def test_5ala_3_hop(self):
""" Regression test to make sure if only one basis
set is specified we get the correct input file
FMO with HOP
"""
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_3_hop.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule)
fragmentation.setFMOHOPFragmentation()
fragmentation.setQMBasis('3-21G')
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share':'share'}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_5ala_3_hop(self):
""" Correct input for HOP with one basis """
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_3_hop.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
fragmentation.setFMOHOPFragmentation()
fragmentation.setQMBasis('3-21G')
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share': 'share'}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_5ala_1_hop(self):
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_1_hop.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule)
fragmentation.setFMOHOPFragmentation()
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share':'share'}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_5ala_1_hop(self):
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_1_hop.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
fragmentation.setFMOHOPFragmentation()
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share': 'share'}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
for i in range(len(fixture)):
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
