def read_spc_dict_from_path(dict_path):
"""
Read species dictionary given the dictionary file path
Args:
dict_path (str): the absolute path to species dictionary
Returns:
spc_dict (OrderedDict): an ordered dictionary has all species information
"""
lib = KineticsLibrary()
spc_dict = lib.get_species(dict_path)
return spc_dict
def create_kinetic_lib(path):
"""
Create an empty kinetic library and an empty species dictionary according to the path
Args:
path (str): The non-existing file path to create kinetic libraries and species dictionary
"""
lib_path = os.path.join(path, 'reactions.py')
if os.path.isfile(lib_path):
logging.warn('File %s is already existed, not overwriting.' %
(lib_path))
# Create an empty kinetics library file
lib = KineticsLibrary()
lib.save(lib_path)
dict_path = os.path.join(path, 'dictionary.txt')
with open(dict_path, 'w+'):
pass
def read_kinetic_lib_from_path(lib_path,
kinetic_db,
overwrite=False,
create=False):
"""
Read RMG kinetic library given its file path. The species dictionary should
be included under the same directory.
Args:
lib_path (str): Path to thermo library file
kinetic_db (RMG KineticsDatabase): RMG database object
"""
if not os.path.exists(lib_path) and create:
create_kinetic_lib(os.path.dirname(lib_path))
lib = KineticsLibrary()
kinetic_db.libraries[lib_path] = lib
kinetic_db.library_order.append(lib_path)
logging.info(
'Created kinetics library {1} at {0} ...'.format(
os.path.split(lib_path)[0],
os.path.split(lib_path)[1]), )
elif lib_path not in kinetic_db.library_order or overwrite:
lib = KineticsLibrary()
try:
lib.load(lib_path,
KineticsDatabase().local_context,
KineticsDatabase().global_context)
except:
logging.error('The library file %s is not vaild.' % (lib_path))
else:
lib.label = lib_path
kinetic_db.libraries[lib.label] = lib
kinetic_db.library_order.append(lib.label)
logging.info(
'Loading kinetics library {1} from {0} ...'.format(
os.path.split(lib_path)[0],
os.path.split(lib_path)[1]), )
else:
logging.warning('The library %s has already been loaded' % (lib_path))
species = speciesList[i]
rdkitmol = species.molecule[0].toRDKitMol(removeHs=False)
species.molecule = [Molecule().fromRDKitMol(rdkitmol)]#[0].toAdjacencyList(removeH=False)
print species.molecule[0].toAdjacencyList(removeH = removeH)
if species.thermo:
thermoLibrary.loadEntry(index = i + 1,
label = species.label,
molecule = species.molecule[0].toAdjacencyList(removeH = removeH),
thermo = species.thermo,
shortDesc = species.thermo.comment
)
else:
logging.warning('Species {0} did not contain any thermo data and was omitted from the thermo library.'.format(str(species)))
# load kinetics library entries
kineticsLibrary = KineticsLibrary()
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index = i+1,
item = reaction,
data = reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
kineticsLibrary.checkForDuplicates()
kineticsLibrary.convertDuplicatesToMulti()
# Assign history to all entries
"""
import argparse
import os
from rmgpy.data.kinetics import KineticsLibrary
from rmgpy import settings
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('inputPath', metavar='INPUT', type=str, nargs=1,
help='the input path of the RMG-Java kinetics library directory')
parser.add_argument('libraryName', metavar='OUTPUT', type=str, nargs=1,
help='the libraryName for the RMG-Py format kinetics library')
args = parser.parse_args()
inputPath = args.inputPath[0]
libraryName = args.libraryName[0]
library = KineticsLibrary()
library.loadOld(inputPath)
try:
os.makedirs(os.path.join(settings['database.directory'], 'kinetics', 'libraries', libraryName))
except:
pass
# Save in Py format
library.save(os.path.join(settings['database.directory'], 'kinetics', 'libraries', libraryName, 'reactions.py'))
library.saveDictionary(os.path.join(settings['database.directory'], 'kinetics', 'libraries', libraryName,'dictionary.txt'))
for i in range(len(species_list)):
species = species_list[i]
if species.thermo:
thermo_library.load_entry(
index=i + 1,
label=species.label,
molecule=species.molecule[0].to_adjacency_list(),
thermo=species.thermo,
)
else:
logging.warning(
"""Species {0} did not contain any thermo data and was omitted from the thermo
library.""".format(str(species)))
# load kinetics library entries
kinetics_library = KineticsLibrary(name=name)
kinetics_library.entries = {}
for i in range(len(reaction_list)):
reaction = reaction_list[i]
entry = Entry(
index=i + 1,
label=str(reaction),
item=reaction,
data=reaction.kinetics,
)
try:
entry.long_desc = 'Originally from reaction library: ' + reaction.library + "\n" + reaction.kinetics.comment
except AttributeError:
entry.long_desc = reaction.kinetics.comment
kinetics_library.entries[i + 1] = entry
# load thermo library entries
thermoLibrary = ThermoLibrary()
for i in range(len(speciesList)):
species = speciesList[i]
if species.thermo:
thermoLibrary.loadEntry(index = i + 1,
label = species.label,
molecule = species.molecule[0].toAdjacencyList(),
thermo = species.thermo,
shortDesc = species.thermo.comment
)
else:
logging.warning('Species {0} did not contain any thermo data and was omitted from the thermo library.'.format(str(species)))
# load kinetics library entries
kineticsLibrary = KineticsLibrary()
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index = i+1,
label = str(reaction),
item = reaction,
data = reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
kineticsLibrary.checkForDuplicates()
kineticsLibrary.convertDuplicatesToMulti()
nargs=1,
help='the input path of the RMG-Java kinetics library directory')
parser.add_argument(
'outputPath',
metavar='OUTPUT',
type=str,
nargs=1,
help=
'the libraryname.py output file for the RMG-Py format kinetics library'
)
args = parser.parse_args()
inputPath = args.inputPath[0]
outputPath = args.outputPath[0]
library = KineticsLibrary()
library.loadOld(inputPath)
# Assign history to entries
user = getUsername() # Pulls username from current git repository
#user = '******'.format(name, email) # If not in git repository, then enter user information manually
event = [
time.asctime(), user, 'action',
'{0} imported this entry from the old RMG database.'.format(user)
]
for label, entry in library.entries.iteritems():
entry.history.append(event)
# Save in Py format
library.save(outputPath)
positional arguments:
INPUT the input path of the RMG-Java kinetics library directory
LIBRARYNAME the libraryname for the RMG-Py format kinetics library
"""
import argparse
import os
from rmgpy.data.kinetics import KineticsLibrary
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('inputPath', metavar='INPUT', type=str, nargs=1,
help='the input path of the RMG-Java kinetics library directory')
parser.add_argument('libraryName', metavar='OUTPUT', type=str, nargs=1,
help='the libraryName for the RMG-Py format kinetics library')
args = parser.parse_args()
inputPath = args.inputPath[0]
libraryName = args.libraryName[0]
library = KineticsLibrary()
library.loadOld(inputPath)
# Save in Py format
library.save(os.path.join('input/kinetics/libraries/', libraryName, 'reactions.py'))
library.saveDictionary(os.path.join('input/kinetics/libraries/', libraryName, 'dictionary.txt'))
# load thermo library entries
thermoLibrary = ThermoLibrary(name=name)
for i in range(len(speciesList)):
species = speciesList[i]
if species.thermo:
thermoLibrary.loadEntry(index = i + 1,
label = species.label,
molecule = species.molecule[0].toAdjacencyList(),
thermo = species.thermo,
shortDesc = species.thermo.comment
)
else:
logging.warning('Species {0} did not contain any thermo data and was omitted from the thermo library.'.format(str(species)))
# load kinetics library entries
kineticsLibrary = KineticsLibrary(name=name)
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index = i+1,
label = str(reaction),
item = reaction,
data = reaction.kinetics,
)
try:
entry.longDesc = 'Originally from reaction library: ' + reaction.library + "\n" + reaction.kinetics.comment
except AttributeError:
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i+1] = entry
"""
This script imports an individual RMG-Java kinetics library from a local directory and saves the output
kinetics library py file into a path of the user's choosing. This py file can be added to the
input/kinetics/libraries folder to be used as an RMG-Py kinetics library.
"""
import argparse
import time
from rmgpy.data.kinetics import KineticsLibrary
from importOldDatabase import getUsername
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('inputPath', metavar='INPUT', type=str, nargs=1,
help='the input path of the RMG-Java kinetics library directory')
parser.add_argument('outputPath', metavar='OUTPUT', type=str, nargs=1,
help='the libraryname.py output file for the RMG-Py format kinetics library')
args = parser.parse_args()
inputPath = args.inputPath[0]
outputPath = args.outputPath[0]
library = KineticsLibrary()
library.loadOld(inputPath)
# Save in Py format
library.save(outputPath)
def chemkin_to_kinetic_lib(chem_path,
dict_path,
name,
save_path='',
use_chemkin_names=True):
"""
Convert a CHEMKIN file into a RMG kinetic library given species dictionary
and the library name.
Args:
chem_path (str): The path to the CHEMKIN file
dict_path (str): The path to a species dictionary
name (str): The name of the new library
save_path (str): The path to the saving directory. By default, the library
will be saved to RMG-database repository
use_chemkin_names (bool): Use the original CHEMKIN species name
"""
# Load the reactions from the CHEMKIN FILE
logging.info('Loading CHEMKIN file %s with species dictionary %s' %
(chem_path, dict_path))
_, rxns = load_chemkin_file(chem_path,
dict_path,
use_chemkin_names=use_chemkin_names)
kinetic_lib = KineticsLibrary(name=name)
kinetic_lib.entries = {}
# Create new entries
for i in range(len(rxns)):
rxn = rxns[i]
entry = Entry(
index=i + 1,
label=str(rxn),
item=rxn,
data=rxn.kinetics,
)
try:
entry.long_desc = 'Originally from reaction library: ' + \
rxn.library + "\n" + rxn.kinetics.comment
except AttributeError:
entry.long_desc = rxn.kinetics.comment
kinetic_lib.entries[i + 1] = entry
logging.info('Adding reaction %s in to the kinetic library %s' %
(entry.label, name))
# Check for duplicates and convert them to multiArrhenius / multiPdepArrehenius
kinetic_lib.check_for_duplicates(mark_duplicates=True)
kinetic_lib.convert_duplicates_to_multi()
# Save the library
if not save_path:
save_path = os.path.join(settings['database.directory'], 'kinetics',
'libraries')
try:
os.makedirs(os.path.join(save_path, name))
except:
pass
logging.info('Saving the kinetic library to %s' %
(os.path.join(save_path, name)))
kinetic_lib.save(os.path.join(save_path, name, 'reactions.py'))
kinetic_lib.save_dictionary(os.path.join(save_path, name,
'dictionary.txt'))
] #[0].toAdjacencyList(removeH=False)
print species.molecule[0].toAdjacencyList(removeH=removeH)
if species.thermo:
thermoLibrary.loadEntry(
index=i + 1,
label=species.label,
molecule=species.molecule[0].toAdjacencyList(removeH=removeH),
thermo=species.thermo,
shortDesc=species.thermo.comment)
else:
logging.warning(
'Species {0} did not contain any thermo data and was omitted from the thermo library.'
.format(str(species)))
# load kinetics library entries
kineticsLibrary = KineticsLibrary()
kineticsLibrary.entries = {}
for i in range(len(reactionList)):
reaction = reactionList[i]
entry = Entry(
index=i + 1,
item=reaction,
data=reaction.kinetics,
)
entry.longDesc = reaction.kinetics.comment
kineticsLibrary.entries[i + 1] = entry
kineticsLibrary.checkForDuplicates()
kineticsLibrary.convertDuplicatesToMulti()
# Assign history to all entries