi-bitwise reproducibility checks and write reference value on failed reproducibility.

Copy a yaFyaml node and everything below it into a cable_yaml_node_t.

Returns a list of coordinate variables to be included in an output stream based on the output grid type.

Deep copy of a node and everything below it.

canopy%fes_cor = 0.0

The directory part of path, including the final /, or nothing if there is none.

Interface for extracting the value from the tile with the largest area fraction in each grid cell for various data types and array ranks. If several tiles share the largest fraction, the first of them is used.

Index of the tile with the largest area fraction in the grid cell described by land_entry. Ties go to the first such tile.

Extracts the value of the largest-area tile in each grid cell from a 1D int32 array.

Extracts the value of the largest-area tile in each grid cell from a 2D int32 array.

Extracts the value of the largest-area tile in each grid cell from a 3D int32 array.

Extracts the value of the largest-area tile in each grid cell from a 1D real32 array.

Extracts the value of the largest-area tile in each grid cell from a 2D real32 array.

Extracts the value of the largest-area tile in each grid cell from a 3D real32 array.

Extracts the value of the largest-area tile in each grid cell from a 1D real64 array.

Extracts the value of the largest-area tile in each grid cell from a 2D real64 array.

Extracts the value of the largest-area tile in each grid cell from a 3D real64 array.

Position of the binding called name, or 0 if there is none.

Interface for extracting the value from the first patch/tile in each grid cell for various data types and array ranks. This is useful for arrays where averaging along the patch/tile dimension does not make sense, or where the array contains the same value everywhere along the patch/tile dimension.

Extracts the first patch value for each grid cell from a 1D integer array.

Extracts the first patch value for each grid cell from a 2D integer array.

Extracts the first patch value for each grid cell from a 3D integer array.

Extracts the first patch value for each grid cell from a 1D 32-bit real array.

Extracts the first patch value for each grid cell from a 2D 32-bit real array.

Extracts the first patch value for each grid cell from a 3D 32-bit real array.

Extracts the first patch value for each grid cell from a 1D 64-bit real array.

Extracts the first patch value for each grid cell from a 2D 64-bit real array.

Extracts the first patch value for each grid cell from a 3D 64-bit real array.

Helper subroutine to get initialise optional scale, div, and offset arguments for accumulate procedures.

Searches for CABLE parameters in the met forcing file, and if it finds any, uses these values to overwrite the values that have already been loaded from the default parameter loading and/or the restart file.

Root extraction : Haverd et al. 2013

Interface for computing the area weighted average over the patch/tile dimension for various data types and array ranks.

Computes the area weighted average over the patch/tile dimension for a 1D 32-bit real array.

Computes the area weighted average over the patch/tile dimension for a 2D 32-bit real array.

Computes the area weighted average over the patch/tile dimension for a 3D 32-bit real array.

Computes the area weighted average over the patch/tile dimension for a 1D 64-bit real array.

Computes the area weighted average over the patch/tile dimension for a 2D 64-bit real array.

Computes the area weighted average over the patch/tile dimension for a 3D 64-bit real array.

MMY : move from subroutine derived_parameters to here since derived_parameters is now an option but compulsory

This subroutine computes the height of the canopy above ground/snow surface when there is snow present.

Infers the appropriate netCDF dimensions for a given output variable based on its data shape and the grid type of the output stream.

Initialise local structure variables for the current MPI rank

Initialize the surface wetness factor of the soil/snow (ssnow_wetfac) array

Accumulate the aggregated data from the source data using the instant aggregation method.

Reset the aggregated data for the instant aggregation method. This is a no-op since instant aggregation always takes the value of the most recent data point.

Returns a parallel I/O decomposition mapping from a memory layout with a local 'land' dimension to a netCDF variable layout with a global 'land' dimension.

Returns a parallel I/O decomposition mapping from a memory layout with a 'land' dimension to a netCDF variable layout with 'x' and 'y' dimensions.

Returns a parallel I/O decomposition mapping from a memory layout with a 'patch' dimension to a netCDF variable layout with a 'land' and 'patch' dimension.

Returns a parallel I/O decomposition mapping from a memory layout with a local 'patch' dimension to a netCDF variable layout with a global 'patch' dimension.

Returns a parallel I/O decomposition mapping from a memory layout with a 'patch' dimension to a netCDF variable layout with 'x', 'y', and 'patch' dimensions.

Whether definition is selected by the entry name of the given section.

This subroutine computes the leaf-area index of a canopy when there is snow present. The formulae assume that the leaf area is distributed uniformly in the vertical within the canopy.

Allocates the luc%%var(imland,mvmax) variables

Allocates the luc%var(mp) variables.

Checks the mass balance and writes the output CNP pool sizes for each plant functional type.

Deallocates the luc%var(mland,mvmax) variables

Deallocates the luc%var(mp) variables

Main driver for the land-use change

Maps luc%var_y(mland,mvmax) to lucmp%var(mp)

Assigns lucmp%var(mp) to luc%var_x(mland,mvmax)

Redistribution of the plant functional type transition to ensure that the change in plant functional type fractions from the state data is consistent with the estimates from previous states and transition.

This subroutine applies the land-use changes to the transfer of the C, N and P pools, the biophysical states, the soil texture and the soil order for each patch. Then it will seed the deforested land.

Assigns luc%var_y to luc%var_x

This SUBROUTINE converts the previously evaluated rate of potential evaporation ssnow_potev from the soil into the associated latent heat flux canopy_fes. The evaluation accounts for whether the water flux is in liquid or solid phase (evaporation or sublimation, dew or frost), the direction of the flux (to or from the soil), and any limits due to a lack of water in the surface layer of the soil column. The SUBROUTINE also evaluates the partition of the latent heat flux between soil canopy_fess and puddle canopy_fesp contributions.

Defines the priority order of sources of parameter values for CABLE, determines the total number of patches over all grid cells, and writes parameter values to CABLE's parameter arrays.

Reading LU input data, zeroing biomass in empty secondary forest tiles and tranferring LUC-based age weights for secondary forest to POP structure

Calculates the energy and water balances at each time step as well as the cumulative balance over the simulation.

Accumulate the aggregated data from the source data using the max aggregation method.

Reset the aggregated data for the max aggregation method.

Accumulate the aggregated data from the source data using the mean aggregation method.

Accumulate the aggregated data from the source data using the min aggregation method.

Reset the aggregated data for the min aggregation method.

Check if an MPI return code signaled an error. If so, print the corresponding message and abort the execution.

Class method to abort execution of an MPI group.

Class method to check if the communicator is defined.

Contructor for mpi_grp_t class.

Contructor for mpi_grp_t using the legacy communicator type.

Class method to split an MPI group.

Overload the default construct for mpi_grp_t

Finalise MPI.

Initialise MPI and set default communicator.

Stub for when MPI is not available

Stub for when MPI is not available

Returns the netCDF dimension(s) corresponding to a given output variable dimension, taking into account the output grid type and reduction method. This function is used to determine the dimensions of netCDF variables based on the in-memory data shapes of CABLE variables as described by cable_output_dim_t instances.

NetCDF type code for the catalogue type name float or int.

Infers the appropriate netCDF variable type for a given output variable.

Factory interface for creating new aggregator instances. The specific type of aggregator created is determined by the type of the source data array provided.

Create a new 0D integer aggregator.

Create a new 1D integer aggregator.

Create a new 2D integer aggregator.

Create a new 3D integer aggregator.

Create a new 0D 32-bit real aggregator.

Create a new 1D 32-bit real aggregator.

Create a new 2D 32-bit real aggregator.

Create a new 3D 32-bit real aggregator.

Create a new 0D 64-bit real aggregator.

Create a new 1D 64-bit real aggregator.

Create a new 2D 64-bit real aggregator.

Create a new 3D 64-bit real aggregator.

The scalar value as an integer. Aborts if it is not one.

The scalar value as a logical (true or false). Aborts otherwise.

The scalar value as a real. Aborts if it is not one.

The text of a scalar node. Aborts for mappings and sequences.

The child_index-th child (1-based) of a mapping or sequence.

The value stored under key. Aborts if this node has no such key.

Shorthand for this%get(key)%as_integer().

Shorthand for this%get(key)%as_logical().

Shorthand for this%get(key)%as_real().

Shorthand for this%get(key)%as_string().

Whether this node is a mapping containing key.

Position of key among the children of a mapping, or 0 if absent.

Number of children of a mapping or sequence. Zero for scalars.

Reset the aggregated data for aggregation methods other than point, min, and max.

Returns the land index corresponding to the given patch index, using cstart and nap to determine the mapping. If the patch index does not lie on any land point, the function aborts.

Select the correct files given the year for filenames following the gswp format

Select the correct files given the year for filenames following the princeton format

Evaluates the integrated similarity function for momentum transfer, $\psi_m(\xi)$.

Evaluates the integrated similarity function for turbulent transfer of scalars, $\psi_s(\xi)$.

This SUBROUTINE evaluates the specific humidity (water vapour mixing ratio) at saturation (in kgkg$^{-1}$), at a given air temperature (in $^{\circ}$C) and air pressure (in hPa) for an array of size mp.

This SUBROUTINE evaluates the specific humidity (water vapour mixing ratio) at saturation (in kgkg$^{-1}$), at a given air temperature (in $^{\circ}$C) and air pressure (in hPa).

The metadata mapping of node as attributes, with templates filled in.

A subroutine rather than a function so that problems, a deferred-length string, is reliably updated for the caller by gfortran.

Read every stream. A subroutine because gfortran drops updates made to the deferred-length string problems inside a function called on the right of an assignment.

Removes transpiration water from soil. We also attribute the negative canopy transpiration (dew) to the wet canopy flux.

Replace the year in the filename with the value of ncciy for the gswp file format.

Replace the year in the filename with the value of ncciy for the princeton format

True if node has key holding a single value; otherwise records a problem.

Calculates the roughness parameters and the aerodynamic contribution to the resistances controlling the fluxes between the land and atmosphere for each land point.

The text of a scalar yaFyaml node. Non-string scalars are rendered in the form they are written in YAML (true/false for booleans).

Offline serial driver.

Sets the global attributes for a given output stream.

calculate snow processes and thermal soil

CLN CHARACTER(LEN=99), INTENT(IN) :: fcnpspin vh_js !! CLN OPEN(91, file=fcnpspin) CLN read(91,*) myearspin CLN901 format(A99) WHERE(xkNlimiting .eq. 0) !Chris Lu 4/June/2012 xkNlimiting = 0.001 END WHERE call totcnppools(1,veg,casamet,casapool,bmcplant,bmnplant,bmpplant,bmclitter,bmnlitter,bmplitter, & bmcsoil,bmnsoil,bmpsoil,bmnsoilmin,bmpsoillab,bmpsoilsorb,bmpsoilocc,bmarea)

Creates an output file, defines its contents, and writes its coordinates.

An output file with the settings of a configured stream.

Accumulate the aggregated data from the source data using the sum aggregation method.

Translate local land index on current MPI rank to global land index

Calculates the amount of water removed from the soil by transpiration.

This SUBROUTINE updates the value of the stability parameter $\xi$ during the iteration loop of the Monin-Obukhov (MO) similarity theory in define_canopy.
$\xi$ quantifies the role that the surface fluxes play in setting the efficiency of turbulent transfer from the land to the atmosphere, and hence the aerodynamic component of the resistance network for those same surface fluxes (an implicit problem which requires iteration to solve).

The output variable for one use of a definition in the configuration.