def write_clr(f, atoms):
"""Write extra color and radius code to a CLR-file (for use with AtomEye).
Hit F12 in AtomEye to use.
See: http://mt.seas.upenn.edu/Archive/Graphics/A/
"""
color = None
radius = None
if atoms.has('color'):
color = atoms.get_array('color')
if atoms.has('radius'):
radius = atoms.get_array('radius')
if color is None:
color = np.zeros([len(atoms),3], dtype=float)
for a in atoms:
color[a.index, :] = default_color[a.get_symbol()]
if radius is None:
radius = np.zeros(len(atoms), dtype=float)
for a in atoms:
radius[a.index] = default_radius[a.get_symbol()]
radius.shape = (-1, 1)
if isinstance(f, str):
f = paropen(f, 'w')
for c1, c2, c3, r in np.append(color, radius, axis=1):
f.write('%f %f %f %f\n' % ( c1, c2, c3, r ))
def write_xyz(fileobj, images):
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if not isinstance(images, (list, tuple)):
images = [images]
symbols = images[0].get_chemical_symbols()
natoms = len(symbols)
for atoms in images:
fileobj.write('%d\n' % natoms)
Strcell = "Lattice=\""
for c in atoms.get_cell()[:]:
Strcell += ('%f %f %f ' % (c[0], c[1], c[2]))
fileobj.write(Strcell[:-1] + "\" Properties=species:S:1:pos:R:3\n")
for s, (x, y, z) in zip(symbols, atoms.get_positions()):
fileobj.write('%-2s %22.15f %22.15f %22.15f\n' % (s, x, y, z))
def write_cube(fileobj, atoms, data=None):
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if isinstance(atoms, list):
if len(atoms) > 1:
raise ValueError('Can only write one configuration '
'to a cube file!')
atoms = atoms[0]
if data is None:
data = np.ones((2, 2, 2))
data = np.asarray(data)
if data.dtype == complex:
data = np.abs(data)
fileobj.write('cube file from ase_ext.n')
fileobj.write('OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n')
cell = atoms.get_cell()
shape = np.array(data.shape)
corner = np.zeros(3)
for i in range(3):
if shape[i] % 2 == 1:
shape[i] += 1
corner += cell[i] / shape[i] / Bohr
fileobj.write('%5d%12.6f%12.6f%12.6f\n' %
(len(atoms), corner[0], corner[1], corner[2]))
for i in range(3):
n = data.shape[i]
d = cell[i] / shape[i] / Bohr
fileobj.write('%5d%12.6f%12.6f%12.6f\n' % (n, d[0], d[1], d[2]))
positions = atoms.get_positions() / Bohr
numbers = atoms.get_atomic_numbers()
for Z, (x, y, z) in zip(numbers, positions):
fileobj.write('%5d%12.6f%12.6f%12.6f%12.6f\n' % (Z, 0.0, x, y, z))
data.tofile(fileobj, sep='\n', format='%e')
def write_mol2_charges(fileobj, images):
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if not isinstance(images, (list, tuple)):
images = [images]
symbols = images[0].get_chemical_symbols()
natoms = len(symbols)
for atoms in images:
fileobj.write('%d\n' % natoms)
Strcell = ""
for c in atoms.get_cell()[:]:
Strcell += ('%f %f %f ' % (c[0], c[1], c[2]))
fileobj.write(Strcell + "\n")
for s, (x, y, z), c in zip(symbols, atoms.get_positions(),
atoms.get_charges()):
fileobj.write('%-2s %22.15f %22.15f %22.15f %22.15f\n' %
(s, x, y, z, c))
def write_exciting(fileobj, images):
"""writes exciting input structure in XML
Parameters
----------
fileobj : File object
Filehandle to which data should be written
images : Atom Object or List of Atoms objects
This function will write the first Atoms object to file
Returns
-------
"""
from lxml import etree as ET
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
root = atoms2etree(images)
fileobj.write(ET.tostring(root, method='xml',
pretty_print=True,
xml_declaration=True,
encoding='UTF-8'))
def initialize(self, file=None, initialwannier='random', seed=None):
"""Re-initialize current rotation matrix.
Keywords are identical to those of the constructor.
"""
Nw = self.nwannier
Nb = self.nbands
if file is not None:
self.Z_dknn, self.U_kww, self.C_kul = load(paropen(file))
elif initialwannier == 'bloch':
# Set U and C to pick the lowest Bloch states
self.U_kww = np.zeros((self.Nk, Nw, Nw), complex)
self.C_kul = []
for U, M, L in zip(self.U_kww, self.fixedstates_k, self.edf_k):
U[:] = np.identity(Nw, complex)
if L > 0:
self.C_kul.append(np.identity(Nb - M, complex)[:, :L])
else:
self.C_kul.append([])
elif initialwannier == 'random':
# Set U and C to random (orthogonal) matrices
self.U_kww = np.zeros((self.Nk, Nw, Nw), complex)
self.C_kul = []
for U, M, L in zip(self.U_kww, self.fixedstates_k, self.edf_k):
U[:] = random_orthogonal_matrix(Nw, seed, real=False)
if L > 0:
self.C_kul.append(
random_orthogonal_matrix(Nb - M, seed=seed,
real=False)[:, :L])
else:
self.C_kul.append(np.array([]))
else:
# Use initial guess to determine U and C
self.C_kul, self.U_kww = self.calc.initial_wannier(
initialwannier, self.kptgrid, self.fixedstates_k, self.edf_k,
self.spin)
self.update()
def write_pdb(fileobj, images):
"""Write images to PDB-file."""
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if not isinstance(images, (list, tuple)):
images = [images]
format = 'ATOM %5d %-4s %8.3f%8.3f%8.3f 0.00 0.00\n'
# RasMol complains if the atom index exceeds 100000. There might
# be a limit of 5 digit numbers in this field.
MAXNUM = 100000
symbols = images[0].get_chemical_symbols()
natoms = len(symbols)
for atoms in images:
fileobj.write('MODEL 1\n')
p = atoms.get_positions()
for a in range(natoms):
x, y, z = p[a]
fileobj.write(format % (a % MAXNUM, symbols[a], x, y, z))
fileobj.write('ENDMDL\n')
def __init__(self, name):
self.f = paropen(name + '.csv', 'w')
def write_xsf(fileobj, images, data=None):
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if not isinstance(images, (list, tuple)):
images = [images]
fileobj.write('ANIMSTEPS %d\n' % len(images))
numbers = images[0].get_atomic_numbers()
pbc = images[0].get_pbc()
if pbc[2]:
fileobj.write('CRYSTAL\n')
elif pbc[1]:
fileobj.write('SLAB\n')
elif pbc[0]:
fileobj.write('POLYMER\n')
else:
fileobj.write('MOLECULE\n')
for n, atoms in enumerate(images):
if pbc.any():
fileobj.write('PRIMVEC %d\n' % (n + 1))
cell = atoms.get_cell()
for i in range(3):
fileobj.write(' %.14f %.14f %.14f\n' % tuple(cell[i]))
fileobj.write('PRIMCOORD %d\n' % (n + 1))
# Get the forces if it's not too expensive:
calc = atoms.get_calculator()
if (calc is not None and
(hasattr(calc, 'calculation_required') and
not calc.calculation_required(atoms,
['energy', 'forces', 'stress']))):
forces = atoms.get_forces()
else:
forces = None
pos = atoms.get_positions()
fileobj.write(' %d 1\n' % len(pos))
for a in range(len(pos)):
fileobj.write(' %2d' % numbers[a])
fileobj.write(' %20.14f %20.14f %20.14f' % tuple(pos[a]))
if forces is None:
fileobj.write('\n')
else:
fileobj.write(' %20.14f %20.14f %20.14f\n' % tuple(forces[a]))
if data is None:
return
fileobj.write('BEGIN_BLOCK_DATAGRID_3D\n')
fileobj.write(' data\n')
fileobj.write(' BEGIN_DATAGRID_3Dgrid#1\n')
data = np.asarray(data)
if data.dtype == complex:
data = np.abs(data)
shape = data.shape
fileobj.write(' %d %d %d\n' % shape)
cell = atoms.get_cell()
origin = np.zeros(3)
for i in range(3):
if not pbc[i]:
origin += cell[i] / shape[i]
fileobj.write(' %f %f %f\n' % tuple(origin))
for i in range(3):
fileobj.write(' %f %f %f\n' %
tuple(cell[i] * (shape[i] + 1) / shape[i]))
for x in range(shape[2]):
for y in range(shape[1]):
fileobj.write(' ')
fileobj.write(' '.join(['%f' % d for d in data[x, y]]))
fileobj.write('\n')
fileobj.write('\n')
fileobj.write(' END_DATAGRID_3D\n')
fileobj.write('END_BLOCK_DATAGRID_3D\n')
def write_cfg(f, a):
"""Write atomic configuration to a CFG-file (native AtomEye format).
See: http://mt.seas.upenn.edu/Archive/Graphics/A/
"""
if isinstance(f, str):
f = paropen(f, 'w')
f.write('Number of particles = %i\n' % len(a))
f.write('A = 1.0 Angstrom\n')
cell = a.get_cell()
for i in range(3):
for j in range(3):
f.write('H0(%1.1i,%1.1i) = %f A\n' % ( i + 1, j + 1, cell[i, j] ))
entry_count = 3
for x in list(a.arrays.keys()):
if not x in cfg_default_fields:
if len(a.get_array(x).shape) == 1:
entry_count += 1
else:
entry_count += a.get_array(x).shape[1]
vels = a.get_velocities()
if type(vels) == np.ndarray:
entry_count += 3
else:
f.write('.NO_VELOCITY.\n')
f.write('entry_count = %i\n' % entry_count)
i = 0
for name, aux in a.arrays.items():
if not name in cfg_default_fields:
if len(aux.shape) == 1:
f.write('auxiliary[%i] = %s [a.u.]\n' % ( i, name ))
i += 1
else:
for j in range(aux.shape[1]):
f.write('auxiliary[%i] = %s_%1.1i [a.u.]\n' % ( i, name, j ))
i += 1
# Distinct elements
spos = a.get_scaled_positions()
for i in a:
el = i.get_symbol()
f.write('%f\n' % ase_ext.data.atomic_masses[ase.data.chemical_symbols.index(el)])
f.write('%s\n' % el)
x, y, z = spos[i.index, :]
s = '%e %e %e ' % ( x, y, z )
if type(vels) == np.ndarray:
vx, vy, vz = vels[i.index, :]
s = s + ' %e %e %e ' % ( vx, vy, vz )
for name, aux in a.arrays.items():
if not name in cfg_default_fields:
if len(aux.shape) == 1:
s += ' %e' % aux[i.index]
else:
s += ( aux.shape[1]*' %e' ) % tuple(aux[i.index].tolist())
f.write('%s\n' % s)
def summary(self,
method='standard',
direction='central',
T=298.,
threshold=10,
freq=None,
log=sys.stdout):
"""Print a summary of the frequencies and derived thermodynamic
properties. The equations for the calculation of the enthalpy and
entropy diverge for zero frequencies and a threshold value is used
to ignore extremely low frequencies (default = 10 cm^-1).
Parameters:
method : string
Can be 'standard'(default) or 'Frederiksen'.
direction: string
Direction for finite differences. Can be one of 'central'
(default), 'forward', 'backward'.
T : float
Temperature in K at which thermodynamic properties are calculated.
threshold : float
Threshold value for low frequencies (default 10 cm^-1).
freq : numpy array
Optional. Can be used to create a summary on a set of known
frequencies.
destination : string or object with a .write() method
Where to print the summary info. Default is to print to
standard output. If another string is given, it creates that
text file and writes the output to it. If a file object (or any
object with a .write(string) function) is given, it writes to that
file.
Notes:
The enthalpy and entropy calculations are very sensitive to low
frequencies and the threshold value must be used with caution."""
if isinstance(log, str):
log = paropen(log, 'a')
write = log.write
s = 0.01 * units._e / units._c / units._hplanck
if freq != None:
hnu = freq / s
else:
hnu = self.get_energies(method, direction)
write('---------------------\n')
write(' # meV cm^-1\n')
write('---------------------\n')
for n, e in enumerate(hnu):
if e.imag != 0:
c = 'i'
e = e.imag
else:
c = ' '
write('%3d %6.1f%s %7.1f%s\n' % (n, 1000 * e, c, s * e, c))
write('---------------------\n')
write('Zero-point energy: %.3f eV\n' %
self.get_zero_point_energy(freq=freq))
write('Thermodynamic properties at %.2f K\n' % T)
write('Enthalpy: %.3f eV\n' % self.get_enthalpy(method=method,
direction=direction,
T=T,
threshold=threshold,
freq=freq))
write('Entropy : %.3f meV/K\n' %
(1E3 * self.get_entropy(method=method,
direction=direction,
T=T,
threshold=threshold,
freq=freq)))
write('T*S : %.3f eV\n' %
(T * self.get_entropy(method=method,
direction=direction,
T=T,
threshold=threshold,
freq=freq)))
write('E->G : %.3f eV\n' %
(self.get_zero_point_energy(freq=freq) + self.get_enthalpy(
method=method,
direction=direction,
T=T,
threshold=threshold,
freq=freq) - T * self.get_entropy(method=method,
direction=direction,
T=T,
threshold=threshold,
freq=freq)))
def __init__(self, logname, descriptions=1, verbosity=1):
self.f = paropen(logname, 'w')
unittest.TextTestRunner.__init__(self, self.f, descriptions, verbosity)
def save(self, file):
"""Save information on localization and rotation matrices to file."""
dump((self.Z_dknn, self.U_kww, self.C_kul), paropen(file, 'w'))
