def test_water():
from ase.calculators.gaussian import Gaussian
from ase.atoms import Atoms
from ase.optimize.lbfgs import LBFGS
from ase.io import read
# First test to make sure Gaussian works
calc = Gaussian(xc='pbe', chk='water.chk', label='water')
calc.clean()
water = Atoms('OHH',
positions=[(0, 0, 0), (1, 0, 0), (0, 1, 0)],
calculator=calc)
opt = LBFGS(water)
opt.run(fmax=0.05)
forces = water.get_forces()
energy = water.get_potential_energy()
positions = water.get_positions()
# Then test the IO routines
water2 = read('water.log')
forces2 = water2.get_forces()
energy2 = water2.get_potential_energy()
positions2 = water2.get_positions()
# Compare distances since positions are different in standard orientation.
dist = water.get_all_distances()
dist2 = read('water.log', index=-1).get_all_distances()
assert abs(energy - energy2) < 1e-7
assert abs(forces - forces2).max() < 1e-9
assert abs(positions - positions2).max() < 1e-6
assert abs(dist - dist2).max() < 1e-6
def write_dftb(filename, atoms):
"""Method to write atom structure in DFTB+ format
(gen format)
"""
import numpy as np
#sort
atoms.set_masses()
masses = atoms.get_masses()
indexes = np.argsort(masses)
atomsnew = Atoms()
for i in indexes:
atomsnew = atomsnew + atoms[i]
if isinstance(filename, str):
myfile = open(filename, 'w')
else: # Assume it's a 'file-like object'
myfile = filename
ispbc = atoms.get_pbc()
box = atoms.get_cell()
if (any(ispbc)):
myfile.write('%8d %2s \n' %(len(atoms), 'S'))
else:
myfile.write('%8d %2s \n' %(len(atoms), 'C'))
chemsym = atomsnew.get_chemical_symbols()
allchem = ''
for i in chemsym:
if i not in allchem:
allchem = allchem + i + ' '
myfile.write(allchem+' \n')
coords = atomsnew.get_positions()
itype = 1
for iatom, coord in enumerate(coords):
if iatom > 0:
if chemsym[iatom] != chemsym[iatom-1]:
itype = itype+1
myfile.write('%5i%5i %19.16f %19.16f %19.16f \n' \
%(iatom+1, itype,
coords[iatom][0], coords[iatom][1], coords[iatom][2]))
# write box
if (any(ispbc)):
#dftb dummy
myfile.write(' %19.16f %19.16f %19.16f \n' %(0, 0, 0))
myfile.write(' %19.16f %19.16f %19.16f \n'
%( box[0][0], box[0][1], box[0][2]))
myfile.write(' %19.16f %19.16f %19.16f \n'
%( box[1][0], box[1][1], box[1][2]))
myfile.write(' %19.16f %19.16f %19.16f \n'
%( box[2][0], box[2][1], box[2][2]))
if type(filename) == str:
myfile.close()
def write_dftb(filename, atoms):
"""Method to write atom structure in DFTB+ format
(gen format)
"""
import numpy as np
#sort
atoms.set_masses()
masses = atoms.get_masses()
indexes = np.argsort(masses)
atomsnew = Atoms()
for i in indexes:
atomsnew = atomsnew + atoms[i]
if isinstance(filename, str):
myfile = open(filename, 'w')
else: # Assume it's a 'file-like object'
myfile = filename
ispbc = atoms.get_pbc()
box = atoms.get_cell()
if (any(ispbc)):
myfile.write('%8d %2s \n' % (len(atoms), 'S'))
else:
myfile.write('%8d %2s \n' % (len(atoms), 'C'))
chemsym = atomsnew.get_chemical_symbols()
allchem = ''
for i in chemsym:
if i not in allchem:
allchem = allchem + i + ' '
myfile.write(allchem + ' \n')
coords = atomsnew.get_positions()
itype = 1
for iatom, coord in enumerate(coords):
if iatom > 0:
if chemsym[iatom] != chemsym[iatom - 1]:
itype = itype + 1
myfile.write('%5i%5i %19.16f %19.16f %19.16f \n' \
%(iatom+1, itype,
coords[iatom][0], coords[iatom][1], coords[iatom][2]))
# write box
if (any(ispbc)):
#dftb dummy
myfile.write(' %19.16f %19.16f %19.16f \n' % (0, 0, 0))
myfile.write(' %19.16f %19.16f %19.16f \n' %
(box[0][0], box[0][1], box[0][2]))
myfile.write(' %19.16f %19.16f %19.16f \n' %
(box[1][0], box[1][1], box[1][2]))
myfile.write(' %19.16f %19.16f %19.16f \n' %
(box[2][0], box[2][1], box[2][2]))
if isinstance(filename, str):
myfile.close()
def read_gen(fileobj):
"""Read structure in GEN format (refer to DFTB+ manual).
Multiple snapshot are not allowed. """
if isinstance(fileobj, str):
fileobj = open(fileobj)
image = Atoms()
lines = fileobj.readlines()
line = lines[0].split()
natoms = int(line[0])
pb_flag = line[1]
if line[1] not in ['C', 'F', 'S']:
raise IOError(
'Error in line #1: only C (Cluster), S (Supercell) or F (Fraction)'
+ 'are valid options')
# Read atomic symbols
line = lines[1].split()
# Define a dictionary with symbols-id
symboldict = dict()
symbolid = 1
for symb in line:
symboldict[symbolid] = symb
symbolid += 1
# Read atoms (GEN format supports only single snapshot)
del lines[:2]
positions = []
symbols = []
for line in lines[:natoms]:
dummy, symbolid, x, y, z = line.split()[:5]
symbols.append(symboldict[int(symbolid)])
positions.append([float(x), float(y), float(z)])
image = Atoms(symbols=symbols, positions=positions)
del lines[:natoms]
# If Supercell, parse periodic vectors.
# If Fraction, translate into Supercell.
if pb_flag == 'C':
return image
else:
# Dummy line: line after atom positions is not uniquely defined
# in gen implementations, and not necessary in DFTB package
del lines[:1]
image.set_pbc([True, True, True])
p = []
for i in range(3):
x, y, z = lines[i].split()[:3]
p.append([float(x), float(y), float(z)])
image.set_cell([(p[0][0], p[0][1], p[0][2]),
(p[1][0], p[1][1], p[1][2]),
(p[2][0], p[2][1], p[2][2])])
if pb_flag == 'F':
frac_positions = image.get_positions()
image.set_scaled_positions(frac_positions)
return image
def test_co_kernel_derivative(self):
direction = np.array([1., 2., 3.])
direction /= np.linalg.norm(direction)
atoms = Atoms(['C', 'O'],
positions=np.array([-0.5 * direction, 0.5 * direction]))
atoms.set_calculator(EMT())
def to_radius(x):
xyzs = x.get_positions()
r = np.sqrt(np.sum((xyzs[1, :] - xyzs[0, :])**2))
dr = np.zeros((1, 6))
dr[0, 0] = (xyzs[0, 0] - xyzs[1, 0]) / r
dr[0, 1] = (xyzs[0, 1] - xyzs[1, 1]) / r
dr[0, 2] = (xyzs[0, 2] - xyzs[1, 2]) / r
dr[0, 3] = (xyzs[1, 0] - xyzs[0, 0]) / r
dr[0, 4] = (xyzs[1, 1] - xyzs[0, 1]) / r
dr[0, 5] = (xyzs[1, 2] - xyzs[0, 2]) / r
return [r], dr
kernel = RBFKernel(constant=100.0, length_scale=0.23)
calc = NCGPRCalculator(input_transform=to_radius,
kernel=kernel,
C1=1e8,
C2=1e8,
opt_restarts=0)
calc.add_data(atoms)
K = calc.build_kernel_matrix()
K_num = np.zeros_like(K)
# kernel value is not tested:
K_num[0, 0] = K[0, 0]
x0 = atoms.get_positions()
dx = 1e-4
def K_fun(x, y):
a = np.array([to_radius(Atoms(['C', 'O'], positions=x))[0]])
b = np.array([to_radius(Atoms(['C', 'O'], positions=y))[0]])
return calc.kernel(a, b, dx=True, dy=True)[0, 0]
for i in range(6):
dxi = np.zeros(6)
dxi[i] = dx
dxi = dxi.reshape((2, 3))
# Test first derivative
K_num[1 + i, 0] = self.num_dx_forth_order(K_fun, x0, x0, dxi)
for j in range(6):
dxj = np.zeros(6)
dxj[j] = dx
dxj = dxj.reshape((2, 3))
K_num[1 + i, 1 + j] = self.num_dxdy_forth_order(
K_fun, x0, x0, dxi, dxj)
# Test symmetry of derivatives
K_num[0, 1 + i] = self.num_dy_forth_order(K_fun, x0, x0, dxi)
np.testing.assert_allclose(K, K_num, atol=1E-5)
def read_geometry(filename, dir='.'):
fh = open(os.path.join(dir, filename), 'rb')
lines = list(filter(read_geometry_filter, fh.readlines()))
# return geometry in ASE format
geometry = []
for line in lines:
sline = line.split()
# find chemical symbol (the symbols in the file are lowercase)
symbol = sline[-1]
for s in chemical_symbols:
if symbol == s.lower():
symbol = s
break
geometry.append(Atom(symbol=symbol, position=sline[:-1]))
fh.close()
atoms = Atoms(geometry)
atoms.set_positions(atoms.get_positions()*Bohr) # convert to Angstrom
return atoms
def unf(phonon, sc_mat, qpoints, knames=None, x=None, xpts=None):
prim = phonon.get_primitive()
prim = Atoms(symbols=prim.get_chemical_symbols(),
cell=prim.get_cell(),
positions=prim.get_positions())
#vesta_view(prim)
sc_qpoints = np.array([np.dot(q, sc_mat) for q in qpoints])
phonon.set_qpoints_phonon(sc_qpoints, is_eigenvectors=True)
freqs, eigvecs = phonon.get_qpoints_phonon()
uf = phonon_unfolder(atoms=prim,
supercell_matrix=sc_mat,
eigenvectors=eigvecs,
qpoints=sc_qpoints,
phase=False)
weights = uf.get_weights()
#ax=plot_band_weight([list(x)]*freqs.shape[1],freqs.T*8065.6,weights[:,:].T*0.98+0.01,xticks=[knames,xpts],style='alpha')
ax = plot_band_weight([list(x)] * freqs.shape[1],
freqs.T * 33.356,
weights[:, :].T * 0.99 + 0.001,
xticks=[knames, xpts],
style='alpha')
return ax
def test_fix_symmetry_shuffle_indices():
atoms = Atoms('AlFeAl6',
cell=[6] * 3,
positions=[[0, 0, 0], [2.9, 2.9, 2.9], [0, 0, 3], [0, 3, 0],
[0, 3, 3], [3, 0, 0], [3, 0, 3], [3, 3, 0]],
pbc=True)
atoms.set_constraint(FixSymmetry(atoms))
at_permut = atoms[[0, 2, 3, 4, 5, 6, 7, 1]]
pos0 = atoms.get_positions()
def perturb(atoms, pos0, at_i, dpos):
positions = pos0.copy()
positions[at_i] += dpos
atoms.set_positions(positions)
new_p = atoms.get_positions()
return pos0[at_i] - new_p[at_i]
dp1 = perturb(atoms, pos0, 1, (0.0, 0.1, -0.1))
dp2 = perturb(atoms, pos0, 2, (0.0, 0.1, -0.1))
pos0 = at_permut.get_positions()
permut_dp1 = perturb(at_permut, pos0, 7, (0.0, 0.1, -0.1))
permut_dp2 = perturb(at_permut, pos0, 1, (0.0, 0.1, -0.1))
assert np.max(np.abs(dp1 - permut_dp1)) < 1.0e-10
assert np.max(np.abs(dp2 - permut_dp2)) < 1.0e-10
force='force',
nproc=1,
chk='water.chk',
label='water')
calc.clean()
water = Atoms('OHH',
positions=[(0, 0, 0), (1, 0, 0), (0, 1, 0)],
calculator=calc)
opt = LBFGS(water)
opt.run(fmax=0.05)
forces = water.get_forces()
energy = water.get_potential_energy()
positions = water.get_positions()
# Then test the IO routines
from ase.io import read
water2 = read('water.log')
forces2 = water2.get_forces()
energy2 = water2.get_potential_energy()
positions2 = water2.get_positions()
#compare distances since positions are different in standard orientation
dist = water.get_all_distances()
dist2 = read('water.log', quantity='structures')[-1].get_all_distances()
assert abs(energy - energy2) < 1e-7
assert abs(forces - forces2).max() < 1e-9
assert abs(positions - positions2).max() < 1e-6
assert abs(dist - dist2).max() < 1e-6
class ifc_parser():
def __init__(self,
symbols,
fname='abinit_ifc.out',
primitive_atoms=None,
cell=np.eye(3)):
with open(fname) as myfile:
self.lines = myfile.readlines()
self.R = []
self.G = []
self.ifc = []
self.atom_positions = []
self.split()
self.read_info()
self.read_lattice()
self.atoms = Atoms(symbols, positions=self.atom_positions, cell=self.R)
self.primitive_atoms = primitive_atoms
self.atoms.set_positions(self.atom_positions)
self.read_ifc()
self.map_ifc_to_primitive_cell()
self.make_model()
def split(self):
lines = self.lines
self.info_lines = []
self.lattice_lines = []
self.ifc_lines = {}
inp_block = False
lat_block = False
ifc_block = False
for iline, line in enumerate(lines):
# input variables
if line.strip().startswith("-outvars_anaddb:"):
inp_block = True
if line.strip().startswith("========="):
inp_block = False
if inp_block:
self.info_lines.append(line.strip())
# lattice vectors
if line.strip().startswith("read the DDB information"):
lat_block = True
if line.strip().startswith("========="):
lat_block = False
if lat_block:
self.lattice_lines.append(line.strip())
# IFC block
if line.strip().startswith(
"Calculation of the interatomic forces"):
ifc_block = True
if line.strip().startswith("========="):
ifc_block = False
if ifc_block:
if line.strip().startswith('generic atom number'):
iatom = int(line.split()[-1])
atom_position = map(float, lines[iline + 1].split()[-3:])
self.atom_positions.append(np.array(atom_position) * Bohr)
if line.find('interaction with atom') != -1:
jinter = int(line.split()[0])
self.ifc_lines[(iatom, jinter)] = lines[iline:iline + 15]
def read_info(self):
self.invars = {}
keys = ('asr', 'chneut', 'dipdip', 'ifcflag', 'ifcana', 'ifcout',
'natifc', 'brav')
lines = self.info_lines
for line in lines:
for key in keys:
val = read_value(line, key)
if val:
self.invars[key] = int(val)
#print(self.invars)
def read_lattice(self):
lines = self.lattice_lines
#print lines
for line in lines:
if line.startswith('R('):
self.R.append(np.array((map(float, line.split()[1:4]))) * Bohr)
self.G.append(np.array((map(float, line.split()[5:8]))) / Bohr)
#print(self.R)
def read_ifc_elem(self, iatom, iinter):
lines = self.ifc_lines[(iatom, iinter)]
w = lines[0].strip().split()
jatom = int(w[-3])
jcell = int(w[-1])
pos_j = [float(x) * Bohr for x in lines[1].strip().split()[-3:]]
distance = float(lines[2].strip().split()[-1]) * Bohr
# check distance
# Fortran format F9.5: some values are not seperated by whitespaces.
# Maybe better fit that in abinit code.
#ifc0= map(float, lines[3].strip().split()[0:3])
#ifc1= map(float, lines[4].strip().split()[0:3])
#ifc2= map(float, lines[5].strip().split()[0:3])
#ifc=np.array([ifc0, ifc1, ifc2]).T * Hartree / Bohr**2
#print lines[3]
ifc0 = map(float,
[lines[3][i * 9 + 1:i * 9 + 9 + 1] for i in range(3)])
ifc1 = map(float,
[lines[4][i * 9 + 1:i * 9 + 9 + 1] for i in range(3)])
ifc2 = map(float,
[lines[5][i * 9 + 1:i * 9 + 9 + 1] for i in range(3)])
ifc = np.array([ifc0, ifc1, ifc2]).T * Hartree / Bohr**2
#ifc = np.array([ifc0, ifc1, ifc2]) * Hartree / Bohr**2
if not ('dipdip' in self.invars and self.invars['dipdip'] == 1):
ifc_ewald = None
ifc_sr = None
else:
ifc0 = map(
float,
[lines[3][i * 9 + 2:i * 9 + 9 + 2] for i in range(3, 6)])
ifc1 = map(
float,
[lines[4][i * 9 + 2:i * 9 + 9 + 2] for i in range(3, 6)])
ifc2 = map(
float,
[lines[5][i * 9 + 2:i * 9 + 9 + 2] for i in range(3, 6)])
#ifc0= map(float, lines[3].strip().split()[3:6])
#ifc1= map(float, lines[4].strip().split()[3:6])
#ifc2= map(float, lines[5].strip().split()[3:6])
ifc_ewald = np.array([ifc0, ifc1, ifc2])
ifc0 = map(
float,
[lines[3][i * 9 + 3:i * 9 + 9 + 3] for i in range(6, 9)])
ifc1 = map(
float,
[lines[4][i * 9 + 3:i * 9 + 9 + 3] for i in range(6, 9)])
ifc2 = map(
float,
[lines[5][i * 9 + 3:i * 9 + 9 + 3] for i in range(6, 9)])
#ifc0= map(float, lines[3].strip().split()[6:9])
#ifc1= map(float, lines[4].strip().split()[6:9])
#ifc2= map(float, lines[5].strip().split()[6:9])
ifc_sr = np.array([ifc0, ifc1, ifc2])
# sanity check
poses = self.atoms.get_positions()
jpos = pos_j
ipos = poses[iatom - 1]
np.array(jpos)
if not np.abs(np.linalg.norm(np.array(jpos) - ipos) - distance) < 1e-5:
print "Warning: distance wrong", "iatom: ", iatom, ipos, "jatom", jatom, jpos
return {
"iatom": iatom,
"jatom": jatom,
"jcell": jcell,
"jpos": pos_j,
"distance": distance,
"ifc": ifc,
"ifc_ewald": ifc_ewald,
"ifc_sr": ifc_sr
}
def read_ifc(self):
natom, niteraction = sorted(self.ifc_lines.keys())[-1]
for iatom in range(1, natom + 1):
for iint in range(1, niteraction + 1):
self.ifc.append(self.read_ifc_elem(iatom, iint))
def map_ifc_to_primitive_cell(self):
if self.primitive_atoms is None:
return
pcell = self.primitive_atoms.get_cell()
new_ifc = []
for ifce in self.ifc:
# remove atoms outside of primitive cell
if ifce['iatom'] <= len(self.primitive_atoms):
jpos = ifce['jpos']
for i, pos in enumerate(self.primitive_atoms.get_positions()):
dis = jpos - pos
R = np.linalg.solve(pcell, dis)
if np.all(
np.isclose(
np.mod(R + 1e-4, [1, 1, 1]), [0, 0, 0],
atol=1e-3)):
jatom = i + 1
#print "Found: " ,jatom
break
ifce['jatom'] = jatom
new_ifc.append(ifce)
self.ifc = new_ifc
def make_model2(self):
pass
def make_model(self):
if self.primitive_atoms is not None:
atoms = self.primitive_atoms
else:
atoms = self.atoms
lat = atoms.get_cell()
apos = atoms.get_scaled_positions()
masses = atoms.get_masses()
orb = []
for pos in apos:
for i in range(3):
orb.append(pos)
#print orb
model = mytb(3, 3, lat=lat, orb=orb)
self.tbmodel = pythtb.tbmodel(3, 3, lat=lat, orb=orb)
#model = self.tbmodel
atom_positions = atoms.get_positions()
hopdict = {}
for ifce in self.ifc:
#print ifce
iatom = ifce['iatom']
jatom = ifce['jatom']
jpos = ifce['jpos']
Ri = atom_positions[iatom - 1]
Rj = atom_positions[jatom - 1]
dis = jpos - Rj
#print self.atoms.get_cell()
R = np.linalg.solve(atoms.get_cell(), dis)
#print R
R = [int(round(x)) for x in R]
if not np.isclose(
np.dot(atoms.get_cell(), R) + atom_positions[jatom - 1],
jpos,
atol=1e-4).all():
print("Warning: Not equal", np.dot(atoms.get_cell(), R) +
atom_positions[jatom - 1], jpos)
#if not np.isclose(np.linalg.norm(jpos-Ri),ifce['distance']):
# print("Warning: Not equal to distance", np.linalg.norm(jpos-Ri), ifce['distance'])
#print R
for a in range(3):
for b in range(3):
i = 3 * (iatom - 1) + a
j = 3 * (jatom - 1) + b
val = ifce['ifc'][a, b] / np.sqrt(masses[iatom - 1] *
masses[jatom - 1])
#print i,j,R
if iatom == jatom and a == b and R == [0, 0, 0]:
model.set_onsite(val, ind_i=i)
else:
if (np.abs(val)) > 0.00000001:
model.set_hop(
val, i, j, R, allow_conjugate_pair=True)
R = tuple(R)
hopdict[(
i,
j,
R, )] = val
#model.set_hop_dis(val,i,j,jpos-Ri)
#print self.atoms.get_positions()
self.model = model
#print(len(hopdict))
for hop in hopdict:
i, j, R = hop
mR = tuple(-np.array(R))
if (
j,
i,
mR, ) not in hopdict:
print "Warning: ", (j, i, mR), "not in IFC"
delta = np.abs(hopdict[(
i,
j,
R, )] - hopdict[(
j,
i,
mR, )])
if delta > 0.000001:
print "Warning: ", (j, i, mR), "differ, delta=", delta
def solve_model(self, output_figure=None, show=False):
my_model = self.model
# generate k-point path and labels
path = np.array([[0.0, 0.0, 0.0], [0.5, 0.0, 0.0], [0.5, 0.5, 0.0],
[0, 0, 0], [0.5, 0.5, 0.5], [.5, 0, 0]])
label = (r'$\Gamma $', r'$X$', r'$M$', r'$\Gamma$', r'$R$', r'X')
(k_vec, k_dist, k_node) = self.tbmodel.k_path(path, 301)
print('---------------------------------------')
print('starting calculation')
print('---------------------------------------')
print('Calculating bands...')
# solve for eigenenergies of hamiltonian on
# the set of k-points from above
evals = my_model.solve_all(k_vec)
s = np.sign(evals)
v = np.sqrt(s * evals)
#v = np.sqrt(np.abs(evals.real)) * np.sign(evals.real)
evals = s * v * 15.633302 * 33.256
# plotting of band structure
print('Plotting bandstructure...')
# First make a figure object
fig, ax = plt.subplots()
# specify horizontal axis details
ax.set_xlim([0, k_node[-1]])
ax.set_xticks(k_node)
ax.set_xticklabels(label)
ax.axhline(y=0, linestyle='--')
for n in range(len(k_node)):
ax.axvline(x=k_node[n], linewidth=0.5, color='k')
# plot bands
for n in range(evals.shape[0]):
ax.plot(k_dist, evals[n])
# put title
ax.set_title("band structure")
ax.set_xlabel("Path in k-space")
ax.set_ylabel("Band energy")
# make an PDF figure of a plot
fig.tight_layout()
if output_figure is not None:
fig.savefig(output_figure)
if show:
plt.show()
print('Done.\n')
def __init__(self, geometry=None, **kwargs) -> None:
if geometry == None:
atoms = Atoms(**kwargs)
elif type(geometry) == ase.atoms.Atoms:
atoms = geometry.copy()
elif Path(geometry).is_file():
if str(Path(geometry).parts[-1]) == "geometry.in.next_step":
atoms = ase.io.read(geometry, format="aims")
else:
try:
atoms = ase.io.read(geometry)
except Exception as excpt:
logger.error(str(excpt))
raise Exception(
"ASE was not able to recognize the file format, e.g., a non-standard cif-format."
)
elif Path(geometry).is_dir():
raise Exception(
"You specified a directory as input. The geometry must be a file."
)
else:
atoms = None
assert type(atoms) == ase.atoms.Atoms, "Atoms not read correctly."
# Get data from another Atoms object:
numbers = atoms.get_atomic_numbers()
positions = atoms.get_positions()
cell = atoms.get_cell()
celldisp = atoms.get_celldisp()
pbc = atoms.get_pbc()
constraint = [c.copy() for c in atoms.constraints]
masses = atoms.get_masses()
magmoms = None
charges = None
momenta = None
if atoms.has("initial_magmoms"):
magmoms = atoms.get_initial_magnetic_moments()
if atoms.has("initial_charges"):
charges = atoms.get_initial_charges()
if atoms.has("momenta"):
momenta = atoms.get_momenta()
self.arrays = {}
super().__init__(
numbers=numbers,
positions=positions,
cell=cell,
celldisp=celldisp,
pbc=pbc,
constraint=constraint,
masses=masses,
magmoms=magmoms,
charges=charges,
momenta=momenta,
)
self._is_1d = None
self._is_2d = None
self._is_3d = None
self._periodic_axes = None
self._check_lattice_vectors()
try:
self.sg = ase.spacegroup.get_spacegroup(self, symprec=1e-2)
except:
self.sg = ase.spacegroup.Spacegroup(1)
self.lattice = self.cell.get_bravais_lattice().crystal_family
from ase.atoms import Atoms
from ase.optimize.lbfgs import LBFGS
# First test to make sure Gaussian works
calc = Gaussian(method='pbepbe', basis='sto-3g', force='force',
nproc=1, chk='water.chk', label='water')
calc.clean()
water = Atoms('OHH',
positions=[(0., 0. ,0. ), (1. ,0. ,0. ), (0. ,1. ,0. )],
calculator=calc)
opt = LBFGS(water)
opt.run(fmax=0.05)
forces = water.get_forces()
energy = water.get_potential_energy()
positions = water.get_positions()
# Then test the IO routines
from ase.io import read
water2 = read('water/water.log')
forces2 = water2.get_forces()
energy2 = water2.get_potential_energy()
positions2 = water2.get_positions()
assert (energy - energy2) < 1e-14
assert (forces.all() - forces2.all()) < 1e-14
assert (positions.all() - positions2.all()) < 1e-14