Prepare properties

src/dxtb/constants/__init__.py

@@ -3,7 +3,7 @@
 """
 
 from . import defaults, xtb
-from .chemistry import ATOMIC_NUMBER, PSE
-from .torch import FLOAT32, FLOAT64, UINT8
-from .units import AA2AU, AU2KCAL, CAL2J, EV2AU, K2AU
-from .xtb import KA, KB, KCN, NCOORD_DEFAULT_CUTOFF, R_SHIFT
+from .chemistry import *
+from .getters import *
+from .units import *
+from .xtb import *

src/dxtb/constants/chemistry.py

@@ -3,6 +3,11 @@
 """
 from __future__ import annotations
 
+import torch
+
+__all__ = ["ATOMIC_MASSES", "ATOMIC_NUMBER", "PSE"]
+
+
 PSE = {
     0: "X",
     1: "H",
@@ -126,3 +131,101 @@
 }
 
 ATOMIC_NUMBER = {sym: num for num, sym in PSE.items()}
+"""Atomic symbol to atomic number."""
+
+
+ATOMIC_MASSES = torch.tensor(
+    [
+        0.0,  # dummy
+        1.00797,
+        4.00260,
+        6.941,
+        9.01218,
+        10.81,
+        12.011,
+        14.0067,
+        15.9994,
+        18.998403,
+        20.179,
+        22.98977,
+        24.305,
+        26.98154,
+        28.0855,
+        30.97376,
+        32.06,
+        35.453,
+        39.948,
+        39.0983,
+        40.08,
+        44.9559,
+        47.90,
+        50.9415,
+        51.996,
+        54.9380,
+        55.847,
+        58.9332,
+        58.70,
+        63.546,
+        65.38,
+        69.72,
+        72.59,
+        74.9216,
+        78.96,
+        79.904,
+        83.80,
+        85.4678,
+        87.62,
+        88.9059,
+        91.22,
+        92.9064,
+        95.94,
+        98.0,
+        101.07,
+        102.9055,
+        106.4,
+        107.868,
+        112.41,
+        114.82,
+        118.69,
+        121.75,
+        126.9045,
+        127.60,
+        131.30,
+        132.9054,
+        137.33,
+        138.9055,
+        140.12,
+        140.9077,
+        144.24,
+        145,
+        150.4,
+        151.96,
+        157.25,
+        158.9254,
+        162.50,
+        164.9304,
+        167.26,
+        168.9342,
+        173.04,
+        174.967,
+        178.49,
+        180.9479,
+        183.85,
+        186.207,
+        190.2,
+        192.22,
+        195.09,
+        196.9665,
+        200.59,
+        204.37,
+        207.2,
+        208.9804,
+        209,
+        210,
+        222,
+    ]
+)
+"""
+Isotope-averaged atom masses in g/mol from
+https://www.angelo.edu/faculty/kboudrea/periodic/structure_mass.htm
+"""

src/dxtb/constants/getters.py

@@ -0,0 +1,44 @@
+"""
+Getter functions for constants
+==============================
+
+This module only contains some convenience functions for collecting constants.
+"""
+from __future__ import annotations
+
+import torch
+
+from .._types import Tensor
+from .chemistry import ATOMIC_MASSES
+from .defaults import TORCH_DTYPE
+from .units import GMOL2AU
+
+__all__ = ["get_atomic_masses"]
+
+
+def get_atomic_masses(
+    numbers: Tensor,
+    atomic_units: bool = True,
+    device: torch.device | None = None,
+    dtype: torch.dtype = TORCH_DTYPE,
+) -> Tensor:
+    """
+    Get isotope-averaged atomic masses for all `numbers`.
+    Parameters
+    ----------
+    numbers : Tensor
+        Atomic numbers in the system.
+    atomic_units : bool, optional
+        Flag for unit conversion. If `True` (default), the atomic masses will
+        be returned in atomic units. If `False`, the unit remains g/mol.
+    device : torch.device | None, optional
+        Device to store the tensor. If `None` (default), the default device is used.
+    dtype : torch.dtype, optional
+        Data type of the tensor. If none is given, it defaults to float32.
+    Returns
+    -------
+    Tensor
+        Atomic masses.
+    """
+    m = ATOMIC_MASSES[numbers].to(device).type(dtype)
+    return m * GMOL2AU if atomic_units is True else m

src/dxtb/constants/units.py

@@ -2,8 +2,66 @@
 Unit conversion factors.
 """
 
-AA2AU = 1.8897261246204404
-"""Factor for conversion from angstrom to atomic units."""
+from scipy.constants import physical_constants
+
+
+def get_constant(constant_name: str) -> float:
+    if constant_name not in physical_constants:
+        raise KeyError(f"Constant '{constant_name}' not found.")
+    return physical_constants[constant_name][0]
+
+
+class CODATA:
+    """CODATA values for various physical constants"""
+
+    h = get_constant("Planck constant")
+    """Planck's constant"""
+
+    c = get_constant("speed of light in vacuum")
+    """Speed of light in vacuum (m/s)"""
+
+    kb = get_constant("Boltzmann constant")
+    """Boltzmann's constant"""
+
+    na = get_constant("Avogadro constant")
+    """Avogadro's number (mol^-1)"""
+
+    e = get_constant("elementary charge")
+    """Elementary charge"""
+
+    alpha = get_constant("fine-structure constant")
+    """Fine structure constant (CODATA2018)"""
+
+    me = get_constant("electron mass")
+    """Rest mass of the electron (kg)"""
+
+    bohr = get_constant("Bohr radius")
+    """Bohr radius (m)"""
+
+
+PI = 3.1415926535897932384626433832795029
+
+# LENGTH
+
+AU2METER = CODATA.bohr
+"""
+Conversion from bohr (a.u.) to meter.
+This equals: 1 bohr = 5.29177210903e-11 m.
+"""
+
+METER2AU = 1.0 / AU2METER
+"""Conversion from meter to atomic units."""
+
+AA2METER = 1e-10
+"""Factor for conversion from Angstrom to meter (1e-10)."""
+
+AA2AU = AA2METER * METER2AU
+"""
+Factor for conversion from angstrom to atomic units.
+This equals: 1 Angstrom = 1.8897261246204404 a.u.
+"""
+
+# ENERGY
 
 EV2AU = 1.0 / 27.21138505
 """Factor for conversion from eletronvolt to atomic units."""
@@ -17,11 +75,69 @@
 CAL2J = 4.184
 """Factor for conversion from Calorie to Joule"""
 
-C2AU = 1.0 / 1.60217653e-19
-"""Factor for conversion from Coulomb to to atomic units"""
+AU2COULOMB = CODATA.e
+"""
+Factor for conversion from atomic units to Coulomb.
+This equals the elementary charge.
+"""
+
+COULOMB2AU = 1.0 / AU2COULOMB
+"""Factor for conversion from Coulomb to atomic units."""
+
+AU2JOULE = get_constant("atomic unit of energy")
+"""Factor for conversion from atomic units to Joule (J = kg·m²·s⁻²)."""
 
-J2AU = 1.0 / 4.3597441775e-18
-"""Factor for conversion from Joule to atomic units"""
+JOULE2AU = 1.0 / AU2JOULE
+"""
+Factor for conversion from Joule (J = kg·m²·s⁻²) to atomic units.
+This equals: 1 Joule = 2.294e+17 Hartree.
+Could also be calculated as: CODATA.me * CODATA.c**2 * CODATA.alpha**2
+"""
 
-VAA2AU = J2AU / (C2AU * AA2AU)
+VAA2AU = JOULE2AU / (COULOMB2AU * AA2AU)
 """Factor for conversion from  V/Å = J/(C·Å) to atomic units"""
+
+
+AU_KG = CODATA.me
+KG_AU = 1.0 / AU_KG
+
+AMU_KG = get_constant("unified atomic mass unit")
+KG_AMU = 1.0 / AMU_KG
+
+AMU_AU = AMU_KG * KG_AU
+AU_AMU = AU_KG * KG_AU
+
+
+AU2GMOL = 1e3 * CODATA.me * CODATA.na
+"""Electron mass (a.u.) to molecular mass per mole (g/mol)"""
+
+GMOL2AU = 1.0 / AU2GMOL
+"""Molecular mass per mole (g/mol) to electron mass (a.u.)"""
+
+
+AU2RCM = AU2JOULE / (CODATA.h * CODATA.c) * 1e-2
+"""Conversion from hartree to reciprocal centimeters"""
+
+RCM2AU = 1.0 / AU2RCM
+"""Conversion from reciprocal centimeters to hartree"""
+
+
+DEBYE2AU = 1e-21 / CODATA.c * COULOMB2AU * METER2AU
+"""
+Conversion from Debye to atomic units.
+This equals: 1 Debye in SI units (C m) = 0.393430 a.u.
+"""
+
+AU2DEBYE = 1.0 / DEBYE2AU
+"""Conversion from atomic units to Debye."""
+
+AMU = 5.485799090649e-4
+AU2KMMOL = (DEBYE2AU / AA2AU) ** 2 / AMU * 42.256
+
+# TIME
+
+AU2SECOND = get_constant("atomic unit of time")
+"""Conversion from atomic units to second. Atomic unit of time (s)."""
+
+SECOND2AU = 1.0 / AU2SECOND
+"""Conversion from second to atomic units."""

src/dxtb/coulomb/secondorder.py

@@ -48,7 +48,11 @@
 from ..utils import batch, cdist, real_pairs
 from .average import AveragingFunction, averaging_function, harmonic_average
 
-__all__ = ["ES2", "new_es2"]
+__all__ = ["ES2", "LABEL_ES2", "new_es2"]
+
+
+LABEL_ES2 = "ES2"
+"""Label for the 'ES2' interaction, coinciding with the class name."""
 
 
 class ES2(Interaction):
@@ -156,10 +160,7 @@ def __init__(
         self.shell_resolved = shell_resolved and lhubbard is not None
 
     def get_cache(
-        self,
-        numbers: Tensor,
-        positions: Tensor,
-        ihelp: IndexHelper,
+        self, numbers: Tensor, positions: Tensor, ihelp: IndexHelper
     ) -> ES2.Cache:
         """
         Obtain the cache object containing the Coulomb matrix.

src/dxtb/coulomb/thirdorder.py

@@ -42,7 +42,11 @@
 from ..interaction import Interaction
 from ..param import Param, get_elem_param
 
-__all__ = ["ES3", "new_es3"]
+__all__ = ["ES3", "LABEL_ES3", "new_es3"]
+
+
+LABEL_ES3 = "ES3"
+"""Label for the 'ES3' interaction, coinciding with the class name."""
 
 
 class ES3(Interaction):