def test_uio66zrbrick_crossterms():
with log.section('NOSETEST', 2):
# Load input data for a ficticious system of an isolated
# UiO-66 brick
name = 'uio66-zr-brick/system.chk'
fn = context.get_fn(os.path.join('systems', name))
data = load_chk(fn)
system = System(data['numbers'],data['pos'],charges=data['charges'],
ffatypes=data['ffatypes'],bonds=data['bonds'],radii=data['radii'])
system.set_standard_masses()
ai = SecondOrderTaylor('ai', coords=system.pos.copy(),
grad=data['gradient'], hess=data['hessian'])
# Run QuickFF
with tmpdir('test_uio66') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
fn_log = os.path.join(dn, 'quickff.log')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=True,
remove_dysfunctional_cross=True,fn_yaff=fn_yaff,fn_sys=fn_sys,log_file=fn_log))
program.run()
# Check force constants of cross terms and corresponding diagonal terms
print("%50s %15s %15s"%("Basename","Cross FC","Diag FC"))
for term in program.valence.terms:
if not term.is_master(): continue
if term.basename.startswith('Cross'):
fc = program.valence.get_params(term.index, only='fc')
for i in [0,1]:
fc_diag = program.valence.get_params(term.diag_term_indexes[i], only='fc')
print("%50s %15.6f %15.6f %50s" % (term.basename,fc,fc_diag,program.valence.terms[term.diag_term_indexes[i]].basename))
if fc_diag==0.0: assert fc==0.0
def test_detect_bonds_cyclopropene_exceptions():
system = get_system_cyclopropene()
# create system without bonds
system = System(system.numbers, system.pos)
# Add bonds between all hydrogen and carbon atoms (unrealistic but useful for testing)
system.detect_bonds({(1, 6): 8.0 * angstrom})
assert system.nbond == 3 + 4 * 3
def test_iter_matches_guaianolide():
system = System.from_file(context.get_fn('test/guaianolide.xyz'))
system.detect_bonds()
system_ref = System.from_file(context.get_fn('test/guaianolide_framework_ordered.xyz'))
system_ref.detect_bonds()
order = np.array(system.iter_matches(system_ref).next())
np.testing.assert_equal(order, [8, 9, 4, 7, 14, 12, 11, 10, 5, 6, 13, 16, 15, 2, 0, 1, 3])
def test_iter_matches_guaianolide():
system = System.from_file(context.get_fn('test/guaianolide.xyz'))
system.detect_bonds()
system_ref = System.from_file(context.get_fn('test/guaianolide_framework_ordered.xyz'))
system_ref.detect_bonds()
order = np.array(system.iter_matches(system_ref).next())
np.testing.assert_equal(order, [8, 9, 4, 7, 14, 12, 11, 10, 5, 6, 13, 16, 15, 2, 0, 1, 3])
def test_uio66zrbrick_crossterms():
with log.section('NOSETEST', 2):
# Load input data for a ficticious system of an isolated
# UiO-66 brick
with path('quickff.data.systems.uio66-zr-brick', 'system.chk') as fn:
data = load_chk(fn)
system = System(data['numbers'],data['pos'],charges=data['charges'],
ffatypes=data['ffatypes'],bonds=data['bonds'],radii=data['radii'])
system.set_standard_masses()
ai = SecondOrderTaylor('ai', coords=system.pos.copy(),
grad=data['gradient'], hess=data['hessian'])
# Run QuickFF
with tmpdir('test_uio66') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
fn_log = os.path.join(dn, 'quickff.log')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=True,
remove_dysfunctional_cross=True,fn_yaff=fn_yaff,fn_sys=fn_sys,log_file=fn_log))
program.run()
# Check force constants of cross terms and corresponding diagonal terms
print("%50s %15s %15s"%("Basename","Cross FC","Diag FC"))
for term in program.valence.terms:
if not term.is_master(): continue
if term.basename.startswith('Cross'):
fc = program.valence.get_params(term.index, only='fc')
for i in [0,1]:
fc_diag = program.valence.get_params(term.diag_term_indexes[i], only='fc')
print("%50s %15.6f %15.6f %50s" % (term.basename,fc,fc_diag,program.valence.terms[term.diag_term_indexes[i]].basename))
if fc_diag==0.0: assert fc==0.0
def test_CAU13_xylene():
host = System.from_file(pkg_resources.resource_filename(__name__, '../../data/test/CAU_13.chk'))
guest = System.from_file(pkg_resources.resource_filename(__name__, '../../data/test/xylene.chk'))
pars_fn = pkg_resources.resource_filename(__name__, '../../data/test/parameters_CAU-13_xylene.txt')
complex = host.merge(guest)
for tailcorrections in False, True:
# Construct force fields
ff_complex = ForceField.generate(complex, pars_fn, tailcorrections=tailcorrections)
ff_host = ForceField.generate(host, pars_fn, tailcorrections=tailcorrections)
ff_exclude = ForceField.generate(complex, pars_fn, nlow=host.natom, tailcorrections=tailcorrections)
# The nlow keyword is meant to exclude all pair interactions when both
# atomic indices are smaller than nlow
# The energy of this force field should be exactly equal to the energy of
# the entire complex (featuring framework-framework, framework-guest, and
# guest-guest interactions) minus the energy of the framework (featuring
# only framework-framework interactions). Note that this is not what is
# usually considered an interaction energy, because for instance guest-guest
# valence interactions are still included.
e_complex = ff_complex.compute()
e_host = ff_host.compute()
e_exclude = ff_exclude.compute()
# Compare energies part by part
nparts = len(ff_complex.parts)
assert len(ff_host.parts)==nparts
assert len(ff_exclude.parts)==nparts
for ipart in range(nparts):
eref = ff_complex.parts[ipart].energy - ff_host.parts[ipart].energy
ecomp = ff_exclude.parts[ipart].energy
print("%20s %15.9f %15.9f"% (ff_exclude.parts[ipart].name, eref, ecomp))
assert np.abs(eref-ecomp)<1e-10
def test_detect_bonds_water_exceptions():
system = get_system_water32()
# create system without bonds
system = System(system.numbers, system.pos)
# Add bonds between hydrogen atoms (unrealistic but useful for testing)
system.detect_bonds({(1,1): 2.0*angstrom})
assert system.nbond >= 96
def test_iter_matches_nobornane_rhodium():
rules = [
('H', '1'),
('C_H1', '6&=1%1'),
('C_H2', '6&=2%1'),
('C_H3', '6&=3%1'),
('C', '6'), # all remaining carbons
('P', '15'),
('Rh', '45'),
]
system = System.from_file(
pkg_resources.resource_filename(
__name__, '../data/test/rhodium_complex_nobornane.xyz'))
system.detect_bonds()
system.detect_ffatypes(rules)
system_ref = System.from_file(
pkg_resources.resource_filename(__name__,
'../data/test/nobornane.xyz'))
system_ref.detect_bonds()
system_ref.detect_ffatypes(rules)
selected = set(next(system.iter_matches(system_ref)))
reference = set([
77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,
95
])
np.testing.assert_equal(selected, reference)
def test_detect_bonds_cyclopropene_exceptions():
system = get_system_cyclopropene()
# create system without bonds
system = System(system.numbers, system.pos)
# Add bonds between all hydrogen and carbon atoms (unrealistic but useful for testing)
system.detect_bonds({(1,6): 8.0*angstrom})
assert system.nbond == 3+4*3
def test_detect_bonds_water_exceptions():
system = get_system_water32()
# create system without bonds
system = System(system.numbers, system.pos)
# Add bonds between hydrogen atoms (unrealistic but useful for testing)
system.detect_bonds({(1, 1): 2.0 * angstrom})
assert system.nbond >= 96
def test_detect_bonds_glycine():
system = get_system_glycine()
check_detect_bonds(system)
system = System(system.numbers, system.pos)
system.detect_bonds()
assert hasattr(system, 'neighs1')
assert hasattr(system, 'neighs2')
assert hasattr(system, 'neighs3')
def test_iter_matches_single_atom():
system = System.from_file(context.get_fn('test/rhodium_complex_nobornane.xyz'))
system.detect_bonds()
system_ref = System(pos=np.zeros((1, 3), float), numbers = np.array([45]))
system_ref.detect_bonds()
selected = set(system.iter_matches(system_ref).next())
reference = set([28])
np.testing.assert_equal(selected, reference)
def test_detect_bonds_glycine():
system = get_system_glycine()
check_detect_bonds(system)
system = System(system.numbers, system.pos)
system.detect_bonds()
assert hasattr(system, 'neighs1')
assert hasattr(system, 'neighs2')
assert hasattr(system, 'neighs3')
def test_supercell_nobonds():
cellpar = 2.867 * angstrom
sys111 = System(
numbers=np.array([26, 26]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]) * cellpar,
ffatypes=['Fe', 'Fe'],
rvecs=np.identity(3) * cellpar,
)
sys333 = sys111.supercell(3, 3, 3)
def test_supercell_nobonds():
cellpar = 2.867*angstrom
sys111 = System(
numbers=np.array([26, 26]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])*cellpar,
ffatypes=['Fe', 'Fe'],
rvecs=np.identity(3)*cellpar,
)
sys333 = sys111.supercell(3,3,3)
def test_iter_matches_single_atom():
system = System.from_file(
pkg_resources.resource_filename(
__name__, '../data/test/rhodium_complex_nobornane.xyz'))
system.detect_bonds()
system_ref = System(pos=np.zeros((1, 3), float), numbers=np.array([45]))
system_ref.detect_bonds()
selected = set(next(system.iter_matches(system_ref)))
reference = set([28])
np.testing.assert_equal(selected, reference)
def write_chk(input_dict,working_directory='.'):
# collect data and initialize Yaff system
if 'cell' in input_dict.keys() and input_dict['cell'] is not None:
system = System(input_dict['numbers'], input_dict['pos']*angstrom, ffatypes=input_dict['ffatypes'], ffatype_ids=input_dict['ffatype_ids'], rvecs=input_dict['cell']*angstrom)
else:
system = System(input_dict['numbers'], input_dict['pos']*angstrom, ffatypes=input_dict['ffatypes'], ffatype_ids=input_dict['ffatype_ids'])
# determine masses, bonds and ffaypes from ffatype_rules
system.detect_bonds()
system.set_standard_masses()
# write dictionary to MolMod CHK file
system.to_file(posixpath.join(working_directory,'system.chk'))
def test_iter_matches_guaianolide():
system = System.from_file(
pkg_resources.resource_filename(__name__,
'../data/test/guaianolide.xyz'))
system.detect_bonds()
system_ref = System.from_file(
pkg_resources.resource_filename(
__name__, '../data/test/guaianolide_framework_ordered.xyz'))
system_ref.detect_bonds()
order = np.array(next(system.iter_matches(system_ref)))
np.testing.assert_equal(
order, [8, 9, 4, 7, 14, 12, 11, 10, 5, 6, 13, 16, 15, 2, 0, 1, 3])
def test_supercell_dipoles():
cellpar = 2.867*angstrom
sys111 = System(
numbers=np.array([26, 26]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])*cellpar,
ffatypes=['Fe', 'Fe'],
dipoles=np.array([[0.1,1.0,2.0],[0.5,0.7,0.9]]),
radii2=np.array([0.0,2.0]),
rvecs=np.identity(3)*cellpar,
)
sys333 = sys111.supercell(3,3,3)
assert (sys333.dipoles == np.tile(np.array([[0.1,1.0,2.0],[0.5,0.7,0.9]]), (27,1))).all()
assert (sys333.radii2 == np.tile(np.array([0.0,2.0]), 27)).all()
def test_supercell_charges():
cellpar = 2.867 * angstrom
sys111 = System(
numbers=np.array([26, 26]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]) * cellpar,
ffatypes=['Fe', 'Fe'],
charges=np.array([0.1, 1.0]),
radii=np.array([0.0, 2.0]),
rvecs=np.identity(3) * cellpar,
)
sys333 = sys111.supercell(3, 3, 3)
assert (sys333.charges == np.tile(np.array([0.1, 1.0]), 27)).all()
assert (sys333.radii == np.tile(np.array([0.0, 2.0]), 27)).all()
def get_yaff_system(self, snapshot=0):
numbers = np.array([
pt[symbol].number
for symbol in self.structure.get_chemical_symbols()
])
if snapshot == 0:
struct = self.structure
else:
struct = self.get_structure(iteration_step=snapshot,
wrap_atoms=False)
pos = struct.positions.reshape(-1, 3) * angstrom
cell = struct.cell
if cell is None:
system = System(numbers,
pos,
ffatypes=self.ffatypes,
ffatype_ids=self.ffatype_ids)
else:
system = System(numbers,
pos,
rvecs=cell * angstrom,
ffatypes=self.ffatypes,
ffatype_ids=self.ffatype_ids)
system.detect_bonds()
system.set_standard_masses()
return system
def test_scopes3():
system = System(numbers=np.array([8, 1, 1, 6, 1, 1, 1, 8, 1]),
pos=np.zeros((9, 3), float),
scopes=['WAT', 'METH'],
scope_ids=np.array([0, 0, 0, 1, 1, 1, 1, 1, 1]),
ffatypes=['O', 'H', 'C', 'H_C', 'H_O'],
ffatype_ids=np.array([0, 1, 1, 2, 3, 3, 3, 0, 4]))
assert (system.scopes == ['WAT', 'METH']).all()
assert (system.scope_ids == np.array([0, 0, 0, 1, 1, 1, 1, 1, 1])).all()
assert (system.ffatypes == ['O', 'H', 'C', 'H_C', 'H_O', 'O']).all()
assert (system.ffatype_ids == np.array([0, 1, 1, 2, 3, 3, 3, 5, 4])).all()
assert system.get_scope(0) == 'WAT'
assert system.get_scope(3) == 'METH'
assert system.get_ffatype(0) == 'O'
assert system.get_ffatype(7) == 'O'
assert system.get_ffatype(8) == 'H_O'
def load_system_xyz(fn):
'''Load atomic numbers, coordinates and cell parameters from fn'''
# Load the cell vectors from the second line.
print 'Loading atomic structure from XYZ file.'
with open(fn) as f:
# Skip one line.
f.next()
# Read rvecs (real-space cell vectors).
real_numbers = []
for word in f.next().split():
try:
real_numbers.append(float(word))
except ValueError:
pass
print 'Detected %i real numbers in title line.' % len(real_numbers)
if len(real_numbers) >= 9:
rvecs = np.array(real_numbers[:9]).reshape(3, 3)*angstrom
print 'Treating system as periodic with the following cell vectors'
print 'in Angstrom. (Cell vectors are displayed as rows.)'
print rvecs/angstrom
else:
print 'I\'m assuming the system is aperiodic because there are less'
print 'than nine real numbers in the title line.'
rvecs = None
# Let Yaff read the rest of the file.
print
return System.from_file(fn, rvecs=rvecs)
def load_chk(self, fn):
"""
Load the atom types, atom type ids and structure by reading a .chk file.
**Arguments**
fn the path to the chk file
"""
system = System.from_file(fn)
system.set_standard_masses()
if len(system.pos.shape) != 2:
raise IOError(
"Something went wrong, positions in CHK file %s should have Nx3 dimensions"
% fn)
if system.cell.rvecs is not None and len(system.cell.rvecs) > 0:
self.structure = Atoms(
positions=system.pos.copy() / angstrom,
numbers=system.numbers,
masses=system.masses,
cell=system.cell.rvecs / angstrom,
pbc=True,
)
else:
self.structure = Atoms(
positions=system.pos.copy() / angstrom,
numbers=system.numbers,
masses=system.masses,
)
if system.ffatypes is not None:
self.ffatypes = system.ffatypes
if system.ffatype_ids is not None:
self.ffatype_ids = system.ffatype_ids
def __init__(self, system, rules=None, cases=None):
self.system = system
self.cases = cases
# Compile the rules if they are present
if cases is None:
if rules is None:
rules = ['!0'] * self.natom
compiled_rules = []
for rule in rules:
if isinstance(rule, str):
rule = atsel_compile(rule)
compiled_rules.append(rule)
self.rules = compiled_rules
self.cases = list(self._iter_cases())
elif rules is not None:
raise ValueError(
'Either rules are cases must be provided, not both.')
# Construct a fake system, a dlist and an iclist for just one ic
self.fake_system = System(numbers=np.zeros(self.natom, int),
pos=np.zeros((self.natom, 3), float),
rvecs=self.system.cell.rvecs)
self.dlist = DeltaList(self.fake_system)
self.iclist = InternalCoordinateList(self.dlist)
self.tangent = np.zeros((self.natom, 3), float)
def load_system_cube(fn):
'''Load system from fn in cube format'''
# TODO: this should be moved into Yaff/MolMod
print 'Loading atomic structure from CUBE file.'
with open(fn) as f:
# Skip two header lines.
f.next()
f.next()
# Read number of atoms.
natom = int(f.next().split()[0])
assert natom > 0
# Read real-space vectors
rvecs = np.zeros((3, 3), float)
for irow in xrange(3):
words = f.next().split()
nrep = int(words[0])
rvecs[irow, 0] = nrep * float(words[1])
rvecs[irow, 1] = nrep * float(words[2])
rvecs[irow, 2] = nrep * float(words[3])
print 'Treating system as periodic with the following cell vectors'
print 'in Angstrom. (Cell vectors are displayed as rows.)'
print rvecs / angstrom
# Read atomic numbers and coordinates
numbers = np.zeros(natom, int)
coordinates = np.zeros((natom, 3), float)
for iatom in xrange(natom):
words = f.next().split()
numbers[iatom] = int(words[0])
coordinates[iatom, 0] = float(words[2])
coordinates[iatom, 1] = float(words[3])
coordinates[iatom, 2] = float(words[4])
print
return System(numbers=numbers, pos=coordinates, rvecs=rvecs)
def load_system_xyz(fn):
'''Load atomic numbers, coordinates and cell parameters from fn'''
# Load the cell vectors from the second line.
print 'Loading atomic structure from XYZ file.'
with open(fn) as f:
# Skip one line.
f.next()
# Read rvecs (real-space cell vectors).
real_numbers = []
for word in f.next().split():
try:
real_numbers.append(float(word))
except ValueError:
pass
print 'Detected %i real numbers in title line.' % len(real_numbers)
if len(real_numbers) >= 9:
rvecs = np.array(real_numbers[:9]).reshape(3, 3) * angstrom
print 'Treating system as periodic with the following cell vectors'
print 'in Angstrom. (Cell vectors are displayed as rows.)'
print rvecs / angstrom
else:
print 'I\'m assuming the system is aperiodic because there are less'
print 'than nine real numbers in the title line.'
rvecs = None
# Let Yaff read the rest of the file.
print
return System.from_file(fn, rvecs=rvecs)
def read_system(name):
# Load system data.
fn = context.get_fn(os.path.join('systems', name))
numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(fn)
# Try to load charges.
charges = None
fns_wpart = glob(os.path.join(os.path.dirname(fn), 'gaussian_mbis.h5'))
if len(fns_wpart) > 0:
with h5.File(fns_wpart[0], 'r') as f:
charges = f['charges'][:]
# Create system object.
system = System(numbers, coords, charges=charges)
system.detect_bonds()
system.set_standard_masses()
# Load ab initio data.
ai = SecondOrderTaylor('ai', coords=system.pos.copy(), energy=energy, grad=grad, hess=hess, pbc=pbc)
return system, ai
def test_remove_duplicate_dipoles():
cellpar = 2.867*angstrom
system1 = System(
numbers=np.array([26, 27]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]])*cellpar,
ffatypes=['A', 'B'],
dipoles=np.array([[0.1,1.0,2.0],[0.5,0.7,0.9]]),
radii2=np.array([0.0,2.0]),
rvecs=np.identity(3)*cellpar,
)
system2 = system1.supercell(1, 2, 1)
system2.cell = system1.cell
system3 = system2.remove_duplicate()
for j, number in enumerate([26, 27]):
#By removing duplicates, atoms might be reordered
i = np.where( system3.numbers == number)[0]
assert system1.radii2[j] == system3.radii2[i]
assert np.all( system1.dipoles[j] == system3.dipoles[i] )
def test_remove_duplicate_dipoles():
cellpar = 2.867 * angstrom
system1 = System(
numbers=np.array([26, 27]),
pos=np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]) * cellpar,
ffatypes=['A', 'B'],
dipoles=np.array([[0.1, 1.0, 2.0], [0.5, 0.7, 0.9]]),
radii2=np.array([0.0, 2.0]),
rvecs=np.identity(3) * cellpar,
)
system2 = system1.supercell(1, 2, 1)
system2.cell = system1.cell
system3 = system2.remove_duplicate()
for j, number in enumerate([26, 27]):
#By removing duplicates, atoms might be reordered
i = np.where(system3.numbers == number)[0]
assert system1.radii2[j] == system3.radii2[i]
assert np.all(system1.dipoles[j] == system3.dipoles[i])
def test_xyz():
system0 = get_system_water32()
with tmpdir(__name__, 'test_xyz') as dirname:
system0.to_file('%s/tmp.xyz' % dirname)
system1 = System.from_file('%s/tmp.xyz' % dirname,
rvecs=system0.cell.rvecs,
ffatypes=system0.ffatypes,
ffatype_ids=system0.ffatype_ids)
compare_water32(system0, system1, 1e-10, xyz=True)
def test_hdf5():
system0 = get_system_water32()
with tmpdir(__name__, 'test_hdf5') as dirname:
fn = '%s/tmp.h5' % dirname
system0.to_file(fn)
with h5.File(fn) as f:
assert 'system' in f
system1 = System.from_file(fn)
compare_water32(system0, system1)
def test_scopes3():
system = System(
numbers=np.array([8, 1, 1, 6, 1, 1, 1, 8, 1]),
pos=np.zeros((9, 3), float),
scopes=['WAT', 'METH'],
scope_ids=np.array([0, 0, 0, 1, 1, 1, 1, 1, 1]),
ffatypes=['O', 'H', 'C', 'H_C', 'H_O'],
ffatype_ids=np.array([0, 1, 1, 2, 3, 3, 3, 0, 4])
)
assert (system.scopes == ['WAT', 'METH']).all()
assert (system.scope_ids == np.array([0, 0, 0, 1, 1, 1, 1, 1, 1])).all()
assert (system.ffatypes == ['O', 'H', 'C', 'H_C', 'H_O', 'O']).all()
assert (system.ffatype_ids == np.array([0, 1, 1, 2, 3, 3, 3, 5, 4])).all()
assert system.get_scope(0) == 'WAT'
assert system.get_scope(3) == 'METH'
assert system.get_ffatype(0) == 'O'
assert system.get_ffatype(7) == 'O'
assert system.get_ffatype(8) == 'H_O'
def test_chk():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_chk')
try:
system0.to_file('%s/tmp.chk' % dirname)
system1 = System.from_file('%s/tmp.chk' % dirname)
compare_water32(system0, system1, 1e-10)
finally:
shutil.rmtree(dirname)
def test_xyz():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_xyz')
try:
system0.to_file('%s/tmp.xyz' % dirname)
system1 = System.from_file('%s/tmp.xyz' % dirname, rvecs=system0.cell.rvecs, ffatypes=system0.ffatypes, ffatype_ids=system0.ffatype_ids)
compare_water32(system0, system1, 1e-10, xyz=True)
finally:
shutil.rmtree(dirname)
def test_xyz():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_xyz')
try:
system0.to_file('%s/tmp.xyz' % dirname)
system1 = System.from_file('%s/tmp.xyz' % dirname, rvecs=system0.cell.rvecs, ffatypes=system0.ffatypes, ffatype_ids=system0.ffatype_ids)
compare_water32(system0, system1, 1e-10, xyz=True)
finally:
shutil.rmtree(dirname)
def test_chk():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_chk')
try:
system0.to_file('%s/tmp.chk' % dirname)
system1 = System.from_file('%s/tmp.chk' % dirname)
compare_water32(system0, system1, 1e-10)
finally:
shutil.rmtree(dirname)
def __init__(self, latency=1.0, name="", yaffpara=None, yaffsys=None, yafflog='yaff.log', rcut=18.89726133921252, alpha_scale=3.5, gcut_scale=1.1, skin=0, smooth_ei=False, reci_ei='ewald', pars=None, dopbc=False, threaded=True):
"""Initialises FFYaff and enables a basic Yaff force field.
Args:
yaffpara: File name of the Yaff parameter file
yaffsys: File name of the Yaff system file
yafflog: File name to which Yaff will write some information about the system and the force field
pars: Optional dictionary, giving the parameters needed by the driver.
**kwargs: All keyword arguments that can be provided when generating
a Yaff force field; see constructor of FFArgs in Yaff code
"""
from yaff import System, ForceField, log
import codecs
import locale
import atexit
# a socket to the communication library is created or linked
super(FFYaff, self).__init__(latency, name, pars, dopbc)
# A bit weird to use keyword argument for a required argument, but this
# is also done in the code above.
if yaffpara is None:
raise ValueError("Must provide a Yaff parameter file.")
if yaffsys is None:
raise ValueError("Must provide a Yaff system file.")
self.yaffpara = yaffpara
self.yaffsys = yaffsys
self.rcut = rcut
self.alpha_scale = alpha_scale
self.gcut_scale = gcut_scale
self.skin = skin
self.smooth_ei = smooth_ei
self.reci_ei = reci_ei
self.yafflog = yafflog
# Open log file
logf = open(yafflog, 'w')
# Tell Python to close the file when the script exits
atexit.register(logf.close)
# Redirect Yaff log to file
log._file = codecs.getwriter(locale.getpreferredencoding())(logf)
self.system = System.from_file(self.yaffsys)
self.ff = ForceField.generate(self.system, self.yaffpara, rcut=self.rcut, alpha_scale=self.alpha_scale, gcut_scale=self.gcut_scale, skin=self.skin, smooth_ei=self.smooth_ei, reci_ei=self.reci_ei)
log._active = False
def __init__(self, latency=1.0, name="", threaded=False, yaffpara=None, yaffsys=None, yafflog='yaff.log', rcut=18.89726133921252, alpha_scale=3.5, gcut_scale=1.1, skin=0, smooth_ei=False, reci_ei='ewald', pars=None, dopbc=False):
"""Initialises FFYaff and enables a basic Yaff force field.
Args:
yaffpara: File name of the Yaff parameter file
yaffsys: File name of the Yaff system file
yafflog: File name to which Yaff will write some information about the system and the force field
pars: Optional dictionary, giving the parameters needed by the driver.
**kwargs: All keyword arguments that can be provided when generating
a Yaff force field; see constructor of FFArgs in Yaff code
"""
from yaff import System, ForceField, log
import codecs
import locale
import atexit
# a socket to the communication library is created or linked
super(FFYaff, self).__init__(latency, name, pars, dopbc, threaded=threaded)
# A bit weird to use keyword argument for a required argument, but this
# is also done in the code above.
if yaffpara is None:
raise ValueError("Must provide a Yaff parameter file.")
if yaffsys is None:
raise ValueError("Must provide a Yaff system file.")
self.yaffpara = yaffpara
self.yaffsys = yaffsys
self.rcut = rcut
self.alpha_scale = alpha_scale
self.gcut_scale = gcut_scale
self.skin = skin
self.smooth_ei = smooth_ei
self.reci_ei = reci_ei
self.yafflog = yafflog
# Open log file
logf = open(yafflog, 'w')
# Tell Python to close the file when the script exits
atexit.register(logf.close)
# Redirect Yaff log to file
log._file = codecs.getwriter(locale.getpreferredencoding())(logf)
self.system = System.from_file(self.yaffsys)
self.ff = ForceField.generate(self.system, self.yaffpara, rcut=self.rcut, alpha_scale=self.alpha_scale, gcut_scale=self.gcut_scale, skin=self.skin, smooth_ei=self.smooth_ei, reci_ei=self.reci_ei)
log._active = False
def test_hdf5_assign_ffatypes():
system0 = get_system_water32()
with tmpdir(__name__, 'test_hdf5_assign_ffatypes') as dirname:
system0.ffatypes = ['O', 'H']
system0.ffatype_ids = np.array([0, 1, 1] * 32)
fn = '%s/tmp.h5' % dirname
system0.to_file(fn)
with h5.File(fn) as f:
assert 'system' in f
system1 = System.from_file(fn)
compare_water32(system0, system1)
def test_scopes2():
system = System(numbers=np.array([8, 1, 1, 6, 1, 1, 1, 8, 1]),
pos=np.zeros((9, 3), float),
scopes=['WAT', 'METH'],
scope_ids=np.array([0, 0, 0, 1, 1, 1, 1, 1, 1]),
ffatypes=['O', 'H', 'C', 'H_C', 'O', 'H_O'],
ffatype_ids=np.array([0, 1, 1, 2, 3, 3, 3, 4, 5]))
assert (system.scopes == ['WAT', 'METH']).all()
assert (system.scope_ids == np.array([0, 0, 0, 1, 1, 1, 1, 1, 1])).all()
assert (system.ffatypes == ['O', 'H', 'C', 'H_C', 'O', 'H_O']).all()
assert (system.ffatype_ids == np.array([0, 1, 1, 2, 3, 3, 3, 4, 5])).all()
def test_lammps_ffconversion_mil53():
fn_system = pkg_resources.resource_filename(
__name__, '../../data/test/system_mil53.chk')
fn_pars = pkg_resources.resource_filename(
__name__, '../../data/test/parameters_mil53.txt')
system = System.from_file(fn_system)
with tmpdir(__name__, 'test_lammps_ffconversion_mil53') as dirname:
ff2lammps(system, fn_pars, dirname)
# No test for correctness, just check that output files are present
assert os.path.isfile(os.path.join(dirname, 'lammps.in'))
assert os.path.isfile(os.path.join(dirname, 'lammps.data'))
def test_hdf5():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_hdf5')
try:
fn = '%s/tmp.h5' % dirname
system0.to_file(fn)
with h5.File(fn) as f:
assert 'system' in f
system1 = System.from_file(fn)
compare_water32(system0, system1)
finally:
shutil.rmtree(dirname)
def test_hdf5():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_hdf5')
try:
fn = '%s/tmp.h5' % dirname
system0.to_file(fn)
with h5.File(fn) as f:
assert 'system' in f
system1 = System.from_file(fn)
compare_water32(system0, system1)
finally:
shutil.rmtree(dirname)
def write_chk(input_dict, working_directory='.'):
# collect data and initialize Yaff system
if 'cell' in input_dict.keys() and input_dict['cell'] is not None:
system = System(input_dict['numbers'], input_dict['pos']*angstrom, rvecs=input_dict['cell']*angstrom, ffatypes=input_dict['ffatypes_man'], ffatype_ids=input_dict['ffatype_ids_man'])
else:
system = System(input_dict['numbers'], input_dict['pos']*angstrom, ffatypes=input_dict['ffatypes_man'], ffatype_ids=input_dict['ffatype_ids_man'])
# determine masses, bonds and ffaypes from ffatype_rules
system.detect_bonds()
system.set_standard_masses()
# write dictionnairy to MolMod CHK file
system.to_file(posixpath.join(working_directory,'input.chk'))
# Reload input.chk as dictionairy and add AI input data
d = load_chk(posixpath.join(working_directory,'input.chk'))
assert isinstance(input_dict['aiener'], float), "AI energy not defined in input, use job.read_abintio(...)"
assert isinstance(input_dict['aigrad'], np.ndarray), "AI gradient not defined in input, use job.read_abintio(...)"
assert isinstance(input_dict['aihess'], np.ndarray), "AI hessian not defined in input, use job.read_abintio(...)"
d['energy'] = input_dict['aiener']
d['grad'] = input_dict['aigrad']
d['hess'] = input_dict['aihess']
dump_chk(posixpath.join(working_directory,'input.chk'), d)
def test_exclusion():
def random_rotation(pos):
com = np.average(pos, axis=0)
pos -= com
while True:
V1 = np.random.rand(); V2 = np.random.rand(); S = V1**2 + V2**2;
if S < 1:
break;
theta = np.array([2*np.pi*(2*V1*np.sqrt(1-S)-0.5), 2*np.pi*(2*V2*np.sqrt(1-S)-0.5), np.pi*((1-2*S)/2)])
R_x = np.array([[1, 0, 0],[0, np.cos(theta[0]), -np.sin(theta[0])],[0, np.sin(theta[0]), np.cos(theta[0])]])
R_y = np.array([[np.cos(theta[1]), 0, np.sin(theta[1])],[0, 1, 0],[-np.sin(theta[1]), 0, np.cos(theta[1])]])
R_z = np.array([[np.cos(theta[2]), -np.sin(theta[2]),0],[np.sin(theta[2]), np.cos(theta[2]),0],[0, 0, 1]])
R = np.dot(R_z, np.dot( R_y, R_x ))
pos_new = np.zeros((len(pos), len(pos[0])))
for i, p in enumerate(pos):
pos_new[i] = np.dot(R, np.array(p).T)
return pos_new + com
def get_adsorbate_pos(adsorbate, rvecs):
pos = adsorbate.pos
pos = random_rotation(pos)
pos -= np.average(pos, axis=0)
new_com = np.random.rand()*rvecs[0] + np.random.rand()*rvecs[1] + np.random.rand()*rvecs[2]
return pos + new_com
# Empty framework
system = System.from_file(pkg_resources.resource_filename(__name__, '../../data/test/CAU_13.chk'))
N_system = len(system.pos)
ff_file = pkg_resources.resource_filename(__name__, '../../data/test/parameters_CAU-13_xylene.txt')
ff = ForceField.generate(system, ff_file)
ff.nlist.update()
E_parts = {part.name:part.compute() for part in ff.parts}
ff_new = ForceField.generate(system, ff_file, exclude_frame=True, n_frame=N_system)
ff_new.nlist.update()
E_parts_new = {part.name:part.compute() for part in ff_new.parts}
# Add 4 adsorbates
adsorbate = System.from_file(pkg_resources.resource_filename(__name__, '../../data/test/xylene.chk'))
pos = system.pos
ffatypes = np.append(system.ffatypes, adsorbate.ffatypes)
bonds = system.bonds
numbers = system.numbers
ffatype_ids = system.ffatype_ids
charges = system.charges
masses = system.masses
for i in range(4):
pos = np.append(pos, get_adsorbate_pos(adsorbate,system.cell.rvecs), axis=0)
bonds = np.append(bonds, adsorbate.bonds + N_system + len(adsorbate.pos) * i,axis=0)
numbers = np.append(numbers, adsorbate.numbers, axis=0)
ffatype_ids = np.append(ffatype_ids, adsorbate.ffatype_ids + max(system.ffatype_ids) + 1, axis=0)
charges = np.append(charges, adsorbate.charges, axis=0)
masses = np.append(masses, adsorbate.masses, axis=0)
# Framework with 4 adsorbates
system = System(numbers, pos, ffatypes=ffatypes, ffatype_ids=ffatype_ids, bonds=bonds,\
rvecs = system.cell.rvecs, charges=charges, masses=masses)
ff = ForceField.generate(system, ff_file)
ff_new = ForceField.generate(system, ff_file, exclude_frame=True, n_frame=N_system)
# Test 100 random configurations
for i in range(100):
new_pos = ff.system.pos
for i in range(4):
new_pos[N_system+i*len(adsorbate.pos):N_system+(i+1)*len(adsorbate.pos)] = get_adsorbate_pos(adsorbate,system.cell.rvecs)
ff.update_pos(new_pos)
ff_new.update_pos(new_pos)
ff.nlist.update()
ff_new.nlist.update()
E_parts_rand = {part.name:part.compute() for part in ff.parts}
E_parts_new_rand = {part.name:part.compute() for part in ff_new.parts}
for key, _ in E_parts.items():
assert (E_parts[key]-E_parts_rand[key]) - (E_parts_new[key]-E_parts_new_rand[key]) < 10e-12
self.make_output()
#settings
with log.section('INIT', 2, timer='Initialization'):
settings = Settings(fn_yaff='pars_cov.txt', plot_traj='All', xyz_traj=True)
#load Gaussian Formatted Checkpoint file
fchk = FCHKFile('gaussian.fchk')
numbers = fchk.fields.get('Atomic numbers')
energy = fchk.fields.get('Total Energy')
coords = fchk.fields.get('Current cartesian coordinates').reshape([len(numbers), 3])
grad = fchk.fields.get('Cartesian Gradient').reshape([len(numbers), 3])
hess = fchk.get_hessian().reshape([len(numbers), 3, len(numbers), 3])
#Construct Yaff System file
system = System(numbers, coords)
system.detect_bonds()
system.set_standard_masses()
#Construct a QuickFF SecondOrderTaylor object containing the AI reference
with log.section('INIT', 2, timer='Initialization'):
ai = SecondOrderTaylor('ai', coords=coords, energy=energy, grad=grad, hess=hess)
#define atom types
rules = [
('H', '1 & =1%8'), #hydrogen atom with one oxygen neighbor
('O', '8 & =2%1'), #oxygen atom with two hydrogen neighbors
]
system.detect_ffatypes(rules)
#construct electrostatic force field from HE charges in gaussian_wpart.h5
