MicroBenthos
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MicroBenthos
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Z
_
__init__() (microbenthos.core.domain.SedimentDBLDomain method)
(microbenthos.core.expression.Expression method)
(microbenthos.core.irradiance.Irradiance method)
(microbenthos.core.irradiance.IrradianceChannel method)
(microbenthos.core.microbes.MicrobialGroup method)
(microbenthos.core.process.Process method)
(microbenthos.core.process.ProcessEvent method)
(microbenthos.core.variable.ModelVariable method)
(microbenthos.model.equation.ModelEquation method)
(microbenthos.model.model.MicroBenthosModel method)
(microbenthos.model.simulation.Simulation method)
_add_diffusion_term() (microbenthos.model.equation.ModelEquation method)
_check_with_importpath() (microbenthos.utils.loader.MicroBenthosSchemaValidator method)
_check_with_model_path() (microbenthos.utils.loader.MicroBenthosSchemaValidator method)
_check_with_sympy_symbol() (microbenthos.utils.loader.MicroBenthosSchemaValidator method)
_check_with_unit_name() (microbenthos.utils.loader.MicroBenthosSchemaValidator method)
_create_entity_into() (microbenthos.model.model.MicroBenthosModel method)
_create_figure() (microbenthos.dataview.plotter.ModelPlotter method)
_create_output_dir() (microbenthos.runners.simulate.SimulationRunner method)
_create_solver() (microbenthos.model.simulation.Simulation method)
_get_label() (microbenthos.dataview.plotter.ModelPlotter method)
_get_term_obj() (microbenthos.model.equation.ModelEquation method)
_init_artist_styles() (microbenthos.dataview.plotter.ModelPlotter method)
_save_data() (in module microbenthos.model.saver)
_save_nested_dict() (in module microbenthos.model.saver)
_setup() (microbenthos.model.model.MicroBenthosModel method)
_sympify() (microbenthos.core.expression.Expression method)
_validate_like_unit() (microbenthos.utils.loader.MicroBenthosSchemaValidator method)
A
add_aliased_path() (microbenthos.dataview.base.ModelData method)
add_attenuation_source() (microbenthos.core.irradiance.IrradianceChannel method)
add_console_logging() (in module microbenthos)
add_derived_data() (microbenthos.dataview.base.ModelData method)
add_diffusion_term_from() (microbenthos.model.equation.ModelEquation method)
add_equation() (microbenthos.model.model.MicroBenthosModel method)
add_event() (microbenthos.core.process.Process method)
add_exporter() (microbenthos.runners.simulate.SimulationRunner method)
add_feature_from() (microbenthos.core.microbes.MicrobialGroup method)
add_formula() (microbenthos.model.model.MicroBenthosModel method)
add_piece() (microbenthos.core.expression.Expression method)
add_process_from() (microbenthos.core.microbes.MicrobialGroup method)
add_source_term_from() (microbenthos.model.equation.ModelEquation method)
aliased_paths (microbenthos.dataview.base.ModelData attribute)
all_entities_setup() (microbenthos.model.model.MicroBenthosModel property)
as_hms() (microbenthos.model.model.ModelClock property)
as_hms_string() (microbenthos.model.model.ModelClock property)
as_latex_string() (microbenthos.model.equation.ModelEquation method)
as_pretty_string() (microbenthos.model.equation.ModelEquation method)
as_source_for() (microbenthos.core.process.Process method)
as_symbolic() (microbenthos.model.equation.ModelEquation method)
as_term() (microbenthos.core.process.Process method)
attenuation_profile() (microbenthos.core.irradiance.IrradianceChannel property)
axes_all() (microbenthos.dataview.plotter.ModelPlotter property)
axes_depth_all() (microbenthos.dataview.plotter.ModelPlotter property)
axes_time_all() (microbenthos.dataview.plotter.ModelPlotter property)
B
base (microbenthos.core.expression.Expression attribute)
BaseExporter (class in microbenthos.exporters.exporter)
biomass() (microbenthos.core.microbes.MicrobialGroup property)
C
can_restore_from() (microbenthos.model.model.MicroBenthosModel method)
cell_size (microbenthos.core.domain.SedimentDBLDomain attribute)
channels (microbenthos.core.irradiance.Irradiance attribute)
check_compatibility() (in module microbenthos.model.resume)
check_constraints() (microbenthos.core.variable.ModelVariable static method)
check_create() (microbenthos.core.variable.ModelVariable static method)
check_domain() (microbenthos.core.entity.DomainEntity method)
check_simulation() (microbenthos.runners.simulate.SimulationRunner method)
check_store() (microbenthos.dataview.base.ModelData method)
(microbenthos.dataview.hdfstore.HDFModelData method)
(microbenthos.dataview.snapshot.SnapshotModelData method)
checkers (microbenthos.utils.loader.MicroBenthosSchemaValidator attribute)
clip_max (microbenthos.core.variable.ModelVariable attribute)
clip_min (microbenthos.core.variable.ModelVariable attribute)
close() (microbenthos.dataview.plotter.ModelPlotter method)
(microbenthos.exporters.exporter.BaseExporter method)
coercers (microbenthos.utils.loader.MicroBenthosSchemaValidator attribute)
condition (microbenthos.core.process.ProcessEvent attribute)
constrain() (microbenthos.core.variable.ModelVariable method)
constraints (microbenthos.core.variable.ModelVariable attribute)
create() (microbenthos.core.variable.ModelVariable method)
create_artists() (microbenthos.dataview.plotter.ModelPlotter method)
create_channel() (microbenthos.core.irradiance.Irradiance method)
create_clock_artist() (microbenthos.dataview.plotter.ModelPlotter method)
create_entity_from() (microbenthos.model.model.MicroBenthosModel method)
create_from() (microbenthos.utils.create.CreateMixin class method)
create_full_equation() (microbenthos.model.model.MicroBenthosModel method)
create_line_artists() (microbenthos.dataview.plotter.ModelPlotter method)
create_mesh() (microbenthos.core.domain.SedimentDBLDomain method)
create_params (microbenthos.core.variable.ModelVariable attribute)
create_var() (microbenthos.core.domain.SedimentDBLDomain method)
CreateMixin (class in microbenthos.utils.create)
D
day_fraction (microbenthos.core.irradiance.Irradiance attribute)
DBL_length (microbenthos.core.domain.SedimentDBLDomain attribute)
default_setters (microbenthos.utils.loader.MicroBenthosSchemaValidator attribute)
define_attenuation() (microbenthos.core.irradiance.IrradianceChannel method)
depths (microbenthos.core.domain.SedimentDBLDomain attribute)
(microbenthos.dataview.base.ModelData attribute)
derived_paths (microbenthos.dataview.base.ModelData attribute)
diff() (microbenthos.core.expression.Expression method)
diffusion_def (microbenthos.model.equation.ModelEquation attribute)
distances (microbenthos.core.domain.SedimentDBLDomain attribute)
domain() (microbenthos.core.entity.DomainEntity property)
(microbenthos.model.model.MicroBenthosModel property)
DomainEntity (class in microbenthos.core.entity)
draw() (microbenthos.dataview.plotter.ModelPlotter method)
E
entities_setup() (microbenthos.model.model.MicroBenthosModel method)
Entity (class in microbenthos.core.entity)
ENTRY_ENV (microbenthos.dataview.base.ModelData attribute)
ENTRY_EQUATIONS (microbenthos.dataview.base.ModelData attribute)
ENTRY_IRRADIANCE (microbenthos.dataview.base.ModelData attribute)
ENTRY_MICROBE_FEATURES (microbenthos.dataview.base.ModelData attribute)
ENTRY_MICROBES (microbenthos.dataview.base.ModelData attribute)
env (microbenthos.model.model.MicroBenthosModel attribute)
eqn_processes (microbenthos.dataview.base.ModelData attribute)
eqn_source_totals (microbenthos.dataview.base.ModelData attribute)
eqn_var_actual (microbenthos.dataview.base.ModelData attribute)
eqn_var_difference (microbenthos.dataview.base.ModelData attribute)
eqn_var_expected (microbenthos.dataview.base.ModelData attribute)
eqn_vars (microbenthos.dataview.base.ModelData attribute)
equations (microbenthos.model.model.MicroBenthosModel attribute)
evaluate() (microbenthos.core.process.Process method)
event_time (microbenthos.core.process.ProcessEvent attribute)
events (microbenthos.core.process.Process attribute)
evolution() (microbenthos.model.simulation.Simulation method)
exporters_activated() (microbenthos.runners.simulate.SimulationRunner method)
expr() (microbenthos.core.expression.Expression method)
(microbenthos.core.process.Process property)
(microbenthos.core.process.ProcessEvent property)
Expression (class in microbenthos.core.expression)
F
fexp() (in module microbenthos.dataview.plotter)
finalize() (microbenthos.model.equation.ModelEquation method)
finalized (microbenthos.model.equation.ModelEquation attribute)
find_subclasses_recursive() (in module microbenthos.utils.loader)
finish() (microbenthos.exporters.exporter.BaseExporter method)
(microbenthos.exporters.graphic.GraphicExporter method)
(microbenthos.exporters.progress.ProgressExporter method)
fipy_solver() (microbenthos.model.simulation.Simulation property)
FIPY_SOLVERS (microbenthos.model.simulation.Simulation attribute)
flabel() (in module microbenthos.dataview.plotter)
fman() (in module microbenthos.dataview.plotter)
frames_outdir() (microbenthos.exporters.graphic.GraphicExporter property)
frepr() (in module microbenthos.dataview.plotter)
from_dict() (microbenthos.core.entity.Entity class method)
from_params() (microbenthos.core.entity.Entity class method)
G
get_data() (microbenthos.dataview.base.ModelData method)
get_data_exporters() (microbenthos.runners.simulate.SimulationRunner method)
get_info() (microbenthos.exporters.exporter.BaseExporter method)
(microbenthos.runners.simulate.SimulationRunner method)
get_node() (microbenthos.dataview.base.ModelData method)
(microbenthos.dataview.hdfstore.HDFModelData method)
(microbenthos.dataview.snapshot.SnapshotModelData method)
get_object() (microbenthos.model.model.MicroBenthosModel method)
get_schema() (in module microbenthos.utils.loader)
get_state() (microbenthos.model.simulation.Simulation method)
GraphicExporter (class in microbenthos.exporters.graphic)
H
has_domain() (microbenthos.core.entity.DomainEntity property)
HDFModelData (class in microbenthos.dataview.hdfstore)
hours_day (microbenthos.core.irradiance.Irradiance attribute)
hours_total (microbenthos.core.irradiance.Irradiance attribute)
I
idx_surface (microbenthos.core.domain.SedimentDBLDomain attribute)
implicit (microbenthos.core.process.Process attribute)
increment_time() (microbenthos.model.model.ModelClock method)
intensities (microbenthos.core.irradiance.IrradianceChannel attribute)
Irradiance (class in microbenthos.core.irradiance)
irradiance_intensities (microbenthos.dataview.base.ModelData attribute)
IrradianceChannel (class in microbenthos.core.irradiance)
is_eager (microbenthos.exporters.exporter.BaseExporter attribute)
(microbenthos.exporters.progress.ProgressExporter attribute)
is_setup() (microbenthos.core.entity.DomainEntity property)
(microbenthos.core.irradiance.Irradiance property)
(microbenthos.core.irradiance.IrradianceChannel property)
K
k0 (microbenthos.core.irradiance.IrradianceChannel attribute)
k_mods (microbenthos.core.irradiance.IrradianceChannel attribute)
k_name() (microbenthos.core.irradiance.IrradianceChannel property)
k_var (microbenthos.core.irradiance.IrradianceChannel attribute)
L
logger (microbenthos.utils.loader.MicroBenthosSchemaValidator attribute)
M
max_sweeps() (microbenthos.model.simulation.Simulation property)
mesh (microbenthos.core.domain.SedimentDBLDomain attribute)
microbe_features (microbenthos.dataview.base.ModelData attribute)
microbenthos
module
microbenthos.cli
module
microbenthos.core
module
microbenthos.core.domain
module
microbenthos.core.entity
module
microbenthos.core.expression
module
microbenthos.core.irradiance
module
microbenthos.core.microbes
module
microbenthos.core.process
module
microbenthos.core.variable
module
microbenthos.dataview
module
microbenthos.dataview.base
module
microbenthos.dataview.hdfstore
module
microbenthos.dataview.plotter
module
microbenthos.dataview.snapshot
module
microbenthos.exporters
module
microbenthos.exporters.exporter
module
microbenthos.exporters.graphic
module
microbenthos.exporters.model_data
module
microbenthos.exporters.progress
module
microbenthos.model
module
microbenthos.model.equation
module
microbenthos.model.model
module
microbenthos.model.resume
module
microbenthos.model.saver
module
microbenthos.model.simulation
module
microbenthos.runners
module
microbenthos.runners.simulate
module
microbenthos.utils
module
microbenthos.utils.create
module
microbenthos.utils.loader
module
microbenthos.utils.log
module
microbenthos.utils.snapshotters
module
microbenthos.utils.yaml_setup
module
MicroBenthosModel (class in microbenthos.model.model)
MicroBenthosSchemaValidator (class in microbenthos.utils.loader)
MicrobialGroup (class in microbenthos.core.microbes)
model (microbenthos.model.equation.ModelEquation attribute)
model() (microbenthos.dataview.plotter.ModelPlotter property)
(microbenthos.model.simulation.Simulation property)
(microbenthos.runners.simulate.SimulationRunner property)
ModelClock (class in microbenthos.model.model)
ModelData (class in microbenthos.dataview.base)
ModelDataExporter (class in microbenthos.exporters.model_data)
ModelEquation (class in microbenthos.model.equation)
ModelPlotter (class in microbenthos.dataview.plotter)
ModelVariable (class in microbenthos.core.variable)
module
microbenthos
microbenthos.cli
microbenthos.core
microbenthos.core.domain
microbenthos.core.entity
microbenthos.core.expression
microbenthos.core.irradiance
microbenthos.core.microbes
microbenthos.core.process
microbenthos.core.variable
microbenthos.dataview
microbenthos.dataview.base
microbenthos.dataview.hdfstore
microbenthos.dataview.plotter
microbenthos.dataview.snapshot
microbenthos.exporters
microbenthos.exporters.exporter
microbenthos.exporters.graphic
microbenthos.exporters.model_data
microbenthos.exporters.progress
microbenthos.model
microbenthos.model.equation
microbenthos.model.model
microbenthos.model.resume
microbenthos.model.saver
microbenthos.model.simulation
microbenthos.runners
microbenthos.runners.simulate
microbenthos.utils
microbenthos.utils.create
microbenthos.utils.loader
microbenthos.utils.log
microbenthos.utils.snapshotters
microbenthos.utils.yaml_setup
N
name (microbenthos.core.entity.Entity attribute)
normalization_rules (microbenthos.utils.loader.MicroBenthosSchemaValidator attribute)
O
obj (microbenthos.model.equation.ModelEquation attribute)
on_domain_set() (microbenthos.core.entity.DomainEntity method)
(microbenthos.core.microbes.MicrobialGroup method)
on_time_updated() (microbenthos.core.entity.Entity method)
(microbenthos.core.irradiance.Irradiance method)
(microbenthos.core.microbes.MicrobialGroup method)
(microbenthos.core.process.Process method)
(microbenthos.core.process.ProcessEvent method)
(microbenthos.model.model.MicroBenthosModel method)
outpath() (microbenthos.exporters.model_data.ModelDataExporter property)
P
params (microbenthos.core.process.Process attribute)
parse_formula() (microbenthos.core.expression.Expression method)
PATH_DEPTHS (microbenthos.dataview.base.ModelData attribute)
PATH_IRRADIANCE_CHANNELS (microbenthos.dataview.base.ModelData attribute)
PATH_TIMES (microbenthos.dataview.base.ModelData attribute)
post_init() (microbenthos.core.entity.Entity method)
prepare() (microbenthos.exporters.exporter.BaseExporter method)
(microbenthos.exporters.graphic.GraphicExporter method)
(microbenthos.exporters.model_data.ModelDataExporter method)
(microbenthos.exporters.progress.ProgressExporter method)
prepare_simulation() (microbenthos.runners.simulate.SimulationRunner method)
Process (class in microbenthos.core.process)
process (microbenthos.core.process.ProcessEvent attribute)
process() (microbenthos.exporters.exporter.BaseExporter method)
(microbenthos.exporters.graphic.GraphicExporter method)
(microbenthos.exporters.model_data.ModelDataExporter method)
(microbenthos.exporters.progress.ProgressExporter method)
processes (microbenthos.core.microbes.MicrobialGroup attribute)
ProcessEvent (class in microbenthos.core.process)
ProgressExporter (class in microbenthos.exporters.progress)
R
read_data_from() (microbenthos.dataview.base.ModelData method)
(microbenthos.dataview.hdfstore.HDFModelData method)
(microbenthos.dataview.snapshot.SnapshotModelData method)
read_metadata_from() (microbenthos.dataview.base.ModelData method)
(microbenthos.dataview.hdfstore.HDFModelData method)
(microbenthos.dataview.snapshot.SnapshotModelData method)
repr_pretty() (microbenthos.core.process.Process method)
restore_from() (microbenthos.core.entity.Entity method)
(microbenthos.core.irradiance.Irradiance method)
(microbenthos.core.irradiance.IrradianceChannel method)
(microbenthos.core.microbes.MicrobialGroup method)
(microbenthos.core.process.Process method)
(microbenthos.core.variable.ModelVariable method)
(microbenthos.model.equation.ModelEquation method)
(microbenthos.model.model.MicroBenthosModel method)
restore_var() (in module microbenthos.utils.snapshotters)
resume_existing_simulation() (microbenthos.runners.simulate.SimulationRunner method)
revert_vars() (microbenthos.model.model.MicroBenthosModel method)
RHS_terms() (microbenthos.model.equation.ModelEquation property)
rules (microbenthos.utils.loader.MicroBenthosSchemaValidator attribute)
run() (microbenthos.runners.simulate.SimulationRunner method)
run_timestep() (microbenthos.model.simulation.Simulation method)
runner (microbenthos.exporters.exporter.BaseExporter attribute)
S
save_definitions() (microbenthos.runners.simulate.SimulationRunner method)
save_run_info() (microbenthos.runners.simulate.SimulationRunner method)
save_snapshot() (in module microbenthos.model.saver)
schema_key (microbenthos.model.model.MicroBenthosModel attribute)
(microbenthos.model.simulation.Simulation attribute)
sediment_length (microbenthos.core.domain.SedimentDBLDomain attribute)
sediment_mask (microbenthos.core.domain.SedimentDBLDomain attribute)
SedimentDBLDomain (class in microbenthos.core.domain)
seed() (microbenthos.core.variable.ModelVariable method)
set_domain() (microbenthos.core.entity.DomainEntity method)
set_porosity() (microbenthos.core.domain.SedimentDBLDomain method)
set_time() (microbenthos.model.model.ModelClock method)
setup() (microbenthos.core.entity.DomainEntity method)
(microbenthos.core.irradiance.Irradiance method)
(microbenthos.core.irradiance.IrradianceChannel method)
(microbenthos.core.microbes.MicrobialGroup method)
(microbenthos.core.process.Process method)
(microbenthos.core.process.ProcessEvent method)
(microbenthos.core.variable.ModelVariable method)
(microbenthos.exporters.exporter.BaseExporter method)
setup_console_logging() (in module microbenthos)
setup_logfile() (microbenthos.runners.simulate.SimulationRunner method)
setup_model() (microbenthos.dataview.plotter.ModelPlotter method)
show() (microbenthos.dataview.plotter.ModelPlotter method)
sim() (microbenthos.exporters.exporter.BaseExporter property)
simtime_days (microbenthos.model.simulation.Simulation attribute)
simtime_lims() (microbenthos.model.simulation.Simulation property)
simtime_step() (microbenthos.model.simulation.Simulation property)
simtime_total() (microbenthos.model.simulation.Simulation property)
Simulation (class in microbenthos.model.simulation)
simulation() (microbenthos.runners.simulate.SimulationRunner property)
SimulationRunner (class in microbenthos.runners.simulate)
snapshot() (microbenthos.core.domain.SedimentDBLDomain method)
(microbenthos.core.entity.Entity method)
(microbenthos.core.irradiance.Irradiance method)
(microbenthos.core.irradiance.IrradianceChannel method)
(microbenthos.core.microbes.MicrobialGroup method)
(microbenthos.core.process.Process method)
(microbenthos.core.variable.ModelVariable method)
(microbenthos.model.equation.ModelEquation method)
(microbenthos.model.model.MicroBenthosModel method)
snapshot_due() (microbenthos.model.simulation.Simulation method)
snapshot_var() (in module microbenthos.utils.snapshotters)
SnapshotModelData (class in microbenthos.dataview.snapshot)
source_coeffs (microbenthos.model.equation.ModelEquation attribute)
source_exprs (microbenthos.model.equation.ModelEquation attribute)
source_formulae (microbenthos.model.equation.ModelEquation attribute)
source_terms (microbenthos.model.equation.ModelEquation attribute)
sources_rate() (microbenthos.model.equation.ModelEquation method)
sources_total (microbenthos.model.equation.ModelEquation attribute)
srepr() (microbenthos.exporters.progress.ProgressExporter method)
started (microbenthos.exporters.exporter.BaseExporter attribute)
started() (microbenthos.model.simulation.Simulation property)
store() (microbenthos.dataview.base.ModelData property)
surface_irrad (microbenthos.core.irradiance.Irradiance attribute)
symbols() (microbenthos.core.expression.Expression method)
T
teardown_logfile() (microbenthos.runners.simulate.SimulationRunner method)
term_diffusion() (microbenthos.model.equation.ModelEquation property)
term_transient() (microbenthos.model.equation.ModelEquation property)
times (microbenthos.dataview.base.ModelData attribute)
total_cells (microbenthos.core.domain.SedimentDBLDomain attribute)
track_budget() (microbenthos.model.equation.ModelEquation property)
Tracked (microbenthos.model.equation.ModelEquation attribute)
tracked (microbenthos.model.equation.ModelEquation attribute)
transport_rate() (microbenthos.model.equation.ModelEquation method)
truncate_model_data() (in module microbenthos.model.resume)
types_mapping (microbenthos.utils.loader.MicroBenthosSchemaValidator attribute)
U
unit_constructor() (in module microbenthos.utils.yaml_setup)
unit_representer() (in module microbenthos.utils.yaml_setup)
update() (microbenthos.dataview.base.ModelData method)
update_artists() (microbenthos.dataview.plotter.ModelPlotter method)
update_domain_info() (microbenthos.dataview.base.ModelData method)
update_equations() (microbenthos.dataview.base.ModelData method)
(microbenthos.model.model.MicroBenthosModel method)
update_intensities() (microbenthos.core.irradiance.IrradianceChannel method)
update_irradiance() (microbenthos.dataview.base.ModelData method)
update_legends() (microbenthos.dataview.plotter.ModelPlotter method)
update_microbes() (microbenthos.dataview.base.ModelData method)
update_simtime_step() (microbenthos.model.simulation.Simulation method)
update_tracked() (microbenthos.dataview.base.ModelData method)
update_tracked_budget() (microbenthos.model.equation.ModelEquation method)
update_vars() (microbenthos.model.model.MicroBenthosModel method)
V
validate_dict() (in module microbenthos.utils.loader)
validate_yaml() (in module microbenthos.utils.loader)
validation_rules (microbenthos.utils.loader.MicroBenthosSchemaValidator attribute)
value() (microbenthos.model.model.ModelClock property)
var (microbenthos.core.variable.ModelVariable attribute)
(microbenthos.model.equation.ModelEquation attribute)
var_in_DBL() (microbenthos.core.domain.SedimentDBLDomain method)
var_in_sediment() (microbenthos.core.domain.SedimentDBLDomain method)
var_quantity() (microbenthos.model.equation.ModelEquation method)
varname (microbenthos.model.equation.ModelEquation attribute)
varpath (microbenthos.model.equation.ModelEquation attribute)
VARS (microbenthos.core.domain.SedimentDBLDomain attribute)
(microbenthos.core.microbes.MicrobialGroup attribute)
video_outpath() (microbenthos.exporters.graphic.GraphicExporter property)
W
write_frame() (microbenthos.exporters.graphic.GraphicExporter method)
Z
zenith_level (microbenthos.core.irradiance.Irradiance attribute)
zenith_time (microbenthos.core.irradiance.Irradiance attribute)
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