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131 fhi aims unclear extraction of species #138

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131 fhi aims unclear extraction of species #138

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f005973
Minor touch ups
Jun 27, 2023
60ce7b5
Make control species repeatable
Jul 14, 2023
60dabe4
Clean `atom_parameters` section and `ControlInOut` parsing
Jul 14, 2023
f5dace3
Add reference to basis function from atom_parameters + TODO: add the …
Jul 17, 2023
45b4231
Add general hash mapper for `MSections` + Store hash by element
Jul 18, 2023
8e7931e
Change dependency from `hashlib` to `nomad.utils`
Jul 18, 2023
4531b47
Clean Gaussian basis sets
Jul 18, 2023
615dd2d
Fix Gaussian parsing
Jul 18, 2023
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213 changes: 66 additions & 147 deletions electronicparsers/fhiaims/metainfo/fhi_aims.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,30 @@ class x_fhi_aims_section_controlIn_basis_func(MSection):
-
''')

x_fhi_aims_controlIn_basis_func_gauss_l = Quantity(
type=np.dtype(np.int32),
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You can use type=np.int32 here and in other quantities.

shape=[],
description='''
"L is an integer number, specifying the angular momentum"
- Manual FHI-aims v201716_2
''')

x_fhi_aims_controlIn_basis_func_gauss_alphas = Quantity(
type=np.dtype(np.float64),
shape=['*'],
unit='1 / meter ** 2',
description='''
"The exponent defining a (primitive) Gaussian function"
- Manual FHI-aims v201716_2
''')

x_fhi_aims_controlIn_basis_func_gauss_coeffs = Quantity(
type=np.dtype(np.float64),
shape=['*'],
description='''
Weights in linearly composed Gaussian functions.
''')

x_fhi_aims_controlIn_basis_func_type = Quantity(
type=str,
shape=[],
Expand Down Expand Up @@ -145,20 +169,6 @@ class x_fhi_aims_section_controlIn_basis_set(MSection):
angular leven for the hartreee part
''')

x_fhi_aims_controlIn_mass = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
mass of the nucleus in atomic mass units
''')

x_fhi_aims_controlIn_nucleus = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
charge of the nucleus
''')

x_fhi_aims_controlIn_outer_grid = Quantity(
type=np.dtype(np.float64),
shape=[],
Expand All @@ -180,84 +190,22 @@ class x_fhi_aims_section_controlIn_basis_set(MSection):
radial multiplier
''')

x_fhi_aims_controlIn_species_name = Quantity(
type=str,
shape=[],
description='''
-
''')

x_fhi_aims_section_controlIn_basis_func = SubSection(
sub_section=SectionProxy('x_fhi_aims_section_controlIn_basis_func'),
repeats=True)


class x_fhi_aims_section_controlInOut_atom_species(MSection):
'''
-
'''

m_def = Section(validate=False)

x_fhi_aims_controlInOut_pure_gaussian = Quantity(
x_fhi_aims_controlIn_hash = Quantity(
type=str,
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_species_charge = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='coulomb',
description='''
-
''')

x_fhi_aims_controlInOut_species_cut_pot_scale = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_species_cut_pot_width = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='meter',
description='''
-
''')

x_fhi_aims_controlInOut_species_cut_pot = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='meter',
description='''
-
''')

x_fhi_aims_controlInOut_species_mass = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='kilogram',
description='''
-
''')

x_fhi_aims_controlInOut_species_name = Quantity(
x_fhi_aims_controlIn_species_name = Quantity(
type=str,
shape=[],
description='''
-
''')

x_fhi_aims_section_controlInOut_basis_func = SubSection(
sub_section=SectionProxy('x_fhi_aims_section_controlInOut_basis_func'),
repeats=True)

x_fhi_aims_section_vdW_TS = SubSection(
sub_section=SectionProxy('x_fhi_aims_section_vdW_TS'),
x_fhi_aims_section_controlIn_basis_func = SubSection(
sub_section=SectionProxy('x_fhi_aims_section_controlIn_basis_func'),
repeats=True)


Expand All @@ -275,78 +223,13 @@ class x_fhi_aims_section_controlInOut_basis_func(MSection):
-
''')

x_fhi_aims_controlInOut_basis_func_gauss_alpha = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='1 / meter ** 2',
description='''
-
''')

x_fhi_aims_controlInOut_basis_func_gauss_l = Quantity(
type=np.dtype(np.int32),
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_basis_func_gauss_N = Quantity(
type=np.dtype(np.int32),
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_basis_func_gauss_weight = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_basis_func_l = Quantity(
type=str,
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_basis_func_n = Quantity(
type=np.dtype(np.int32),
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_basis_func_occ = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_basis_func_primitive_gauss_alpha = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='1 / meter ** 2',
description='''
-
''')

x_fhi_aims_controlInOut_basis_func_radius = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_basis_func_type = Quantity(
type=str,
shape=[],
description='''
-
''')


class x_fhi_aims_section_eigenvalues_group_ZORA(MSection):
'''
Expand Down Expand Up @@ -1386,10 +1269,46 @@ class AtomParameters(simulation.method.AtomParameters):

m_def = Section(validate=False, extends_base_section=True)

x_fhi_aims_section_controlInOut_atom_species = SubSection(
sub_section=SectionProxy('x_fhi_aims_section_controlInOut_atom_species'),
x_fhi_aims_controlInOut_pure_gaussian = Quantity(
type=str,
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_species_cut_pot_scale = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
-
''')

x_fhi_aims_controlInOut_species_cut_pot_width = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='meter',
description='''
-
''')

x_fhi_aims_controlInOut_species_cut_pot = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='meter',
description='''
-
''')

x_fhi_aims_section_vdW_TS = SubSection(
sub_section=SectionProxy('x_fhi_aims_section_vdW_TS'),
repeats=True)

x_fhi_aims_section_controlIn_basis_set = Quantity(
type=Reference(SectionProxy('x_fhi_aims_section_controlIn_basis_set')),
shape=[],
description='''-''',
)


class HubbardKanamoriModel(simulation.method.HubbardKanamoriModel):

Expand Down
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