def get_bands_node(self):
bnode = DataFactory('array.bands')()
bdat, bkp, bgnu = self.get_bands_plot()
if not (bdat and bkp):
return None
with open(bkp) as bk:
self.line(bk) # contains num kpoints
kp = re.split(self.empty_line, bk.read())
kp = filter(None, kp)
kp = map(self.splitlines, kp)
kp = filter(None, kp[0])
kp = np.array(kp)
bnode.set_kpoints(kp[:, :3], weights=kp[:, 3])
with open(bdat) as bd:
data = re.split(self.empty_line, bd.read())
data = filter(None, data)
data = map(self.splitlines, data)
data = np.array(data)
bnode.set_bands(data[:, :, 1].transpose())
kppath = self._calc.inp.settings.get_dict().get('kpoint_path')
kpl = [[kpp[0], kpp[1:4]] for kpp in kppath]
kpl.append([kppath[-1][4], kppath[-1][5:8]])
counter = {i[0]: 0 for i in kpl}
kplab = []
for kpi in kpl:
ci = counter[kpi[0]]
idx = self._find_special_kpoint(kp[:, :3], kpi[1], num=ci)
kplab.append((idx, kpi[0]))
counter[kpi[0]] += 1
bnode.labels = kplab
return bnode
def convert_kpoints(kpoints):
"""Convert the k-points output from string to float."""
if kpoints is None:
return False, None
kpoints_node = DataFactory('array.kpoints')()
kpoints_node.set_kpoints([[float(x) for x in k.split()]
for k in kpoints])
return True, kpoints_node
def read_ibzkpt(self):
ibz = self.get_file('IBZKPT')
if not ibz:
self.logger.warning('IBZKPT not found')
return None
kpp = KpParser(ibz)
kpout = DataFactory('array.kpoints')()
kpout.set_kpoints(kpp.kpoints,
weights=kpp.weights,
cartesian=kpp.cartesian)
return kpout
def vasp_kpoints(request, aiida_env):
"""Fixture: (kpoints object, resulting KPOINTS)"""
from aiida.orm import DataFactory
if request.param == 'mesh':
kpoints = DataFactory('array.kpoints')()
kpoints.set_kpoints_mesh([2, 2, 2])
ref_kpoints = _ref_kp_mesh()
elif request.param == 'list':
kpoints = DataFactory('array.kpoints')()
kpoints.set_kpoints([[0., 0., 0.], [0., 0., .5]], weights=[1., 1.])
ref_kpoints = _ref_kp_list()
return kpoints, ref_kpoints
def _get_kpoints(self):
"""Create a DB Node for the IBZKPT file"""
kpp = self._parsers['IBZKPT']
if kpp is None:
return {'kpoints': None}
kpout = DataFactory('array.kpoints')()
kpout.set_kpoints(kpp.kpoints,
weights=kpp.weights,
cartesian=kpp.cartesian)
return {'kpoints': kpout}
def _get_bands(self):
"""
Create a bands and a kpoints node from values in eigenvalue.
:returns: bsnode, kpout
* bsnode: BandsData containing eigenvalues from EIGENVAL
and occupations from vasprun.xml
* kpout: KpointsData containing kpoints from EIGENVAL,
both bsnode as well as kpnode come with cell unset
"""
eig = self.get_file('EIGENVAL')
if not eig:
return {'bands': None, 'kpoints': None}
_, kpoints, bands = EigParser.parse_eigenval(eig)
bsnode = DataFactory('array.bands')()
kpout = DataFactory('array.kpoints')()
# Take the output structure if available.
structure = None
if 'structure' in self._output_nodes:
structure = self._output_nodes['structure']
if structure is None:
structure = self._calc.inp.structure
bsnode.set_cell(structure.get_ase().get_cell())
kpout.set_cell(structure.get_ase().get_cell())
if self._calc.inp.kpoints.get_attrs().get('array|kpoints'):
bsnode.set_kpointsdata(self._calc.inp.kpoints)
if self._calc.inp.kpoints.labels:
bsnode.labels = self._calc.inp.kpoints.labels
else:
bsnode.set_kpoints(kpoints[:, :3],
weights=kpoints[:, 3],
cartesian=False)
bsnode.set_bands(bands,
occupations=self._parsers['vasprun.xml'].occupations)
kpout.set_kpoints(kpoints[:, :3],
weights=kpoints[:, 3],
cartesian=False)
return {'bands': bsnode, 'kpoints': kpout}
def read_eigenval(self):
'''
Create a bands and a kpoints node from values in eigenvalue.
returns: bsnode, kpout
- bsnode: BandsData containing eigenvalues from EIGENVAL
and occupations from vasprun.xml
- kpout: KpointsData containing kpoints from EIGENVAL,
both bsnode as well as kpnode come with cell unset
'''
eig = self.get_file('EIGENVAL')
if not eig:
self.logger.warning('EIGENVAL not found')
return None, None, None
header, kp, bs = EigParser.parse_eigenval(eig)
bsnode = DataFactory('array.bands')()
kpout = DataFactory('array.kpoints')()
structure = None # get output structure if not static
if self.vrp.is_md or self.vrp.is_relaxation:
structure = self.read_cont()
if self.vrp.is_md: # set cell from input or output structure
cellst = structure
else:
cellst = self._calc.inp.structure
bsnode.set_cell(cellst.get_ase().get_cell())
kpout.set_cell(cellst.get_ase().get_cell())
if self._calc.inp.kpoints.get_attrs().get('array|kpoints'):
bsnode.set_kpointsdata(self._calc.inp.kpoints)
if self._calc.inp.kpoints.labels:
bsnode.labels = self._calc.inp.kpoints.labels
else:
bsnode.set_kpoints(kp[:, :3], weights=kp[:, 3], cartesian=False)
bsnode.set_bands(bs, occupations=self.vrp.occupations)
kpout.set_kpoints(kp[:, :3], weights=kp[:, 3], cartesian=False)
return bsnode, kpout, structure
def kpoints_list():
kpoints = DataFactory('array.kpoints')()
kpoints.set_kpoints([[0., 0., 0.], [0., 0., .5]], weights=[1., 1.])
return kpoints
