def test_reduce1(self):
atom = Atoms(['C', 'Au'])
atom = atom.sub(0)
atom = atom.reduce()
assert_true(atom[0] == Atom[6])
assert_true(len(atom) == 1)
assert_true(len(atom.atom) == 1)
def test_reorder1(self):
atom = Atoms(['C', 'Au'])
atom = atom.sub(1)
atom = atom.reorder()
assert_true(atom[0] == Atom['Au'])
assert_true(len(atom) == 1)
assert_true(len(atom.atom) == 2)
def test_atoms_set():
a1 = Atom(1)
a2 = Atom(2)
a3 = Atom(3)
a = Atoms(a1, 3)
assert len(a) == 3
assert len(a.atom) == 1
a[1] = a2
assert len(a) == 3
assert len(a.atom) == 2
# Add the atom, but do not specify any
# atoms to have the species
a[[]] = a3
assert len(a) == 3
assert len(a.atom) == 3
for atom in a:
assert atom in [a1, a2]
assert atom != a3
found = 0
for atom, i_s in a.iter(True):
if atom == a1:
assert len(i_s) == 2
found += 1
elif atom == a2:
assert len(i_s) == 1
found += 1
elif atom == a3:
assert len(i_s) == 0
found += 1
assert found == 3
def test_create1(self):
atom1 = Atoms([self.C, self.C3, self.Au])
atom2 = Atoms(['C', 'C', 'Au'])
atom3 = Atoms(['C', 6, 'Au'])
atom4 = Atoms(['Au', 6, 'C'])
assert_true(atom2 == atom3)
assert_true(atom2 == atom4)
def test_remove1():
atom = Atoms(['C', 'Au'])
atom = atom.remove(1)
atom = atom.reduce()
assert atom[0] == Atom[6]
assert len(atom) == 1
assert len(atom.atom) == 1
def read_geometry(self, velocity=False, species_Z=False):
""" Returns a `Geometry` object from the XV file
Parameters
----------
species_Z : bool, optional
if ``True`` the atomic numbers are the species indices (useful when
reading the ChemicalSpeciesLabel block simultaneously).
velocity : bool, optional
also return the velocities in the file
Returns
-------
Geometry
velocity : only if `velocity` is true.
"""
sc = self.read_supercell()
# Read number of atoms
na = int(self.readline())
xyz = np.empty([na, 3], np.float64)
vel = np.empty([na, 3], np.float64)
atms = [None] * na
sp = np.empty([na], np.int32)
for ia in range(na):
line = list(map(float, self.readline().split()[:8]))
sp[ia] = int(line[0])
if species_Z:
atms[ia] = Atom(sp[ia])
else:
atms[ia] = Atom(int(line[1]))
xyz[ia, :] = line[2:5]
vel[ia, :] = line[5:8]
xyz *= Bohr2Ang
vel *= Bohr2Ang
# Ensure correct sorting
max_s = sp.max()
sp -= 1
# Ensure we can remove the atom after having aligned them
atms2 = Atoms(AtomUnknown(1000), na=na)
for i in range(max_s):
idx = (sp[:] == i).nonzero()[0]
if len(idx) == 0:
# Always ensure we have "something" for the unoccupied places
atms2[idx] = AtomUnknown(1000 + i)
else:
atms2[idx] = atms[idx[0]]
geom = Geometry(xyz, atms2.reduce(), sc=sc)
if velocity:
return geom, vel
return geom
def read_geometry(self):
""" Read geometry from the contained file """
# First we read in the geometry
sc = self.read_supercell()
# Try and go to the first model record
in_model, l = self._step_record('MODEL')
idx = []
tags = []
xyz = []
Z = []
if in_model:
l = self.readline()
def is_atom(line):
return l.startswith('ATOM') or l.startswith('HETATM')
def is_end_model(line):
return l.startswith('ENDMDL') or l == ''
while not is_end_model(l):
if is_atom(l):
idx.append(int(l[6:11]))
tags.append(l[12:16].strip())
xyz.append(
[float(l[30:38]),
float(l[38:46]),
float(l[46:54])])
Z.append(l[76:78].strip())
l = self.readline()
# First sort all atoms according to the idx array
idx = np.array(idx)
idx = np.argsort(idx)
xyz = np.array(xyz)[idx, :]
tags = [tags[i] for i in idx]
Z = [Z[i] for i in idx]
# Create the atom list
atoms = Atoms(Atom(Z[0], tag=tags[0]), na=len(Z))
for i, a in enumerate(map(Atom, Z, tags)):
try:
s = atoms.specie_index(a)
except:
s = len(atoms.atom)
atoms._atom.append(a)
atoms._specie[i] = s
return Geometry(xyz, atoms, sc=sc)
def test_get1(self):
atoms = Atoms(['C', 'C', 'Au'])
assert_true(atoms[2] == Atom('Au'))
assert_true(atoms[0] == Atom('C'))
assert_true(atoms[1] == Atom('C'))
assert_true(atoms[0:2] == [Atom('C')] * 2)
assert_true(atoms[1:] == [Atom('C'), Atom('Au')])
def test_get1():
atoms = Atoms(['C', 'C', 'Au'])
assert atoms[2] == Atom('Au')
assert atoms[0] == Atom('C')
assert atoms[1] == Atom('C')
assert atoms[0:2] == [Atom('C')]*2
assert atoms[1:] == [Atom('C'), Atom('Au')]
def read_basis(self):
""" Returns a set of atoms corresponding to the basis-sets in the ORB_INDX file
The specie names have a short field in the ORB_INDX file, hence the name may
not necessarily be the same as provided in the species block
"""
# First line contains no no_s
line = self.readline().split()
no = int(line[0])
self.readline()
self.readline()
pt = PeriodicTable()
def crt_atom(spec, orbs):
i = pt.Z(spec)
if isinstance(i, int):
return Atom(i, orbs)
else:
return Atom(-1, orbs, tag=spec)
# Now we begin by reading the atoms
atom = []
orbs = []
specs = []
ia = 1
for _ in range(no):
line = self.readline().split()
i_a = int(line[1])
if i_a != ia:
if i_s not in specs:
atom.append(crt_atom(spec, orbs))
specs.append(i_s)
ia = i_a
orbs = []
i_s = int(line[2]) - 1
if i_s in specs:
continue
spec = line[3]
nlmz = list(map(int, line[5:9]))
P = line[9] == 'T'
rc = float(line[11]) * Bohr2Ang
# Create the orbital
o = AtomicOrbital(n=nlmz[0],
l=nlmz[1],
m=nlmz[2],
Z=nlmz[3],
P=P,
spherical=Orbital(rc))
orbs.append(o)
if i_s not in specs:
atom.append(crt_atom(spec, orbs))
specs.append(i_s)
# Now re-arrange the atoms and create the Atoms object
return Atoms([atom[i] for i in specs])
def test_iter1(self):
# Add new atoms to the set
atom = Atoms(['C', 'C'])
for a, idx in atom:
assert_true(a == Atom[6])
assert_true(len(idx) == 2)
atom = Atoms(['C', 'Au', 'C', 'Au'])
for i, aidx in enumerate(atom):
a, idx = aidx
if i == 0:
assert_true(a == Atom[6])
assert_true((idx == [0, 2]).all())
elif i == 1:
assert_true(a == Atom['Au'])
assert_true((idx == [1, 3]).all())
assert_true(len(idx) == 2)
def test_set1(self):
# Add new atoms to the set
atom = Atoms(['C', 'C'])
assert_true(atom[0] == Atom('C'))
assert_true(atom[1] == Atom('C'))
atom[1] = Atom('Au')
assert_true(atom[0] == Atom('C'))
assert_true(atom[1] == Atom('Au'))
def test_set1():
# Add new atoms to the set
atom = Atoms(['C', 'C'])
assert atom[0] == Atom('C')
assert atom[1] == Atom('C')
atom[1] = Atom('Au')
assert atom[0] == Atom('C')
assert atom[1] == Atom('Au')
def test_charge_diff():
o1 = Orbital(1., 1.)
o2 = Orbital(1., .5)
a1 = Atom(5, [o1, o2, o1, o2])
a2 = Atom(5, [o1, o2, o1, o2, o1, o1])
a = Atoms([a1, a2])
assert len(a.q0) == 2
assert a.q0.sum() == pytest.approx(8)
assert np.allclose(a.q0, [3, 5])
def read_atom(self):
""" Reads a the atoms and returns an `Atoms` object """
self.readline()
_, ns = map(int, self.readline().split()[:2])
species = self.readline().split()[:ns] # species
orbs = self.readline().split()[:ns] # orbs per species
# Create list of species with correct # of orbitals per specie
species = [Atom(s, orbs=int(o)) for s, o in zip(species, orbs)]
return Atoms(species)
def test_set2():
# Add new atoms to the set
atom = Atoms(['C', 'C'])
assert atom[0] == Atom('C')
assert atom[1] == Atom('C')
assert len(atom.atom) == 1
atom[1] = Atom('Au', [-1] * 2)
assert atom[0] == Atom('C')
assert atom[1] != Atom('Au')
assert atom[1] == Atom('Au', [-1] * 2)
assert len(atom.atom) == 2
def test_set2(self):
# Add new atoms to the set
atom = Atoms(['C', 'C'])
assert_true(atom[0] == Atom('C'))
assert_true(atom[1] == Atom('C'))
assert_true(len(atom.atom) == 1)
atom[1] = Atom('Au', orbs=2)
assert_true(atom[0] == Atom('C'))
assert_false(atom[1] == Atom('Au'))
assert_true(atom[1] == Atom('Au', orbs=2))
assert_true(len(atom.atom) == 2)
def test_replace1():
# Add new atoms to the set
atom = Atoms(['C'] * 10 + ['B'] * 2)
atom[range(1, 4)] = Atom('Au', [-1] * 2)
assert atom[0] == Atom('C')
for i in range(1, 4):
assert atom[i] != Atom('Au')
assert atom[i] == Atom('Au', [-1] * 2)
assert atom[4] != Atom('Au')
assert atom[4] != Atom('Au', [-1] * 2)
assert len(atom.atom) == 3
atom.replace(atom[0], Atom('C', [-1] * 2))
assert atom[0] == Atom('C', [-1] * 2)
assert len(atom.atom) == 3
assert atom[0] == Atom('C', [-1] * 2)
for i in range(4, 10):
assert atom[i] == Atom('C', [-1] * 2)
for i in range(1, 4):
assert atom[i] == Atom('Au', [-1] * 2)
for i in range(10, 12):
assert atom[i] == Atom('B')
def test_append1():
# Add new atoms to the set
atom1 = Atoms(['C', 'C'])
assert atom1[0] == Atom('C')
assert atom1[1] == Atom('C')
atom2 = Atoms([Atom('C', tag='DZ'), Atom[6]])
assert atom2[0] == Atom('C', tag='DZ')
assert atom2[1] == Atom('C')
atom = atom1.append(atom2)
assert atom[0] == Atom('C')
assert atom[1] == Atom('C')
assert atom[2] == Atom('C', tag='DZ')
assert atom[3] == Atom('C')
atom = atom1.append(Atom(6, tag='DZ'))
assert atom[0] == Atom('C')
assert atom[1] == Atom('C')
assert atom[2] == Atom('C', tag='DZ')
atom = atom1.append([Atom(6, tag='DZ'), Atom[6]])
assert atom[0] == Atom('C')
assert atom[1] == Atom('C')
assert atom[2] == Atom('C', tag='DZ')
assert atom[3] == Atom('C')
def test_set3():
# Add new atoms to the set
atom = Atoms(['C'] * 10)
atom[range(1, 4)] = Atom('Au', [-1] * 2)
assert atom[0] == Atom('C')
for i in range(1, 4):
assert atom[i] != Atom('Au')
assert atom[i] == Atom('Au', [-1] * 2)
assert atom[4] != Atom('Au')
assert atom[4] != Atom('Au', [-1] * 2)
assert len(atom.atom) == 2
atom[1:4] = Atom('C')
assert len(atom.atom) == 2
def test_set3(self):
# Add new atoms to the set
atom = Atoms(['C'] * 10)
atom[range(1, 4)] = Atom('Au', orbs=2)
assert_true(atom[0] == Atom('C'))
for i in range(1, 4):
assert_false(atom[i] == Atom('Au'))
assert_true(atom[i] == Atom('Au', orbs=2))
assert_false(atom[4] == Atom('Au'))
assert_false(atom[4] == Atom('Au', orbs=2))
assert_true(len(atom.atom) == 2)
atom[1:4] = Atom('C')
assert_true(len(atom.atom) == 2)
def test_create1(setup):
atom1 = Atoms([setup.C, setup.C3, setup.Au])
atom2 = Atoms(['C', 'C', 'Au'])
atom3 = Atoms(['C', 6, 'Au'])
atom4 = Atoms(['Au', 6, 'C'])
assert atom2 == atom3
assert atom2 != atom4
assert atom2.hassame(atom4)
def test_reduce1():
atom = Atoms(['C', 'Au'])
atom = atom.sub(0)
atom1 = atom.reduce()
assert atom[0] == Atom[6]
assert len(atom) == 1
assert len(atom.atom) == 2
assert atom1[0] == Atom[6]
assert atom1[0] != Atom[8]
assert len(atom1) == 1
assert len(atom1.atom) == 1
atom.reduce(True)
assert atom[0] == Atom[6]
assert len(atom) == 1
assert len(atom.atom) == 1
def read_geometry(self):
""" Returns Geometry object from a Siesta.nc file """
# Read supercell
sc = self.read_supercell()
xyz = np.array(self._value('xa'), np.float64)
xyz.shape = (-1, 3)
if 'BASIS' in self.groups:
basis = self.read_basis()
species = self.groups['BASIS'].variables['basis'][:] - 1
atom = Atoms([basis[i] for i in species])
else:
atom = Atom(1)
xyz *= Bohr2Ang
# Create and return geometry object
geom = Geometry(xyz, atom, sc=sc)
return geom
def test_iter1():
# Add new atoms to the set
atom = Atoms(['C', 'C'])
for a in atom.iter():
assert a == Atom[6]
for a, idx in atom.iter(True):
assert a == Atom[6]
assert len(idx) == 2
atom = Atoms(['C', 'Au', 'C', 'Au'])
for i, aidx in enumerate(atom.iter(True)):
a, idx = aidx
if i == 0:
assert a == Atom[6]
assert (idx == [0, 2]).all()
elif i == 1:
assert a == Atom['Au']
assert (idx == [1, 3]).all()
assert len(idx) == 2
def test_reorder1():
atom = Atoms(['C', 'Au'])
atom = atom.sub(1)
atom1 = atom.reorder()
# Check we haven't done anything to the original Atoms object
assert atom[0] == Atom['Au']
assert atom.specie[0] == 1
assert len(atom) == 1
assert len(atom.atom) == 2
assert atom1[0] == Atom['Au']
assert atom1.specie[0] == 0
assert len(atom1) == 1
assert len(atom1.atom) == 2
# Do in-place
atom.reorder(True)
assert atom[0] == Atom['Au']
assert atom.specie[0] == 0
assert len(atom) == 1
assert len(atom.atom) == 2
def test_replace2():
# Add new atoms to the set
atom = Atoms(['C'] * 10 + ['B'] * 2)
atom.replace(range(1, 4), Atom('Au', [-1] * 2))
assert atom[0] == Atom('C')
for i in range(1, 4):
assert atom[i] != Atom('Au')
assert atom[i] == Atom('Au', [-1] * 2)
assert atom[4] != Atom('Au')
assert atom[4] != Atom('Au', [-1] * 2)
assert len(atom.atom) == 3
# Second replace call (equivalent to replace_atom)
atom.replace(atom[0], Atom('C', [-1] * 2))
assert atom[0] == Atom('C', [-1] * 2)
assert len(atom.atom) == 3
assert atom[0] == Atom('C', [-1] * 2)
for i in range(4, 10):
assert atom[i] == Atom('C', [-1] * 2)
for i in range(1, 4):
assert atom[i] == Atom('Au', [-1] * 2)
for i in range(10, 12):
assert atom[i] == Atom('B')
def test_len(setup):
atom = Atoms([setup.C, setup.C3, setup.Au])
assert len(atom) == 3
assert len(atom.q0) == 3
def test_create_map():
atom = Atoms(map(lambda x: x, [1, 2, 3]))
assert len(atom) == 3
def test_create2():
atom = Atoms(Atom(6, R=1.45), na=2)
atom = Atoms(atom, na=4)
assert atom[0].maxR() == 1.45
for ia in range(len(atom)):
assert atom.maxR(True)[ia] == 1.45
