def test_1(self):
"""
Test post functionality of /tools/chemkin/
"""
chemFile = os.path.join(rmgpy.getPath(),'tools','data','diffmodels','chem1.inp')
dictFile = os.path.join(rmgpy.getPath(),'tools','data','diffmodels','species_dictionary1.txt')
with open(chemFile) as cf, open(dictFile) as df:
response = self.client.post('/tools/chemkin/', {'ChemkinFile': cf, 'DictionaryFile': df})
self.assertEqual(response.status_code, 200)
folder = os.path.join(settings.MEDIA_ROOT,'rmg','tools','chemkin')
# Check if inputs were correctly uploaded
chemInput = os.path.join(folder,'chemkin','chem.inp')
dictInput = os.path.join(folder,'RMG_Dictionary.txt')
self.assertTrue(os.path.isfile(chemInput),'Chemkin file was not uploaded')
self.assertTrue(os.path.isfile(dictInput),'Dictionary file was not uploaded')
# Check if outputs were correctly generated
htmlOutput = os.path.join(folder,'output.html')
self.assertTrue(os.path.isfile(htmlOutput),'HTML Output was not generated')
# Clean up
shutil.rmtree(folder)
def test_1(self):
"""
Test basic functionality of /tools/compare/
"""
chemFile1 = os.path.join(rmgpy.getPath(),'tools','data','diffmodels','chem1.inp')
dictFile1 = os.path.join(rmgpy.getPath(),'tools','data','diffmodels','species_dictionary1.txt')
chemFile2 = os.path.join(rmgpy.getPath(),'tools','data','diffmodels','chem2.inp')
dictFile2 = os.path.join(rmgpy.getPath(),'tools','data','diffmodels','species_dictionary2.txt')
with open(chemFile1) as cf1, open(dictFile1) as df1, open(chemFile2) as cf2, open(dictFile2) as df2:
response = self.client.post('/tools/compare/', {'ChemkinFile1': cf1, 'DictionaryFile1': df1, 'ChemkinFile2': cf2, 'DictionaryFile2': df2})
self.assertEqual(response.status_code, 200)
folder = os.path.join(settings.MEDIA_ROOT,'rmg','tools','compare')
# Check if inputs were correctly uploaded
chemInput1 = os.path.join(folder,'chem1.inp')
dictInput1 = os.path.join(folder,'RMG_Dictionary1.txt')
chemInput2 = os.path.join(folder,'chem2.inp')
dictInput2 = os.path.join(folder,'RMG_Dictionary2.txt')
self.assertTrue(os.path.isfile(chemInput1),'Chemkin file 1 was not uploaded')
self.assertTrue(os.path.isfile(dictInput1),'Dictionary file 1 was not uploaded')
self.assertTrue(os.path.isfile(chemInput2),'Chemkin file was 2 not uploaded')
self.assertTrue(os.path.isfile(dictInput2),'Dictionary file 2 was not uploaded')
# Check if outputs were correctly generated
htmlOutput = os.path.join(folder,'diff.html')
self.assertTrue(os.path.isfile(htmlOutput),'HTML Output was not generated')
shutil.rmtree(folder)
def test_1(self):
"""
Test basic functionality of /tools/flux/
"""
inputFile = os.path.join(rmgpy.getPath(),'tools','data','flux','input.py')
chemFile = os.path.join(rmgpy.getPath(),'tools','data','flux','chemkin','chem.inp')
dictFile = os.path.join(rmgpy.getPath(),'tools','data','flux','chemkin','species_dictionary.txt')
with open(inputFile) as nf, open(chemFile) as cf, open(dictFile) as df:
response = self.client.post('/tools/flux/', {'InputFile': nf, 'ChemkinFile': cf, 'DictionaryFile': df,
'MaxNodes': 50, 'MaxEdges': 50, 'TimeStep': 1.25,
'ConcentrationTolerance': 1e-6, 'SpeciesRateTolerance': 1e-6})
self.assertEqual(response.status_code, 200)
folder = os.path.join(settings.MEDIA_ROOT,'rmg','tools','flux')
# Check if inputs were correctly uploaded
pyInput = os.path.join(folder,'input.py')
chemInput = os.path.join(folder,'chem.inp')
dictInput = os.path.join(folder,'species_dictionary.txt')
self.assertTrue(os.path.isfile(pyInput),'RMG input file was not uploaded')
self.assertTrue(os.path.isfile(chemInput),'Chemkin file was not uploaded')
self.assertTrue(os.path.isfile(dictInput),'Dictionary file was not uploaded')
# Check if outputs were correctly generated
videoOutput = os.path.join(folder,'1','flux_diagram.avi')
species = os.path.join(folder,'species')
self.assertTrue(os.path.isfile(videoOutput),'Video output was not generated')
self.assertTrue(os.path.isdir(species),'Species directory was not generated')
shutil.rmtree(folder)
def test_3(self):
"""
Test basic functionality of /tools/merge_models/
"""
chemFile1 = os.path.join(rmgpy.getPath(), 'tools', 'data',
'diffmodels', 'chem1.inp')
dictFile1 = os.path.join(rmgpy.getPath(), 'tools', 'data',
'diffmodels', 'species_dictionary1.txt')
chemFile2 = os.path.join(rmgpy.getPath(), 'tools', 'data',
'diffmodels', 'chem2.inp')
dictFile2 = os.path.join(rmgpy.getPath(), 'tools', 'data',
'diffmodels', 'species_dictionary2.txt')
with open(chemFile1) as cf1, open(dictFile1) as df1, open(
chemFile2) as cf2, open(dictFile2) as df2:
response = self.client.post(
'/tools/merge_models/', {
'ChemkinFile1': cf1,
'DictionaryFile1': df1,
'ChemkinFile2': cf2,
'DictionaryFile2': df2
})
self.assertEqual(response.status_code, 200)
folder = os.path.join(settings.MEDIA_ROOT, 'rmg', 'tools', 'compare')
# Check if inputs were correctly uploaded
chemInput1 = os.path.join(folder, 'chem1.inp')
dictInput1 = os.path.join(folder, 'RMG_Dictionary1.txt')
chemInput2 = os.path.join(folder, 'chem2.inp')
dictInput2 = os.path.join(folder, 'RMG_Dictionary2.txt')
self.assertTrue(os.path.isfile(chemInput1),
'Chemkin file 1 was not uploaded')
self.assertTrue(os.path.isfile(dictInput1),
'Dictionary file 1 was not uploaded')
self.assertTrue(os.path.isfile(chemInput2),
'Chemkin file was 2 not uploaded')
self.assertTrue(os.path.isfile(dictInput2),
'Dictionary file 2 was not uploaded')
# Check if outputs were correctly generated
chemOutput = os.path.join(folder, 'chem.inp')
dictOutput = os.path.join(folder, 'species_dictionary.txt')
logOutput = os.path.join(folder, 'merging_log.txt')
self.assertTrue(os.path.isfile(chemOutput),
'CHEMKIN file was not generated')
self.assertTrue(os.path.isfile(dictOutput),
'Species dictionary was not generated')
self.assertTrue(os.path.isfile(logOutput),
'Merging log file was not generated')
shutil.rmtree(folder)
def test_1(self):
"""
Test basic functionality of /tools/flux/
"""
inputFile = os.path.join(rmgpy.getPath(), 'tools', 'data', 'flux',
'input_simple.py')
chemFile = os.path.join(rmgpy.getPath(), 'tools', 'data', 'flux',
'chemkin', 'chem.inp')
dictFile = os.path.join(rmgpy.getPath(), 'tools', 'data', 'flux',
'chemkin', 'species_dictionary.txt')
with open(inputFile) as nf, open(chemFile) as cf, open(dictFile) as df:
response = self.client.post(
'/tools/flux/', {
'InputFile': nf,
'ChemkinFile': cf,
'DictionaryFile': df,
'MaxNodes': 50,
'MaxEdges': 50,
'TimeStep': 1.25,
'ConcentrationTolerance': 1e-6,
'SpeciesRateTolerance': 1e-6
})
self.assertEqual(response.status_code, 200)
folder = os.path.join(settings.MEDIA_ROOT, 'rmg', 'tools', 'flux')
# Check if inputs were correctly uploaded
pyInput = os.path.join(folder, 'input.py')
chemInput = os.path.join(folder, 'chem.inp')
dictInput = os.path.join(folder, 'species_dictionary.txt')
self.assertTrue(os.path.isfile(pyInput),
'RMG input file was not uploaded')
self.assertTrue(os.path.isfile(chemInput),
'Chemkin file was not uploaded')
self.assertTrue(os.path.isfile(dictInput),
'Dictionary file was not uploaded')
# Check if outputs were correctly generated
videoOutput = os.path.join(folder, '1', 'flux_diagram.avi')
species = os.path.join(folder, 'species')
self.assertTrue(os.path.isfile(videoOutput),
'Video output was not generated')
self.assertTrue(os.path.isdir(species),
'Species directory was not generated')
shutil.rmtree(folder)
def getGitCommit(self):
import subprocess
from rmgpy import getPath
try:
return subprocess.check_output(['git', 'log',
'--format=%H%n%cd', '-1'],
cwd=getPath()).splitlines()
except:
return '', ''
def createOutput(self):
"""
Generate output html file from the path containing chemkin and dictionary files.
"""
import subprocess
import rmgpy
command = ("python", os.path.join(rmgpy.getPath(), "..", "generateReactions.py"), self.input)
subprocess.check_call(command, cwd=self.path)
def createOutput(self):
"""
Generate output html file from the path containing chemkin and dictionary files.
"""
import subprocess
import rmgpy
command = (
'python',
os.path.join(rmgpy.getPath(), '..', 'generateReactions.py'),
self.input,
)
subprocess.check_call(command, cwd=self.path)
def createOutput(self):
"""
Generate output html file from the path containing chemkin and dictionary files.
"""
import subprocess
import rmgpy
command = ('python',
os.path.realpath(os.path.join(rmgpy.getPath(), '..', 'scripts', 'generateReactions.py')),
self.input,
)
subprocess.check_call(command, cwd=self.path)
def setUp(self): """ A function run before each unit test in this class. """ RMGpy_path = os.path.normpath(os.path.join(getPath(),'..')) fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles') self.mop1 = QMCalculator(software = 'mopac', method = 'pm3', fileStore = fileStore ) self.mop2 = QMCalculator(software = 'mopac', method = 'pm6', ) self.mop3 = QMCalculator(software = 'mopac', method = 'pm7', fileStore = fileStore ) self.mop4 = QMCalculator(software = 'mopac', method = 'pm8', fileStore = fileStore ) self.gauss1 = QMCalculator(software = 'gaussian', method = 'pm3', ) self.gauss2 = QMCalculator(software = 'gaussian', method = 'pm6', fileStore = fileStore ) self.gauss3 = QMCalculator(software = 'gaussian', method = 'pm7', fileStore = fileStore ) self.molpro1 = QMCalculator(software = 'molpro', method = 'mp2', fileStore = fileStore ) self.qmmol1 = QMCalculator(fileStore=fileStore) self.qmmol1.RMG_bin_path = os.path.join(RMGpy_path, 'testing', 'qm', 'bin') self.qmmol2 = QMCalculator(fileStore=fileStore) self.qmmol2.RMG_bin_path = os.path.join(RMGpy_path, 'testing', 'hexadiene', 'input.py')
def test_1(self):
"""
Test post functionality of /tools/chemkin/
"""
chemFile = os.path.join(rmgpy.getPath(), 'tools', 'data', 'diffmodels',
'chem1.inp')
dictFile = os.path.join(rmgpy.getPath(), 'tools', 'data', 'diffmodels',
'species_dictionary1.txt')
with open(chemFile) as cf, open(dictFile) as df:
response = self.client.post('/tools/chemkin/', {
'ChemkinFile': cf,
'DictionaryFile': df
})
self.assertEqual(response.status_code, 200)
folder = os.path.join(settings.MEDIA_ROOT, 'rmg', 'tools', 'chemkin')
# Check if inputs were correctly uploaded
chemInput = os.path.join(folder, 'chemkin', 'chem.inp')
dictInput = os.path.join(folder, 'RMG_Dictionary.txt')
self.assertTrue(os.path.isfile(chemInput),
'Chemkin file was not uploaded')
self.assertTrue(os.path.isfile(dictInput),
'Dictionary file was not uploaded')
# Check if outputs were correctly generated
htmlOutput = os.path.join(folder, 'output.html')
self.assertTrue(os.path.isfile(htmlOutput),
'HTML Output was not generated')
# Clean up
shutil.rmtree(folder)
def setUp(self): """ A function run before each unit test in this class. """ RMGpy_path = os.path.normpath(os.path.join(getPath(),'..')) self.settings1 = QMSettings(software = 'mopac', method = 'pm3', fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles'), scratchDirectory = None, onlyCyclics = False, maxRadicalNumber = 0, ) self.settings2 = QMSettings()
def setUp(self):
"""
A function run before each unit test in this class.
"""
RMGpy_path = os.path.normpath(os.path.join(getPath(),'..'))
self.settings1 = QMSettings(software = 'mopac',
method = 'pm3',
fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles'),
scratchDirectory = None,
onlyCyclics = False,
maxRadicalNumber = 0,
)
self.settings2 = QMSettings()
def setUp(self):
"""
A function run before each unit test in this class.
"""
RMGpy_path = os.path.normpath(os.path.join(getPath(),'..'))
qm = QMCalculator(software = 'gaussian',
method = 'pm6',
fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles'),
scratchDirectory = os.path.join(RMGpy_path, 'testing', 'qm', 'QMscratch'),
)
if not os.path.exists(qm.settings.fileStore):
os.makedirs(qm.settings.fileStore)
self.qmmol1 = GaussianMolPM6(mol1, qm.settings)
def setUp(self):
"""
A function run before each unit test in this class.
"""
RMGpy_path = os.path.normpath(os.path.join(getPath(),'..'))
qm = QMCalculator(software = 'gaussian',
method = 'pm6',
fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles'),
scratchDirectory = os.path.join(RMGpy_path, 'testing', 'qm', 'QMscratch'),
)
if not os.path.exists(qm.settings.fileStore):
os.makedirs(qm.settings.fileStore)
self.qmmol1 = GaussianMolPM6(mol1, qm.settings)
def test_1(self):
"""
Test basic functionality of /tools/populate_reactions/
"""
from rmgpy.chemkin import loadChemkinFile
from rmgpy.rmg.model import ReactionModel
inputFile = os.path.join(rmgpy.getPath(), 'tools', 'data', 'generate',
'input.py')
with open(inputFile) as fp:
response = self.client.post('/tools/populate_reactions/',
{'InputFile': fp})
self.assertEqual(response.status_code, 200)
folder = os.path.join(settings.MEDIA_ROOT, 'rmg', 'tools',
'populateReactions')
# Check if inputs were correctly uploaded
pyInput = os.path.join(folder, 'input.txt')
self.assertTrue(os.path.isfile(pyInput),
'RMG input file was not uploaded')
# Check if outputs were correctly generated
htmlOutput = os.path.join(folder, 'output.html')
chemOutput = os.path.join(folder, 'chemkin', 'chem.inp')
dictOutput = os.path.join(folder, 'chemkin', 'species_dictionary.txt')
self.assertTrue(os.path.isfile(htmlOutput),
'HTML Output was not generated')
self.assertTrue(os.path.isfile(chemOutput),
'CHEMKIN file was not generated')
self.assertTrue(os.path.isfile(dictOutput),
'Species dictionary was not generated')
# Check that the output is not empty
model = ReactionModel()
model.species, model.reactions = loadChemkinFile(
chemOutput, dictOutput)
self.assertTrue(model.species, 'No species were generated')
self.assertTrue(model.reactions, 'No reactions were generated')
shutil.rmtree(folder)
def setUp(self):
"""
A function run before each unit test in this class.
"""
RMGpy_path = os.path.normpath(os.path.join(getPath(), '..'))
qm = QMCalculator(software='mopac',
method='pm7',
fileStore=os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles'),
scratchDirectory=os.path.join(RMGpy_path, 'testing', 'qm', 'QMscratch'),
)
if not os.path.exists(qm.settings.fileStore):
os.makedirs(qm.settings.fileStore)
mol1 = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
self.qmmol1 = MopacMolPM7(mol1, qm.settings)
def setUp(self):
"""
A function run before each unit test in this class.
"""
RMGpy_path = os.path.normpath(os.path.join(getPath(), ".."))
qm = QMCalculator(
software="mopac",
method="pm3",
fileStore=os.path.join(RMGpy_path, "testing", "qm", "QMfiles"),
scratchDirectory=os.path.join(RMGpy_path, "testing", "qm", "QMscratch"),
)
if not os.path.exists(qm.settings.fileStore):
os.makedirs(qm.settings.fileStore)
self.qmmol1 = MopacMolPM3(mol1, qm.settings)
def setUp(self):
"""
A function run before each unit test in this class.
"""
RMGpy_path = os.path.normpath(os.path.join(getPath(), '..'))
qm = QMCalculator(software='mopac',
method='pm7',
fileStore=os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles'),
scratchDirectory=os.path.join(RMGpy_path, 'testing', 'qm', 'QMscratch'),
)
if not os.path.exists(qm.settings.fileStore):
os.makedirs(qm.settings.fileStore)
mol1 = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
self.qmmol1 = MopacMolPM7(mol1, qm.settings)
def setUp(self):
"""
A function run before each unit test in this class.
"""
rmg_path = os.path.normpath(os.path.join(getPath(), '..'))
self.fileStore = os.path.join(rmg_path, 'testing', 'qm', 'QMfiles')
self.mop1 = QMCalculator(software='mopac',
method='pm3',
fileStore=self.fileStore)
self.mop2 = QMCalculator(
software='mopac',
method='pm6',
)
self.mop3 = QMCalculator(software='mopac',
method='pm7',
fileStore=self.fileStore)
self.mop4 = QMCalculator(software='mopac',
method='pm8',
fileStore=self.fileStore)
self.gauss1 = QMCalculator(
software='gaussian',
method='pm3',
)
self.gauss2 = QMCalculator(software='gaussian',
method='pm6',
fileStore=self.fileStore)
self.gauss3 = QMCalculator(software='gaussian',
method='pm7',
fileStore=self.fileStore)
self.molpro1 = QMCalculator(software='molpro',
method='mp2',
fileStore=self.fileStore)
self.qmmol1 = QMCalculator(fileStore=self.fileStore)
self.qmmol2 = QMCalculator(fileStore=self.fileStore)
def test_1(self):
"""
Test basic functionality of /tools/populate_reactions/
"""
from rmgpy.chemkin import loadChemkinFile
from rmgpy.rmg.model import ReactionModel
inputFile = os.path.join(rmgpy.getPath(),'tools','data','generate','input.py')
with open(inputFile) as fp:
response = self.client.post('/tools/populate_reactions/', {'InputFile': fp})
self.assertEqual(response.status_code, 200)
folder = os.path.join(settings.MEDIA_ROOT,'rmg','tools','populateReactions')
# Check if inputs were correctly uploaded
pyInput = os.path.join(folder,'input.txt')
self.assertTrue(os.path.isfile(pyInput),'RMG input file was not uploaded')
# Check if outputs were correctly generated
htmlOutput = os.path.join(folder,'output.html')
chemOutput = os.path.join(folder,'chemkin','chem.inp')
dictOutput = os.path.join(folder,'chemkin','species_dictionary.txt')
self.assertTrue(os.path.isfile(htmlOutput),'HTML Output was not generated')
self.assertTrue(os.path.isfile(chemOutput),'CHEMKIN file was not generated')
self.assertTrue(os.path.isfile(dictOutput),'Species dictionary was not generated')
# Check that the output is not empty
model = ReactionModel()
model.species, model.reactions = loadChemkinFile(chemOutput, dictOutput)
self.assertTrue(model.species,'No species were generated')
self.assertTrue(model.reactions, 'No reactions were generated')
shutil.rmtree(folder)
def setUp(self): """ A function run before each unit test in this class. """ RMGpy_path = os.path.normpath(os.path.join(getPath(),'..')) fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles') if not os.path.exists(fileStore): os.makedirs(fileStore) self.mop1 = QMCalculator(fileStore=fileStore) self.mop1.settings.software = 'mopac' self.mop1.settings.method = 'pm3' self.mop1.settings.onlyCyclics = False self.mop1.settings.maxRadicalNumber = 0 self.mop2 = QMCalculator() self.mop2.settings.software = 'mopac' self.mop2.settings.method = 'pm6' self.mop2.settings.onlyCyclics = False self.mop2.settings.maxRadicalNumber = 0 self.mop3 = QMCalculator(fileStore=fileStore) self.mop3.settings.software = 'mopac' self.mop3.settings.method = 'pm7' self.mop3.settings.onlyCyclics = False self.mop3.settings.maxRadicalNumber = 0 self.mop4 = QMCalculator(fileStore=fileStore) self.mop4.settings.software = 'mopac' self.mop4.settings.method = 'pm8' self.mop4.settings.onlyCyclics = False self.mop4.settings.maxRadicalNumber = 0 self.gauss1 = QMCalculator() self.gauss1.settings.software = 'gaussian' self.gauss1.settings.method = 'pm3' self.gauss1.settings.onlyCyclics = False self.gauss1.settings.maxRadicalNumber = 0 self.gauss2 = QMCalculator(fileStore=fileStore) self.gauss2.settings.software = 'gaussian' self.gauss2.settings.method = 'pm6' self.gauss2.settings.onlyCyclics = False self.gauss2.settings.maxRadicalNumber = 0 self.gauss3 = QMCalculator(fileStore=fileStore) self.gauss3.settings.software = 'gaussian' self.gauss3.settings.method = 'pm7' self.gauss3.settings.onlyCyclics = False self.gauss3.settings.maxRadicalNumber = 0 self.molpro1 = QMCalculator(fileStore=fileStore) self.molpro1.settings.software = 'molpro' self.molpro1.settings.method = 'mp2' self.molpro1.settings.onlyCyclics = False self.molpro1.settings.maxRadicalNumber = 0 self.qmmol1 = QMCalculator(fileStore=fileStore) self.qmmol1.RMG_bin_path = os.path.join(RMGpy_path, 'testing', 'qm', 'bin') self.qmmol2 = QMCalculator(fileStore=fileStore) self.qmmol2.RMG_bin_path = os.path.join(RMGpy_path, 'testing', 'hexadiene', 'input.py')
def setUp(self): """ A function run before each unit test in this class. """ RMGpy_path = os.path.normpath(os.path.join(getPath(),'..')) fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles') if not os.path.exists(fileStore): os.makedirs(fileStore) self.mop1 = QMCalculator(fileStore=fileStore) self.mop1.settings.software = 'mopac' self.mop1.settings.method = 'pm3' self.mop1.settings.onlyCyclics = False self.mop1.settings.maxRadicalNumber = 0 self.mop2 = QMCalculator() self.mop2.settings.software = 'mopac' self.mop2.settings.method = 'pm6' self.mop2.settings.onlyCyclics = False self.mop2.settings.maxRadicalNumber = 0 self.mop3 = QMCalculator(fileStore=fileStore) self.mop3.settings.software = 'mopac' self.mop3.settings.method = 'pm7' self.mop3.settings.onlyCyclics = False self.mop3.settings.maxRadicalNumber = 0 self.mop4 = QMCalculator(fileStore=fileStore) self.mop4.settings.software = 'mopac' self.mop4.settings.method = 'pm8' self.mop4.settings.onlyCyclics = False self.mop4.settings.maxRadicalNumber = 0 self.gauss1 = QMCalculator() self.gauss1.settings.software = 'gaussian' self.gauss1.settings.method = 'pm3' self.gauss1.settings.onlyCyclics = False self.gauss1.settings.maxRadicalNumber = 0 self.gauss2 = QMCalculator(fileStore=fileStore) self.gauss2.settings.software = 'gaussian' self.gauss2.settings.method = 'pm6' self.gauss2.settings.onlyCyclics = False self.gauss2.settings.maxRadicalNumber = 0 self.gauss3 = QMCalculator(fileStore=fileStore) self.gauss3.settings.software = 'gaussian' self.gauss3.settings.method = 'pm7' self.gauss3.settings.onlyCyclics = False self.gauss3.settings.maxRadicalNumber = 0 self.molpro1 = QMCalculator(fileStore=fileStore) self.molpro1.settings.software = 'molpro' self.molpro1.settings.method = 'mp2' self.molpro1.settings.onlyCyclics = False self.molpro1.settings.maxRadicalNumber = 0 self.qmmol1 = QMCalculator(fileStore=fileStore) self.qmmol1.RMG_bin_path = os.path.join(RMGpy_path, 'testing', 'qm', 'bin') self.qmmol2 = QMCalculator(fileStore=fileStore) self.qmmol2.RMG_bin_path = os.path.join(RMGpy_path, 'testing', 'hexadiene', 'input.py')
from rmgpy.qm.main import QMCalculator
from rmgpy.molecule import Molecule
from rmgpy.qm.mopac import MopacMolPM3, MopacMolPM6, MopacMolPM7
mopacEnv = os.getenv('MOPAC_DIR', default="/opt/mopac")
if os.path.exists(os.path.join(mopacEnv , 'MOPAC2012.exe')):
executablePath = os.path.join(mopacEnv , 'MOPAC2012.exe')
elif os.path.exists(os.path.join(mopacEnv , 'MOPAC2009.exe')):
executablePath = os.path.join(mopacEnv , 'MOPAC2009.exe')
else:
executablePath = os.path.join(mopacEnv , '(MOPAC 2009 or 2012)')
qm = QMCalculator()
qm.settings.software = 'mopac'
RMGpy_path = os.path.normpath(os.path.join(getPath(),'..'))
qm.settings.fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles')
qm.settings.scratchDirectory = None
qm.settings.onlyCyclics = False
qm.settings.maxRadicalNumber = 0
mol1 = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
class TestMopacMolPM3(unittest.TestCase):
"""
Contains unit tests for the Geometry class.
"""
@unittest.skipIf(os.path.exists(executablePath)==False, "MOPAC not found. Try resetting your environment variables if you want to use it.")
def setUp(self):
"""
# DEALINGS IN THE SOFTWARE.
#
################################################################################
import os
import unittest
import shutil
from nose.plugins.attrib import attr
from main import RMG
from rmgpy import settings
from rmgpy.data.rmg import RMGDatabase
from rmgpy import getPath
from rmgpy.rmg.model import CoreEdgeReactionModel
###################################################
originalPath = getPath()
@attr('functional')
class TestMain(unittest.TestCase):
@classmethod
def setUpClass(cls):
"""A function that is run ONCE before all unit tests in this class."""
cls.testDir = os.path.join(originalPath, 'rmg', 'test_data', 'mainTest')
cls.outputDir = 'output'
cls.databaseDirectory = settings['database.directory']
cls.seedThermo = os.path.join(cls.databaseDirectory, 'thermo', 'libraries', 'testSeed.py')
cls.seedKinetics = os.path.join(cls.databaseDirectory, 'kinetics', 'libraries', 'testSeed')
cls.seedThermoEdge = os.path.join(cls.databaseDirectory, 'thermo', 'libraries', 'testSeed_edge.py')
cls.seedKineticsEdge = os.path.join(cls.databaseDirectory, 'kinetics', 'libraries', 'testSeed_edge')
# DEALINGS IN THE SOFTWARE.
#
################################################################################
import os
import unittest
import shutil
from main import RMG
from rmgpy import settings
from rmgpy.data.rmg import RMGDatabase
from rmgpy import getPath
from rmgpy.rmg.model import CoreEdgeReactionModel
###################################################
originalPath = getPath()
class TestMain(unittest.TestCase):
@classmethod
def setUpClass(cls):
"""A function that is run ONCE before all unit tests in this class."""
cls.testDir = os.path.join(originalPath, 'rmg', 'test_data', 'mainTest')
cls.outputDir = 'output'
cls.databaseDirectory = settings['database.directory']
cls.seedThermo = os.path.join(cls.databaseDirectory, 'thermo', 'libraries', 'testSeed.py')
cls.seedKinetics = os.path.join(cls.databaseDirectory, 'kinetics', 'libraries', 'testSeed')
cls.seedThermoEdge = os.path.join(cls.databaseDirectory, 'thermo', 'libraries', 'testSeed_edge.py')
cls.seedKineticsEdge = os.path.join(cls.databaseDirectory, 'kinetics', 'libraries', 'testSeed_edge')
from rmgpy.qm.main import QMCalculator
from rmgpy.molecule import Molecule
from rmgpy.qm.gaussian import GaussianMolPM3, GaussianMolPM6
gaussEnv = os.getenv('GAUSS_EXEDIR') or os.getenv('g09root') or os.getenv(
'g03root') or ""
if os.path.exists(os.path.join(gaussEnv, 'g09')):
executablePath = os.path.join(gaussEnv, 'g09')
elif os.path.exists(os.path.join(gaussEnv, 'g03')):
executablePath = os.path.join(gaussEnv, 'g03')
else:
executablePath = os.path.join(gaussEnv, '(g03 or g09)')
qm = QMCalculator()
qm.settings.software = 'gaussian'
RMGpy_path = os.path.normpath(os.path.join(getPath(), '..'))
qm.settings.fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles')
qm.settings.scratchDirectory = None
qm.settings.onlyCyclics = False
qm.settings.maxRadicalNumber = 0
mol1 = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
class TestGaussianMolPM3(unittest.TestCase):
"""
Contains unit tests for the Geometry class.
"""
@unittest.skipIf(
os.path.exists(executablePath) == False,
"Gaussian not found. Try resetting your environment variables if you want to use it."