diff --git a/wien2kparser/metainfo/wien2k.py b/wien2kparser/metainfo/wien2k.py
index e939b3678b64e6e62d3bb1621898bfe691bc2402..f36fd86411ea36747692815751cc6d89a6d42688 100644
--- a/wien2kparser/metainfo/wien2k.py
+++ b/wien2kparser/metainfo/wien2k.py
@@ -152,8 +152,7 @@ class section_scf_iteration(public.section_scf_iteration):
a_legacy=LegacyDefinition(name='x_wien2k_iteration_number'))
x_wien2k_nr_of_independent_atoms = Quantity(
- type=np.dtype(np.int32),
- shape=[],
+ type=int,
description='''
number of independent atoms in the cell
''',
@@ -377,27 +376,27 @@ class section_scf_iteration(public.section_scf_iteration):
x_wien2k_for_x_gl = Quantity(
type=np.dtype(np.float64),
- shape=[],
+ shape=['x_wien2k_nr_of_independent_atoms'],
description='''
- force on atom xx in mRy/bohr (in the global coordinate system of the unit cell (in
+ force on inequivalent atom xx (in the global coordinate system of the unit cell (in
the same way as the atomic positions are specified)): Fx
''',
a_legacy=LegacyDefinition(name='x_wien2k_for_x_gl'))
x_wien2k_for_y_gl = Quantity(
type=np.dtype(np.float64),
- shape=[],
+ shape=['x_wien2k_nr_of_independent_atoms'],
description='''
- force on atom xx in mRy/bohr (in the global coordinate system of the unit cell (in
+ force on inequivalent atom xx in (in the global coordinate system of the unit cell (in
the same way as the atomic positions are specified)): Fy
''',
a_legacy=LegacyDefinition(name='x_wien2k_for_y_gl'))
x_wien2k_for_z_gl = Quantity(
type=np.dtype(np.float64),
- shape=[],
+ shape=['x_wien2k_nr_of_independent_atoms'],
description='''
- force on atom xx in mRy/bohr (in the global coordinate system of the unit cell (in
+ force on inequivalent atom xx in (in the global coordinate system of the unit cell (in
the same way as the atomic positions are specified)): Fz
''',
a_legacy=LegacyDefinition(name='x_wien2k_for_z_gl'))
@@ -410,6 +409,14 @@ class section_scf_iteration(public.section_scf_iteration):
''',
a_legacy=LegacyDefinition(name='x_wien2k_atom_nr'))
+ x_wien2k_atom_mult = Quantity(
+ type=np.dtype(np.int32),
+ shape=['x_wien2k_nr_of_independent_atoms'],
+ description='''
+ atom multiplicity
+ ''',
+ a_legacy=LegacyDefinition(name='x_wien2k_atom_mult'))
+
x_wien2k_sphere_nr = Quantity(
type=str,
shape=[],
diff --git a/wien2kparser/parser_wien2k.py b/wien2kparser/parser_wien2k.py
index 935f81e62fa2bc7c73e31ab0a71baa0952931751..92769dc6f26fc8499f474ed0babcdd1f8ab42aa5 100644
--- a/wien2kparser/parser_wien2k.py
+++ b/wien2kparser/parser_wien2k.py
@@ -56,6 +56,7 @@ class Wien2kContext(object):
self.scfIterNr = 0
self.spinPol = None
self.eTot = None
+ self.forces = None
def startedParsing(self, path, parser):
"""called when parsing starts"""
@@ -139,6 +140,9 @@ class Wien2kContext(object):
if self.eTot is not None:
backend.addValue("energy_total", self.eTot)
+ if self.forces is not None:
+ backend.addArrayValues('atom_forces', self.forces)
+
mainFile = self.parser.fIn.fIn.name
eigvalKpoint=[]
@@ -206,16 +210,6 @@ class Wien2kContext(object):
if atom_labels is not None:
backend.addArrayValues('atom_labels', np.asarray(atom_labels))
- # atom force
- atom_force = []
- for i in ['x', 'y', 'z']:
- api = section['x_wien2k_for_' + i]
- if api is not None:
- atom_force.append(api)
- if atom_force:
- # need to transpose array since its shape is [number_of_atoms,3] in\the metadata
- backend.addArrayValues('atom_forces', np.transpose(np.asarray(atom_force)))
-
# Parse the structure file
mainFile = self.parser.fIn.fIn.name
fName = mainFile[:-4] + ".struct"
@@ -291,6 +285,22 @@ class Wien2kContext(object):
if eTot is not None:
self.eTot = eTot[0]
+ # save the forces
+ fx = section['x_wien2k_for_x_gl']
+ fy = section['x_wien2k_for_y_gl']
+ fz = section['x_wien2k_for_z_gl']
+ if fx is not None and fy is not None and fz is not None:
+ backend.addArrayValues('x_wien2k_for_x_gl', fx)
+ backend.addArrayValues('x_wien2k_for_y_gl', fy)
+ backend.addArrayValues('x_wien2k_for_z_gl', fz)
+ # account for atom multiplicities
+ self.forces=[]
+ for i,a in enumerate(section['x_wien2k_atom_mult']):
+ for _ in range(a):
+ self.forces.append([fx[i], fy[i], fz[i]])
+ print (self.forces)
+
+
# description of the input
mainFileDescription = SM(
name = 'root',
@@ -331,8 +341,10 @@ mainFileDescription = SM(
SM(r":NOE\s*:\s*NUMBER\sOF\sELECTRONS\s*=\s*(?P<x_wien2k_noe>[0-9.]+)"),
SM(r":FER\s*:\sF E R M I - ENERGY\W\w*\W\w*M\W*=\s*(?P<energy_reference_fermi_iteration__rydberg>[-+0-9.]+)"),
SM(r":GMA\s*:\s*POTENTIAL\sAND\sCHARGE\sCUT-OFF\s*(?P<x_wien2k_cutoff>[0-9.]+)\s*Ry\W\W[0-9.]+"),
- SM(r":CHA(?P<x_wien2k_atom_nr>[-+0-9]+):\s*TOTAL\s*\w*\s*CHARGE INSIDE SPHERE\s*(?P<x_wien2k_sphere_nr>[-+0-9]+)\s*=\s*(?P<x_wien2k_tot_val_charge_sphere>[0-9.]+)",repeats = True),
- SM(r":CHA\s*:\s*TOTAL\s*\w*\s*CHARGE INSIDE\s*\w*\s*CELL\s=\s*(?P<x_wien2k_tot_val_charge_cell>[-+0-9.]+)"),
+ SM(r":POS[0-9]*:\s*ATOM\s*[-0-9.]+\s*X,Y,Z\s*=[-0-9. ]+MULT=\s*(?P<x_wien2k_atom_mult>[0-9]+)\s*ZZ=\s*[0-9.]+.*", repeats = True),
+ #FIXME: this is repeating interleaved with the previous matcher and likely need its own submatcher
+# SM(r":CHA(?P<x_wien2k_atom_nr>[-+0-9]+):\s*TOTAL\s*\w*\s*CHARGE INSIDE SPHERE\s*(?P<x_wien2k_sphere_nr>[-+0-9]+)\s*=\s*(?P<x_wien2k_tot_val_charge_sphere>[0-9.]+)",repeats = True),
+# SM(r":CHA\s*:\s*TOTAL\s*\w*\s*CHARGE INSIDE\s*\w*\s*CELL\s=\s*(?P<x_wien2k_tot_val_charge_cell>[-+0-9.]+)"),
SM(r":SUM\s*:\s*SUM OF EIGENVALUES\s*=\s*(?P<energy_sum_eigenvalues_scf_iteration__rydberg>[-+0-9.]+)"),
SM(r":RTO(?P<x_wien2k_atom_nr>[-+0-9]+)\s*:\s*[0-9]+\s*(?P<x_wien2k_density_at_nucleus_valence>[-+0-9.]+)\s*(?P<x_wien2k_density_at_nucleus_semicore>[-+0-9.]+)\s*(?P<x_wien2k_density_at_nucleus_core>[-+0-9.]+)\s*(?P<x_wien2k_density_at_nucleus_tot>[0-9.]+)",repeats = True),
#FIXME: followig matchers work just for cases without spin polarization
@@ -350,7 +362,7 @@ mainFileDescription = SM(
SM(r":MMTOT:\s*(TOTAL|SPIN) MAGNETIC MOMENT IN CELL\s*=\s*(?P<x_wien2k_mmtot>[-+0-9.]+)"),
SM(r":ENE\s*:\s*\W*\w*\W*\s*TOTAL\s*ENERGY\s*IN\s*Ry\s*=\s*(?P<energy_total_scf_iteration__rydberg>[-+0-9.]+)"),
SM(r":FOR[0-9]*:\s*(?P<x_wien2k_atom_nr>[0-9]+).ATOM\s*(?P<x_wien2k_for_abs>[0-9.]+)\s*(?P<x_wien2k_for_x>[-++0-9.]+)\s*(?P<x_wien2k_for_y>[-+0-9.]+)\s*(?P<x_wien2k_for_z>[-+0-9.]+)\s*partial\sforces", repeats = True),
- SM(r":FGL[0-9]*:\s*(?P<x_wien2k_atom_nr>[0-9]+).ATOM\s*(?P<x_wien2k_for_x_gl>[-+0-9.]+)\s*(?P<x_wien2k_for_y_gl>[-+0-9.]+)\s*(?P<x_wien2k_for_z_gl>[-+0-9.]+)\s*partial\sforces", repeats = True)
+ SM(r":FGL[0-9]*:\s*(?P<x_wien2k_atom_nr>[0-9]+).ATOM\s*(?P<x_wien2k_for_x_gl__mrydberg_bohr_1>[-+0-9.]+)\s*(?P<x_wien2k_for_y_gl__mrydberg_bohr_1>[-+0-9.]+)\s*(?P<x_wien2k_for_z_gl__mrydberg_bohr_1>[-+0-9.]+)\s*total\sforces", repeats = True),
]
)
]