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Coop coordination #280

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Coop coordination #280

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86dd213
Add elements coordination in schemas.py
juliette1996 Sep 11, 2020
4432fe3
Update workflow_coop.py with coordination number
juliette1996 Sep 11, 2020
6541d2a
Add a description of elements_coordination option
juliette1996 Sep 14, 2020
d19ef53
Add nano-CAT to setup.py
juliette1996 Sep 14, 2020
472e2e7
Variable assignment in workflow_coop.py
juliette1996 Sep 14, 2020
6a4c11f
fixed logger error
felipeZ Sep 14, 2020
6058891
update changelog
felipeZ Sep 14, 2020
133697d
Merge branch 'master' into coop_coordination
felipeZ Sep 14, 2020
bb0820b
Create input_test_coop_coordination.yml
juliette1996 Sep 14, 2020
67c44f0
Test coordination functionality of coop workflow
juliette1996 Sep 14, 2020
1d62551
Merge branch 'master' into coop_coordination
felipeZ Sep 14, 2020
c822be2
Update yml input test
juliette1996 Oct 15, 2020
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5 changes: 4 additions & 1 deletion nanoqm/workflows/schemas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -303,7 +303,10 @@ def merge(d1: Dict[str, Any], d2: Dict[str, Any]) -> Dict[str, Any]:
#: Input for a Crystal Orbital Overlap Population calculation
dict_coop = {
# List of the two elements to calculate the COOP for
"coop_elements": list}
"coop_elements": list,
# Coordination number to be considered for each of the two elements
Optional("elements_coordination", default=None): Or(None, list)
}


dict_merged_single_points = merge(dict_general_options, dict_single_points)
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27 changes: 22 additions & 5 deletions nanoqm/workflows/workflow_coop.py
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Expand Up @@ -10,12 +10,16 @@
__all__ = ['workflow_crystal_orbital_overlap_population']

import logging
from typing import List, Tuple
from typing import List, Tuple, Union

import numpy as np

from scm.plams import Molecule

from qmflows.parsers.xyzParser import readXYZ

from nanoCAT.recipes import coordination_number
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nanoCAT must be included in the library requirements at setup.py


from ..common import (DictConfig, MolXYZ, h2ev,
number_spherical_functions_per_atom, retrieve_hdf5_data)
from ..integrals.multipole_matrices import compute_matrix_multipole
Expand Down Expand Up @@ -44,11 +48,14 @@ def workflow_crystal_orbital_overlap_population(config: DictConfig):
# Converting the xyz-file to a mol-file
mol = readXYZ(config.path_traj_xyz)

if config.elements_coordination is not None:
geometry = Molecule(config.path_traj_xyz)

# Computing the indices of the atomic orbitals of the two selected
# elements, and the overlap matrix that contains only elements related to
# the two elements
el_1_orbital_ind, el_2_orbital_ind, overlap_reduced = compute_overlap_and_atomic_orbitals(
mol, config)
mol, config, geometry)

# Compute the crystal orbital overlap population between the two selected
# elements
Expand Down Expand Up @@ -83,7 +90,8 @@ def get_eigenvalues_coefficients(config: DictConfig) -> Tuple[np.ndarray, np.nda


def compute_overlap_and_atomic_orbitals(
mol: MolXYZ, config: DictConfig) -> Tuple[List[int], List[int], List[int]]:
mol: MolXYZ, config: DictConfig,
geometry: Union[Molecule, None]) -> Tuple[List[int], List[int], List[int]]:
"""Compute the indices of the atomic orbitals of the two selected elements.

Computes the overlap matrix, containing only the elements related to those two elements.
Expand All @@ -102,8 +110,17 @@ def compute_overlap_and_atomic_orbitals(
element_1 = config["coop_elements"][0]
element_2 = config["coop_elements"][1]

element_1_index = [i for i, s in enumerate(mol) if element_1.lower() in s]
element_2_index = [i for i, s in enumerate(mol) if element_2.lower() in s]
if config["elements_coordination"] is None:
element_1_index = [i for i, s in enumerate(mol) if element_1.lower() in s]
element_2_index = [i for i, s in enumerate(mol) if element_2.lower() in s]

# For the two selected elements, only the indices corresponding to a given coordination number
else:
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Fyi, you can also make nano-CAT an optional dependency and then raise any potential ImportErrors whenever a code branch is reached that does require nano-CAT:

from typing import Optional
try:
    from nanoCAT import coordination_number
    NANOCAT_EX: Optional[ImportError] = None
except ImportError as ex:
    NANOCAT_EX = ex


def compute_overlap_and_atomic_orbitals(...):
    if config["elements_coordination"] is None:
        ...
    elif NANOCAT_EX is not None:
        raise NANOCAT_EX
    else:
        coord = coordination_number(geometry)
        ...

coord = coordination_number(geometry)
cn_1 = config["elements_coordination"][0]
cn_2 = config["elements_coordination"][1]
element_1_index = [i - 1 for i in coord[element_1][cn_1]]
element_2_index = [i - 1 for i in coord[element_2][cn_2]]

# Making a list of the indices of the atomic orbitals for each of the two
# elements
Expand Down