Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

131 fhi aims unclear extraction of species #138

Open
wants to merge 8 commits into
base: develop
Choose a base branch
from
Open

131 fhi aims unclear extraction of species #138

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
213 changes: 66 additions & 147 deletions electronicparsers/fhiaims/metainfo/fhi_aims.py
View file
Open in desktop
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),
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
Loading