Update Contaminant Structure Model

CMakeLists.txt

@@ -29,7 +29,12 @@ set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} ${debug_flags}")
 set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${release_flags}")
 
 # Sources to compile - everything except those matching the regex
-file(GLOB_RECURSE sources src/*.f90 vendor/*.f90)
+file(GLOB_RECURSIVE sources
+    src/*.f90
+    src/Data/*.f90
+    src/Contaminant/*.f90
+    vendor/*.f90
+)
 list(FILTER sources EXCLUDE REGEX ".*vendor/feh/example/.*f90$")
 list(FILTER sources EXCLUDE REGEX ".*vendor/feh/tests/.*f90$")
 list(FILTER sources EXCLUDE REGEX ".*vendor/datetime-fortran/tests/.*f90$")
@@ -47,4 +52,4 @@ file(WRITE "src/VersionModule.f90" ${version_file_new})
 # Compile to executable and link to NetCDF
 add_executable(nanofase ${sources})
 target_include_directories(nanofase PUBLIC "${NETCDF_INCLUDES}")
-target_link_libraries(nanofase PRIVATE "${NETCDF_LIBRARIES_F90}")
+target_link_libraries(nanofase PRIVATE "${NETCDF_LIBRARIES_F90}")

Makefile.example

@@ -32,90 +32,92 @@ COMP_META = $(COMPILE_TIME) $(GIT_HASH) $(GIT_RELEASE)
 AUTOPARALLEL = 0
 N_THREADS = 4
 ifeq ($(AUTOPARALLEL), 1)
-	COMMON_FLAGS += -floop-parallelize-all -ftree-parallelize-loops=${N_THREADS}
+    COMMON_FLAGS += -floop-parallelize-all -ftree-parallelize-loops=${N_THREADS}
 endif
 
 # Objects to generate, in dependency order
 OBJECTS_ = ErrorInstance.o \
-	Result.o \
-	ErrorHandler.o \
-	ErrorCriteria.o \
-	mo_types.o \
-	mo_netcdf.o \
-	datetime_module.o \
-	sparskit.o \
-	Spoof.o \
-	mod_strptime.o \
-	VersionModule.o \
-	DefaultsModule.o \
-	GlobalsModule.o \
-	UtilModule.o \
-	LoggerModule.o \
-	DataInputModule.o \
-	AbstractBiotaModule.o \
-	BiotaSoilModule.o \
-	BiotaWaterModule.o \
-	AbstractReactorModule.o \
-	ReactorModule.o \
-	FineSedimentModule.o \
-	AbstractBedSedimentLayerModule.o \
-	BedSedimentLayerModule.o \
-	AbstractBedSedimentModule.o \
-	BedSedimentModule.o \
-	DiffuseSourceModule.o \
-	PointSourceModule.o \
-	FlowModule.o \
-	WaterBodyModule.o \
-	ReachModule.o \
-	RiverReachModule.o \
-	EstuaryReachModule.o \
-	AbstractSoilLayerModule.o \
-	SoilLayerModule.o \
-	AbstractSoilProfileModule.o \
-	SoilProfileModule.o \
-	CropModule.o \
-	AbstractGridCellModule.o \
-	GridCellModule.o \
-	AbstractEnvironmentModule.o \
-	EnvironmentModule.o \
-	NetCDFOutputModule.o \
-	NetCDFAggregatedOutputModule.o \
-	DataOutputModule.o \
-	CheckpointModule.o \
-	main.o 
+    Result.o \
+    ErrorHandler.o \
+    ErrorCriteria.o \
+    mo_types.o \
+    mo_netcdf.o \
+    datetime_module.o \
+    sparskit.o \
+    Spoof.o \
+    mod_strptime.o \
+    VersionModule.o \
+    DefaultsModule.o \
+    GlobalsModule.o \
+    UtilModule.o \
+    LoggerModule.o \
+    DataInputModule.o \
+    ContaminantModule.o \
+    FlowModule.o \
+    AbstractBiotaModule.o \
+    BiotaSoilModule.o \
+    BiotaWaterModule.o \
+    AbstractReactorModule.o \
+    ReactorModule.o \
+    FineSedimentModule.o \
+    AbstractBedSedimentLayerModule.o \
+    BedSedimentLayerModule.o \
+    AbstractBedSedimentModule.o \
+    BedSedimentModule.o \
+    DiffuseSourceModule.o \
+    PointSourceModule.o \
+    AbstractSoilLayerModule.o \
+    SoilLayerModule.o \
+    AbstractSoilProfileModule.o \
+    SoilProfileModule.o \
+    CropModule.o \
+    WaterBodyModule.o \
+    ReachModule.o \
+    RiverReachModule.o \
+    EstuaryReachModule.o \
+    AbstractGridCellModule.o \
+    GridCellModule.o \
+    AbstractEnvironmentModule.o \
+    EnvironmentModule.o \
+    NetCDFOutputModule.o \
+    NetCDFAggregatedOutputModule.o \
+    DataOutputModule.o \
+    CheckpointModule.o \
+    main.o
 
 # Add the build dir to each object name
 OBJECTS = $(addprefix build/, $(OBJECTS_))
 
 # Where to look for the source files
 VPATH = vendor/feh/src \
-	vendor/mo_netcdf/src \
-	vendor/datetime-fortran/src \
-	vendor/spoof/src \
-	src \
-	src/Data \
-	src/Logger \
-	src/Biota \
-	src/Reactor \
-	src/BedSedimentLayer \
-	src/BedSediment \
-	src/Source \
-	src/WaterBody \
-	src/Soil \
-	src/GridCell \
-	src/Environment
+    vendor/mo_netcdf/src \
+    vendor/datetime-fortran/src \
+    vendor/spoof/src \
+    src \
+    src/Data \
+    src/Logger \
+    src/Biota \
+    src/Reactor \
+    src/BedSedimentLayer \
+    src/BedSediment \
+    src/Source \
+    src/WaterBody \
+    src/Soil \
+    src/GridCell \
+    src/Environment \
+    src/Contaminant
 
 # Write the model version (from git) to file
 MODEL_VERSION := $(shell sed -i "s/\".*\"/\"${GIT_RELEASE}\"/g" src/VersionModule.f90)
 
 $(EXEC_FILE): $(OBJECTS)
-	$(FC) $(FLAGS) -o $(BUILD_DIR)/$@ $^ $(NETCDF)
-	echo $(COMP_META) > $(BUILD_DIR)/comp_meta
+    $(FC) $(FLAGS) -o $(BUILD_DIR)/$@ $^ $(NETCDF)
+    echo $(COMP_META) > $(BUILD_DIR)/comp_meta
 $(BUILD_DIR)/%.o: %.f90
-	$(FC) -c $< -o $@ -J$(BUILD_DIR) $(FLAGS) $(NETCDF)
+    $(FC) -c $< -o $@ -J$(BUILD_DIR) $(FLAGS) $(NETCDF)
 release: FLAGS = ${RELEASE_FLAGS} ${COMMON_FLAGS}
 release: $(EXEC_FILE)
 fast: FLAGS = ${FAST_FLAGS} ${COMMON_FLAGS}
 fast: $(EXEC_FILE)
 clean:
-	rm -f $(BUILD_DIR)/*.mod $(BUILD_DIR)/*.o $(BUILD_DIR)/$(EXEC_FILE) $(BUILD_DIR)/comp_meta
+    rm -f $(BUILD_DIR)/*.mod $(BUILD_DIR)/*.o $(BUILD_DIR)/$(EXEC_FILE) $(BUILD_DIR)/comp_meta

config.example/test-scenario.example.nml

@@ -1,104 +1,94 @@
 !! NanoFASE model test scenario example config file
 !! ------------------------------------------------
-!! This file provideds a full list of config options that can be provided to
-!! the NanoFASE model. When used as is (alongside the data stored at 
-!! data.example/test-scenario.nc), this runs the model for a 12-cell,
-!! 10-timestep test scenario.
+!! This file provides the main configuration options for the model run.
 
-! One of the quirks of Fortran namelist files is that you can't saved implicitly sized
-! arrays to variables in Fortran code without knowing their length. The way around this
-! is to specify the array lengths as separate variables in a group read in before the
-! arrays themselves. This is that group.
 &allocatable_array_sizes
-n_soil_layers = 3                                       ! Number of soil layers to model
-n_sediment_layers = 4                                   ! Number of sediment layers to model
-n_nm_size_classes = 5                                   ! Number of NM size classes
-n_spm_size_classes = 5                                  ! Number of SPM size classes
-n_fractional_compositions = 2                           ! Number of fractional compositions for sediment
+    n_soil_layers = 3                 ! Number of soil layers to model
+    n_sediment_layers = 4             ! Number of sediment layers to model
+    n_contaminant_size_classes = 5    ! Number of contaminant size classes
+    n_spm_size_classes = 5            ! Number of SPM size classes
+    n_fractional_compositions = 2     ! Number of fractional compositions for sediment
 /
 
-! Control the config options specific to the NMs
-&nanomaterial
-nm_size_classes = 10e-9, 30e-9, 100e-9, 300e-9, 1000e-9 ! Diameter of NM in each binned size class [m]
-n_nm_forms = 1                                          ! Number of NM forms (core, shell, coating, corona etc)
-n_nm_extra_states = 2                                   ! Number of extra NM states, other than heteroaggregated to SPM
-/ 
+&contaminant
+    n_contaminant_extra_states = 2    ! Number of extra contaminant states, other than heteroaggregated to SPM
+    n_contaminant_forms = 2           ! Number of contaminant forms (e.g., pristine, transformed)
+/
 
-! Paths to data. For info on compiling data for the NanoFASE model, see the nanofase-data repo: https://github.com/NERC-CEH/nanofase-data
 &data
-input_file = "data.example/test-scenario.nc"            ! Path to NetCDF input data, which includes most of the spatial and temporally resolved data
-constants_file = "data.example/constants_test-scenario.nml" ! Path to constants namelist file, which includes most of the non-spatiotemporal input data 
-output_path = "output/"                                 ! Path to store the output data
+    input_file = "data.example/test-scenario.nc"            ! Path to NetCDF input data
+    constants_file = "data.example/constants_test-scenario.nml" ! Path to constants namelist file
+    output_path = "output/"                                 ! Path to store the output data
 /
 
 &output
-write_csv = .true.                                      ! Should we write output data to CSV files?
-write_netcdf = .true.                                   ! Should we write output data to a NetCDF file?
-netcdf_write_mode = 'end'                               ! When should we write to the NetCDF file? Every time step ('itr') or at the end of the run ('end'). Every time step is slower, end uses much more memory
-write_metadata_as_comment = .true.                      ! Should output data metadata (e.g. column descriptions) be included as comments at top of CSV files?
-include_waterbody_breakdown = .false.                   ! For surface water and sediment output, include breakdown over waterbodies or aggregate at grid cell level?
-include_sediment_layer_breakdown = .true.               ! Include breakdown of data over sediment layers?
-include_soil_layer_breakdown = .false.                  ! Include breaedown of data over soil layers?
-include_soil_state_breakdown = .false.                  ! Include breakdown of NM state - free vs attached to soil matrix
-soil_pec_units = 'kg/kg'                                ! What units to use for soil PEC - kg/kg or kg/m3? NOT CURRENTLY IN USE
-sediment_pec_units = 'kg/kg'                            ! What units to use for sediment PEC - kg/kg or kg/m3? NOT CURRENTLY IN USE
-include_soil_erosion_yields = .true.                    ! Should soil erosion yields be included in soil output?
-include_sediment_fluxes = .true.                        ! Should sediment fluxes to/from waterbodies be included?
+    write_csv = .true.
+    write_netcdf = .true.
+    netcdf_write_mode = 'end'
+    write_metadata_as_comment = .true.
+    include_waterbody_breakdown = .false.
+    include_sediment_layer_breakdown = .true.
+    include_soil_layer_breakdown = .false.
+    include_soil_state_breakdown = .false.
+    soil_pec_units = 'kg/kg'
+    sediment_pec_units = 'kg/kg'
+    include_soil_erosion_yields = .true.
+    include_sediment_fluxes = .true.
+    include_spm_size_class_breakdown = .false.
+    write_compartment_stats = .false.
 /
 
 &run
-description = "12 cell, 10 timestep test scenario"      ! Not used by model, but included in output data
-write_to_log = .false.                                  ! Should we write logs to file?
-timestep = 86400                                        ! Length of each time step, in seconds
-n_timesteps = 10                                        ! Number of time steps
-start_date = "2015-01-01"                               ! Start date for model run, in YYYY-MM-DD format
-epsilon = 1e-20,                                        ! Precision for numerical simulations
-error_output = .true.                                   ! Should error handling be turned on? Be careful if not, things might go wrong!
-trigger_warnings = .false.                              ! Should errors that are non-critical (warnings) be triggered (printed to the console)?
-log_file_path = "log/"                                  ! Where to place model logs
-output_hash = ""                                        ! Append all output file names with this value. Useful for parallel model runs. Max 32 characters (e.g. hex string).
-ignore_nm = .false.                                     ! If .true., this tells the model we're not interested in NM and misses out costly computations. Useful for sediment calibration, NM PECs will be invalid
-warm_up_period = 10                                     ! Warm up period before main simulation begin.
-simulation_mask = ""                                    ! Path to simulation mask, if only running for part of the data's area (empty string indicates no mask)
+    description = "12 cell, 10 timestep test scenario"
+    write_to_log = .false.
+    timestep = 86400
+    n_timesteps = 10
+    start_date = "2015-01-01"
+    epsilon = 1e-20
+    error_output = .true.
+    trigger_warnings = .false.
+    log_file_path = "log/"
+    output_hash = ""
+    ignore_contaminant = .false.
+    warm_up_period = 10
+    simulation_mask = ""
+    bash_colors = .true.
 /
 
-! Checkpointing is the ability to save a model run so that it can be reinstated from file. This is useful if, for example,
-! you want to have a standard "warm-up" period for the model which you don't want to run every time you run the model.
-! The checkpoint file is a binary file and this may cause issues transferring to different architectures
 &checkpoint
-checkpoint_file = "./checkpoint.dat"                    ! Location of checkpoint file to read from and/or save to
-save_checkpoint = .false.                               ! Save a checkpoint file when the run is finished? Defaults to false
-reinstate_checkpoint = .false.                          ! Reinstate a checkpoint from checkpoint_file? Defaults to false
-preserve_timestep = .false.                             ! Should the timestep from the checkpoint be used as a starting timestep in a reinstated run?
+    checkpoint_file = "./checkpoint.dat"
+    save_checkpoint = .false.
+    reinstate_checkpoint = .false.
+    preserve_timestep = .false.
+    save_checkpoint_after_warm_up = .false.
 /
 
 &steady_state
-run_to_steady_state = .false.                           ! Should the model be run until steady state by iterating over current simulation input data?
-mode = 'sediment_size_distribution'                     ! Mode defines what variable will be used to assess steady state
-delta = 1e-4
+    run_to_steady_state = .false.
+    mode = 'sediment_size_distribution'
+    delta = 1e-4
 /
 
 &soil
-soil_layer_depth = 0.05, 0.15, 0.2                      ! Depth of each soil layer. Array of length &allocatable_array_sizes > n_soil_layers
-include_bioturbation = .true.                           ! Should bioturbation be modelled?
-include_attachment = .true.                             ! Should attachment be modelled?
-include_soil_erosion = .true.                           ! Should soil erosion be modelled?
+    soil_layer_depth = 0.05, 0.15, 0.2
+    include_bioturbation = .true.
+    include_attachment = .true.
+    include_soil_erosion = .true.
+    include_clay_enrichment = .false.
 /
 
 &sediment
-sediment_layer_depth = 0.01, 0.01, 0.01, 0.01           ! Depth of each sediment layer. Array of length &allocatable_array_sizes > n_sediment_layers
-spm_size_classes = 0.002e-3, 0.06e-3, 0.2e-3, 0.6e-3, 2.0e-3    ! Diameter of SPM in each binned size class [m]
-include_bed_sediment = .true.                           ! Should bed sediment be modelled?
-sediment_particle_densities = 1500, 2600                ! Density of sediment particles in each fractional composition class [kg/m3]
+    sediment_layer_depth = 0.01, 0.01, 0.01, 0.01
+    spm_size_classes = 0.002e-3, 0.06e-3, 0.2e-3, 0.6e-3, 2.0e-3
 /
 
 &water
-min_stream_slope = 0.0001                               ! Impose a minimum stream slope. Defaults to 0.0001, must be greater than 0
-min_estuary_timestep = 3600                             ! Minimum timestep length to use when modelling estuarine dynamics [s]. Defaults to 1 hour
-include_estuary = .true.                                ! Should we model estuaries, or treat them as rivers?
-include_bank_erosion = .true.                           ! Should we model the input of sediment via bank erosion?
+    min_stream_slope = 0.0001
+    min_estuary_timestep = 3600
+    include_estuary = .true.
+    include_bank_erosion = .true.
 /
 
 &sources
-include_point_sources = .true.                          ! Should point sources be included?
+    include_point_sources = .true.
 /