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Commit 430c1f8c authored by Ask Hjorth Larsen's avatar Ask Hjorth Larsen
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parse multiple configurations

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parser/parser-gulp/main.py
+ 77
− 44
View file @ 430c1f8c
......@@ -113,37 +113,47 @@ time to end of optimisation
class GulpContext(object):
def __init__(self):
self.data = {}
self.spacegroup = None
self.current_raw_cell = None
self.npbc = None
def startedParsing(self, fname, parser):
pass
def onClose_section_system(self, backend, gindex, section):
data = self.data
print(list(data.keys()))
ctable = data.pop('gulp_coordinate_table', None)
symbols = ctable[:, 0]
gulp_labels = ctable[:, 1]
positions = ctable[:, 2:5].astype(float)
if self.npbc is None:
self.npbc = section['x_gulp_pbc'][0]
assert self.npbc in range(4)
pbc = np.zeros(3, bool)
pbc[:self.npbc] = True
assert sum(pbc) == self.npbc
# charge, occupancy?
spacegroup = section['x_gulp_space_group']
if self.spacegroup is None:
spacegroup = section['x_gulp_space_group']
if spacegroup is not None:
spacegroup = spacegroup[0]
self.spacegroup = spacegroup
if spacegroup is None:
#print(list(self.data.keys()))
npbc = section['x_gulp_pbc'][0]
pbc = np.zeros(3, bool)
pbc[:npbc] = True
self.current_raw_cell = data.pop('cell', self.current_raw_cell)
if self.npbc > 0:
assert self.current_raw_cell is not None
if npbc == 0:
cell3d = np.identity(3)
else:
cell = data['cell']
assert npbc in [0, 1, 2, 3]
assert cell.shape == (npbc, 3)
cell3d = np.identity(3)
cell3d[:npbc, :] = cell
if self.spacegroup is None:
cell3d = np.identity(3)
if self.npbc > 0:
cell = self.current_raw_cell
assert cell.shape == (self.npbc, 3), cell.shape
cell3d[:self.npbc, :] = cell
# use Atoms to get scaled positions/cell right:
atoms = Atoms([0] * len(positions), cell=cell3d,
......@@ -157,9 +167,7 @@ class GulpContext(object):
sym = '%s-%s' % (sym, label)
atom_labels.append(sym)
assert sum(atoms.pbc) == npbc
else:
group = section['x_gulp_patterson_group']
# group may be none ---- no spacegroup
cellpar = [section['x_gulp_cell_a'],
section['x_gulp_cell_b'],
......@@ -169,7 +177,7 @@ class GulpContext(object):
section['x_gulp_cell_gamma']]
for x in cellpar:
assert len(x) == 1
num = get_spacegroup_number(spacegroup[0])
num = get_spacegroup_number(self.spacegroup)
atoms_by_label = {}
for i, (s, l, p) in enumerate(zip(symbols, gulp_labels, positions)):
......@@ -195,11 +203,10 @@ class GulpContext(object):
# Also, the ordering may be messed up.
# This is torturous.
atom_positions = np.array(atom_positions)
assert section['x_gulp_pbc'][0] == 3
backend.addArrayValues('atom_labels', np.asarray(atom_labels))
backend.addArrayValues('configuration_periodic_dimensions',
np.array(atoms.pbc))
np.array(pbc))
backend.addValue('number_of_atoms', len(atom_labels))
# The cell can be infinite in some directions.
# In that case the cell value will just be one (it has to have some value!!)
......@@ -328,17 +335,63 @@ def get_input_system_sm():
SM(r'-+', name='bar'),
# We need to skip the 'Region 1' headers, so stop criterion is the empty line!
context.multi_sm('gulp_coordinate_table',
r'-+',
r'-----+',
#No. Atomic x y z Charge Occupancy
# Label (Frac) (Frac) (Frac) (e) (Frac)
#
# 1 La c 0.333333 0.666667 0.245000 * 9.00000 1.000000
r'\s*\d+\s+(\S+)\s+(\S)[\s\*]+(\S+)[\s\*]+(\S+)[\s\*]+(\S+)[\s\*]+(\S+)[\s\*]+(\S+)',
r'$^')
r'\s*\d+\s+(\S+)\s+(\S+)[\s\*]+(\S+)[\s\*]+(\S+)[\s\*]+(\S+)[\s\*]+(\S+)[\s\*]+(\S+)',
r'----+')
]),
])
return m
def get_optimise_sm():
m = SM(r'\s*Start of bulk optimisation :',
name='opt-start',
repeats=True,
sections=['section_system',
'section_single_configuration_calculation'],
subMatchers=[
SM(r'\s*Components of energy :',
name='e-components',
subMatchers=[
SM(r'\s*Total lattice energy\s*=\s*(?P<energy_total__eV>\S+)\s*eV',
name='etotal')
]),
SM(r'\s*Final (asymmetric unit|fractional) coordinates( of atoms)?\s*:',
subMatchers=[
context.multi_sm('gulp_coordinate_table',
r'-------------+',
# This table is slightly differently formatted than the one from the input
#--------------------------------------------------------------------------------
# No. Atomic x y z Radius
# Label (Frac) (Frac) (Frac) (Angs)
#--------------------------------------------------------------------------------
# 1 La c 0.333333 0.666667 0.248457 0.000000
# 2 O c 0.000000 0.000000 0.000000 0.000000
r'\s*\d+\s*(\S+)\s*(\S+)\s*(\S+)\s*(\S+)\s*(\S+)\s*(\S+)',
r'^$')
]),
SM(r'\s*Final Cartesian lattice vectors \(Angstroms\) :',
subMatchers=[
context.multi_sm(r'cell',
r'',
r'\s*(\S+)\s*(\S+)\s*(\S+)')
]),
SM(r'\s*Final cell parameters and derivatives :',
name='finalcell',
subMatchers=[
SM(r'\s*a\s*(?P<x_gulp_cell_a>\S+)\s+Angstrom', name='a'),
SM(r'\s*b\s*(?P<x_gulp_cell_b>\S+)\s+Angstrom', name='b'),
SM(r'\s*c\s*(?P<x_gulp_cell_c>\S+)\s+Angstrom', name='c'),
SM(r'\s*alpha\s*(?P<x_gulp_cell_alpha>\S+)\s+Degrees', name='alpha'),
SM(r'\s*beta\s*(?P<x_gulp_cell_beta>\S+)\s+Degrees', name='beta'),
SM(r'\s*gamma\s*(?P<x_gulp_cell_gamma>\S+)\s+Degrees', name='gamma'),
])
])
return m
infoFileDescription = SM(
name='root',
weak=True,
......@@ -349,27 +402,7 @@ infoFileDescription = SM(
SM(r'\*\s*Version\s*=\s*(?P<program_version>\S+)',
name='version'),
get_input_system_sm(),
#SM(r'\s*\*+\s*Optimisation achieved\s*\*+',
# name='opt-output',
# sections=['section_system',
# 'section_single_configuration_calculation'],
# subMatchers=[
# SM(r'\s*Final energy\s*=\s*(?P<energy_total__eV>\S+)\s*eV',
# name='energy'),
#ArraySM(
#
# ]),
#ArraySM(r'\s*Brillouin zone sampling points\s*:',
# r'\s*\d+\s+\S+\s+\S+\s+\S+\s+\S+',
#get_array('eigenvalues_kpoints', 1, 4))
#SM(r'\s*Brillouin zone sampling points\s*:',
# name='BZ sampling header',
# subMatchers=[
# SM(r'-+', name='bar'),
# ArraySM(r'',
# r'\s*\d+\s+\S+\s+\S+\s+\S+\s+\S+',
# get_array('x_
# ])
get_optimise_sm(), # note British spelling
SM(r'x^',
name='impossible') # 'Parse' the whole file
])
......
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