Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update kineticsGroups.py #1

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Update kineticsGroups.py #1

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
38 changes: 19 additions & 19 deletions kineticsGroups.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -311,7 +311,7 @@ def generateKineticsGroupValues(family, database, trainingSetLabels, method):

x, residues, rank, s = numpy.linalg.lstsq(A, b)

# Store the results
# updating and storing the results
family.groups.top[0].data = Arrhenius(
A = (math.exp(x[-3]),kunits),
n = x[-2],
Expand All @@ -337,7 +337,7 @@ def generateKineticsGroupValues(family, database, trainingSetLabels, method):
Ea = entry.data.Ea.value / 1000.
print '%-39s %11.3f %11.3f %11.3f' % (label, logA, n, Ea)
print '--------------------------------------- ----------- ----------- -----------'
for i, group in enumerate(groupList):
for group in enumerate(groupList):
label = group.label
logA = math.log10(group.data.A.value)
n = group.data.n.value
Expand Down Expand Up @@ -389,7 +389,7 @@ def generateKineticsGroupValues(family, database, trainingSetLabels, method):
Ea = (x[-1,2]*1000.,"J/mol"),
T0 = (1,"K"),
)
for i, group in enumerate(groupList):
for group in enumerate(groupList):
group.data = Arrhenius(
A = (math.exp(x[i,0]),kunits),
n = x[i,1],
Expand All @@ -398,23 +398,23 @@ def generateKineticsGroupValues(family, database, trainingSetLabels, method):
)

# Print the results
print '======================================= =========== =========== ==========='
print 'Group log A (SI) n Ea (kJ/mol) '
print '======================================= =========== =========== ==========='
print ('======================================= =========== =========== ===========')
print ('Group log A (SI) n Ea (kJ/mol)')
print ('======================================= =========== =========== ===========')
entry = family.groups.top[0]
label = ', '.join(['%s' % (top.label) for top in family.groups.top])
logA = math.log10(entry.data.A.value)
n = entry.data.n.value
Ea = entry.data.Ea.value / 1000.
print '%-39s %11.3f %11.3f %11.3f' % (label, logA, n, Ea)
print '--------------------------------------- ----------- ----------- -----------'
print ('--------------------------------------- ----------- ----------- -----------')
for i, group in enumerate(groupList):
label = group.label
logA = math.log10(group.data.A.value)
n = group.data.n.value
Ea = group.data.Ea.value / 1000.
print '%-39s %11.3f %11.3f %11.3f' % (label, logA, n, Ea)
print '======================================= =========== =========== ==========='
print ('======================================= =========== =========== ===========')

# Add a note to the history of each changed item indicating that we've generated new group values
changed = False
Expand All @@ -441,7 +441,7 @@ def generateKineticsGroupValues(family, database, trainingSetLabels, method):

return changed

################################################################################
print ('################################################################################')

def evaluateKineticsGroupValues(family, database, testSetLabels, mode, plot):
"""
Expand All @@ -461,7 +461,7 @@ def evaluateKineticsGroupValues(family, database, testSetLabels, mode, plot):
testSetLabels.append(label)
testSetLabels.append('{0}_RMG_Java'.format(label))

print 'Categorizing reactions in test sets for {0}'.format(family.label)
print ('Categorizing reactions in test sets for {0}'.format(family.label))
testSets = createDataSet(testSetLabels, family, database)

# For each entry in each test set, determine the kinetics as predicted by
Expand Down Expand Up @@ -604,11 +604,11 @@ def onpick(event):
reaction, template, entry, kmodel, kdata = testSet[ind]
kunits = 'm^3/(mol*s)' if len(reaction.reactants) == 2 else 's^-1'
print label
print 'template = [%s]' % (', '.join([g.label for g in template]))
print 'entry = %r' % (entry)
print '%s' % (reaction)
print 'k_data = %9.2e %s' % (xdata[ind], kunits)
print 'k_model = %9.2e %s' % (ydata[ind], kunits)
print ('template = [%s]' % (', '.join([g.label for g in template]))
print ('entry = %r' % (entry))
print ('%s' % (reaction))
print ('k_data = %9.2e %s' % (xdata[ind], kunits))
print ('k_model = %9.2e %s' % (ydata[ind], kunits))

connection_id = fig.canvas.mpl_connect('pick_event', onpick)

Expand Down Expand Up @@ -815,12 +815,12 @@ def getFromJava(args):
testSetLabels = ['PrIMe'],
)
except (VerySpecificException, Exception) as e:
print "FAILED on "+family
print "EXCEPTION: "+str(e)
print ("FAILED on "+family)
print ("EXCEPTION: "+str(e))
failures.append(family)
else:
successes.append(family)
print 'COMPLETED making RMG-Java kinetics for:'
print ('COMPLETED making RMG-Java kinetics for:')
for family in successes:
print " "+family
print 'FAILED while making RMG-Java kinetics for:'
Expand Down Expand Up @@ -869,4 +869,4 @@ def getFromJava(args):
break
else:
parser.print_help()
print 'ArgumentError: {0}'.format(e)
print ('ArgumentError: {0}'.format(e))