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_2form8wat_2(self):
filename = "temp.inp"
otherfile = self.fixtures + "/2form8wat_2.fixture"
molecule = fileToMol("tests/2form8wat.pdb")
fragmentation = Fragmentation(molecule)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
fragmentation.setFMOEFPWatersFromLayer(1)
directories = {'share':''}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("3.0")
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
ignoring = False
for i in range(len(fixture)):
if "EFRAG" in generated[i] or "EFRAG" in fixture[i]:
ignoring = True
if ignoring:
if "END" in generated[i] or "END" in fixture[i]:
ignoring = False
if not ignoring:
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
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_2form8wat_2(self):
filename = "temp.inp"
otherfile = self.fixtures + "/2form8wat_2.fixture"
molecule = fileToMol("tests/2form8wat.pdb")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
fragmentation.setFMOEFPWatersFromLayer(1)
directories = {'share': ''}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("3.0")
gamessfmo.setup()
gamessfmo.writeFile(filename)
generated = ReadStringListFromFile(filename)
fixture = ReadStringListFromFile(otherfile)
self.assertEqual(len(generated), len(fixture))
ignoring = False
for i in range(len(fixture)):
if "EFRAG" in generated[i] or "EFRAG" in fixture[i]:
ignoring = True
if ignoring:
if "END" in generated[i] or "END" in fixture[i]:
ignoring = False
if not ignoring:
self.assertEqual(generated[i], fixture[i])
self.delete_file(filename)
def test_water_1(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_1.fixture"
gamessfmo = GamessFMO(self.fragmentation)
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_water_1(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_1.fixture"
molecule = fileToMol("tests/watercluster4.xyz")
fragmentation = Fragmentation(molecule)
directories = {'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_water_1(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_1.fixture"
molecule = fileToMol("tests/watercluster4.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
directories = {'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_water_4(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_4.fixture"
self.fragmentation.beginFragmentation()
self.fragmentation.doFragmentation()
self.fragmentation.finishFragmentation()
gamessfmo = GamessFMO(self.fragmentation)
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)
def test_5ala_2_afo(self):
filename = "temp.inp"
otherfile = self.fixtures + "/5ala_2_afo.fixture"
molecule = fileToMol("tests/5ala.xyz")
fragmentation = Fragmentation(molecule)
fragmentation.setQMBasis('3-21G:6-31G(d)')
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_water_5(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_5.fixture"
molecule = fileToMol("tests/watercluster4.xyz")
fragmentation = Fragmentation(molecule)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share':''}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setActiveAtomsDistance(1.0)
gamessfmo.setBufferMaxDistance(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_water_5(self):
filename = "temp.inp"
otherfile = self.fixtures + "/water_5.fixture"
molecule = fileToMol("tests/watercluster4.xyz")
fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.finishFragmentation()
directories = {'share': ''}
gamessfmo = GamessFMO(fragmentation, directories)
gamessfmo.setCentralFragmentID(1)
gamessfmo.setBoundariesFromString("1.0")
gamessfmo.setActiveAtomsDistance(1.0)
gamessfmo.setBufferMaxDistance(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)