diff --git a/parser/parser-gulp/main.py b/parser/parser-gulp/main.py
index f688891fa9596769fbcb9e44c27b17885bd4a61d..55f9b0c6c2535683a55303993c6492d7e9e42081 100644
--- a/parser/parser-gulp/main.py
+++ b/parser/parser-gulp/main.py
@@ -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
])