def test_dihedral_ethene(self):
mol = XYZFile("input/ethene.xyz").get_molecule()
c = mol.coordinates.copy()
self.assertAlmostEqual(ic.dihed_cos(c[2], c[0], c[3], c[5])[0], 1.0)
self.assertAlmostEqual(ic.dihed_angle(c[2], c[0], c[3], c[5])[0], 0.0)
for i in xrange(1000):
angle = numpy.random.uniform(-numpy.pi, numpy.pi)
radius = numpy.random.uniform(0, 5*angstrom)
offset = numpy.random.uniform(0, 5*angstrom)
c[5] = [
offset,
-radius*numpy.cos(angle),
radius*numpy.sin(angle),
]
self.assertAlmostEqual(ic.dihed_cos(c[2], c[0], c[3], c[5])[0], numpy.cos(angle))
self.assertAlmostEqual(ic.dihed_angle(c[2], c[0], c[3], c[5])[0], angle)
def cart_to_zmat(self, coordinates):
N = len(self.graph.numbers)
result = numpy.zeros(N, dtype=self.dtype)
for i in xrange(N):
ref0 = self.old_index[i]
rel1 = -1
rel2 = -1
rel3 = -1
distance = 0
angle = 0
dihed = 0
if i > 0:
ref1 = self.get_new_ref([ref0])
distance = numpy.linalg.norm(coordinates[ref0]-coordinates[ref1])
rel1 = i - self.new_index[ref1]
if i > 1:
ref2 = self.get_new_ref([ref0, ref1])
angle, = ic.bend_angle(coordinates[ref0], coordinates[ref1], coordinates[ref2])
rel2 = i - self.new_index[ref2]
if i > 2:
ref3 = self.get_new_ref([ref0, ref1, ref2])
dihed, = ic.dihed_angle(coordinates[ref0], coordinates[ref1], coordinates[ref2], coordinates[ref3])
rel3 = i - self.new_index[ref3]
result[i] = (self.graph.numbers[i], distance, rel1, angle, rel2, dihed, rel3)
return result
def cart_to_zmat(self, coordinates):
"""Convert cartesian coordinates to ZMatrix format
Argument:
coordinates -- Cartesian coordinates (numpy array Nx3)
The coordinates must match with the graph that was used to initialize
the ZMatrixGenerator object.
"""
N = len(self.graph.numbers)
if coordinates.shape != (N, 3):
raise ValueError("The shape of the coordinates must be (%i, 3)" % N)
result = numpy.zeros(N, dtype=self.dtype)
for i in xrange(N):
ref0 = self.old_index[i]
rel1 = -1
rel2 = -1
rel3 = -1
distance = 0
angle = 0
dihed = 0
if i > 0:
ref1 = self._get_new_ref([ref0])
distance = numpy.linalg.norm(coordinates[ref0]-coordinates[ref1])
rel1 = i - self.new_index[ref1]
if i > 1:
ref2 = self._get_new_ref([ref0, ref1])
angle, = ic.bend_angle(coordinates[[ref0, ref1, ref2]])
rel2 = i - self.new_index[ref2]
if i > 2:
ref3 = self._get_new_ref([ref0, ref1, ref2])
dihed, = ic.dihed_angle(coordinates[[ref0, ref1, ref2, ref3]])
rel3 = i - self.new_index[ref3]
result[i] = (self.graph.numbers[i], distance, rel1, angle, rel2, dihed, rel3)
return result
def cart_to_zmat(self, coordinates):
N = len(self.graph.numbers)
result = numpy.zeros(N, dtype=self.dtype)
for i in xrange(N):
ref0 = self.old_index[i]
rel1 = -1
rel2 = -1
rel3 = -1
distance = 0
angle = 0
dihed = 0
if i > 0:
ref1 = self.get_new_ref([ref0])
distance = numpy.linalg.norm(coordinates[ref0] -
coordinates[ref1])
rel1 = i - self.new_index[ref1]
if i > 1:
ref2 = self.get_new_ref([ref0, ref1])
angle, = ic.bend_angle(coordinates[ref0], coordinates[ref1],
coordinates[ref2])
rel2 = i - self.new_index[ref2]
if i > 2:
ref3 = self.get_new_ref([ref0, ref1, ref2])
dihed, = ic.dihed_angle(coordinates[ref0], coordinates[ref1],
coordinates[ref2], coordinates[ref3])
rel3 = i - self.new_index[ref3]
result[i] = (self.graph.numbers[i], distance, rel1, angle, rel2,
dihed, rel3)
return result
def test_dihedral_ethene():
mol = Molecule.from_file("input/ethene.xyz")
c = mol.coordinates.copy()
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] - 1.0) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0]) < 1e-5
for i in xrange(1000):
angle = np.random.uniform(-np.pi, np.pi)
radius = np.random.uniform(0, 5*angstrom)
offset = np.random.uniform(0, 5*angstrom)
c[5] = [
offset,
-radius*np.cos(angle),
-radius*np.sin(angle),
]
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] - np.cos(angle)) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0] - angle) < 1e-5
def test_dihedral_ethene():
mol = Molecule.from_file(context.get_fn("test/ethene.xyz"))
c = mol.coordinates.copy()
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] - 1.0) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0]) < 1e-5
for i in xrange(1000):
angle = np.random.uniform(-np.pi, np.pi)
radius = np.random.uniform(0, 5 * angstrom)
offset = np.random.uniform(0, 5 * angstrom)
c[5] = [
offset,
-radius * np.cos(angle),
-radius * np.sin(angle),
]
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] -
np.cos(angle)) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0] - angle) < 1e-5
def test_dihedral_ethene():
mol = Molecule.from_file(
pkg_resources.resource_filename(__name__, "../data/test/ethene.xyz"))
c = mol.coordinates.copy()
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] - 1.0) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0]) < 1e-5
for i in range(1000):
angle = np.random.uniform(-np.pi, np.pi)
radius = np.random.uniform(0, 5 * angstrom)
offset = np.random.uniform(0, 5 * angstrom)
c[5] = [
offset,
-radius * np.cos(angle),
-radius * np.sin(angle),
]
assert abs(ic.dihed_cos([c[2], c[0], c[3], c[5]])[0] -
np.cos(angle)) < 1e-5
assert abs(ic.dihed_angle([c[2], c[0], c[3], c[5]])[0] - angle) < 1e-5
def get_dihedral_angle(term, system):
dihed = term.get_atoms()
if system.cell.nvec > 0:
d10 = system.pos[dihed[0]] - system.pos[dihed[1]]
d12 = system.pos[dihed[2]] - system.pos[dihed[1]]
d23 = system.pos[dihed[3]] - system.pos[dihed[2]]
system.cell.mic(d10)
system.cell.mic(d12)
system.cell.mic(d23)
return _dihed_angle_low(d10, d12, d23, 0)[0]
else:
rs = np.array([system.pos[j] for j in dihed])
return dihed_angle(rs)[0]
def get_dihedral_angle(term, system):
dihed = term.get_atoms()
if system.cell.nvec>0:
d10 = system.pos[dihed[0]] - system.pos[dihed[1]]
d12 = system.pos[dihed[2]] - system.pos[dihed[1]]
d23 = system.pos[dihed[3]] - system.pos[dihed[2]]
system.cell.mic(d10)
system.cell.mic(d12)
system.cell.mic(d23)
return _dihed_angle_low(d10, d12, d23, 0)[0]
else:
rs = np.array([system.pos[j] for j in dihed])
return dihed_angle(rs)[0]
def init_part_fun(self, nma, partf):
"""See :meth:`tamkin.partf.StatFys.init_part_fun`"""
if nma.periodic:
raise NotImplementedError("Rotors in periodic systems are not supported yet")
self.center = nma.coordinates[self.rot_scan.dihedral[1]]
self.axis = nma.coordinates[self.rot_scan.dihedral[2]] - self.center
self.axis /= numpy.linalg.norm(self.axis)
self.moment, self.reduced_moment = compute_moments(
nma.coordinates, nma.masses3, self.center, self.axis, self.rot_scan.top_indexes
)
if self.large_fixed:
moment = self.moment
else:
moment = self.reduced_moment
from molmod.ic import dihed_angle
self.nma_angle = dihed_angle(nma.coordinates[self.rot_scan.dihedral])[0]
# the energy levels
if self.rot_scan.potential is None:
# free rotor
self.energy_levels = numpy.zeros(self.num_levels, float)
for i in xrange(self.num_levels-1):
index = i/2+1
self.energy_levels[i+1] = index**2/(2*moment)
self.hb = None
self.v_coeffs = None
self.v_ref = 0.0
else:
# hindered rotor
self.hb = HarmonicBasis(self.num_levels, 2*numpy.pi)
angles, energies = self.potential
self.v_coeffs = self.hb.fit_fn(angles, energies, self.dofmax,
self.rotsym, self.even, self.v_threshold)
self.energy_levels = self.hb.solve(moment, self.v_coeffs)
self.energy_levels = self.energy_levels[:self.num_levels]
# the cancelation frequency based on the scan
if self.cancel_freq == 'scan':
force_constant = self.hb.eval_deriv2(numpy.array([self.nma_angle]), self.v_coeffs)[0]
self.cancel_freq = numpy.sqrt(force_constant/moment)/(2*numpy.pi)
# scaling factors
self.freq_scaling = partf.vibrational.freq_scaling
self.zp_scaling = partf.vibrational.zp_scaling
self.classical = partf.vibrational.classical
def cart_to_zmat(self, coordinates):
"""Convert cartesian coordinates to ZMatrix format
Argument:
coordinates -- Cartesian coordinates (numpy array Nx3)
The coordinates must match with the graph that was used to initialize
the ZMatrixGenerator object.
"""
N = len(self.graph.numbers)
if coordinates.shape != (N, 3):
raise ValueError("The shape of the coordinates must be (%i, 3)" %
N)
result = np.zeros(N, dtype=self.dtype)
for i in range(N):
ref0 = self.old_index[i]
rel1 = -1
rel2 = -1
rel3 = -1
distance = 0
angle = 0
dihed = 0
if i > 0:
ref1 = self._get_new_ref([ref0])
distance = np.linalg.norm(coordinates[ref0] -
coordinates[ref1])
rel1 = i - self.new_index[ref1]
if i > 1:
ref2 = self._get_new_ref([ref0, ref1])
angle, = ic.bend_angle(coordinates[[ref0, ref1, ref2]])
rel2 = i - self.new_index[ref2]
if i > 2:
ref3 = self._get_new_ref([ref0, ref1, ref2])
dihed, = ic.dihed_angle(coordinates[[ref0, ref1, ref2, ref3]])
rel3 = i - self.new_index[ref3]
result[i] = (self.graph.numbers[i], distance, rel1, angle, rel2,
dihed, rel3)
return result
def init_part_fun(self, nma, partf):
"""See :meth:`tamkin.partf.StatFys.init_part_fun`"""
if nma.periodic:
raise NotImplementedError(
"Rotors in periodic systems are not supported yet")
self.center = nma.coordinates[self.rot_scan.dihedral[1]]
self.axis = nma.coordinates[self.rot_scan.dihedral[2]] - self.center
self.axis /= np.linalg.norm(self.axis)
self.moment, self.reduced_moment = compute_moments(
nma.coordinates, nma.masses3, self.center, self.axis,
self.rot_scan.top_indexes)
if self.large_fixed:
moment = self.moment
else:
moment = self.reduced_moment
from molmod.ic import dihed_angle
self.nma_angle = dihed_angle(
nma.coordinates[self.rot_scan.dihedral])[0]
# the energy levels
if self.rot_scan.potential is None:
# free rotor
self.energy_levels = np.zeros(self.num_levels, float)
for i in xrange(self.num_levels - 1):
index = i / 2 + 1
self.energy_levels[i + 1] = index**2 / (2 * moment)
self.hb = None
self.v_coeffs = None
self.v_ref = 0.0
else:
# hindered rotor
self.hb = HarmonicBasis(self.num_levels, 2 * np.pi)
angles, energies = self.potential
self.v_coeffs = self.hb.fit_fn(angles, energies, self.dofmax,
self.rotsym, self.even,
self.v_threshold)
self.energy_levels = self.hb.solve(moment, self.v_coeffs)
self.energy_levels = self.energy_levels[:self.num_levels]
# the cancelation frequency based on the scan
if self.hb is None:
if not isinstance(self.cancel_freq, float):
raise ValueError(
'No cancelation frequency was computed for rotor "%s"' %
self.name)
else:
force_constant = self.hb.eval_deriv2(np.array([self.nma_angle]),
self.v_coeffs)[0]
scan_cancel_freq = np.sqrt(force_constant / moment) / (2 * np.pi)
if self.cancel_freq == 'scan':
self.cancel_freq = scan_cancel_freq
elif abs(self.cancel_freq -
scan_cancel_freq) > 0.3 * abs(self.cancel_freq):
print 'WARNING: The cancelation frequency of rotor "%s" obtained with MBH (%.1f cm^-1) deviates a lot from the one derived from the scan (%.1f cm^-1).' % (
self.name, self.cancel_freq /
(lightspeed / centimeter), scan_cancel_freq /
(lightspeed / centimeter))
# print a warning is the cancelation frequency is rather high.
if self.cancel_freq > 500 * (lightspeed / centimeter):
print 'WARNING: the cancelation frequency of rotor "%s" is rather high: %.1f cm^-1.' % (
self.name, self.cancel_freq / (lightspeed / centimeter))
elif self.cancel_freq <= 0:
print 'WARNING: the cancelation frequency of rotor "%s" is negative: %.1f cm^-1.' % (
self.name, self.cancel_freq / (lightspeed / centimeter))
# scaling factors
self.freq_scaling = partf.vibrational.freq_scaling
self.zp_scaling = partf.vibrational.zp_scaling
self.classical = partf.vibrational.classical
def dihedral(self, *atoms):
''' IUPAC sign convention'''
return ic.dihed_angle([self.coordinates[i]
for i in atoms])[0] / units.deg
def dihedral(self, *atoms):
''' IUPAC sign convention'''
return ic.dihed_angle([self.coordinates[i]
for i in atoms])[0] / units.deg
mol = Molecule.from_file(filename)
# setup stuff
mol.set_default_graph()
mol.set_default_symbols()
return mol
if __name__ == "__main__":
# initialize molecule
mol = setup("1IRA_R_B_clean.pdb")
# all bonds of degree 3
for bond in kth_bonds(mol, 3):
# find the coordinates of the bonds
bond_coor = list(map(lambda x: mol.coordinates[x], bond))
# print symbols of bond and bond angle in degrees
to_print = [bond]+symbolify(mol, bond)+[bend_angle(bond_coor)[0]/deg]
pretty(to_print, "\t")
# all bonds of degree 4
for bond in kth_bonds(mol, 4):
# find the coordinates of the bonds
bond_coor = list(map(lambda x: mol.coordinates[x], bond))
# print symbols of bond and dihed angle in degrees
to_print = [bond]+symbolify(mol, bond)+[dihed_angle(bond_coor)[0]/deg]
pretty(to_print, "\t")
def init_dihedral_terms(self, thresshold=20 * deg):
'''
Initialize the dihedral potentials from the local topology. The
dihedral potential will be one of the two following possibilities:
The multiplicity m is determined from the local topology, i.e.
the number of neighbors of the central two atoms in the dihedral
If the equilibrium value of all instances of the torsion are
within `thresshold` of 0 deg or per/2 with per = 180deg/m,
the following potential will be chosen:
0.5*K*(1-cos(m*psi-m*psi0)) with psi0 = 0 or 360/(2*m)
'''
with log.section('VAL', 3, 'Initializing'):
#get all dihedrals
from molmod.ic import dihed_angle, _dihed_angle_low
ffatypes = [
self.system.ffatypes[fid] for fid in self.system.ffatype_ids
]
dihedrals = {}
for dihedral in self.system.iter_dihedrals():
dihedral, types = term_sort_atypes(ffatypes, dihedral,
'dihedral')
if types in dihedrals.keys():
dihedrals[types].append(dihedral)
else:
dihedrals[types] = [dihedral]
#loop over all distinct dihedral types
ncos = 0
for types, diheds in dihedrals.iteritems():
psi0s = np.zeros(len(diheds), float)
ms = np.zeros(len(diheds), float)
for i, dihed in enumerate(diheds):
if self.system.cell.nvec > 0:
d10 = self.system.pos[dihed[0]] - self.system.pos[
dihed[1]]
d12 = self.system.pos[dihed[2]] - self.system.pos[
dihed[1]]
d23 = self.system.pos[dihed[3]] - self.system.pos[
dihed[2]]
self.system.cell.mic(d10)
self.system.cell.mic(d12)
self.system.cell.mic(d23)
psi0s[i] = _dihed_angle_low(d10, d12, d23, 0)[0]
else:
rs = np.array([self.system.pos[j] for j in dihed])
psi0s[i] = dihed_angle(rs)[0]
n1 = len(self.system.neighs1[dihed[1]])
n2 = len(self.system.neighs1[dihed[2]])
ms[i] = get_multiplicity(n1, n2)
nan = False
for m in ms:
if np.isnan(m): nan = True
if nan or None in ms or ms.std() > 1e-3:
ms_string = str(ms)
if nan: ms_string = 'nan'
log.warning('missing dihedral for %s (m is %s)' %
('.'.join(types), ms_string))
continue
m = int(np.round(ms.mean()))
rv = get_restvalue(psi0s, m, thresshold=thresshold, mode=1)
if rv is not None:
#a regular Cosine term is used for the dihedral potential
for dihed in diheds:
term = self.add_term(Cosine, [DihedAngle(*dihed)],
types, ['HC_FC_DIAG'],
['au', 'kjmol', 'deg'])
self.set_params(term.index, rv0=rv, m=m)
ncos += 1
else:
#no dihedral potential could be determine, hence it is ignored
log.warning(
'missing dihedral for %s (could not determine rest value from %s)'
% ('.'.join(types), str(psi0s / deg)))
continue
log.dump('Added %i Cosine dihedral terms' % ncos)
def init_part_fun(self, nma, partf):
"""See :meth:`tamkin.partf.StatFys.init_part_fun`"""
if nma.periodic:
raise NotImplementedError("Rotors in periodic systems are not supported yet")
self.center = nma.coordinates[self.rot_scan.dihedral[1]]
self.axis = nma.coordinates[self.rot_scan.dihedral[2]] - self.center
self.axis /= np.linalg.norm(self.axis)
self.moment, self.reduced_moment = compute_moments(
nma.coordinates, nma.masses3, self.center, self.axis, self.rot_scan.top_indexes
)
if self.large_fixed:
moment = self.moment
else:
moment = self.reduced_moment
from molmod.ic import dihed_angle
self.nma_angle = dihed_angle(nma.coordinates[self.rot_scan.dihedral])[0]
# the energy levels
if self.rot_scan.potential is None:
# free rotor
self.energy_levels = np.zeros(self.num_levels, float)
for i in xrange(self.num_levels-1):
index = i/2+1
self.energy_levels[i+1] = index**2/(2*moment)
self.hb = None
self.v_coeffs = None
self.v_ref = 0.0
else:
# hindered rotor
self.hb = HarmonicBasis(self.num_levels, 2*np.pi)
angles, energies = self.potential
self.v_coeffs = self.hb.fit_fn(angles, energies, self.dofmax,
self.rotsym, self.even, self.v_threshold)
self.energy_levels = self.hb.solve(moment, self.v_coeffs)
self.energy_levels = self.energy_levels[:self.num_levels]
# the cancelation frequency based on the scan
if self.hb is None:
if not isinstance(self.cancel_freq, float):
raise ValueError('No cancelation frequency was computed for rotor "%s"' % self.name)
else:
force_constant = self.hb.eval_deriv2(np.array([self.nma_angle]), self.v_coeffs)[0]
scan_cancel_freq = np.sqrt(force_constant/moment)/(2*np.pi)
if self.cancel_freq == 'scan':
self.cancel_freq = scan_cancel_freq
elif abs(self.cancel_freq - scan_cancel_freq) > 0.3*abs(self.cancel_freq):
print 'WARNING: The cancelation frequency of rotor "%s" obtained with MBH (%.1f cm^-1) deviates a lot from the one derived from the scan (%.1f cm^-1).' % (
self.name, self.cancel_freq/(lightspeed/centimeter), scan_cancel_freq/(lightspeed/centimeter)
)
# print a warning is the cancelation frequency is rather high.
if self.cancel_freq > 500*(lightspeed/centimeter):
print 'WARNING: the cancelation frequency of rotor "%s" is rather high: %.1f cm^-1.' % (
self.name, self.cancel_freq/(lightspeed/centimeter)
)
elif self.cancel_freq <= 0:
print 'WARNING: the cancelation frequency of rotor "%s" is negative: %.1f cm^-1.' % (
self.name, self.cancel_freq/(lightspeed/centimeter)
)
# scaling factors
self.freq_scaling = partf.vibrational.freq_scaling
self.zp_scaling = partf.vibrational.zp_scaling
self.classical = partf.vibrational.classical