def test_gaff(self, smiles):
import foyer
import mbuild as mb
# These tests are smiles strings
cmpd = mb.load(smiles, smiles=True)
ff = commpare.identify_forcefields()['GAFF']
structure = ff.apply(cmpd)
# Enlarge box to avoid cutoff issues
bbox = cmpd.boundingbox
bbox.lengths *= 10
if any(bbox.lengths < 10):
bbox.lengths = [100, 100, 100]
structure.box = [
bbox.lengths[0], bbox.lengths[1], bbox.lengths[2], 90, 90, 90
]
energies = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance': 10,
'ref_energy':
1 / 4.184
})
print(smiles)
print(energies)
print('=' * 20)
def test_small_systems(self):
import foyer
# These tests are gro/top files
path_to_foyer_unit_tests = os.path.join(foyer.__path__[0],
'opls_validation/')
# Walk through each unit test folder, loading energy and print out
unit_dirs = [
folder for folder in os.listdir(path_to_foyer_unit_tests)
if (os.path.isdir(os.path.join(path_to_foyer_unit_tests, folder))
and 'oplsaa.ff' not in folder)
]
for unit_test_dir in unit_dirs:
os.chdir(os.path.join(path_to_foyer_unit_tests, unit_test_dir))
top_file = glob.glob("*.top")[0]
gro_file = glob.glob("*.gro")[0]
structure = pmd.load_file(top_file, xyz=gro_file)
energies = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance':
10,
'ref_energy':
1 / 4.184
})
print(unit_test_dir)
print(energies)
print('=' * 20)
def test_small_systems(self):
import validate
path_to_amb_unit_tests = os.path.join(validate.__path__[0],
'tests/amber/unit_tests')
# Walk through each unit test folder, loading energy and print out
unit_dirs = [
folder for folder in os.listdir(path_to_amb_unit_tests)
if os.path.isdir(os.path.join(path_to_amb_unit_tests, folder))
]
for unit_test_dir in unit_dirs:
print(unit_test_dir)
os.chdir(os.path.join(path_to_amb_unit_tests, unit_test_dir))
# Maybe there's a better way to validate the contents of each
# unit test directory?
prmtop_files = glob.glob("*.prmtop")
crd_files = []
crd_files.extend(glob.glob("*.crd"))
crd_files.extend(glob.glob("*.inpcrd"))
if len(prmtop_files) > 0 and len(crd_files) > 0:
structure = pmd.load_file(prmtop_files[0], xyz=crd_files[0])
energies = commpare.spawn_engine_simulations(
structure,
engines=['openmm', 'gromacs'],
hoomd_kwargs={
'ref_distance': 10,
'ref_energy': 1 / 4.184
})
print(energies)
print('=' * 20)
def test_conversions(self):
# Check to see if we can correctly spawn engine simulations
eth = Alkane(n=10)
cmpd = mb.fill_box(eth, n_compounds=10, box=[10, 10, 10])
ff = foyer.Forcefield(name='oplsaa')
structure = ff.apply(cmpd)
df = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance': 10,
'ref_energy': 1 / 4.184
})
assert df is not None
def test_small_systems(self):
import validate
path_to_gmx_unit_tests = os.path.join(validate.__path__[0],
'tests/gromacs/unit_tests')
# Walk through each unit test folder, loading energy and print out
unit_dirs = [
folder for folder in os.listdir(path_to_gmx_unit_tests)
if os.path.isdir(os.path.join(path_to_gmx_unit_tests, folder))
]
for unit_test_dir in unit_dirs:
print(unit_test_dir)
os.chdir(os.path.join(path_to_gmx_unit_tests, unit_test_dir))
top_file = glob.glob("*.top")[0]
gro_file = glob.glob("*.gro")[0]
structure = pmd.load_file(top_file, xyz=gro_file)
energies = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance':
10,
'ref_energy':
1 / 4.184
})
print(energies)
print('=' * 20)
def test_mbuild_examples(self):
import mbuild as mb
from mbuild.examples import (Alkane, Methane, Ethane, PMPCLayer,
AlkaneMonolayer)
import foyer
for i in range(4, 20):
my_alkane = Alkane(n=i)
ff = foyer.Forcefield(name='oplsaa')
structure = ff.apply(my_alkane)
bbox = my_alkane.boundingbox
bbox.lengths *= 10
if any(bbox.lengths < 10):
bbox.lengths = [100, 100, 100]
structure.box = [
bbox.lengths[0], bbox.lengths[1], bbox.lengths[2], 90, 90, 90
]
structure.combining_rule = 'lorentz'
energies = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance':
10,
'ref_energy':
1 / 4.184
})
print('Alkane, n={}'.format(i))
print(energies)
print('=' * 20)
eth = Ethane()
structure = ff.apply(eth)
bbox = eth.boundingbox
bbox.lengths *= 10
if any(bbox.lengths < 10):
bbox.lengths = [100, 100, 100]
structure.box = [
bbox.lengths[0], bbox.lengths[1], bbox.lengths[2], 90, 90, 90
]
structure.combining_rule = 'lorentz'
energies = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance': 10,
'ref_energy':
1 / 4.184
})
print("Ethane")
print(energies)
print('=' * 20)
methan = Methane()
structure = ff.apply(methan)
bbox = methan.boundingbox
bbox.lengths *= 10
if any(bbox.lengths < 10):
bbox.lengths = [100, 100, 100]
structure.box = [
bbox.lengths[0], bbox.lengths[1], bbox.lengths[2], 90, 90, 90
]
structure.combining_rule = 'lorentz'
energies = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance': 10,
'ref_energy':
1 / 4.184
})
print("Methane")
print(energies)
print('=' * 20)