pygcc.read_db

Created on Wed Mar 17 16:02:22 2021

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

Copyright (c) 2020 - 2021, 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/>.

Module Contents

Classes

db_reader

Class to read direct-access and source thermodynamic database

Functions

findcodecs(filename)

Function to find the name of the encoding used to decode or encode any file

Attributes

J_to_cal

pygcc.read_db.J_to_cal = 4.184
pygcc.read_db.findcodecs(filename)[source]

Function to find the name of the encoding used to decode or encode any file

class pygcc.read_db.db_reader(**kwargs)[source]

Class to read direct-access and source thermodynamic database

Parameters:

  • dbaccess (string) – filename and location of the direct-access/sequential-access database, optional, default is speq21

  • dbBerman_dir (string) – filename and location of the Berman mineral database, optional

  • dbHP_dir (string) – filename and location of the supcrtbl mineral and gas database, optional

  • sourcedb (string) – filename of the source database, optional

  • sourcedb – filename of the source database, optional

  • sourceformat (string) – specify the source database format, either ‘GWB’ or ‘EQ36’, optional

  • dbaccessformat (string, optional) – specify the direct-access/sequential-access database format, either ‘speq’ or ‘supcrtbl’, default is ‘speq’

  • sourcedb_codecs (string) – specify the name of the encoding used to decode or encode the sourcedb file, optional

  • dbaccess_codecs (string) – specify the name of the encoding used to decode or encode the dbaccess file, optional

Returns:

  • dbaccessdic (dict) – dictionary of minerals, gases, redox and aqueous species

  • dbaccess (string) – direct-access database file name

  • sourcedic (dict) – dictionary of reaction coefficients and species

  • specielist (list) – list of species segmented into the different categories [element, basis, redox, aqueous, minerals, gases, oxides]

  • speciecat (list) – list of species categories listed in ‘specielist’

  • chargedic (dict) – dictionary of charges of species

  • MWdic (dict) – dictionary of MW of species

  • Mineraltype (dict) – mineral type for minerals

  • fugacity_info (dict) – fugacity information as stored in new tdat database for chi and critical ppts

  • Sptype (dict) – specie types and eq3/6 and revised date info

  • Elemlist (dict) – dictionary of elements and coefficients

Examples

>>> ps = db_reader(sourcedb = './default_db/thermo.com.dat',
                   sourceformat = 'gwb',
                   dbaccess = './default_db/speq21.dat')
>>> ps.sourcedic, ps.dbaccessdic, ps.specielist
kwargs
__calc__(**kwargs)[source]
readAqspecdb()[source]

This function reads direct access thermodynamic database and can add other database sources at the bottom returns all constants of Maier-Kelley power function for minerals and gases (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] ) and

aqueous species (dG [cal/mol], dH [cal/mol], S [cal/mol-K], V [cm3/mol], 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] ) packed into a dbacess dictionary. In addition, the function can read Berman’s mineral 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]). In addition, the function can read supcrtbl’s mineral and gas 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 [-])

Parameters:

  • database (dbHP_dir filename and location of the supcrtbl (Holland and Powell) mineral and gas) –

  • database –

  • database –

Returns:

  • dbaccessdic dictionary of minerals, gases, redox and aqueous species

  • dbaccess dat file name

Usage:

[dbaccessdic, dbname] = readAqspecdb(dbaccess)

readSourceGWBdb()[source]

This function reads source GWB thermodynamic database and reaction coefficients of ‘eh’ and ‘e-’ has been added at the bottom returns all reaction coefficients and species, group species into redox, minerals, gases, oxides and aqueous species :param sourcedb: :type sourcedb: filename of the source database

Returns:

  • sourcedic (dictionary of reaction coefficients and species)

  • specielist (list of species segmented into the different categories) – [element, basis, redox, aqueous, minerals, gases, oxides]

  • speciecat (list of species categories listed in ‘specielist’)

  • chargedic (dictionary of charges of species)

  • MWdic (dictionary of MW of species)

  • Mineraltype (mineral type for minerals)

  • fugacity_info (fugacity information as stored in new tdat database for chi and critical ppts)

Usage:

[sourcedic, specielist, chargedic, MWdic, Mineraltype, fugacity_info, activity_model] = readSourceGWBdb()

readSourceEQ36db()[source]

This function reads source EQ3/6 thermodynamic database and reaction coefficients of ‘eh’ and ‘e-’ has been added at the bottom returns all reaction coefficients and species, group species into basis, auxiliary basis, minerals, gases, liquids and aqueous species :param sourcedb: :type sourcedb: filename of the source database

Returns:

  • sourcedic (dictionary of reaction coefficients and species)

  • specielist (list of species segmented into the different categories) – [element, basis, redox, aqueous, minerals, gases, oxides]

  • speciecat (list of species categories listed in ‘specielist’)

  • chargedic (dictionary of charges of species and DHazero info)

  • MWdic (dictionary of MW of species)

  • Sptype (specie types and eq3/6 and revised date info)

  • Elemlist (dictionary of elements and coefficients)

Usage:

[sourcedic, specielist, chargedic, MWdic, block_info, Elemlist, act_param] = readSourceEQ36db(sourcedb)