sutra.removal_functions module

class sutra.removal_functions.MicrobialRemoval(organism: Organism = 'carotovorum', alpha0_suboxic=None, alpha0_anoxic=None, alpha0_deeply_anoxic=None, pH0_suboxic=None, pH0_anoxic=None, pH0_deeply_anoxic=None, mu1_suboxic=None, mu1_anoxic=None, mu1_deeply_anoxic=None, organism_diam=None)

Bases: object

Class to calculate removal (rate) for a given microbial organism.

organism: object

The microbial organism object with the microbial organism (mbo) of interest

organism_dict: dictionary
‘alpha0’: float

reference_collision_efficiency [-] per redox zone (‘suboxic’, ‘anoxic’, deeply_anoxic’)

‘pH0’: float

reference pH for calculating collision efficiency [-] per redox zone (‘suboxic’, ‘anoxic’, deeply_anoxic’)

‘organism_diam’: float

diameter of pathogen/species [m]

‘mu1’: float

inactivation coefficient [1/day] per redox zone (‘suboxic’, ‘anoxic’, deeply_anoxic’)

calc_advective_microbial_removal(grainsize=0.00025, temp_water=11.0, rho_water=999.703, pH=7.5, por_eff=0.33, conc_start=1.0, conc_gw=0.0, redox='anoxic', distance_traveled=1.0, traveltime=100.0, mu1=None, alpha0=None, pH0=None, organism_diam=None)

Calculate the advective microbial removal of microbial organisms from source to end_point.

For more information about the advective microbial removal calculation:

BTO2012.015: Ch 6.7 (page 71-74)

Parameters

  • lambda (float) – ‘removal rate’ [day-1] (redox dependent) –> calculated

  • redox (str) – redox condition [‘suboxic’,’anoxic’,’deeply_anoxic’]

  • mu1 (float) – inactivation coefficient [day-1]

  • por_eff (float) – effective porosity [-]

  • grainsize (float) – grain diameter of sediment [m]

  • pH (float) – pH of the water [-]

  • pH0 (float) – reference pH for which alpha0 was determined

  • temp_water (float) – Water temperature [degrees celcius]

  • rho_water (float) – Water density [kg m-3]

  • alpha (float) – ‘sticky coefficient’ [-], pH corrected

  • alpha0 (float) – ‘reference sticky coefficient’, for a reference pH [pH0]

  • organism_diam (float) – organism/species diameter [m]

  • v_por (float) – porewater velocity [m/d]

  • conc_start (float) – starting concentration

  • conc_gw (float) – initial groundwater concentration

  • distance_traveled (float) – distance between points [m]

  • traveltime (float) – time between start and endpoint [days]

  • Calculates –

  • ----------- –

  • C_final (float) – final concentration [N/L]

Return type

C_final

calc_lambda(redox='anoxic', mu1=0.149, mu1_std=0.0932, por_eff=0.33, grainsize=0.00025, pH=7.5, temp_water=10.0, rho_water=999.703, alpha0=0.001, pH0=7.5, organism_diam=2.33e-08, v_por=0.01)

For more information about the advective microbial removal calculation: BTO2012.015: Ch 6.7 (page 71-74)

Calculate removal coefficient lambda [/day].

Parameters

  • redox (str) – redox condition [‘suboxic’,’anoxic’,’deeply_anoxic’]

  • mu1 (float) – inactivation coefficient [day-1]

  • por_eff (float) – effective porosity [-]

  • grainsize (float) – grain diameter of sediment [m]

  • pH (float) – pH of the water [-]

  • pH0 (float) – reference pH for which alpha0 was determined

  • temp_water (float) – Water temperature [degrees celcius]

  • rho_water (float) – Water density [kg m-3]

  • alpha (float) – ‘sticky coefficient’ [-], pH corrected

  • alpha0 (float) – ‘reference sticky coefficient’, for a reference pH [pH0]

  • organism_diam (float) – Organism/species diameter [m]

  • v_por (float) – porewater velocity [m/d]

  • const_BM (float) – Boltzmann constant [1,38 × 10-23 J K-1]

  • Calculates –

  • ------------ –

  • lambda (float) – k_att + mu_1 ‘removal rate’ [day-1]

  • k_att (float) – attachmant rate [day-1]

Return type

lambda, k_att

class sutra.removal_functions.Organism(organism_name, removal_function='mbo')

Bases: object

Placeholder class which includes removal parameters for a selection of microbial organisms (‘mbo’). For now dictionary includes the plant pathogens: ‘solani’ (Dickeya solani), ‘carotovorum’ (Pectobacterium carotovorum), and ‘solanacearum’ (Ralstonia solanacearum).

removal_paramaters_dict: dict .. attribute:: organism_name

species_name of the substance

type

String

'alpha0'

reference_collision_efficiency [-] per redox zone (‘suboxic’, ‘anoxic’, deeply_anoxic’)

Type

float

'pH0'

reference pH for calculating collision efficiency [-] per redox zone (‘suboxic’, ‘anoxic’, deeply_anoxic’)

Type

float

'organism_diam'

diameter of pathogen/species [m]

Type

float

'mu1'

inactivation coefficient [1/day] per redox zone (‘suboxic’, ‘anoxic’, deeply_anoxic’)

Type

float