def readSorptionDatabase(self):
"""
Read the sorption database
"""
with open('testdata/gwb_sorption_testdata.dat', 'r') as dbfile:
dblist = dbfile.readlines()
# Parse the database
self.sorption_db = gwb_reader.readDatabase(dblist)
def main():
"""
Parse the thermodynamic database and convert the data to
the MOOSE JSON format
Usage: database_converter.py -i filename --format format -o output_name
For help text: database_converter.py --help
"""
# Command-line options
opt = command_line_options()
# Read the entire database file into a list
with open(opt.input, 'r') as dbfile:
dblist = dbfile.readlines()
# Parse data using appropriate reader
if opt.format == 'gwb':
db = gwb_reader.readDatabase(dblist)
elif opt.format == 'eq36':
db = eq36_reader.readDatabase(dblist)
# Combine all of the database data into a single dictionary
database = {}
# Header information
database['Header'] = {}
database['Header']['title'] = 'MOOSE thermodynamic database'
database['Header']['original'] = os.path.abspath(opt.input)
database['Header']['date'] = datetime.datetime.now().strftime(
"%H:%M %d-%m-%Y")
database['Header']['original format'] = db.format
if db.header:
database['Header']['original header'] = db.header
if db.activity_model:
database['Header']['activity model'] = db.activity_model
if db.fugacity_model:
database['Header']['fugacity model'] = db.fugacity_model
database['Header']['temperatures'] = db.temperatures
database['Header']['pressures'] = db.pressures
if db.activity_model == 'debye-huckel':
database['Header']['adh'] = db.adh
database['Header']['bdh'] = db.bdh
database['Header']['bdot'] = db.bdot
if db.neutral_species:
database['Header']['neutral species'] = db.neutral_species
if db.elements:
database['elements'] = db.elements
if db.basis_species:
database['basis species'] = db.basis_species
if db.secondary_species:
database['secondary species'] = db.secondary_species
if db.mineral_species:
database['mineral species'] = db.mineral_species
if db.gas_species:
database['gas species'] = db.gas_species
if db.redox_couples:
database['redox couples'] = db.redox_couples
if db.oxides:
database['oxides'] = db.oxides
if db.sorbing_minerals:
database['sorbing minerals'] = db.sorbing_minerals
if db.surface_species:
database['surface species'] = db.surface_species
# Write out the database to JSON format
with open(opt.output, 'w') as output:
json.dump(database, output, indent=2)
sys.stdout.write("Finished parsing " + opt.input +
". Output written to " + opt.output + "\n")
sys.exit(0)