import math
from dataclasses import dataclass
from typing import TYPE_CHECKING, List, Optional, Tuple
import numpy as np
from numpy.typing import NDArray
if TYPE_CHECKING:
import h5py
from scm.libbase import UnifiedChemicalSystem as ChemicalSystem
def has_bonds(mol: "ChemicalSystem") -> bool:
return len(mol.bonds) > 0
def has_ff_atom_types(mol: "ChemicalSystem") -> bool:
return all(atom.forcefield is not None and atom.forcefield.type is not None for atom in mol.atoms)
def has_ff_charges(mol: "ChemicalSystem") -> bool:
return all(atom.forcefield is not None and atom.forcefield.charge is not None for atom in mol.atoms)
def has_complete_ff_input(mol: "ChemicalSystem") -> bool:
return has_bonds(mol) and has_ff_atom_types(mol) and has_ff_charges(mol)
def guess_spin_settings(mol: "ChemicalSystem") -> Tuple[bool, int]:
num_electrons = sum(atom.Z for atom in mol.atoms)
num_electrons -= round(mol.charge)
spinpol = num_electrons % 2
unrestricted = num_electrons % 2 == 1
return unrestricted, spinpol
def reject_outliers(data: NDArray, m: float = 16):
d = np.abs(data - np.median(data))
mdev = 0.6745 * np.median(d)
s = d / mdev if mdev != 0.0 else 0.0
# print("Number of discarded outliers:", data.size-data[s<m].size)
# print("Discarded outliers:", data[s>=m])
return data[s < m]
@dataclass
class OLEDPropertiesSpeciesSummmary:
species_name: str
species_smiles: str
species_nummol: int
# Ground state properties:
IP_mean: float
IP_sigma: float
EA_mean: float
EA_sigma: float
Dmag_mean: float
Dmag_sigma: float
Dorient_mean: float
Dorient_mean_uncertainty: float
# Exciton properties:
S1_mean: Optional[float] = None
S1_sigma: Optional[float] = None
T1_mean: Optional[float] = None
T1_sigma: Optional[float] = None
TDMmag_mean: Optional[float] = None
TDMmag_sigma: Optional[float] = None
TDMorient_mean: Optional[float] = None
TDMorient_mean_uncertainty: Optional[float] = None
def __str__(self) -> str:
ret = f"""\
Summary for species: {self.species_name}
---------------------{"-" * len(self.species_name)}
SMILES: {self.species_smiles}
Number of molecules: {self.species_nummol}
Energies:
IP: Ionization potential.
IP = {self.IP_mean:.2f} +- {self.IP_sigma:.3f} eV
EA: Electron affinity.
EA = {self.EA_mean:.2f} +- {self.EA_sigma:.3f} eV
Static dipole moments:
Magnitude:
|d| = {self.Dmag_mean:.2f} +- {self.Dmag_sigma:.2f} Debye
Orientation: theta = angle(d, e_z)
<cos(theta)> = {self.Dorient_mean:.3f} (uncertainty of mean = {self.Dorient_mean_uncertainty:.3f})
(in range [-1:1] with 0 being isotropic)
"""
if (
self.S1_mean is not None
and self.S1_sigma is not None
and self.T1_mean is not None
and self.T1_sigma is not None
and self.TDMorient_mean is not None
and self.TDMorient_mean_uncertainty is not None
):
ret += f"""\
Exciton energies:
S1: Energy of 1st excited singlet state with respect to the ground state.
S1 = {self.S1_mean:.2f} +- {self.S1_sigma:.3f} eV
T1: Energy of 1st excited triplet state with respect to the ground state.
T1 = {self.T1_mean:.2f} +- {self.T1_sigma:.3f} eV
Transition dipole moments: S0 -> S1
Magnitude:
|d| = {self.TDMmag_mean:.2f} +- {self.TDMmag_sigma:.2f} Debye
Orientation: theta = angle(d, e_z)
<cos(theta)^2> = {self.TDMorient_mean:.3f} (uncertainty of mean = {self.TDMorient_mean_uncertainty:.3f})
(in range [0:1] with 1/3 being isotropic)
"""
return ret
[docs]class OLEDPropertiesSummary:
"""A summary of the results of the OLEDProperties workflow."""
[docs] def __init__(self, f: "h5py.File", outlier_Zmax: float = 16):
"""Calculates a summary of the results on an HDF5 file.
:param f: The HDF5 file to summarize.
:type f: h5py.File
:param outlier_Zmax: The modified Z score above which a datapoint is excluded as an outlier. Defaults to 16.
:type outlier_Zmax: float, optional
"""
self.species_summaries: List[OLEDPropertiesSpeciesSummmary] = []
molSpec = f["molecules/species"][:]
IP = f["energies/IP"][:]
EA = f["energies/EA"][:]
Dmag = np.linalg.norm(f["static_multipole_moments/dipole_moment"][()], axis=1)
Dorient = []
for imol in range(f["static_multipole_moments/dipole_moment"].shape[0]):
d = f["static_multipole_moments/dipole_moment"][imol, :]
Dorient.append(np.dot(d / np.linalg.norm(d), [0, 0, 1]))
Dorient = np.array(Dorient)
if "exciton_energies" in f:
S1 = f["exciton_energies/S1"][:]
T1 = f["exciton_energies/T1"][:]
TDMmag = np.linalg.norm(f["transition_dipole_moments/S1_S0"][()], axis=1)
TDMorient = []
for imol in range(f["transition_dipole_moments/S1_S0"].shape[0]):
d = f["transition_dipole_moments/S1_S0"][imol, :]
TDMorient.append(np.dot(d / np.linalg.norm(d), [0, 0, 1]) ** 2)
TDMorient = np.array(TDMorient)
for spec, specName in enumerate(f["species/name"]):
# Ground state properties:
species_summary = OLEDPropertiesSpeciesSummmary(
species_name=specName.decode("ascii"),
species_smiles=f["species/smiles"][spec].decode("ascii"),
species_nummol=int(((molSpec == spec)).sum()),
IP_mean=reject_outliers(IP[(molSpec == spec) & (~np.isnan(IP))], outlier_Zmax).mean(),
IP_sigma=reject_outliers(IP[(molSpec == spec) & (~np.isnan(IP))], outlier_Zmax).std(),
EA_mean=reject_outliers(EA[(molSpec == spec) & (~np.isnan(EA))], outlier_Zmax).mean(),
EA_sigma=reject_outliers(EA[(molSpec == spec) & (~np.isnan(EA))], outlier_Zmax).std(),
Dmag_mean=reject_outliers(Dmag[(molSpec == spec) & (~np.isnan(Dmag))], outlier_Zmax).mean(),
Dmag_sigma=reject_outliers(Dmag[(molSpec == spec) & (~np.isnan(Dmag))], outlier_Zmax).std(),
Dorient_mean=Dorient[(molSpec == spec) & (~np.isnan(Dorient))].mean(),
Dorient_mean_uncertainty=(
Dorient[(molSpec == spec) & (~np.isnan(Dorient))].std()
/ math.sqrt(((molSpec == spec) & (~np.isnan(Dorient))).sum())
),
)
# Exciton properties:
species_summary.S1_mean = reject_outliers(S1[(molSpec == spec) & (~np.isnan(S1))], outlier_Zmax).mean()
species_summary.S1_sigma = reject_outliers(S1[(molSpec == spec) & (~np.isnan(S1))], outlier_Zmax).std()
species_summary.T1_mean = reject_outliers(T1[(molSpec == spec) & (~np.isnan(T1))], outlier_Zmax).mean()
species_summary.T1_sigma = reject_outliers(T1[(molSpec == spec) & (~np.isnan(T1))], outlier_Zmax).std()
species_summary.TDMmag_mean = TDMmag[(molSpec == spec) & (~np.isnan(TDMmag))].mean()
species_summary.TDMmag_sigma = TDMmag[(molSpec == spec) & (~np.isnan(TDMmag))].std()
species_summary.TDMorient_mean = TDMorient[(molSpec == spec) & (~np.isnan(TDMorient))].mean()
species_summary.TDMorient_mean_uncertainty = TDMorient[
(molSpec == spec) & (~np.isnan(TDMorient))
].std() / math.sqrt(((molSpec == spec) & (~np.isnan(TDMorient))).sum())
self.species_summaries.append(species_summary)
[docs] def __str__(self) -> str:
"""Produces a human readable summary of the results.
The same summary is also printed at the end of an ``oled-properties`` workflow run.
"""
return "\n".join(str(s) for s in self.species_summaries)
[docs] def as_yaml(self) -> str:
"""Returns a a summary of the calculation in a YAML format that can be imported into Bumblebee Web."""
ret = """\
---
materials:
"""
for i, ss in enumerate(self.species_summaries):
ret += f"""\
- id: {i+1}
name: {ss.species_name}
description: {ss.species_smiles}
homo: {-ss.IP_mean:.2f}
lumo: {-ss.EA_mean:.2f}
sigma_homo: {ss.IP_sigma:.3f}
sigma_lumo: {ss.EA_sigma:.3f}
singlet: {ss.S1_mean:.2f}
triplet: {ss.T1_mean:.2f}
sigma_singlet: {ss.S1_sigma:.3f}
sigma_triplet: {ss.T1_sigma:.3f}
dipole_strength: {ss.Dmag_mean:.2f}
transition_dipole_anisotropy: {ss.TDMorient_mean:.3f}
"""
ret += f"""\
compositions:
- id: 0
name: {" + ".join(s.species_name for s in self.species_summaries)} (AMS)
description: Calculated by the AMS OLED workflows
fractions:
"""
for i, ss in enumerate(self.species_summaries):
ret += f"""\
- material_id: {i+1}
fraction: {ss.species_nummol / sum(s.species_nummol for s in self.species_summaries)}
"""
return ret
