Heavy metals
From MohidWiki
Introduction
In MOHID the distribution of contaminants is parameterized by using the ratio between the adsorbed particulate concentration and the dissolved concentration (see Adsorption/Desorption ). Physically, the partition coefficient (Johansson et al., 2001) illustrates particle affinity and represents the chemical equilibrium of numerous processes such adsorption onto particulate matter, precipitation and dissolution. Pollutants transport in the adsorbed phase is strongly connected with cohesive sediment transport due to the affinity of many contaminants for the solid phase. Once adsorbed to the sediments, these substances are transported by the sediments (Fernandes L., 2005).
In MOHID the partition coefficient is defined through a keyword (keyword PARTITION_FRACTION). The concentration of the contaminant in the water is described by the following equations (1) and (2):
(1)
(2)
where:
Cd is the concentration of the contaminant in the dissolved phase (mol/l)
Cp is the concentration of the contaminant in the particulate phase (mol/l)
r is the transfer rate from particulate to dissolved phase (1/sec) (keyword PARTITION_RATE)
pd is the dissolved fraction (dimensionless)
ps is the solid fraction (dimensionless)
For each contaminant phase it is necessary to specify opposite phase through the keyword PARTITION_COUPLE. For example, for the contaminant dissolved arsenic, the opposite phase is particulate arsenic.
It is assumed that particulate and dissolved phases must have equal partition rates. Also, the sum of particulate and dissolved phases’ fractions must be equal to 1.
In MOHID, the transfer rate depends on the cohesive sediment concentration. A coefficient Rs is defined as (eq.3):
(3)
SedimentRefConcentration is a cohesive sediment reference concentration (keyword SED_REF_CONC). Particulate and dissolved phases of the same contaminant must have equal cohesive sediment reference concentration. The transfer rate is equal to r for Rs > 1 and equal to r x Rs for Rs<1
Eulerian Applications
Example input files
File WaterProperty_X.dat
OUTPUT_TIME : 0. 3600. <beginproperty> NAME : particulate copper UNITS : mg/l DESCRIPTION : No description was given. PARTICULATE : 1 BOUNDARY_INITIALIZATION : EXTERIOR DEFAULTBOUNDARY : 0.0 BOUNDARY_CONDITION : 2 ADVECTION_DIFFUSION : 1 ADVECTION_H_IMP_EXP : 0 INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0. IS_COEF : 0.001 PARTITION : 1 DISCHARGES : 1 VERTICAL_MOVEMENT : 1 BOTTOM_FLUXES : 1 OUTPUT_HDF : 1 TIME_SERIE : 0 BOX_TIME_SERIE : 0 PARTITION : 1 PARTITION_FRACTION : 0.7 PARTITION_RATE : 5e-5 PARTITION_COUPLE : dissolved copper USE_SED_REF_CONC : 1 SED_REF_CONC : 2. <endproperty> <beginproperty> NAME : dissolved copper UNITS : mg/l DESCRIPTION : No description was given. PARTICULATE : 0 BOUNDARY_INITIALIZATION : EXTERIOR DEFAULTBOUNDARY : 0.02 BOUNDARY_CONDITION : 2 ADVECTION_DIFFUSION : 1 ADVECTION_H_IMP_EXP : 0 INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0.02 IS_COEF : 0.001 PARTITION : 1 DISCHARGES : 1 VERTICAL_MOVEMENT : 0 BOTTOM_FLUXES : 0 OUTPUT_HDF : 1 TIME_SERIE : 0 BOX_TIME_SERIE : 0 PARTITION : 1 PARTITION_FRACTION : 0.3 PARTITION_RATE : 5e-5 PARTITION_COUPLE : particulate copper USE_SED_REF_CONC : 1 SED_REF_CONC : 2. <endproperty> <beginproperty> NAME : particulate zinc UNITS : mg/l DESCRIPTION : No description was given. PARTICULATE : 1 BOUNDARY_INITIALIZATION : EXTERIOR DEFAULTBOUNDARY : 0.0 BOUNDARY_CONDITION : 2 ADVECTION_DIFFUSION : 1 ADVECTION_H_IMP_EXP : 0 INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0. IS_COEF : 0.001 PARTITION : 1 DISCHARGES : 1 VERTICAL_MOVEMENT : 1 BOTTOM_FLUXES : 1 OUTPUT_HDF : 1 TIME_SERIE : 0 BOX_TIME_SERIE : 0 PARTITION : 1 PARTITION_FRACTION : 0.7 PARTITION_RATE : 5e-5 PARTITION_COUPLE : dissolved zinc USE_SED_REF_CONC : 1 SED_REF_CONC : 2. <endproperty> <beginproperty> NAME : dissolved zinc UNITS : mg/l DESCRIPTION : No description was given. PARTICULATE : 0 BOUNDARY_INITIALIZATION : EXTERIOR DEFAULTBOUNDARY : 0.02 BOUNDARY_CONDITION : 2 ADVECTION_DIFFUSION : 1 ADVECTION_H_IMP_EXP : 0 INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0.02 IS_COEF : 0.001 PARTITION : 1 DISCHARGES : 1 VERTICAL_MOVEMENT : 0 BOTTOM_FLUXES : 0 OUTPUT_HDF : 1 TIME_SERIE : 0 BOX_TIME_SERIE : 0 PARTITION : 1 PARTITION_FRACTION : 0.3 PARTITION_RATE : 5e-5 PARTITION_COUPLE : particulate zinc USE_SED_REF_CONC : 1 SED_REF_CONC : 2. <endproperty> <beginproperty> NAME : particulate metal UNITS : mg/l DESCRIPTION : No description was given. PARTICULATE : 1 BOUNDARY_INITIALIZATION : EXTERIOR DEFAULTBOUNDARY : 0.0 BOUNDARY_CONDITION : 2 ADVECTION_DIFFUSION : 1 ADVECTION_H_IMP_EXP : 0 INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0. IS_COEF : 0.001 PARTITION : 1 DISCHARGES : 1 VERTICAL_MOVEMENT : 1 BOTTOM_FLUXES : 1 OUTPUT_HDF : 1 TIME_SERIE : 0 BOX_TIME_SERIE : 0 PARTITION : 1 PARTITION_FRACTION : 0.7 PARTITION_RATE : 5e-5 PARTITION_COUPLE : dissolved metal USE_SED_REF_CONC : 1 SED_REF_CONC : 2. <endproperty> <beginproperty> NAME : dissolved metal UNITS : mg/l DESCRIPTION : No description was given. PARTICULATE : 0 BOUNDARY_INITIALIZATION : EXTERIOR DEFAULTBOUNDARY : 0.02 BOUNDARY_CONDITION : 2 ADVECTION_DIFFUSION : 1 ADVECTION_H_IMP_EXP : 0 INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0.02 IS_COEF : 0.001 PARTITION : 1 DISCHARGES : 1 VERTICAL_MOVEMENT : 0 BOTTOM_FLUXES : 0 OUTPUT_HDF : 1 TIME_SERIE : 0 BOX_TIME_SERIE : 0 PARTITION : 1 PARTITION_FRACTION : 0.3 PARTITION_RATE : 5e-5 PARTITION_COUPLE : particulate metal USE_SED_REF_CONC : 1 SED_REF_CONC : 2. <endproperty>
File InterfaceSedimentWater_X.dat
OUTPUT_TIME : 0 3600 <begin_rugosity> INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0.0025 <end_rugosity> <begin_critical_shear_erosion> INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0.2 <end_critical_shear_erosion> <begin_critical_shear_deposition> INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0.1 <end_critical_shear_deposition> <begin_erosion_rate> INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0.00005 <end_erosion_rate> <beginproperty> NAME : cohesive sediment UNITS : kg/m2 DESCRIPTION : cohesive sediment mass PARTICULATE : 1 WATER_FLUXES : 1 EROSION : 1 DEPOSITION : 1 MASS_LIMITATION : 1 MASS_MIN : 0. INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0.00001 TIME_SERIE : 0 BOX_TIME_SERIE : 0 OUTPUT_HDF : 1 <endproperty> <beginproperty> NAME : particulate copper UNITS : kg/m2 DESCRIPTION : PON mass PARTICULATE : 1 WATER_FLUXES : 1 EROSION : 1 DEPOSITION : 1 MASS_LIMITATION : 1 MASS_MIN : 0. INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0. TIME_SERIE : 0 BOX_TIME_SERIE : 0 OUTPUT_HDF : 1 <endproperty> <beginproperty> NAME : particulate zinc UNITS : kg/m2 DESCRIPTION : PON mass PARTICULATE : 1 WATER_FLUXES : 1 EROSION : 1 DEPOSITION : 1 MASS_LIMITATION : 1 MASS_MIN : 0. INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0. TIME_SERIE : 0 BOX_TIME_SERIE : 0 OUTPUT_HDF : 1 <endproperty> <beginproperty> NAME : particulate metal UNITS : kg/m2 DESCRIPTION : PON mass PARTICULATE : 1 WATER_FLUXES : 1 EROSION : 1 DEPOSITION : 1 MASS_LIMITATION : 1 MASS_MIN : 0. INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0. TIME_SERIE : 0 BOX_TIME_SERIE : 0 OUTPUT_HDF : 1 <endproperty>
File FreeVerticalMovement_X.dat
<beginproperty> NAME : cohesive sediment WS_VALUE : 0.00001 WS_TYPE : 1 DEPOSITION : 1 <endproperty> <beginproperty> NAME : particulate copper WS_VALUE : 0.00001 WS_TYPE : 1 DEPOSITION : 1 <endproperty> <beginproperty> NAME : particulate zinc WS_VALUE : 0.00001 WS_TYPE : 1 DEPOSITION : 1 <endproperty> <beginproperty> NAME : particulate metal WS_VALUE : 0.00001 WS_TYPE : 1 DEPOSITION : 1 <endproperty>
File Discharges_X.dat
<begindischarge> NAME : Discharge I_CELL : 28 J_CELL : 8 K_CELL : 1 ALTERNATIVE_LOCATIONS : 1 DEFAULT_FLOW_VALUE : 50 <<beginproperty>> NAME : cohesive sediment UNITS : psu DEFAULTVALUE : 50 <<endproperty>> <<beginproperty>> NAME : particulate copper UNITS : mg/l DEFAULTVALUE : 0.02 <<endproperty>> <<beginproperty>> NAME : dissolved copper UNITS : mg/l DEFAULTVALUE : 0.02 <<endproperty>> <<beginproperty>> NAME : particulate zinc UNITS : mg/l DEFAULTVALUE : 0.02 <<endproperty>> <<beginproperty>> NAME : dissolved zinc UNITS : mg/l DEFAULTVALUE : 0.02 <<endproperty>> <<beginproperty>> NAME : particulate metal UNITS : mg/l DEFAULTVALUE : 0.02 <<endproperty>> <<beginproperty>> NAME : dissolved metal UNITS : mg/l DEFAULTVALUE : 0.02 <<endproperty>> <enddischarge>
Lagrangian Applications
Example input files
File Model_X.dat
START : 2008 6 1 12 0 0 END : 2008 6 5 12 0 0 DT : 30. VARIABLEDT : 0 GMTREFERENCE : 0 SPLITTING : Double_Splitting LAGRANGEANE : 1 LAGRANGIAN : 1
File Lagrangian_X.dat
OUTPUT_TIME : 0 3600. DT_PARTIC : 30. OUTPUT_CONC : 2 <BeginOrigin> ORIGIN_NAME : Emission (60um) OLD : 0 GROUP_ID : 2 EMISSION_SPATIAL : Point EMISSION_TEMPORAL : Continuous DT_EMIT : 150 FLOW : 1 FLOAT : 0 MOVEMENT : SullivanAllen VARVELHX : 0.0 VARVELH : 0.03 TURB_V : Profile POSITION_CELLS : 7.5 27.5 DEPTH_METERS : 0. NBR_PARTIC : 1 SEDIMENTATION : Stokes D50 : 0.06 MIN_SED_VELOCITY : 0.0 DEPOSITION : 1 TAU_ERO : 0.2 TAU_DEP : 0.1 BOTTOM_DISTANCE : 0.1 BOTTOM_EMISSION : 0 TIME_DECAY : 172800. EROSION_RATE : 0.05 <<BeginProperty>> NAME : sediment UNITS : mg/l CONCENTRATION : 10. AMBIENT_CONC : 1 <<EndProperty>> <<BeginProperty>> NAME : particulate zinc UNITS : mg/l CONCENTRATION : 0.02 AMBIENT_CONC : 0 PARTITION_WATER : 1 PARTITION_COEF_WATER : 0.7 PARTITION_RATE_WATER : 5e-5 PARTITION_COUPLE_WATER : 0.02 PARTITION_SED : 1 PARTITION_COEF_SED : 0.9 PARTITION_RATE_SED : 5e-5 PARTITION_COUPLE_SED : 0.02 <<EndProperty>> <EndOrigin> <BeginOrigin> ORIGIN_NAME : Emission (40um) OLD : 0 GROUP_ID : 1 EMISSION_SPATIAL : Point EMISSION_TEMPORAL : Continuous DT_EMIT : 150 FLOW : 1 FLOAT : 0 MOVEMENT : SullivanAllen VARVELHX : 0.0 VARVELH : 0.03 TURB_V : Profile POSITION_CELLS : 7.5 27.5 DEPTH_METERS : 0. NBR_PARTIC : 1 SEDIMENTATION : Stokes D50 : 0.04 MIN_SED_VELOCITY : 0.0 DEPOSITION : 1 TAU_ERO : 0.2 TAU_DEP : 0.1 BOTTOM_DISTANCE : 0.1 BOTTOM_EMISSION : 0 TIME_DECAY : 172800. EROSION_RATE : 0.05 <<BeginProperty>> NAME : sediment UNITS : mg/l CONCENTRATION : 10. AMBIENT_CONC : 1 <<EndProperty>> <<BeginProperty>> NAME : particulate copper UNITS : mg/l CONCENTRATION : 0.02 AMBIENT_CONC : 0 PARTITION_WATER : 1 PARTITION_COEF_WATER : 0.7 PARTITION_RATE_WATER : 5e-5 PARTITION_COUPLE_WATER : 0.02 PARTITION_SED : 1 PARTITION_COEF_SED : 0.9 PARTITION_RATE_SED : 5e-5 PARTITION_COUPLE_SED : 0.02 <<EndProperty>> <EndOrigin> <BeginOrigin> ORIGIN_NAME : Emission (20um) OLD : 0 GROUP_ID : 1 EMISSION_SPATIAL : Point EMISSION_TEMPORAL : Continuous DT_EMIT : 150 FLOW : 1 FLOAT : 0 MOVEMENT : SullivanAllen VARVELHX : 0.0 VARVELH : 0.03 TURB_V : Profile POSITION_CELLS : 7.5 27.5 DEPTH_METERS : 0. NBR_PARTIC : 1 SEDIMENTATION : Stokes D50 : 0.02 MIN_SED_VELOCITY : 0.0 DEPOSITION : 1 TAU_ERO : 0.2 TAU_DEP : 0.1 BOTTOM_DISTANCE : 0.1 BOTTOM_EMISSION : 0 TIME_DECAY : 172800. EROSION_RATE : 0.05 <<BeginProperty>> NAME : sediment UNITS : mg/l CONCENTRATION : 10. AMBIENT_CONC : 1 <<EndProperty>> <<BeginProperty>> NAME : particulate copper UNITS : mg/l CONCENTRATION : 0.02 AMBIENT_CONC : 0 PARTITION_WATER : 1 PARTITION_COEF_WATER : 0.7 PARTITION_RATE_WATER : 5e-5 PARTITION_COUPLE_WATER : 0.02 PARTITION_SED : 1 PARTITION_COEF_SED : 0.9 PARTITION_RATE_SED : 5e-5 PARTITION_COUPLE_SED : 0.02 <<EndProperty>> <EndOrigin> <BeginOrigin> ORIGIN_NAME : Emission (10um) OLD : 0 GROUP_ID : 1 EMISSION_SPATIAL : Point EMISSION_TEMPORAL : Continuous DT_EMIT : 150 FLOW : 1 FLOAT : 0 MOVEMENT : SullivanAllen VARVELHX : 0.0 VARVELH : 0.03 TURB_V : Profile POSITION_CELLS : 7.5 27.5 DEPTH_METERS : 0. NBR_PARTIC : 1 SEDIMENTATION : Stokes D50 : 0.01 MIN_SED_VELOCITY : 0.0 DEPOSITION : 1 TAU_ERO : 0.2 TAU_DEP : 0.1 BOTTOM_DISTANCE : 0.1 BOTTOM_EMISSION : 0 TIME_DECAY : 172800. EROSION_RATE : 0.05 <<BeginProperty>> NAME : sediment UNITS : mg/l CONCENTRATION : 10. AMBIENT_CONC : 1 <<EndProperty>> <<BeginProperty>> NAME : particulate copper UNITS : mg/l CONCENTRATION : 0.02 AMBIENT_CONC : 0 PARTITION_WATER : 1 PARTITION_COEF_WATER : 0.7 PARTITION_RATE_WATER : 5e-5 PARTITION_COUPLE_WATER : 0.02 PARTITION_SED : 1 PARTITION_COEF_SED : 0.9 PARTITION_RATE_SED : 5e-5 PARTITION_COUPLE_SED : 0.02 <<EndProperty>> <EndOrigin> <BeginOrigin> ORIGIN_NAME : Emission (2um) OLD : 0 GROUP_ID : 1 EMISSION_SPATIAL : Point EMISSION_TEMPORAL : Continuous DT_EMIT : 150 FLOW : 1 FLOAT : 0 MOVEMENT : SullivanAllen VARVELHX : 0.0 VARVELH : 0.03 TURB_V : Profile POSITION_CELLS : 7.5 27.5 DEPTH_METERS : 0. NBR_PARTIC : 1 SEDIMENTATION : Stokes D50 : 0.02 MIN_SED_VELOCITY : 0.0 DEPOSITION : 1 TAU_ERO : 0.2 TAU_DEP : 0.1 BOTTOM_DISTANCE : 0.1 BOTTOM_EMISSION : 0 TIME_DECAY : 172800. EROSION_RATE : 0.05 <<BeginProperty>> NAME : sediment UNITS : mg/l CONCENTRATION : 10. AMBIENT_CONC : 1 <<EndProperty>> <<BeginProperty>> NAME : particulate copper UNITS : mg/l CONCENTRATION : 0.02 AMBIENT_CONC : 0 PARTITION_WATER : 1 PARTITION_COEF_WATER : 0.7 PARTITION_RATE_WATER : 5e-5 PARTITION_COUPLE_WATER : 0.02 PARTITION_SED : 1 PARTITION_COEF_SED : 0.9 PARTITION_RATE_SED : 5e-5 PARTITION_COUPLE_SED : 0.02 <<EndProperty>> <EndOrigin>
References
Johasson, H., Lindstrom, M., Hakanson, L., (2001). On the Modelling of particulate and dissolved fractions of substances in aquatic systems – sedimentological and ecological interactions, Ecological Modelling, 137, 225-240
Fernandes L., (2005). Modelling of arsenic Dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon.
