`pygcc.species_eos`

Created on Wed Mar 17 16:02:22 2021

@author: adedapo.awolayo and Ben Tutolo, University of Calgary

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

Functions implemented here include gas, mineral and aqueous species equation of state

Module Contents

Classes

heatcap

Class to heat capacity for mineral and gases using Maier-Kelley powerlaw, Haas-Fisher powerlaw, Holland and Powell and Berman's function

Functions

`Element_counts`(formula)	This function calculates the elemental composition of a substance given by its chemical formula
`supcrtaq`(TC, P, specieppt[, Dielec_method, ThermoInUnit])	This function evaluates the Gibbs free energy of aqueous species at T and P

Attributes

`J_to_cal`
`KJ_to_cal`

pygcc.species_eos.J_to_cal = 4.184

pygcc.species_eos.KJ_to_cal

pygcc.species_eos.Element_counts(formula)[source]

This function calculates the elemental composition of a substance given by its chemical formula It was a modified version of https://github.com/cgohlke/molmass/blob/master/molmass/molmass.py

Parameters:: formula (string) – Chemical formula
Returns:: elements – dictionary of elemental composition and their respective number of atoms
Return type:: dict

Usage:

[elements] = Element_counts(formula)
Examples of valid formulas are “H2O”, “[2H]2O”, “CH3COOH”, “EtOH”, “CuSO4:5H2O”, “(COOH)2”, “AgCuRu4(H)2[CO]12{PPh3}2”, “CGCGAATTCGCG”, and, “MDRGEQGLLK” .

class pygcc.species_eos.heatcap(**kwargs)[source]

Class to heat capacity for mineral and gases using Maier-Kelley powerlaw, Haas-Fisher powerlaw, Holland and Powell and Berman’s function

Parameters:

T (float, vector) – Temperature [°C]
P (float, vector) – Pressure [bar]
Species_ppt (array) –

Properties such as Supcrt92 (dG [cal/mol], dH [cal/mol], S [cal/mol-K], V [cm3/mol] a [cal/mol-K], b [*10**3 cal/mol/K^2],
c [*10^-5 cal/mol/K], Ttrans [K], Htr [cal/mol], Vtr [cm³/mol], dPdTtr [bar/K] ): Berman’s database

properties such as (dG [J/mol], dH [J/mol], S [J/mol-K], V [cm³/mol], k0, k1, k2, k3, v1 [*10^5 K^-1], v2 [*10^5 K^-2], v3 [*10^5 bar^-1], v4 [*10^8 bar^-2], dTdP [K/bar], Tlambda [K], Tref [K], l1 [(J/mol)^0.5/K], l2 [(J/mol)^0.5/K^2], DtH, d0 [J/mol], d1 [J/mol], d2 [J/mol], d3 [J/mol], d4 [J/mol], d5 [J/mol], Tmin [K], Tmax [K]): Supcrtbl’s database properties such as (dG [kJ/mol], dH [kJ/mol], S [J/mol-K], V [J/bar], a [kJ/mol-K], b [*10^5 kJ/mol/K^2], c [kJ-mol-K], d [kJ/mol/K^0.5], alpha [*10^5 K^-1], kappa0 [kbar], kappa0_d [kbar], kappa0_dd [kbar], n_atom [-], Tc0 [K], Smax [J/mol-K], Vmax [J/bar], dH [KJ/mol], dV [J/bar], W [kJ/mol], Wv [J/bar], n [-], SF [-]), etc
Species (string) – species name, optional for all cases except gases, Coesite and Quartz
method (string) – specify either ‘SUPCRT’ or ‘berman88’ or ‘HP11’ or ‘HF76’ to carry-out any mineral or gas heat capacity calculations, default is ‘SUPCRT’

Returns:

dG (float, vector) – Gibbs Energy [cal/mol]
dCp (float, vector) – Heat capacity [cal/mol/K]

Examples

>>> # Example with Maier-Kelley powerlaw function as implemented in SUPCRT92
>>> from pygcc.pygcc_utils import db_reader
>>> ps = db_reader() # utilizes the default direct-access database, speq21
>>> sp = heatcap( T = 100, P = 50, Species = 'H2S(g)', Species_ppt = ps.dbaccessdic['H2S(g)'], method = 'SUPCRT')
>>> sp.dG, sp.dCp
    -11782.47165818, 8.58416135
>>> sp = heatcap( T = 100, P = 50, Species_ppt = ps.dbaccessdic['Quartz'], method = 'SUPCRT',
                      Species = 'Quartz')
>>> sp.dG, sp.dCp
    -205292.75498942, 12.34074489

>>> # Example with Haas-Fisher powerlaw function
>>> from pygcc.pygcc_utils import db_reader
>>> ps = db_reader() # utilizes the default direct-access database, speq21
>>> sp = heatcap( T = 100, P = 50, Species_ppt = ps.dbaccessdic['ss_Anorthite'], method = 'HF76',
                 Species = 'ss_Anorthite')
>>> sp.dG, sp.dCp
    -960440.79915641, 57.46776903

>>> # Example with Berman's function
>>> from pygcc.pygcc_utils import db_reader
>>> # utilizes the default speq21 and specified Berman dataset database
>>> ps = db_reader(dbBerman_dir = './default_db/Berman.dat')
>>> sp = heatcap( T = 100, P = 50, Species_ppt = ps.dbaccessdic['Quartz'], method = 'berman88',
                 Species = 'Quartz')
>>> sp.dG, sp.dCp
    -205472.3365716, 12.32381279

>>> # Example with Holland and Powell's function
>>> from pygcc.pygcc_utils import db_reader
>>> # utilizes the default speq21 and specified SUPCRTBL (HP2011) dataset database
>>> ps = db_reader(dbHP_dir = './default_db/supcrtbl.dat')
>>> sp = heatcap( T = 100, P = 50, Species_ppt = ps.dbaccessdic['Hematite'], method = 'HP11',
                 Species = 'Hematite')
>>> sp.dG, sp.dCp
    -179494.62259123, 28.09545987

References

Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K.(1978). Summary and critique of the thermodynamic properties of rock-forming minerals.
Kelley K. K (1960) Contributions to the data on theoretical metallurgy. XIII. High temperature heat content, heat capacity and entropy data for elements and inorganic compounds US Bur Mines Bull 548: 232 p
Haas JL Jr, Fisher JR (1976) Simultaneous evaluation and correlation of thermodynamic data. American Journal of Science 276:525-545
Berman, R. G. (1988). Internally-consistent thermodynamic data for minerals in the system Na2O-K2O-CaO-MgO-FeO-Fe2O3-Al2O3-SiO2-TiO2-H2O-CO2. Journal of petrology, 29(2), 445-522.
Berman RG, Brown TH (1985) Heat Capacities of minerals in the system Na2O-K2O-CaO-MgO-FeO-Fe2O3-Al2O3-SiO2-TiO2-H2O-CO2: Representation, estimation, and high temperature extrapolation. Contrib Mineral Petrol 89:168-183
Holland, T. and Powell, R., 2011. An improved and extended internally consistent thermodynamic dataset for phases of petrological interest, involving a new equation of state for solids. Journal of Metamorphic Geology. 29, 333–383.
Holland, T.J.B. and Powell, R., 1998. An internally-consistent thermodynamic dataset for phases of petrological interest. Journal of Metamorphic Geology, 16, 309–344.
Zimmer, K., Zhang, Y.L., Lu, P., Chen, Y.Y., Zhang, G.R., Dalkilic, M. and Zhu, C. (2016) SUPCRTBL: A revised and extended thermodynamic dataset and software package of SUPCRT92. Computer and Geosciences 90:97-111

kwargs

__calc__(**kwargs)[source]

heatcapusgscal(TC, P, species)[source]

This function evaluates Gibbs energy and heat capacity as a function of temperature and pressure for any mineral or gas specie using Haas and Fisher (1976)’s heat capacity parameter fit (utilized for solid-solutions)

Parameters:

TC (float, vector) – Temperature [°C]
P (float, vector) – Pressure [bar]
species (array) – Properties such as [dG [cal/ml], dH [cal/mol], S [cal/mol-K], V [cm³/mol], a [cal/mol-K], b [cal/mol/K^2], c [cal/mol/K], g [cal/mol/K^0.5], f [cal/mol/K^3] )

Returns:

delGfPT (float, vector) – Gibbs Energy [cal/mol]
delCp (float, vector) – Heat capacity [cal/mol/K]

References

Haas JL Jr, Fisher JR (1976) Simultaneous evaluation and correlation of thermodynamic data. American Journal of Science 276:525-545

heatcap_Berman(TC, P, species)[source]

This function evaluates Gibbs energy and heat capacity as a function of temperature and pressure for any mineral or gas specie using Berman (1988) equations and datasets with Berman and Brown (1985)’s heat capacity parameter fit

Parameters:

TC (float, vector) – Temperature [°C]
P (float, vector) – Pressure [bar]
species (array) –

Properties such as [dG [J/mol], dH [J/mol], S [J/mol-K], V [cm³/mol], k0, k1, k2, k3,
v1 [*10^5 K^-1], v2 [*10^5 K^-2], v3 [*10^5 bar^-1], v4 [*10^8 bar^-2], dTdP [K/bar], Tlambda [K], Tref [K], l1 [(J/mol)^0.5/K], l2 [(J/mol)^0.5/K^2], DtH, d0 [J/mol], d1 [J/mol], d2 [J/mol], d3 [J/mol], d4 [J/mol], d5 [J/mol], Tmin [K], Tmax [K]]

Returns:

delGfPT (float, vector) – Gibbs Energy [cal/mol]
delCp (float, vector) – Heat capacity [cal/mol/K]

References

Berman, R. G. (1988). Internally-consistent thermodynamic data for minerals in the system Na2O-K2O-CaO-MgO-FeO-Fe2O3-Al2O3-SiO2-TiO2-H2O-CO2. Journal of petrology, 29(2), 445-522.
Berman RG, Brown TH (1985) Heat Capacities of minerals in the system Na2O-K2O-CaO-MgO-FeO-Fe2O3-Al2O3-SiO2-TiO2-H2O-CO2: Representation, estimation, and high temperature extrapolation. Contrib Mineral Petrol 89:168-183

heatcapsup(TC, P, species, **kwargs)[source]

This function evaluates Gibbs energy and heat capacity as a function of temperature and pressure for any mineral or gas specie using Helgeson et al (1978) equations and Maier-Kelley power function for heat capacity as implemented in SUPCRT92

Parameters:

TC (float, vector) – Temperature [°C]
P (float, vector) – Pressure [bar]
species (array) –

Properties such as ( dG [cal/mol], dH [cal/mol], S [cal/mol-K], V [cm³/mol], a [cal/mol-K],
b [*10^3 cal/mol/K^2], c [*10^-5 cal/mol/K], Ttrans [K], Htr [cal/mol], Vtr [cm³/mol], dPdTtr [bar/K] ), etc
spec_name (string) – species name, optional for all cases except gases, Coesite and Quartz

Returns:

delGfPT (float, vector) – Gibbs Energy [cal/mol]
delCp (float, vector) – Heat capacity [cal/mol/K]

References

Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K.(1978). Summary and critique of the thermodynamic properties of rock-forming minerals.
Kelley K. K (1960) Contributions to the data on theoretical metallurgy. XIII. High temperature heat content, heat capacity and entropy data for elements and inorganic compounds US Bur Mines Bull 548: 232 p

heatcaphp(TC, P, species)[source]

This function evaluates Gibbs energy and heat capacity as a function of temperature and pressure for any mineral or gas specie using Holland and Powell (2011)’s heat capacity parameter fit and database based on SUPCRTBL

Parameters:

TC (float, vector) – Temperature [°C]
P (float, vector) – Pressure [bar]
species (array) –

Properties such as [dG [kJ/mol], dH [kJ/mol], S [J/mol-K], V [J/bar], a [kJ/mol-K],
b [*10^5 kJ/mol/K^2], c [kJ-mol-K], d [kJ/mol/K^0.5], alpha [*10^5 K^-1], kappa0 [kbar], kappa0_d [kbar], kappa0_dd [kbar], n_atom [-], Tc0 [K], Smax [J/mol-K], Vmax [J/bar], dH [KJ/mol], dV [J/bar], W [kJ/mol], Wv [J/bar], n [-], SF [-]]

Returns:

delGfPT (float, vector) – Gibbs Energy [cal/mol]
delCp (float, vector) – Heat capacity [cal/mol/K]

References

Holland, T. and Powell, R., 2011. An improved and extended internally consistent thermodynamic dataset for phases of petrological interest, involving a new equation of state for solids. Journal of Metamorphic Geology. 29, 333–383.
Zimmer, K., Zhang, Y.L., Lu, P., Chen, Y.Y., Zhang, G.R., Dalkilic, M. and Zhu, C. (2016) SUPCRTBL: A revised and extended thermodynamic dataset and software package of SUPCRT92. Computer and Geosciences 90:97-111
Holland, T.J.B. and Powell, R., 1998. An internally-consistent thermodynamic dataset for phases of petrological interest. Journal of Metamorphic Geology, 16, 309–344.

pygcc.species_eos.supcrtaq(TC, P, specieppt, Dielec_method=None, ThermoInUnit='cal', **rhoE)[source]

This function evaluates the Gibbs free energy of aqueous species at T and P using the revised HKF equation of state

Parameters:

TC (float, vector) – Temperature [°C]
P (float, vector) – Pressure [bar]
specieppt (array) – Properties such as (dG [cal/mol], dH [cal/mol], S [cal/mol-K], a1 [10 cal/mol/bar], a2 [*10*-2 cal/mol], a3 [cal-K/mol/bar], a4 [10*-4 cal-K/mol], c1 [cal/mol/K], c2 [10*-4 cal-K/mol], ω [10*-5 cal/mol] )
Dielec_method (string) – specify either ‘FGL97’ or ‘JN91’ or ‘DEW’ as the method to calculate dielectric constant (optional), if not specified default - ‘JN91’
ThermoInUnit (string) – specify either ‘cal’ or ‘KJ’ as the input units for species properties (optional), if not specified default - ‘cal’
rhoE (dict) – dictionary of water properties like density (rho) and dielectric factor (E) (optional)

Returns:

delG – Gibbs energy [cal/mol]

Return type:

float, vector

Usage

The general usage of supcrtaq without the optional arguments is as follows:

Not on steam saturation curve:

delG = supcrtaq(TC, P, specieppt)

where T is temperature in celsius and P is pressure in bar

On steam saturation curve:

delG = supcrtaq(TC, ‘T’, specieppt),

where T is temperature in celsius, followed with a quoted char ‘T’

delG = supcrtaq(P, ‘P’, specieppt),

where P is pressure in bar, followed with a quoted char ‘P’.

Meanwhile, usage with any specific dielectric constant method (‘FGL97’) for condition not on steam saturation curve is as follows. Default method is ‘JN91’

delG = supcrtaq(TC, P, specieppt, Dielec_method = ‘FGL97’)

Examples

>>> from pygcc.pygcc_utils import db_reader
>>> ps = db_reader() # utilizes the default direct-access database, speq21
>>> delG = supcrtaq( 100, 50, ps.dbaccessdic['H2S(aq)'], Dielec_method = 'JN91')
    -9221.81721068
>>> delG = supcrtaq( 100, 50, ps.dbaccessdic['H2S(aq)'], Dielec_method = 'FGL97')
    -9221.6542038

References

Johnson JW, Oelkers EH, Helgeson HC. 1992. SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000°C. Computers & Geosciences 18(7): 899-947. doi: 10.1016/0098-3004(92)90029-Q

pygcc.species_eos

Module Contents

Classes

Functions

Attributes

Usage:

Usage

`pygcc.species_eos`