# -*- coding: utf-8 -*-
"""Class for the ogs KINETRIC REACTION file."""
from ogs5py.fileclasses.base import BlockFile
[docs]class KRC(BlockFile):
"""
Class for the ogs KINETRIC REACTION file.
Parameters
----------
task_root : str, optional
Path to the destiny model folder.
Default: cwd+"ogs5model"
task_id : str, optional
Name for the ogs task.
Default: "model"
Notes
-----
Main-Keywords (#):
- MICROBE_PROPERTIES
- REACTION
- BLOB_PROPERTIES
- KINREACTIONDATA
Sub-Keywords ($) per Main-Keyword:
- MICROBE_PROPERTIES
- MICROBENAME
- _drmc__PARAMETERS
- MONOD_REACTION_NAME
- REACTION
- NAME
- TYPE
- BACTERIANAME
- EQUATION
- RATECONSTANT
- GROWTH
- MONODTERMS
- THRESHHOLDTERMS
- INHIBITIONTERMS
- PRODUCTIONTERMS
- PRODUCTIONSTOCH
- BACTERIAL_YIELD
- ISOTOPE_FRACTIONATION
- BACTERIA_SPECIFIC_CAPACITY
- TEMPERATURE_DEPENDENCE
- _drmc_
- STANDARD_GIBBS_ENERGY
- EXCHANGE_PARAMETERS
- SORPTION_TYPE
- NAPL_PROPERTIES
- REACTION_ORDER
- MINERALNAME
- CHEMAPPNAME
- EQUILIBRIUM_CONSTANT
- RATE_EXPONENTS
- REACTIVE_SURFACE_AREA
- PRECIPITATION_BY_BASETERM_ONLY
- PRECIPITATION_FACTOR
- PRECIPITATION_EXPONENT
- BASETERM
- MECHANISMTERM
- SWITCH_OFF_GEOMETRY
- BLOB_PROPERTIES
- NAME
- D50
- DM
- DS
- UI
- NAPL_CONTENT_INI
- NAPL_CONTENT_RES
- GRAIN_SPHERE_RATIO
- TORTUOSITY
- LENGTH
- CALC_SHERWOOD
- CALC_SHERWOOD_MODIFIED
- SHERWOOD_MODEL
- GEOMETRY
- GAS_DISSOLUTION
- INTERFACIAL_AREA
- KINREACTIONDATA
- SOLVER_TYPE
- RELATIVE_ERROR
- MIN_TIMESTEP
- INITIAL_TIMESTEP
- BACTERIACAPACITY
- MIN_BACTERIACONC
- MIN_CONCENTRATION_REPLACE
- SURFACES
- ALLOW_REACTIONS
- NO_REACTIONS
- COPY_CONCENTRATIONS
- LAGNEAU_BENCHMARK
- SCALE_DCDT
- SORT_NODES
- OMEGA_THRESHOLD
- REACTION_DEACTIVATION
- DEBUG_OUTPUT
- ACTIVITY_MODEL
Standard block:
None
Keyword documentation:
https://ogs5-keywords.netlify.com/ogs/wiki/public/doc-auto/by_ext/krc
Reading routines:
https://github.com/ufz/ogs5/blob/master/FEM/rf_kinreact.cpp
MICROBE_PROPERTIES :
https://github.com/ufz/ogs5/blob/master/FEM/rf_kinreact.cpp#L232
REACTION :
https://github.com/ufz/ogs5/blob/master/FEM/rf_kinreact.cpp#L1549
BLOB_PROPERTIES :
https://github.com/ufz/ogs5/blob/master/FEM/rf_kinreact.cpp#L2622
KINREACTIONDATA :
https://github.com/ufz/ogs5/blob/master/FEM/rf_kinreact.cpp#L3185
See Also
--------
add_block
"""
MKEYS = [
"MICROBE_PROPERTIES",
"REACTION",
"BLOB_PROPERTIES",
"KINREACTIONDATA",
]
# these are not sorted at the moment
SKEYS = [
[ # MICROBE_PROPERTIES
"MICROBENAME",
"_drmc__PARAMETERS",
"MONOD_REACTION_NAME",
],
[ # REACTION
"NAME",
"TYPE",
"BACTERIANAME",
"EQUATION",
"RATECONSTANT",
"GROWTH",
"MONODTERMS",
"THRESHHOLDTERMS",
"INHIBITIONTERMS",
"PRODUCTIONTERMS",
"PRODUCTIONSTOCH",
"BACTERIAL_YIELD",
"ISOTOPE_FRACTIONATION",
"BACTERIA_SPECIFIC_CAPACITY",
"TEMPERATURE_DEPENDENCE",
"_drmc_",
"STANDARD_GIBBS_ENERGY",
"EXCHANGE_PARAMETERS",
"SORPTION_TYPE",
"NAPL_PROPERTIES",
"REACTION_ORDER",
"MINERALNAME",
"CHEMAPPNAME",
"EQUILIBRIUM_CONSTANT",
"RATE_EXPONENTS",
"REACTIVE_SURFACE_AREA",
"PRECIPITATION_BY_BASETERM_ONLY",
"PRECIPITATION_FACTOR",
"PRECIPITATION_EXPONENT",
"BASETERM",
"MECHANISMTERM",
"SWITCH_OFF_GEOMETRY",
],
[ # BLOB_PROPERTIES
"NAME",
"D50",
# "CALC_SHERWOOD",
"DM",
"DS",
"UI",
"NAPL_CONTENT_INI",
"NAPL_CONTENT_RES",
"GRAIN_SPHERE_RATIO",
"TORTUOSITY",
"LENGTH",
"CALC_SHERWOOD",
"CALC_SHERWOOD_MODIFIED",
"SHERWOOD_MODEL",
"GEOMETRY",
"GAS_DISSOLUTION",
"INTERFACIAL_AREA",
],
[ # KINREACTIONDATA
"SOLVER_TYPE",
"RELATIVE_ERROR",
"MIN_TIMESTEP",
"INITIAL_TIMESTEP",
"BACTERIACAPACITY",
"MIN_BACTERIACONC",
"MIN_CONCENTRATION_REPLACE",
"SURFACES",
"ALLOW_REACTIONS",
"NO_REACTIONS",
"COPY_CONCENTRATIONS",
"LAGNEAU_BENCHMARK",
"SCALE_DCDT",
"SORT_NODES",
"OMEGA_THRESHOLD",
"REACTION_DEACTIVATION",
"DEBUG_OUTPUT",
"ACTIVITY_MODEL",
"REALATIVE_ERROR", # really?
"MAX_TIMESTEP", # really?
],
]
STD = {}
def __init__(self, **OGS_Config):
super().__init__(**OGS_Config)
self.file_ext = ".krc"