'''
MIT License
Copyright (c) [2022] [Temitope Ajayi]
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
'''
[docs]
class Water(object):
[docs]
def __init__(self, primary_species, temperature, pressure):
"""Initialization of Parameters (Water composition)
Parameters
-----------
primary_species : PrimarySpecies
Primary specie present in the water composition
temperature : float
Temperature of the solution (°C). Note that this temperature is used only for initial speciation
calculations for this water, before the water composition is assigned to different grid block
pressure : float
Pressure of the solution (bar). This value can be omitted, in which case PT is assumed 1 bar
Returns
--------
"""
self.pressure = pressure
self.temperature = temperature
self.primary_species = primary_species
[docs]
class ReactGas(object):
[docs]
def __init__(self, name, fugacity_flag, partial_pressure):
"""Initialization of Parameters (React Gas)
Parameters
-----------
name : string
Name of the gaseous species present in the system
partial_pressure : float
Initial partial pressure of the gaseous species (in bars)
fugacity_flag : int
Flag depicting if fugacity is enabled or not
Returns
--------
"""
start_index = name.find('\'')
if start_index >= 0:
name = name.replace("'", "")
self.partial_pressure = partial_pressure
self.name = name
self.fugacity_flag = fugacity_flag
[docs]
class WaterComp(object):
[docs]
def __init__(self, primary_species, icon, nrguess, ctot, nameq='*', qksat=0.0, naads_min=None,
sdens=None, imod=None, capac=None):
"""Initialization of Parameters (Water composition)
Parameters
-----------
primary_species : PrimarySpecies
Primary specie present in the water composition
icon : int
Flag indicating the type of constraint controlling the input concentration of the aqueous species
1: input values of CTOT represent total amounts (in moles) for aqueous species, and total
kilogram s for liquid H2O
2: the total concentration of the species will be computed such that the saturation index
of mineral or gas equals qksat at temperature and pressure TC2
and PT, respectively.
3: input values of ctot represent the known activity of the specific species (i.e., not
total concentration) at temperature and pressure TC2 and PT, respectively.
4: the total concentration of the species is adjusted to yield charge balance. Use only
with a charged species
nrguess : float
initial guess (trial) value for the concentration of the individual primary species (not total
concentration), in moles/kg H2O (molal) for species other than H2O and in kg for H2O.
ctot : float
If icon=1, CTOT is total moles of aqueous species, and total amount (in kg) of liquid water for
H2O
nameq : string
Name of mineral or gas (in quotes) to use with option ICON=2. Names must match exactly
those previously listed as minerals or gases in the definition of the chemical system
qksat : float
desired value of mineral log(Q/K) or gas log(fugacity) when option icon=2 is used
sdens : float
Sorption site density in molsites/m2mineral for this surface species
imod : int
Adsorption model type
0 surface complexation without electrostatic terms
1 constant capacitance model
2 double diffuse layer model, linear
3 double diffuse layer model, Gouy-Chapman (most common)
capac : float
Capacitance in F m–2. Must be entered only if imod=1
Returns
--------
"""
self.primary_species = primary_species
self.icon = icon
self.nrguess = nrguess
self.ctot = ctot
self.nameq = nameq
self.qksat = qksat
self.naads_min = naads_min
self.sdens = sdens
self.imod = imod
self.capac = capac
[docs]
class PrimarySpecies(object):
[docs]
def __init__(self, name, notrans):
"""Initialization of Parameters
Parameters
-----------
name : string
Name of the primary species,
notrans : int
Flag for transport and surface complexation options; 0 species (component) will be transported,
1 no transport for this species (component)
Returns
--------
"""
self.NOTRANS = notrans
start_index = name.find('\'')
if start_index >= 0:
name = name.replace("'", "")
self.NAME = name
[docs]
def get_name_trans(self):
""" Function that retrieves the name of primary species and flag for transport and surface complexation options
Parameters
-----------
Returns
--------
parameter : list
List containing name of primary species and flag for transport and surface complexation options
"""
parameter = [self.NAME, self.NOTRANS]
return parameter