def setUp(self):
for virtvar in ['boundaries', 'celltype']:
assert getattr(self,virtvar) is not None, 'Virtual "%s"!' % virtvar
# Basic unit cell information:
pbc_c = {'zero' : (False,False,False), \
'periodic': (True,True,True), \
'mixed' : (True, False, True)}[self.boundaries]
a, b = self.a, 2**0.5*self.a
cell_cv = {'general' : np.array([[0,a,a],[a/2,0,a/2],[a/2,a/2,0]]),
'rotated' : np.array([[0,0,b],[b/2,0,0],[0,b/2,0]]),
'inverted' : np.array([[0,0,b],[0,b/2,0],[b/2,0,0]]),
'orthogonal': np.diag([b, b/2, b/2])}[self.celltype]
cell_cv = np.array([(4-3*pbc)*c_v for pbc,c_v in zip(pbc_c, cell_cv)])
# Decide how many kpoints to sample from the 1st Brillouin Zone
kpts_c = np.ceil((10/Bohr)/np.sum(cell_cv**2,axis=1)**0.5).astype(int)
kpts_c = tuple(kpts_c*pbc_c + 1-pbc_c)
bzk_kc = kpts2ndarray(kpts_c)
self.gamma = len(bzk_kc) == 1 and not bzk_kc[0].any()
#p = InputParameters()
#Z_a = self.atoms.get_atomic_numbers()
#xcfunc = XC(p.xc)
#setups = Setups(Z_a, p.setups, p.basis, p.lmax, xcfunc)
#symmetry, weight_k, self.ibzk_kc = reduce_kpoints(self.atoms, bzk_kc,
# setups, p.usesymm)
self.ibzk_kc = bzk_kc.copy() # don't use symmetry reduction of kpoints
self.nibzkpts = len(self.ibzk_kc)
self.ibzk_kv = kpoint_convert(cell_cv, skpts_kc=self.ibzk_kc)
# Parse parallelization parameters and create suitable communicators.
#parsize_domain, parsize_bands = create_parsize_minbands(self.nbands, world.size)
parsize_domain, parsize_bands = world.size//gcd(world.size, self.nibzkpts), 1
assert self.nbands % np.prod(parsize_bands) == 0
domain_comm, kpt_comm, band_comm = distribute_cpus(parsize_domain,
parsize_bands, self.nspins, self.nibzkpts)
# Set up band descriptor:
self.bd = BandDescriptor(self.nbands, band_comm)
# Set up grid descriptor:
N_c = np.round(np.sum(cell_cv**2, axis=1)**0.5 / self.h)
N_c += 4-N_c % 4 # makes domain decomposition easier
self.gd = GridDescriptor(N_c, cell_cv, pbc_c, domain_comm, parsize_domain)
self.assertEqual(self.gamma, np.all(~self.gd.pbc_c))
# What to do about kpoints?
self.kpt_comm = kpt_comm
if debug and world.rank == 0:
comm_sizes = tuple([comm.size for comm in [world, self.bd.comm, \
self.gd.comm, self.kpt_comm]])
print '%d world, %d band, %d domain, %d kpt' % comm_sizes
def setUp(self):
for virtvar in ['boundaries', 'celltype']:
assert getattr(self,virtvar) is not None, 'Virtual "%s"!' % virtvar
# Basic unit cell information:
pbc_c = {'zero' : (False,False,False), \
'periodic': (True,True,True), \
'mixed' : (True, False, True)}[self.boundaries]
a, b = self.a, 2**0.5*self.a
cell_cv = {'general' : np.array([[0,a,a],[a/2,0,a/2],[a/2,a/2,0]]),
'rotated' : np.array([[0,0,b],[b/2,0,0],[0,b/2,0]]),
'inverted' : np.array([[0,0,b],[0,b/2,0],[b/2,0,0]]),
'orthogonal': np.diag([b, b/2, b/2])}[self.celltype]
cell_cv = np.array([(4-3*pbc)*c_v for pbc,c_v in zip(pbc_c, cell_cv)])
# Decide how many kpoints to sample from the 1st Brillouin Zone
kpts_c = np.ceil((10/Bohr)/np.sum(cell_cv**2,axis=1)**0.5).astype(int)
kpts_c = tuple(kpts_c*pbc_c + 1-pbc_c)
bzk_kc = kpts2ndarray(kpts_c)
self.gamma = len(bzk_kc) == 1 and not bzk_kc[0].any()
#p = InputParameters()
#Z_a = self.atoms.get_atomic_numbers()
#xcfunc = XC(p.xc)
#setups = Setups(Z_a, p.setups, p.basis, p.lmax, xcfunc)
#symmetry, weight_k, self.ibzk_kc = reduce_kpoints(self.atoms, bzk_kc,
# setups, p.usesymm)
self.ibzk_kc = bzk_kc.copy() # don't use symmetry reduction of kpoints
self.nibzkpts = len(self.ibzk_kc)
self.ibzk_kv = kpoint_convert(cell_cv, skpts_kc=self.ibzk_kc)
# Parse parallelization parameters and create suitable communicators.
#parsize, parsize_bands = create_parsize_minbands(self.nbands, world.size)
parsize, parsize_bands = world.size//gcd(world.size, self.nibzkpts), 1
assert self.nbands % np.prod(parsize_bands) == 0
domain_comm, kpt_comm, band_comm = distribute_cpus(parsize,
parsize_bands, self.nspins, self.nibzkpts)
# Set up band descriptor:
self.bd = BandDescriptor(self.nbands, band_comm)
# Set up grid descriptor:
N_c = np.round(np.sum(cell_cv**2, axis=1)**0.5 / self.h)
N_c += 4-N_c % 4 # makes domain decomposition easier
self.gd = GridDescriptor(N_c, cell_cv, pbc_c, domain_comm, parsize)
self.assertEqual(self.gamma, np.all(~self.gd.pbc_c))
# What to do about kpoints?
self.kpt_comm = kpt_comm
if debug and world.rank == 0:
comm_sizes = tuple([comm.size for comm in [world, self.bd.comm, \
self.gd.comm, self.kpt_comm]])
print '%d world, %d band, %d domain, %d kpt' % comm_sizes
def get_bandpath_fcc(ase_atom, npoints=30):
# Set-up the band-path via special points
from ase.dft.kpoints import ibz_points, kpoint_convert, get_bandpath
points = ibz_points['fcc']
G = points['Gamma']
X = points['X']
W = points['W']
K = points['K']
L = points['L']
kpts_reduced, kpath, sp_points = get_bandpath([L, G, X, W, K, G],
ase_atom.cell, npoints=npoints)
kpts_cartes = kpoint_convert(ase_atom.cell, skpts_kc=kpts_reduced)
return kpts_reduced, kpts_cartes, kpath, sp_points
def get_bandpath_fcc(ase_atom, npoints=30):
# Set-up the band-path via special points
from ase.dft.kpoints import ibz_points, kpoint_convert, get_bandpath
points = ibz_points['fcc']
G = points['Gamma']
X = points['X']
W = points['W']
K = points['K']
L = points['L']
kpts_reduced, kpath, sp_points = get_bandpath([L, G, X, W, K, G],
ase_atom.cell, npoints=npoints)
kpts_cartes = kpoint_convert(ase_atom.cell, skpts_kc=kpts_reduced)
return kpts_reduced, kpts_cartes, kpath, sp_points
def get_bandpath_fcc(ase_atom, npoints=30):
# Set-up the band-path via special points
from ase.dft.kpoints import ibz_points, kpoint_convert, get_bandpath
points = ibz_points["fcc"]
G = points["Gamma"]
X = points["X"]
W = points["W"]
K = points["K"]
L = points["L"]
kpts_reduced, kpath, sp_points = get_bandpath([L, G, X, W, K, G], ase_atom.cell, npoints=npoints)
kpts_cartes = kpoint_convert(ase_atom.cell, skpts_kc=kpts_reduced)
return kpts_reduced, kpts_cartes, kpath, sp_points
def get_bandpath_as_aims_strings(self, pbc=[True, True, True]):
"""This function sets up the band path according to Setyawan-Curtarolo conventions.
Returns:
list: List of strings containing the k-path sections.
"""
from ase.dft.kpoints import parse_path_string, kpoint_convert
atoms = self.structure.atoms
atoms.pbc = pbc
path = parse_path_string(
atoms.cell.get_bravais_lattice(pbc=atoms.pbc).bandpath().path)
# list Of lists of path segments
points = atoms.cell.get_bravais_lattice(
pbc=atoms.pbc).bandpath().special_points
segments = []
for seg in path:
section = [(i, j) for i, j in zip(seg[:-1], seg[1:])]
segments.append(section)
output_bands = []
index = 1
for seg in segments:
output_bands.append(
"## Brillouin Zone section Nr. {:d}\n".format(index))
for sec in seg:
dist = np.array(points[sec[1]]) - np.array(points[sec[0]])
length = np.linalg.norm(
kpoint_convert(atoms.cell, skpts_kc=dist))
npoints = np.int_(np.round(np.asarray(length) * 20))
vec1 = "{:.6f} {:.6f} {:.6f}".format(*points[sec[0]])
vec2 = "{:.6f} {:.6f} {:.6f}".format(*points[sec[1]])
output_bands.append(
"{vec1} \t {vec2} \t {npoints} \t {label1} {label2}".
format(
label1=sec[0],
label2=sec[1],
npoints=npoints,
vec1=vec1,
vec2=vec2,
))
index += 1
return output_bands
def read_pw_out(fileobj, index=-1, results_required=True):
"""Reads Quantum ESPRESSO output files.
The atomistic configurations as well as results (energy, force, stress,
magnetic moments) of the calculation are read for all configurations
within the output file.
Will probably raise errors for broken or incomplete files.
Parameters
----------
fileobj : file|str
A file like object or filename
index : slice
The index of configurations to extract.
results_required : bool
If True, atomistic configurations that do not have any
associated results will not be included. This prevents double
printed configurations and incomplete calculations from being
returned as the final configuration with no results data.
Yields
------
structure : Atoms
The next structure from the index slice. The Atoms has a
SinglePointCalculator attached with any results parsed from
the file.
"""
if isinstance(fileobj, str):
fileobj = open(fileobj, 'rU')
# work with a copy in memory for faster random access
pwo_lines = fileobj.readlines()
# TODO: index -1 special case?
# Index all the interesting points
indexes = {
_PW_START: [],
_PW_END: [],
_PW_CELL: [],
_PW_POS: [],
_PW_MAGMOM: [],
_PW_FORCE: [],
_PW_TOTEN: [],
_PW_STRESS: [],
_PW_FERMI: [],
_PW_HIGHEST_OCCUPIED: [],
_PW_HIGHEST_OCCUPIED_LOWEST_FREE: [],
_PW_KPTS: [],
_PW_BANDS: [],
_PW_BANDSTRUCTURE: [],
_PW_ELECTROSTATIC_EMBEDDING: [],
_PW_NITER: [],
_PW_DONE: [],
_PW_WALLTIME: []
}
for idx, line in enumerate(pwo_lines):
for identifier in indexes:
if identifier in line:
indexes[identifier].append(idx)
# Configurations are either at the start, or defined in ATOMIC_POSITIONS
# in a subsequent step. Can deal with concatenated output files.
all_config_indexes = sorted(indexes[_PW_START] + indexes[_PW_POS])
# Slice only requested indexes
# setting results_required argument stops configuration-only
# structures from being returned. This ensures the [-1] structure
# is one that has results. Two cases:
# - SCF of last configuration is not converged, job terminated
# abnormally.
# - 'relax' and 'vc-relax' re-prints the final configuration but
# only 'vc-relax' recalculates.
if results_required:
results_indexes = sorted(indexes[_PW_TOTEN] + indexes[_PW_FORCE] +
indexes[_PW_STRESS] + indexes[_PW_MAGMOM] +
indexes[_PW_BANDS] +
indexes[_PW_ELECTROSTATIC_EMBEDDING] +
indexes[_PW_BANDSTRUCTURE])
# Prune to only configurations with results data before the next
# configuration
results_config_indexes = []
for config_index, config_index_next in zip(
all_config_indexes, all_config_indexes[1:] + [len(pwo_lines)]):
if any([
config_index < results_index < config_index_next
for results_index in results_indexes
]):
results_config_indexes.append(config_index)
# slice from the subset
image_indexes = results_config_indexes[index]
else:
image_indexes = all_config_indexes[index]
# Extract initialisation information each time PWSCF starts
# to add to subsequent configurations. Use None so slices know
# when to fill in the blanks.
pwscf_start_info = dict((idx, None) for idx in indexes[_PW_START])
if isinstance(image_indexes, int):
image_indexes = [image_indexes]
for image_index in image_indexes:
# Find the nearest calculation start to parse info. Needed in,
# for example, relaxation where cell is only printed at the
# start.
if image_index in indexes[_PW_START]:
prev_start_index = image_index
else:
# The greatest start index before this structure
prev_start_index = [
idx for idx in indexes[_PW_START] if idx < image_index
][-1]
# add structure to reference if not there
if pwscf_start_info[prev_start_index] is None:
pwscf_start_info[prev_start_index] = parse_pwo_start(
pwo_lines, prev_start_index)
# Get the bounds for information for this structure. Any associated
# values will be between the image_index and the following one,
# EXCEPT for cell, which will be 4 lines before if it exists.
for next_index in all_config_indexes:
if next_index > image_index:
break
else:
# right to the end of the file
next_index = len(pwo_lines)
# Get the structure
# Use this for any missing data
prev_structure = pwscf_start_info[prev_start_index]['atoms']
if image_index in indexes[_PW_START]:
structure = prev_structure.copy() # parsed from start info
else:
if _PW_CELL in pwo_lines[image_index - 5]:
# CELL_PARAMETERS would be just before positions if present
cell, cell_alat = get_cell_parameters(pwo_lines[image_index -
5:image_index])
else:
cell = prev_structure.cell
cell_alat = pwscf_start_info[prev_start_index]['alat']
# give at least enough lines to parse the positions
# should be same format as input card
n_atoms = len(prev_structure)
positions_card = get_atomic_positions(
pwo_lines[image_index:image_index + n_atoms + 1],
n_atoms=n_atoms,
cell=cell,
alat=cell_alat)
# convert to Atoms object
symbols = [
label_to_symbol(position[0]) for position in positions_card
]
tags = [label_to_tag(position[0]) for position in positions_card]
positions = [position[1] for position in positions_card]
constraint_idx = [position[2] for position in positions_card]
constraint = get_constraint(constraint_idx)
structure = Atoms(symbols=symbols,
positions=positions,
cell=cell,
constraint=constraint,
pbc=True,
tags=tags)
# Extract calculation results
# Energy
energy = None
for energy_index in indexes[_PW_TOTEN]:
if image_index < energy_index < next_index:
energy = float(
pwo_lines[energy_index].split()[-2]) * units['Ry']
# Electrostatic enbedding energy
elec_embedding_energy = None
for eee_index in indexes[_PW_ELECTROSTATIC_EMBEDDING]:
if image_index < eee_index < next_index:
elec_embedding_energy = float(
pwo_lines[eee_index].split()[-2]) * units['Ry']
# Number of iterations
n_iterations = None
for niter_index in indexes[_PW_NITER]:
if image_index < niter_index < next_index:
n_iterations = int(
pwo_lines[niter_index].split('#')[1].split()[0])
# Forces
forces = None
for force_index in indexes[_PW_FORCE]:
if image_index < force_index < next_index:
# Before QE 5.3 'negative rho' added 2 lines before forces
# Use exact lines to stop before 'non-local' forces
# in high verbosity
if not pwo_lines[force_index + 2].strip():
force_index += 4
else:
force_index += 2
# assume contiguous
forces = [[float(x) for x in force_line.split()[-3:]]
for force_line in pwo_lines[force_index:force_index +
len(structure)]]
forces = np.array(forces) * units['Ry'] / units['Bohr']
# Stress
stress = None
for stress_index in indexes[_PW_STRESS]:
if image_index < stress_index < next_index:
sxx, sxy, sxz = pwo_lines[stress_index + 1].split()[:3]
_, syy, syz = pwo_lines[stress_index + 2].split()[:3]
_, _, szz = pwo_lines[stress_index + 3].split()[:3]
stress = np.array([sxx, syy, szz, syz, sxz, sxy], dtype=float)
# sign convention is opposite of ase
stress *= -1 * units['Ry'] / (units['Bohr']**3)
# Magmoms
magmoms = None
for magmoms_index in indexes[_PW_MAGMOM]:
if image_index < magmoms_index < next_index:
magmoms = [
float(mag_line.split('=')[-1])
for mag_line in pwo_lines[magmoms_index + 1:magmoms_index +
1 + len(structure)]
]
# Fermi level / highest occupied level and lowest unoccupied level
efermi = None
lumo_ene = None
for fermi_index in indexes[_PW_FERMI]:
if image_index < fermi_index < next_index:
efermi = float(pwo_lines[fermi_index].split()[-2])
if efermi is None:
for ho_index in indexes[_PW_HIGHEST_OCCUPIED]:
if image_index < ho_index < next_index:
efermi = float(pwo_lines[ho_index].split()[-1])
if efermi is None:
for holf_index in indexes[_PW_HIGHEST_OCCUPIED_LOWEST_FREE]:
if image_index < holf_index < next_index:
efermi = float(pwo_lines[holf_index].split()[-2])
lumo_ene = float(pwo_lines[holf_index].split()[-1])
# K-points
ibzkpts = None
weights = None
kpoints_warning = "Number of k-points >= 100: " + \
"set verbosity='high' to print them."
for kpts_index in indexes[_PW_KPTS]:
nkpts = int(pwo_lines[kpts_index].split()[4])
kpts_index += 2
if pwo_lines[kpts_index].strip() == kpoints_warning:
continue
# QE prints the k-points in units of 2*pi/alat
# with alat defined as the length of the first
# cell vector
cell = structure.get_cell()
alat = np.linalg.norm(cell[0])
ibzkpts = []
weights = []
for i in range(nkpts):
L = pwo_lines[kpts_index + i].split()
weights.append(float(L[-1]))
coord = np.array([L[-6], L[-5], L[-4].strip('),')],
dtype=float)
coord *= 2 * np.pi / alat
coord = kpoint_convert(cell, ckpts_kv=coord)
ibzkpts.append(coord)
ibzkpts = np.array(ibzkpts)
weights = np.array(weights)
# Bands
kpts = None
kpoints_warning = "Number of k-points >= 100: " + \
"set verbosity='high' to print the bands."
for bands_index in indexes[_PW_BANDS] + indexes[_PW_BANDSTRUCTURE]:
if image_index < bands_index < next_index:
bands_index += 2
if pwo_lines[bands_index].strip() == kpoints_warning:
continue
assert ibzkpts is not None
spin, bands, eigenvalues = 0, [], [[], []]
while True:
L = pwo_lines[bands_index].replace('-', ' -').split()
if len(L) == 0:
if len(bands) > 0:
eigenvalues[spin].append(bands)
bands = []
elif L == ['occupation', 'numbers']:
# Skip the lines with the occupation numbers
bands_index += len(eigenvalues[spin][0]) // 8 + 1
elif L[0] == 'k' and L[1].startswith('='):
pass
elif 'SPIN' in L:
if 'DOWN' in L:
spin += 1
else:
try:
bands.extend(map(float, L))
except ValueError:
break
bands_index += 1
if spin == 1:
assert len(eigenvalues[0]) == len(eigenvalues[1])
# assert len(eigenvalues[0]) == len(ibzkpts), \
# (np.shape(eigenvalues), len(ibzkpts))
kpts = []
for s in range(spin + 1):
for w, k, e in zip(weights, ibzkpts, eigenvalues[s]):
kpt = SinglePointKPoint(w, s, k, eps_n=e)
kpts.append(kpt)
# Convergence
job_done = False
for done_index in indexes[_PW_DONE]:
if image_index < done_index < next_index:
job_done = True
# Walltime
walltime = None
for wt_index in indexes[_PW_WALLTIME]:
if image_index < wt_index < next_index:
walltime = time_to_float(pwo_lines[wt_index].split()[-2])
# Put everything together
calc = SinglePointDFTCalculator(structure,
energy=energy,
forces=forces,
stress=stress,
magmoms=magmoms,
efermi=efermi,
ibzkpts=ibzkpts)
calc.results['homo_energy'] = efermi
calc.results['lumo_energy'] = lumo_ene
calc.results['electrostatic embedding'] = elec_embedding_energy
calc.results['iterations'] = n_iterations
calc.results['job done'] = job_done
calc.results['walltime'] = walltime
calc.kpts = kpts
structure.calc = calc
yield structure
def plot_bands(scftype, basis, ngs, nmp=None):
# Set-up the unit cell
from ase.lattice import bulk
from ase.dft.kpoints import ibz_points, kpoint_convert, get_bandpath
ase_atom = bulk('C', 'diamond', a=3.5668*ANG2BOHR)
print "Cell volume =", ase_atom.get_volume(), "Bohr^3"
# Set-up the band-path via special points
points = ibz_points['fcc']
G = points['Gamma']
X = points['X']
W = points['W']
K = points['K']
L = points['L']
band_kpts, x, X = get_bandpath([L, G, X, W, K, G], ase_atom.cell, npoints=30)
abs_kpts = kpoint_convert(ase_atom.cell, skpts_kc=band_kpts)
# Build the cell
cell = pbcgto.Cell()
cell.unit = 'B'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell
cell.basis = 'gth-%s'%(basis)
#cell.basis = 'gth-szv'
#cell.basis = 'gth-dzvp'
cell.pseudo = 'gth-pade'
cell.gs = np.array([ngs,ngs,ngs])
cell.verbose = 7
cell.build(None,None)
# Perform the gamma-point SCF
if scftype == 'dft':
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
elif scftype == 'hf':
mf = pbchf.RHF(cell, exxdiv=None)
else:
scaled_mp_kpts = ase.dft.kpoints.monkhorst_pack((nmp,nmp,nmp))
abs_mp_kpts = cell.get_abs_kpts(scaled_mp_kpts)
if scftype == 'kdft':
mf = pbcdft.KRKS(cell, abs_mp_kpts)
mf.xc = 'lda,vwn'
else:
mf = pbchf.KRHF(cell, abs_mp_kpts, exxdiv='vcut_sph')
mf.analytic_int = False
mf.scf()
print "SCF evals =", mf.mo_energy
# Proceed along k-point band-path
e_kn = []
efermi = -99
for kpt in abs_kpts:
e, c = mf.get_bands(kpt)
print kpt, e
e_kn.append(e)
if e[4-1] > efermi:
efermi = e[4-1]
for k, ek in enumerate(e_kn):
e_kn[k] = ek-efermi
# Write the bands to stdout
f = open('bands_%s_%s_%d_%d.dat'%(scftype,basis,ngs,nmp),'w')
f.write("# Special points:\n")
for point, label in zip(X,['L', 'G', 'X', 'W', 'K', 'G']):
f.write("# %0.6f %s\n"%(point,label))
for kk, ek in zip(x, e_kn):
f.write("%0.6f "%(kk))
for ekn in ek:
f.write("%0.6f "%(ekn))
f.write("\n")
f.close()
# Plot the band structure via matplotlib
emin = -1.0
emax = 1.0
plt.figure(figsize=(8, 4))
nbands = cell.nao_nr()
for n in range(nbands):
plt.plot(x, [e_kn[i][n] for i in range(len(x))])
for p in X:
plt.plot([p, p], [emin, emax], 'k-')
plt.plot([0, X[-1]], [0, 0], 'k-')
plt.xticks(X, ['$%s$' % n for n in ['L', r'\Gamma', 'X', 'W', 'K', r'\Gamma']])
plt.axis(xmin=0, xmax=X[-1], ymin=emin, ymax=emax)
plt.xlabel('k-vector')
plt.ylabel('Energy [au]')
#plt.show()
if nmp is None:
plt.savefig('bands_%s_%s_%d.png'%(scftype,basis,ngs))
else:
plt.savefig('bands_%s_%s_%d_%d.png'%(scftype,basis,ngs,nmp))
