def kinetics_checkChildParentRelationships(self, family_name):
"""
This test checks that groups' parent-child relationships are correct in the database.
"""
from rmgpy.data.base import Database
originalFamily = self.database.kinetics.families[family_name]
family = Database()
family.entries = originalFamily.groups.entries
for nodeName, childNode in family.entries.iteritems():
#top nodes and product nodes don't have parents by definition, so they get an automatic pass:
if childNode in originalFamily.groups.top or childNode in originalFamily.forwardTemplate.products:
continue
parentNode = childNode.parent
# Check whether the node has proper parents unless it is the top reactant or product node
# The parent should be more general than the child
nose.tools.assert_true(
family.matchNodeToChild(parentNode, childNode),
"In {family} family, group {parent} is not a proper parent of its child {child}."
.format(family=family_name, parent=parentNode, child=nodeName))
#check that parentNodes which are LogicOr do not have an ancestor that is a Group
#If it does, then the childNode must also be a child of the ancestor
if isinstance(parentNode, LogicOr):
ancestorNode = childNode
while ancestorNode not in originalFamily.groups.top and isinstance(
ancestorNode, LogicOr):
ancestorNode = ancestorNode.parent
if isinstance(ancestorNode, Group):
nose.tools.assert_true(
family.matchNodeToChild(ancestorNode, childNode),
"In {family} family, group {ancestor} is not a proper ancestor of its child {child}."
.format(family=family_name,
ancestor=ancestorNode,
child=nodeName))
def kinetics_checkSiblingsForParents(self, family_name):
"""
This test checks that siblings in a tree are not actually parent/child
"""
from rmgpy.data.base import Database
originalFamily = self.database.kinetics.families[family_name]
family = Database()
family.entries = originalFamily.groups.entries
for nodeName, node in family.entries.iteritems():
#Some families also construct a 2-level trees for the products
#(root with all entries down one level) We don't care about this
#tree as it is not used in searching, so we ignore products
if node in originalFamily.forwardTemplate.products: continue
for index, child1 in enumerate(node.children):
for child2 in node.children[index + 1:]:
#Don't check a node against itself
if child1 is child2: continue
nose.tools.assert_false(
family.matchNodeToChild(child1, child2),
"In family {0}, node {1} is written as a sibling of {2}, when it is actually a parent."
.format(family_name, child1, child2))
nose.tools.assert_false(
family.matchNodeToChild(child2, child1),
"In family {0}, node {1} is written as a sibling of {2}, when it is actually a parent."
.format(family_name, child2, child1))
def apply_LSRs(self, delta_atomic_adsoprtion_energies):
self.rmg_spcs = Database().get_species(self.dictionary_filename,
resonance=False)
for species in self.surf.species():
rmg_spcs = self.rmg_spcs[species.name]
self._correct_binding_energy(rmg_spcs,
delta_atomic_adsoprtion_energies,
False)
def kinetics_checkGroupsNonidentical(self, family_name):
"""
This test checks that the groups are non-identical.
"""
from rmgpy.data.base import Database
originalFamily = self.database.kinetics.families[family_name]
family = Database()
family.entries = originalFamily.groups.entries
entriesCopy = copy(family.entries)
for nodeName, nodeGroup in family.entries.iteritems():
del entriesCopy[nodeName]
for nodeNameOther, nodeGroupOther in entriesCopy.iteritems():
nose.tools.assert_false(family.matchNodeToNode(nodeGroup, nodeGroupOther), "Group {group} in {family} family was found to be identical to group {groupOther}".format(group=nodeName, family=family_name, groupOther=nodeNameOther))
def save_pictures(git_path="", species_path="", overwrite=False):
"""
Save a folder full of molecule pictures, needed for the pretty dot files.
Saves them in the results directory, in a subfolder "species_pictures".
Unless you set overwrite=True, it'll leave alone files that are
already there.
"""
dictionary_filename = git_path + "/base/chemkin/species_dictionary.txt"
specs = Database().get_species(dictionary_filename, resonance=False)
images_dir = os.path.join(species_path)
os.makedirs(images_dir, exist_ok=True)
for name, species in specs.items():
filepath = os.path.join(images_dir, name + ".png")
if not overwrite and os.path.exists(filepath):
continue
species.molecule[0].draw(filepath)
self.delEa = delEa
self.A = A
self.n = n
self.Ea_old = Ea_old
self.Ea_new = Ea_new
def setParam(self, A, n, Ea):
self.A = A
self.n = n
self.Ea_old = Ea
def setModEa(self, Ea):
self.Ea_new = Ea
database = Database()
species_dict = database.getSpecies(
'/home/slakman.b/Code/mech_C8_EF_paper/V3/RMG_Dictionary.txt')
reaction_list = []
family_list = ['H_Abstraction', 'intra_H_migration']
with open('/home/slakman.b/Code/mech_C8_EF_paper/V3/chem.inp',
'r') as mech_file:
for line in mech_file:
if line.strip().startswith('REACTIONS'): break
for line in mech_file:
if line.strip().startswith('!'): break
if 'H_Abstraction' in line or 'intra_H_migration' in line:
reaction_list.append(line.strip())
def setUp(self):
"""
A function run before each unit test in this class.
"""
# Set up a dummy database
self.database = Database()
