def main(file_name):
xyz_file = XYZFile(file_name)
frames = xyz_file.geometries
# titles = xyz_file.titles
# Unit cell, decide how to make this general
matrix = np.array([[
1.4731497044857509E+01, 3.2189795740722255E-02, 4.5577626559295564E-02
], [
4.2775481701113616E-02, 2.1087874593411915E+01, -2.8531114198383896E-02
], [
6.4054385616337750E-02, 1.3315840416191497E-02, 1.4683043045316882E+01
]])
matrix *= angstrom
cell = UnitCell(matrix)
frac = UnitCell.to_fractional(cell, frames)
xmin = np.min(frac[:, :, 0])
ymin = np.min(frac[:, :, 1])
zmin = np.min(frac[:, :, 2])
frac[:, :, 0] -= -0.5 # xmin
frac[:, :, 1] -= -0.5 # ymin
frac[:, :, 2] -= -0.5 # zmin
decimals = np.modf(frac)[0]
# decimals[:,:,0] += xmin
# decimals[:,:,1] += ymin
# decimals[:,:,2] += zmin
frac_wrapped = np.where(decimals < 0, 1 + decimals, decimals)
# frac_wrapped[:,:,0] += xmin
# frac_wrapped[:,:,1] += ymin
# frac_wrapped[:,:,2] += zmin
cart_wrapped = UnitCell.to_cartesian(cell, frac_wrapped)
xyz_file.geometries = cart_wrapped
xyz_file.write_to_file(file_name.rsplit(".", 1)[0] + "_wrapped.xyz")
def from_cell_str(cls, unit_cell_str, sub=slice(None)):
sub = fix_slice(sub)
if "," in unit_cell_str:
parameters = list(parse_unit(word) for word in unit_cell_str.split(",") if len(word) > 0)
if len(parameters) == 1:
a = parameters[0]
single = numpy.array([[a,0,0],[0,a,0],[0,0,a]], float)
elif len(parameters) == 3:
a,b,c = parameters
single = numpy.array([[[a,0,0],[0,b,0],[0,0,c]]], float)
elif len(parameters) == 6:
a,b,c,alpha,beta,gamma = parameters
uc = UnitCell(
numpy.array([[1,0,0],[0,1,0],[0,0,1]], float),
numpy.array([True, True, True]),
)
uc.set_parameterst(numpy.array([a,b,c]), numpy.array([alpha,beta,gamma]))
single = uc.cell
elif len(parameters) == 9:
single = numpy.array(parameters,float).reshape((3,3)).transpose()
else:
raise ValueError("If the --cell option contains comma's, one, three, six or nine value(s) are expected.")
data = single.reshape((3,3,1))
else:
data = [
[
load_track("%s.%s.%s" % (unit_cell_str, v, c), sub)
for v in "abc"
]
for c in "xyz"
]
return cls(data)
def test_radius_indexes_2d(self):
uc = UnitCell(numpy.identity(3, float), numpy.array([True, True, False]))
indexes = uc.get_radius_indexes(0.5)
expected_indexes = numpy.array([
[-1, -1, 0],
[-1, 0, 0],
[-1, 1, 0],
[ 0, -1, 0],
[ 0, 0, 0],
[ 0, 1, 0],
[ 1, -1, 0],
[ 1, 0, 0],
[ 1, 1, 0],
])
self.assertArraysEqual(indexes, expected_indexes)
def test_distance_matrix_periodic(self):
for i in xrange(1000):
N = 6
unit_cell = UnitCell(
numpy.random.uniform(0,1,(3,3)),
numpy.random.randint(0,2,3).astype(bool),
)
fractional = numpy.random.uniform(0,1,(N,3))
coordinates = unit_cell.to_cartesian(fractional)
from molmod.ext import molecules_distance_matrix
dm = molecules_distance_matrix(coordinates, unit_cell.matrix,
unit_cell.reciprocal)
for i in xrange(N):
for j in xrange(i,N):
delta = coordinates[j]-coordinates[i]
delta = unit_cell.shortest_vector(delta)
distance = numpy.linalg.norm(delta)
self.assertAlmostEqual(dm[i,j], distance)
def test_default_graph_periodic(self):
molecule = Molecule.from_file("input/lau.xyz")
uc = UnitCell.from_parameters3(
numpy.array([14.587, 12.877, 7.613])*angstrom,
numpy.array([90.000, 111.159, 90.000])*deg
)
uc = uc.alignment_c*uc
molecule = molecule.copy_with(unit_cell=uc)
molecule.set_default_graph()
self.assertEqual(molecule.graph.num_edges, 4*molecule.size/3)
def test_parameters(self):
for counter in xrange(100):
in_lengths = numpy.random.uniform(0.5, 1, (3,))
in_angles = numpy.random.uniform(0.3, numpy.pi/2, (3,))
try:
uc = UnitCell.from_parameters3(in_lengths, in_angles)
except ValueError, e:
continue
out_lengths, out_angles = uc.parameters
self.assertArraysAlmostEqual(in_lengths, out_lengths)
self.assertArraysAlmostEqual(in_angles, out_angles)
def get_random_ff(self):
N = 6
mask = numpy.zeros((N,N), bool)
for i in xrange(N):
for j in xrange(i):
mask[i,j] = True
from molmod.ext import molecules_distance_matrix
while True:
unit_cell = UnitCell(
numpy.random.uniform(0,3,(3,3)),
numpy.random.randint(0,2,3).astype(bool),
)
fractional = numpy.random.uniform(0,1,(N,3))
coordinates = unit_cell.to_cartesian(fractional)
if numpy.random.randint(0,2):
unit_cell = None
dm = molecules_distance_matrix(coordinates)
else:
dm = molecules_distance_matrix(coordinates, unit_cell.matrix, unit_cell.reciprocal)
if dm[mask].min() > 1.0:
break
edges = set([])
while len(edges) < 2*N:
v1 = numpy.random.randint(N)
while True:
v2 = numpy.random.randint(N)
if v2 != v1:
break
edges.add(frozenset([v1,v2]))
edges = tuple(edges)
numbers = numpy.random.randint(6, 10, N)
graph = MolecularGraph(edges, numbers)
ff = ToyFF(graph, unit_cell)
return ff, coordinates, dm, mask, unit_cell
def _setup_grid(self, cutoff, unit_cell, grid):
"""Choose a proper grid for the binning process"""
if grid is None:
# automatically choose a decent grid
if unit_cell is None:
grid = cutoff / 2.9
else:
# The following would be faster, but it is not reliable
# enough yet.
#grid = unit_cell.get_optimal_subcell(cutoff/2.0)
divisions = np.ceil(unit_cell.spacings / cutoff)
divisions[divisions < 1] = 1
grid = unit_cell / divisions
if isinstance(grid, float):
grid_cell = UnitCell(
np.array([[grid, 0, 0], [0, grid, 0], [0, 0, grid]]))
elif isinstance(grid, UnitCell):
grid_cell = grid
else:
raise TypeError(
"Grid must be None, a float or a UnitCell instance.")
if unit_cell is not None:
# The columns of integer_matrix are the unit cell vectors in
# fractional coordinates of the grid cell.
integer_matrix = grid_cell.to_fractional(
unit_cell.matrix.transpose()).transpose()
if abs((integer_matrix - np.round(integer_matrix)) *
self.unit_cell.active).max() > 1e-6:
raise ValueError(
"The unit cell vectors are not an integer linear combination of grid cell vectors."
)
integer_matrix = integer_matrix.round()
integer_cell = UnitCell(integer_matrix, unit_cell.active)
else:
integer_cell = None
return grid_cell, integer_cell
def test_distances_intra_random_periodic(self):
for i in xrange(10):
coordinates = numpy.random.uniform(0,1,(20,3))
while True:
unit_cell = UnitCell(
numpy.random.uniform(0,5,(3,3)),
numpy.random.randint(0,2,3).astype(bool),
)
if unit_cell.spacings.min() > 0.5:
break
coordinates = unit_cell.to_cartesian(coordinates)*3-unit_cell.matrix.sum(axis=1)
cutoff = numpy.random.uniform(1, 6)
pair_search = PairSearchIntra(coordinates, cutoff, unit_cell)
self.verify_bins_intra_periodic(pair_search.bins)
distances = [
(frozenset([i0, i1]), distance)
for i0, i1, delta, distance
in pair_search
]
self.verify_distances_intra(coordinates, cutoff, distances, unit_cell)
def _setup_grid(self, cutoff, unit_cell, grid):
"""Choose a proper grid for the binning process"""
if grid is None:
# automatically choose a decent grid
if unit_cell is None:
grid = cutoff/2.9
else:
# The following would be faster, but it is not reliable
# enough yet.
#grid = unit_cell.get_optimal_subcell(cutoff/2.0)
divisions = numpy.ceil(unit_cell.spacings/cutoff)
divisions[divisions<1] = 1
grid = unit_cell/divisions
if isinstance(grid, float):
grid_cell = UnitCell(numpy.array([
[grid, 0, 0],
[0, grid, 0],
[0, 0, grid]
]))
elif isinstance(grid, UnitCell):
grid_cell = grid
else:
raise TypeError("Grid must be None, a float or a UnitCell instance.")
if unit_cell is not None:
# The columns of integer_matrix are the unit cell vectors in
# fractional coordinates of the grid cell.
integer_matrix = grid_cell.to_fractional(unit_cell.matrix.transpose()).transpose()
if abs((integer_matrix - numpy.round(integer_matrix))*self.unit_cell.active).max() > 1e-6:
raise ValueError("The unit cell vectors are not an integer linear combination of grid cell vectors.")
integer_matrix = integer_matrix.round()
integer_cell = UnitCell(integer_matrix, unit_cell.active)
else:
integer_cell = None
return grid_cell, integer_cell
def test_distances_inter_random_periodic(self):
for i in xrange(10):
fractional0 = numpy.random.uniform(0,1,(20,3))
fractional1 = numpy.random.uniform(0,1,(20,3))
while True:
unit_cell = UnitCell(
numpy.random.uniform(0,5,(3,3)),
numpy.random.randint(0,2,3).astype(bool),
)
if unit_cell.spacings.min() > 0.5:
break
coordinates0 = unit_cell.to_cartesian(fractional0)*3-unit_cell.matrix.sum(axis=1)
coordinates1 = unit_cell.to_cartesian(fractional1)*3-unit_cell.matrix.sum(axis=1)
cutoff = numpy.random.uniform(1, 6)
pair_search = PairSearchInter(coordinates0, coordinates1, cutoff, unit_cell)
self.verify_bins_inter_periodic(pair_search.bins0, pair_search.bins1)
distances = [
((i0, i1), distance)
for i0, i1, delta, distance
in pair_search
]
self.verify_distances_inter(coordinates0, coordinates1, cutoff, distances, unit_cell)
def iter_unit_cells(unit_cell_str, sub=None):
sub = fix_slice(sub)
if len(unit_cell_str) == 0:
uc = UnitCell(
numpy.array([[1,0,0],[0,1,0],[0,0,1]], float),
numpy.array([False,False,False]),
)
while True:
yield uc
if "," in unit_cell_str:
parameters = list(parse_unit(word) for word in unit_cell_str.split(",") if len(word) > 0)
if len(parameters) == 1:
a= parameters[0]
uc = UnitCell(
numpy.array([[a,0,0],[0,a,0],[0,0,a]], float),
numpy.array([True, True, True]),
)
elif len(parameters) == 3:
a,b,c = parameters
uc = UnitCell(
numpy.array([[a,0,0],[0,b,0],[0,0,c]], float),
numpy.array([True, True, True]),
)
elif len(parameters) == 6:
a,b,c,alpha,beta,gamma = parameters
uc = UnitCell.from_parameters3(
numpy.array([a,b,c]),
numpy.array([alpha,beta,gamma])
)
elif len(parameters) == 9:
uc = UnitCell(
numpy.array(parameters, float).reshape((3,3)),
numpy.array([True, True, True]),
)
else:
raise ValueError("If the --cell option contains comma's, one, three, six or nine value(s) are expected.")
while True:
yield uc
else:
filenames = ["%s.%s" % (unit_cell_str, suffix) for suffix in ["a.x", "a.y", "a.z", "b.x", "b.y", "b.z", "c.x", "c.y", "c.z"]]
dtype = numpy.dtype([("cell", float, (3,3))])
mtr = MultiTracksReader(filenames, dtype, sub=sub)
for row in mtr:
yield UnitCell(
numpy.array(row["cell"], float),
numpy.array([True, True, True]),
)
def test_distances_intra_lau_periodic(self):
coordinates = XYZFile("input/lau.xyz").geometries[0]
cutoff = periodic.max_radius*2
unit_cell = UnitCell.from_parameters3(
numpy.array([14.59, 12.88, 7.61])*angstrom,
numpy.array([ 90.0, 111.0, 90.0])*deg,
)
pair_search = PairSearchIntra(coordinates, cutoff, unit_cell)
self.verify_bins_intra_periodic(pair_search.bins)
distances = [
(frozenset([i0, i1]), distance)
for i0, i1, delta, distance
in pair_search
]
self.verify_distances_intra(coordinates, cutoff, distances, unit_cell)
def apply_to(self, x, columns=False):
"""Apply this transformation to the given object
The argument can be several sorts of objects:
* ``numpy.array`` with shape (3, )
* ``numpy.array`` with shape (N, 3)
* ``numpy.array`` with shape (3, N), use ``columns=True``
* ``Translation``
* ``Rotation``
* ``Complete``
* ``UnitCell``
In case of arrays, the 3D vectors are transformed. In case of trans-
formations, a transformation is returned that consists of this
transformation applied AFTER the given translation. In case of a unit
cell, a unit cell with rotated cell vectors is returned. (The
translational part does not affect the unit cell.)
This method is equivalent to self*x.
"""
if isinstance(x, numpy.ndarray) and len(
x.shape) == 2 and x.shape[0] == 3 and columns:
return numpy.dot(self.r, x) + self.t.reshape((3, 1))
if isinstance(x, numpy.ndarray) and (
x.shape == (3, ) or
(len(x.shape) == 2 and x.shape[1] == 3)) and not columns:
return numpy.dot(x, self.r.transpose()) + self.t
elif isinstance(x, Complete):
return Complete(numpy.dot(self.r, x.r),
numpy.dot(self.r, x.t) + self.t)
elif isinstance(x, Translation):
return Complete(self.r, numpy.dot(self.r, x.t) + self.t)
elif isinstance(x, Rotation):
return Complete(numpy.dot(self.r, x.r), self.t)
elif isinstance(x, UnitCell):
return UnitCell(numpy.dot(self.r, x.matrix), x.active)
else:
raise ValueError("Can not apply this rotation to %s" % x)
def load_molecule_cp2k(fn_sp, fn_freq, multiplicity=1, is_periodic=True):
"""Load a molecule with the Hessian from a CP2K computation
Arguments:
| fn_sp -- The filename of the single point .out file containing the
energy and the forces.
| fn_freq -- The filename of the frequency .out file containing the
hessian
Optional arguments:
| multiplicity -- The spin multiplicity of the electronic system
[default=1]
| is_periodic -- True when the system is periodic in three dimensions.
False when the systen is aperiodic. [default=True]
| unit_cell -- The unit cell vectors for periodic structures
"""
# auxiliary routine to read atoms
def atom_helper(f):
# skip some lines
for i in xrange(3):
f.readline()
# read the atom lines until an empty line is encountered
numbers = []
coordinates = []
masses = []
while True:
line = f.readline()
if len(line.strip()) == 0:
break
symbol = line[14:19].strip()[:2]
atom = periodic[symbol]
if atom is None:
symbol = symbol[:1]
atom = periodic[symbol]
if atom is None:
numbers.append(0)
else:
numbers.append(atom.number)
coordinates.append(
[float(line[22:33]),
float(line[34:45]),
float(line[46:57])])
masses.append(float(line[72:]))
numbers = np.array(numbers)
coordinates = np.array(coordinates) * angstrom
masses = np.array(masses) * amu
return numbers, coordinates, masses
# auxiliary routine to read forces
def force_helper(f, skip, offset):
# skip some lines
for i in xrange(skip):
f.readline()
# Read the actual forces
tmp = []
while True:
line = f.readline()
if line == "\n":
break
if line == "":
raise IOError("End of file while reading gradient (forces).")
words = line.split()
try:
tmp.append([
float(words[offset]),
float(words[offset + 1]),
float(words[offset + 2])
])
except StandardError:
break
return -np.array(tmp) # force to gradient
# go through the single point file: energy and gradient
energy = None
gradient = None
with open(fn_sp) as f:
while True:
line = f.readline()
if line == "":
break
if line.startswith(" ENERGY|"):
energy = float(line[58:])
elif line.startswith(" MODULE") and "ATOMIC COORDINATES" in line:
numbers, coordinates, masses = atom_helper(f)
elif line.startswith(" FORCES|"):
gradient = force_helper(f, 0, 1)
break
elif line.startswith(' ATOMIC FORCES in [a.u.]'):
gradient = force_helper(f, 2, 3)
break
if energy is None or gradient is None:
raise IOError(
"Could not read energy and/or gradient (forces) from single point file."
)
# go through the freq file: lattic vectors and hessian
with open(fn_freq) as f:
vectors = np.zeros((3, 3), float)
for line in f:
if line.startswith(" CELL"):
break
for axis in range(3):
line = f.next()
vectors[:, axis] = np.array(
[float(line[29:39]),
float(line[39:49]),
float(line[49:59])])
unit_cell = UnitCell(vectors * angstrom)
free_indices = _load_free_low(f)
if len(free_indices) > 0:
total_size = coordinates.size
free_size = len(free_indices)
hessian = np.zeros((total_size, total_size), float)
i2 = 0
while i2 < free_size:
num_cols = min(5, free_size - i2)
f.next() # skip two lines
f.next()
for j in xrange(free_size):
line = f.next()
words = line.split()
for i1 in xrange(num_cols):
hessian[free_indices[i2 + i1], free_indices[j]] = \
float(words[i1 + 2])
i2 += num_cols
else:
raise IOError("Could not read hessian from freq file.")
# symmetrize
hessian = 0.5 * (hessian + hessian.transpose())
# cp2k prints a transformed hessian, here we convert it back to the normal
# hessian in atomic units.
conv = 1e-3 * np.array([masses, masses, masses]).transpose().ravel()**0.5
hessian *= conv
hessian *= conv.reshape((-1, 1))
return Molecule(numbers,
coordinates,
masses,
energy,
gradient,
hessian,
multiplicity,
0,
is_periodic,
unit_cell=unit_cell)
def load_molecule_vasp(contcar, outcar_freq, energy=None, multiplicity=1, is_periodic=True):
"""Load a molecule from VASP 4.6.X and 5.3.X output files
Arguments:
| contcar -- A CONTCAR file with the structure used as POSCAR file for the
Hessian/frequency calculation in VASP. Do not use the CONTCAR file
generated by the frequency calculation. Use the CONTCAR from the
preceding geometry optimization instead. The energy without
entropy (but not the extrapolation to sigma=0) is used.
| outcar_freq -- The OUTCAR file of the Hessian/frequency calculation.
Optional arguments:
| energy -- The potential energy, which overrides the contents of outcar_freq.
| multiplicity -- The spin multiplicity of the electronic system
[default=1]
| is_periodic -- True when the system is periodic in three dimensions.
False when the systen is nonperiodic. [default=True].
"""
# Read atomic symbols, coordinates and cell vectors from CONTCAR
symbols = []
coordinates = []
with open(contcar) as f:
# Skip title.
f.next().strip()
# Read scale for rvecs.
rvec_scale = float(f.next())
# Read rvecs. VASP uses one row per cell vector.
rvecs = np.fromstring(f.next()+f.next()+f.next(), sep=' ').reshape(3, 3)
rvecs *= rvec_scale*angstrom
unit_cell = UnitCell(rvecs)
# Read symbols
unique_symbols = f.next().split()
# Read atom counts per symbol
symbol_counts = [int(w) for w in f.next().split()]
assert len(symbol_counts) == len(unique_symbols)
natom = sum(symbol_counts)
# Construct array with atomic numbers.
numbers = []
for iunique in xrange(len(unique_symbols)):
number = periodic[unique_symbols[iunique]].number
numbers.extend([number]*symbol_counts[iunique])
numbers = np.array(numbers)
# Check next line
while f.next() != 'Direct\n':
continue
# Load fractional coordinates
fractional = np.zeros((natom, 3), float)
for iatom in xrange(natom):
words = f.next().split()
fractional[iatom, 0] = float(words[0])
fractional[iatom, 1] = float(words[1])
fractional[iatom, 2] = float(words[2])
coordinates = unit_cell.to_cartesian(fractional)
# Read energy, gradient, Hessian and masses from outcar_freq. Note that the first
# energy/force calculation is done on the unperturbed input structure.
with open(outcar_freq) as f:
# Loop over the POTCAR sections in the OUTCAR file
number = None
masses = np.zeros(natom, float)
while True:
line = f.next()
if line.startswith(' VRHFIN ='):
symbol = line[11:line.find(':')].strip()
number = periodic[symbol].number
elif line.startswith(' POMASS ='):
mass = float(line[11:line.find(';')])*amu
masses[numbers==number] = mass
elif number is not None and line.startswith('------------------------------'):
assert masses.min() > 0
break
# Go to the first gradient
for line in f:
if line.startswith(' POSITION'):
break
# Skip one line and read the gradient
f.next()
gradient = np.zeros((natom, 3), float)
gunit = electronvolt/angstrom
for iatom in xrange(natom):
words = f.next().split()
gradient[iatom, 0] = -float(words[3])*gunit
gradient[iatom, 1] = -float(words[4])*gunit
gradient[iatom, 2] = -float(words[5])*gunit
if energy is None:
# Go to the first energy
for line in f:
if line.startswith(' FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV)'):
break
# Skip three lines and read energy
f.next()
f.next()
f.next()
energy = float(f.next().split()[3])*electronvolt
# Go to the second derivatives
for line in f:
if line.startswith(' SECOND DERIVATIVES (NOT SYMMETRIZED)'): break
# Skip one line.
f.next()
# Load free atoms (not fixed in space).
keys = f.next().split()
nfree_dof = len(keys)
indices_free = [3*int(key[:-1])+{'X': 0, 'Y': 1, 'Z': 2}[key[-1]]-3 for key in keys]
assert nfree_dof % 3 == 0
# Load the actual Hessian
hunit = electronvolt/angstrom**2
hessian = np.zeros((3*natom, 3*natom), float)
for ifree0 in xrange(nfree_dof):
line = f.next()
irow = indices_free[ifree0]
# skip first col
words = line.split()[1:]
assert len(words) == nfree_dof
for ifree1 in xrange(nfree_dof):
icol = indices_free[ifree1]
hessian[irow, icol] = -float(words[ifree1])*hunit
# Symmetrize the Hessian
hessian = 0.5*(hessian + hessian.T)
return Molecule(
numbers, coordinates, masses, energy, gradient, hessian,
multiplicity=multiplicity, periodic=is_periodic, unit_cell=unit_cell)
def load_molecule_vasp(contcar,
outcar_freq,
outcar_energy=None,
energy=None,
multiplicity=1,
is_periodic=True):
"""Load a molecule from VASP 4.6.X and 5.3.X output files
Arguments:
| contcar -- A CONTCAR file with the structure used as POSCAR file for the
Hessian/frequency calculation in VASP. Do not use the CONTCAR file
generated by the frequency calculation. Use the CONTCAR from the
preceding geometry optimization instead.
| outcar_freq -- The OUTCAR file of the Hessian/frequency calculation. Also the
gradient and the energy are read from this file. The energy
without entropy (but not the extrapolation to sigma=0) is used.
Optional arguments:
| outcar_energy -- When given, the (first) energy without entropy is read from
this file (not the extrapolation to sigma=0) instead of
reading the energy from the freq output
| energy -- The potential energy, which overrides the contents of outcar_freq.
| multiplicity -- The spin multiplicity of the electronic system
[default=1]
| is_periodic -- True when the system is periodic in three dimensions.
False when the systen is nonperiodic. [default=True].
"""
# auxiliary function to read energy:
def read_energy_without_entropy(f):
# Go to the first energy
for line in f:
if line.startswith(
' FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV)'):
break
# Skip three lines and read energy
next(f)
next(f)
next(f)
return float(next(f).split()[3]) * electronvolt
# Read atomic symbols, coordinates and cell vectors from CONTCAR
symbols = []
coordinates = []
with open(contcar) as f:
# Skip title.
next(f).strip()
# Read scale for rvecs.
rvec_scale = float(next(f))
# Read rvecs. VASP uses one row per cell vector.
rvecs = np.fromstring(next(f) + next(f) + next(f),
sep=' ').reshape(3, 3)
rvecs *= rvec_scale * angstrom
unit_cell = UnitCell(rvecs)
# Read symbols
unique_symbols = next(f).split()
# Read atom counts per symbol
symbol_counts = [int(w) for w in next(f).split()]
assert len(symbol_counts) == len(unique_symbols)
natom = sum(symbol_counts)
# Construct array with atomic numbers.
numbers = []
for iunique in range(len(unique_symbols)):
number = periodic[unique_symbols[iunique]].number
numbers.extend([number] * symbol_counts[iunique])
numbers = np.array(numbers)
# Check next line
while next(f) != 'Direct\n':
continue
# Load fractional coordinates
fractional = np.zeros((natom, 3), float)
for iatom in range(natom):
words = next(f).split()
fractional[iatom, 0] = float(words[0])
fractional[iatom, 1] = float(words[1])
fractional[iatom, 2] = float(words[2])
coordinates = unit_cell.to_cartesian(fractional)
if outcar_energy is not None and energy is None:
with open(outcar_energy) as f:
energy = read_energy_without_entropy(f)
# Read energy, gradient, Hessian and masses from outcar_freq. Note that the first
# energy/force calculation is done on the unperturbed input structure.
with open(outcar_freq) as f:
# Loop over the POTCAR sections in the OUTCAR file
number = None
masses = np.zeros(natom, float)
while True:
line = next(f)
if line.startswith(' VRHFIN ='):
symbol = line[11:line.find(':')].strip()
number = periodic[symbol].number
elif line.startswith(' POMASS ='):
mass = float(line[11:line.find(';')]) * amu
masses[numbers == number] = mass
elif number is not None and line.startswith(
'------------------------------'):
assert masses.min() > 0
break
# Go to the first gradient
for line in f:
if line.startswith(' POSITION'):
break
# Skip one line and read the gradient
next(f)
gradient = np.zeros((natom, 3), float)
gunit = electronvolt / angstrom
for iatom in range(natom):
words = next(f).split()
gradient[iatom, 0] = -float(words[3]) * gunit
gradient[iatom, 1] = -float(words[4]) * gunit
gradient[iatom, 2] = -float(words[5]) * gunit
if energy is None:
energy = read_energy_without_entropy(f)
# Go to the second derivatives
for line in f:
if line.startswith(' SECOND DERIVATIVES (NOT SYMMETRIZED)'): break
# Skip one line.
next(f)
# Load free atoms (not fixed in space).
keys = next(f).split()
nfree_dof = len(keys)
indices_free = [
3 * int(key[:-1]) + {
'X': 0,
'Y': 1,
'Z': 2
}[key[-1]] - 3 for key in keys
]
assert nfree_dof % 3 == 0
# Load the actual Hessian
hunit = electronvolt / angstrom**2
hessian = np.zeros((3 * natom, 3 * natom), float)
for ifree0 in range(nfree_dof):
line = next(f)
irow = indices_free[ifree0]
# skip first col
words = line.split()[1:]
assert len(words) == nfree_dof
for ifree1 in range(nfree_dof):
icol = indices_free[ifree1]
hessian[irow, icol] = -float(words[ifree1]) * hunit
# Symmetrize the Hessian
hessian = 0.5 * (hessian + hessian.T)
return Molecule(numbers,
coordinates,
masses,
energy,
gradient,
hessian,
multiplicity=multiplicity,
periodic=is_periodic,
unit_cell=unit_cell)
def test_add_periodicities(self):
for counter in xrange(100):
uc0 = UnitCell(numpy.identity(3, float), numpy.zeros(3,bool))
uc1 = uc0.add_cell_vector(numpy.random.uniform(-2,2,3))
uc2 = uc1.add_cell_vector(numpy.random.uniform(-2,2,3))
uc3 = uc2.add_cell_vector(numpy.random.uniform(-2,2,3))
def test_shortest_vector(self):
raise SkipTest
# simple cases
uc = UnitCell(numpy.identity(3,float)*3)
self.assertArraysAlmostEqual(uc.shortest_vector([3, 0, 1]), numpy.array([0, 0, 1]))
self.assertArraysAlmostEqual(uc.shortest_vector([-3, 0, 1]), numpy.array([0, 0, 1]))
self.assertArraysAlmostEqual(uc.shortest_vector([-2, 0, 1]), numpy.array([1, 0, 1]))
self.assertArraysAlmostEqual(uc.shortest_vector([-1.6, 1, 1]), numpy.array([1.4, 1, 1]))
self.assertArraysAlmostEqual(uc.shortest_vector([-1.4, 1, 1]), numpy.array([-1.4, 1, 1]))
# simple cases
uc = UnitCell(numpy.identity(3,float)*3, numpy.array([True, False, False]))
self.assertArraysAlmostEqual(uc.shortest_vector([3, 0, 1]), numpy.array([0, 0, 1]))
self.assertArraysAlmostEqual(uc.shortest_vector([3, 0, 3]), numpy.array([0, 0, 3]))
# random tests
for uc_counter in xrange(1000):
uc = self.get_random_uc(full=False)
for r_counter in xrange(10):
r0 = numpy.random.normal(0, 10, 3)
r1 = uc.shortest_vector(r0)
change = r1 - r0
self.assert_(numpy.dot(change, r0) <= 0)
#self.assert_(numpy.linalg.norm(r0) >= numpy.linalg.norm(r1))
index = uc.to_fractional(r0-r1)
self.assertArraysAlmostEqual(index, numpy.round(index), doabs=True)
index = uc.to_fractional(r1)
self.assert_(index.max()<0.5)
self.assert_(index.max()>=-0.5)
r0 = numpy.random.normal(0, 10, (10,3))
r1 = uc.shortest_vector(r0)
for i in xrange(10):
r1_row_bis = uc.shortest_vector(r0[i])
self.assertArraysAlmostEqual(r1_row_bis, r1[i], doabs=True)
def test_shortest_vector_trivial(self):
uc = UnitCell(numpy.identity(3, float))
half = numpy.array([0.5,0.5,0.5])
self.assertArraysEqual(uc.shortest_vector(half), -half)
self.assertArraysEqual(uc.shortest_vector(-half), -half)
def test_shortest_vector_aperiodic(self):
unit_cell = UnitCell(numpy.identity(3, float), numpy.zeros(3, bool))
shortest = unit_cell.shortest_vector(numpy.ones(3, float))
expected = numpy.ones(3, float)
self.assertArraysAlmostEqual(shortest, expected)
def test_radius_indexes_2d_graphical(self):
#uc = UnitCell(numpy.array([
# [2.0, 1.0, 0.0],
# [0.0, 0.2, 0.0],
# [0.0, 0.0, 10.0],
#]))
#radius = 0.8
uc = UnitCell(numpy.array([
[1.0, 1.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 10.0],
]))
radius = 5.3
#uc = UnitCell(numpy.array([
# [1.0, 1.0, 0.0],
# [0.0, 1.0, 0.0],
# [0.0, 0.0, 1.0],
#]))
#radius = 0.9
fracs = numpy.arange(-0.5, 0.55, 0.1)
import pylab
from matplotlib.patches import Circle, Polygon
from matplotlib.lines import Line2D
pylab.clf()
for i0 in fracs:
for i1 in fracs:
center = uc.to_cartesian([i0,i1,0.0])
pylab.gca().add_artist(Circle((center[0], center[1]), radius, fill=True, fc='#7777AA', ec='none'))
pylab.gca().add_artist(Circle((0, 0), radius, fill=True, fc='#0000AA', ec='none'))
ranges = uc.get_radius_ranges(radius)
indexes = uc.get_radius_indexes(radius)
for i in xrange(-ranges[0]-1, ranges[0]+1):
start = uc.to_cartesian([i+0.5, -ranges[1]-0.5, 0])
end = uc.to_cartesian([i+0.5, ranges[1]+0.5, 0])
pylab.gca().add_artist(Line2D([start[0], end[0]], [start[1], end[1]], color="k", linewidth=1))
for i in xrange(-ranges[1]-1, ranges[1]+1):
start = uc.to_cartesian([-ranges[0]-0.5, i+0.5, 0])
end = uc.to_cartesian([ranges[0]+0.5, i+0.5, 0])
pylab.gca().add_artist(Line2D([start[0], end[0]], [start[1], end[1]], color="k", linewidth=1))
for i in xrange(-ranges[0], ranges[0]+1):
start = uc.to_cartesian([i, -ranges[1]-0.5, 0])
end = uc.to_cartesian([i, ranges[1]+0.5, 0])
pylab.gca().add_artist(Line2D([start[0], end[0]], [start[1], end[1]], color="k", linewidth=0.5, linestyle="--"))
for i in xrange(-ranges[1], ranges[1]+1):
start = uc.to_cartesian([-ranges[0]-0.5, i, 0])
end = uc.to_cartesian([ranges[0]+0.5, i, 0])
pylab.gca().add_artist(Line2D([start[0], end[0]], [start[1], end[1]], color="k", linewidth=0.5, linestyle="--"))
for i0,i1,i2 in indexes:
if i2 != 0:
continue
corners = uc.to_cartesian(numpy.array([
[i0-0.5, i1-0.5, 0.0],
[i0-0.5, i1+0.5, 0.0],
[i0+0.5, i1+0.5, 0.0],
[i0+0.5, i1-0.5, 0.0],
]))
pylab.gca().add_artist(Polygon(corners[:,:2], fill=True, ec='none', fc='r', alpha=0.5))
corners = uc.to_cartesian(numpy.array([
[-ranges[0]-0.5, -ranges[1]-0.5, 0.0],
[-ranges[0]-0.5, +ranges[1]+0.5, 0.0],
[+ranges[0]+0.5, +ranges[1]+0.5, 0.0],
[+ranges[0]+0.5, -ranges[1]-0.5, 0.0],
]))
pylab.xlim(1.1*corners[:,:2].min(), 1.1*corners[:,:2].max())
pylab.ylim(1.1*corners[:,:2].min(), 1.1*corners[:,:2].max())
#pylab.xlim(-1.5*radius, 1.5*radius)
#pylab.ylim(-1.5*radius, 1.5*radius)
pylab.savefig("output/radius_indexes_2d.png")
def test_radius_ranges_2d(self):
uc = UnitCell(numpy.identity(3, float), numpy.array([True, True, False]))
self.assertArraysEqual(uc.get_radius_ranges(3), numpy.array([3,3,0]))