def __init__(self, name=None, atoms=None, multipoles=('cartesian',2), sym=False):
Multipole.__init__(self, name)
self.sym = sym
self.set_atoms(atoms)
self.set_groups()
self.set_sym_sites()
self.set_multipole_matrix(multipoles)
def macclaurin_test():
# setup the grid
g = Grid(128, 256, rlim=(0, 0.5), zlim=(-0.5, 0.5))
# create a MacLaurin spheriod on the grid
ms = MacLaurinSpheroid(g, 0.25, 0.1)
# plot the density
dens = ms.density()
plt.clf()
plt.imshow(np.transpose(dens),
origin="lower",
interpolation="nearest",
extent=[g.rlim[0], g.rlim[1], g.zlim[0], g.zlim[1]])
ax = plt.gca()
ax.set_aspect("equal")
plt.savefig("dens.png")
# plot the analytic potential
phi_analytic = ms.phi()
plt.clf()
plt.imshow(np.log10(np.abs(np.transpose(phi_analytic))),
origin="lower",
interpolation="nearest",
extent=[g.rlim[0], g.rlim[1], g.zlim[0], g.zlim[1]])
plt.colorbar()
ax = plt.gca()
ax.set_aspect("equal")
plt.savefig("phi_analytic.png")
# compute the multipole expansion and sample the potential
center = (0.0, 0.0)
m = Multipole(g, 12, 2 * g.dr, center=center)
m.compute_expansion(dens)
phi = g.scratch_array()
for i in range(g.nr):
for j in range(g.nz):
phi[i, j] = m.phi(g.r[i], g.z[j])
# plot the potential
plt.clf()
plt.imshow(np.log10(np.abs(np.transpose(phi))),
origin="lower",
interpolation="nearest",
extent=[g.rlim[0], g.rlim[1], g.zlim[0], g.zlim[1]])
plt.colorbar()
ax = plt.gca()
ax.set_aspect("equal")
plt.savefig("phi.png")
def __init__(self, center, count, name=None, ff=None, sym=False):
self.carbon = center
self.oxygen = filter(lambda a: a.element=='O', center.neighbors)[0]
self.hydrogens = filter(lambda a: a.element=='H', center.neighbors)
Multipole.__init__(self, name, ff)
self.atoms = [self.carbon, self.oxygen]
self.name = 'CO_%i' % count
self.carbon.name = 'C%i_CO' % count
self.oxygen.name = 'O%i_CO' % count
if len(self.hydrogens)==1:
self.hydrogens[0].name='H%i_CO' % count
def __init__(self, element=None, coordinates=None, index=None, multipoles=None, representation=None, sym=False):
if multipoles is None: multipoles = {}
self.sym = sym
Multipole.__init__(self, name=element, origin=coordinates, representation=representation)
Atom.__init__(self, index=index, element=element, coordinates=coordinates)
try:
charge = multipoles['charge']
except KeyError:
charge = 0.
center = FFSite(index=index, element=element, coordinates=coordinates, charge=charge, attachment=self)
self.add_site(center)
self.frame = None
def get_dipole_norm(self):
dipole = Multipole.get_dipole(self)
CX = np.zeros(3)
for a in self.nonhydrogens:
CX += a.coordinates - self.center.coordinates
sign = np.sign(np.dot(dipole, CX))
return sign*np.linalg.norm(dipole)
def __init__(self, data):
self.data = data
try:
name = data['name']
except KeyError:
name = None
try:
self.theory = data['theory']
except KeyError:
self.theory = None
try:
representation = data['representation']
except KeyError:
representation = None
try:
sym = data['symmetry']
except KeyError:
sym = False
try:
self.energy = data['energy']
except KeyError:
self.energy = None
try:
atoms = data['atoms']
except KeyError:
atoms = None
try:
self.hybrid_atoms = data['hybridizations']
except KeyError:
self.hybrid_atoms = {}
logger.info('Start assembling %s Molecule\ntheory: %r\nsymmetry: %r\nrepresentation: %r' % (name, self.theory, sym, representation))
Multipole.__init__(self, name=name, representation=representation)
MoleculeWithFrames.__init__(self, name=name, atoms=atoms, sym=sym, framed_atoms=self.hybrid_atoms.keys())
self.set_hybridizations()
self.set_frames_from_sites() # in case extra points are loaded from the file
self.set_sym_sites()
if representation is not None:
self.set_multipole_matrix()
logger.info("Names of equivalent sites: %s" % self.sites_names_eq)
logger.info("Names of non-equivalent sites: %s" % self.sites_names_noneq)
logger.info('%s Molecule is created' % (self.name))
def __init__(self, center, count, name=None, ff=None, sym=False):
self.center = center
self.nonhydrogens = filter(lambda a: a.element!='H', center.neighbors)
self.hydrogens = filter(lambda a: a.element=='H', center.neighbors)
Multipole.__init__(self, name, origin=self.get_origin())
self.atoms = [center] + self.hydrogens
cname = self.center.element
if self.hydrogens:
neighbor_name = 'H'
neighbors = self.hydrogens
else:
neighbor_name = self.nonhydrogens[0].element
neighbors = self.nonhydrogens
if [neighbor_name]*3==[a.element for a in neighbors]:
self.name = cname + neighbor_name + '3_%i' % (count)
self.type = cname + neighbor_name + '3'
self.center.name = '%s%i_%s%s3' % (cname, count, cname, neighbor_name)
elif [neighbor_name]*2==[a.element for a in neighbors]:
self.name = cname + neighbor_name + '2_%i' % (count)
self.type = cname + neighbor_name + '2'
self.center.name = '%s%i_%s%s2'% (cname, count, cname, neighbor_name)
elif [neighbor_name]*1==[a.element for a in neighbors]:
self.name = cname + neighbor_name + '1_%i' % (count)
self.type = cname + neighbor_name + '1'
self.center.name = '%s%i_%s%s1'% (cname, count, cname, neighbor_name)
elif [neighbor_name]*4 == [a.element for a in neighbors]:
self.name = cname + neighbor_name+'4'
self.type = cname + neighbor_name+'4'
self.center.name = cname
else:
raise ValueError('Not a buired group')
for i,a in enumerate(neighbors):
if sym is True:
a.name = neighbor_name + center.name[1:]
else:
a.name = neighbor_name + center.name[1:] + '_' + str(i)