def find_important_reactions(rmg, tolerance):
"""
This function:
- loops over all the species involved in a specific reaction
- decides whether the specific reaction is important for the species.
Whenever it is found that a reaction is important for a species, we break
the species loop, and keep the reaction in the model.
Returns:
a list of rxns that can be removed.
"""
global reactions
# run the simulation, creating concentration profiles for each reaction system defined in input.
simdata = simulate_all(rmg)
reduce_reactions = [ReductionReaction(rxn) for rxn in reactions]
"""
Tolerance to decide whether a reaction is unimportant for the formation/destruction of a species
Tolerance is a floating point value between 0 and 1.
A high tolerance means that many reactions will be deemed unimportant, and the reduced model will be drastically
smaller.
A low tolerance means that few reactions will be deemed unimportant, and the reduced model will only differ from the full
model by a few reactions.
"""
CHUNKSIZE = 40
boolean_array = []
for chunk in chunks(reduce_reactions,CHUNKSIZE):
N = len(chunk)
partial_results = list(map_(WorkerWrapper(assess_reaction), chunk, [rmg.reactionSystems] * N, [tolerance] * N, [simdata] * N))
boolean_array.extend(partial_results)
important_rxns = []
for isImport, rxn in zip(boolean_array, reduce_reactions):
logging.debug('Is rxn {rxn} important? {isImport}'.format(**locals()))
if isImport:
important_rxns.append(rxn)
return [rxn.rmg_reaction for rxn in important_rxns]
def find_important_reactions(rmg, tolerance):
"""
This function:
- loops over all the species involved in a specific reaction
- decides whether the specific reaction is important for the species.
Whenever it is found that a reaction is important for a species, we break
the species loop, and keep the reaction in the model.
Returns:
a list of rxns that can be removed.
"""
global reactions
# run the simulation, creating concentration profiles for each reaction system defined in input.
simdata = simulate_all(rmg)
reduce_reactions = [ReductionReaction(rxn) for rxn in reactions]
"""
Tolerance to decide whether a reaction is unimportant for the formation/destruction of a species
Tolerance is a floating point value between 0 and 1.
A high tolerance means that many reactions will be deemed unimportant, and the reduced model will be drastically
smaller.
A low tolerance means that few reactions will be deemed unimportant, and the reduced model will only differ from the full
model by a few reactions.
"""
CHUNKSIZE = 40
boolean_array = []
for chunk in chunks(reduce_reactions, CHUNKSIZE):
N = len(chunk)
partial_results = list(
map_(WorkerWrapper(assess_reaction), chunk,
[rmg.reactionSystems] * N, [tolerance] * N, [simdata] * N))
boolean_array.extend(partial_results)
important_rxns = []
for isImport, rxn in zip(boolean_array, reduce_reactions):
logging.debug('Is rxn {rxn} important? {isImport}'.format(**locals()))
if isImport:
important_rxns.append(rxn)
return [rxn.rmg_reaction for rxn in important_rxns]
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# SCOOP 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with SCOOP. If not, see <http://www.gnu.org/licenses/>.
#
"""
Shows how to develop a program working with or without scoop launched
providing serial map fallback. This example works even if SCOOP isn't
installed.
"""
try:
from scoop.futures import map as map_
except ImportError:
map_ = map
def helloWorld(value):
return "Hello World from Future #{0}".format(value)
if __name__ == "__main__":
returnValues = list(map_(helloWorld, range(16)))
print("\n".join(returnValues))
#
# SCOOP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# SCOOP 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with SCOOP. If not, see <http://www.gnu.org/licenses/>.
#
"""
Shows how to develop a program working with or without scoop launched
providing serial map fallback. This example works even if SCOOP isn't
installed.
"""
try:
from scoop.futures import map as map_
except ImportError:
map_ = map
def helloWorld(value):
return "Hello World from Future #{0}".format(value)
if __name__ == "__main__":
returnValues = list(map_(helloWorld, range(16)))
print("\n".join(returnValues))
