Update/constant file (grimme-lab#112)

* New file which contains all constants used in the program Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * updated the wrong placed import statement Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Added a new ordner named data containing constants.py and parameters.py Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * moved the covalent radii to the parameters file and give both in angstroem. Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * move get_cov_radii, indent else after return, make tests faster Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * update CHANGELOG.md accordingly§ Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> --------- Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> Co-authored-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de>
jonathan-schoeps · Jan 24, 2025 · 11f7393 · 11f7393
1 parent 16933c5
commit 11f7393
Show file tree

Hide file tree

Showing 11 changed files with 436 additions and 397 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - to set the elemental composition it is now possible to use dicts with not only int but also the element symbols (str)
 - dict keys for elemental compositions will now always be checked for validity
 - Renamed GP3-xTB to g-xTB
+- Moved constants and (empirical) parameters to the `data` module
+
+### Deprecated
 - Nothing will be printed while multiple molecules are generated in parallel, tqdm-based progress bar instead
 - Some debugging statements from generate had to be removed (esp. w.r.t. early stopping)
 

diff --git a/src/mindlessgen/data/__init__.py b/src/mindlessgen/data/__init__.py
@@ -0,0 +1,24 @@
+"""
+This file is used to import all the constants from the constants.py file and the parameters.py file.
+"""
+
+from mindlessgen.data.constants import (
+    PSE,
+    PSE_NUMBERS,
+    PSE_SYMBOLS,
+    BOHR2AA,
+    AA2BOHR,
+)
+
+from mindlessgen.data.parameters import (
+    MAX_ELEM,
+)
+
+__all__ = [
+    "PSE",
+    "PSE_NUMBERS",
+    "PSE_SYMBOLS",
+    "BOHR2AA",
+    "AA2BOHR",
+    "MAX_ELEM",
+]
diff --git a/src/mindlessgen/data/constants.py b/src/mindlessgen/data/constants.py
@@ -0,0 +1,132 @@
+"""
+This module contains the constans which are used in the project.
+"""
+
+PSE: dict[int, str] = {
+    0: "X",
+    1: "H",
+    2: "He",
+    3: "Li",
+    4: "Be",
+    5: "B",
+    6: "C",
+    7: "N",
+    8: "O",
+    9: "F",
+    10: "Ne",
+    11: "Na",
+    12: "Mg",
+    13: "Al",
+    14: "Si",
+    15: "P",
+    16: "S",
+    17: "Cl",
+    18: "Ar",
+    19: "K",
+    20: "Ca",
+    21: "Sc",
+    22: "Ti",
+    23: "V",
+    24: "Cr",
+    25: "Mn",
+    26: "Fe",
+    27: "Co",
+    28: "Ni",
+    29: "Cu",
+    30: "Zn",
+    31: "Ga",
+    32: "Ge",
+    33: "As",
+    34: "Se",
+    35: "Br",
+    36: "Kr",
+    37: "Rb",
+    38: "Sr",
+    39: "Y",
+    40: "Zr",
+    41: "Nb",
+    42: "Mo",
+    43: "Tc",
+    44: "Ru",
+    45: "Rh",
+    46: "Pd",
+    47: "Ag",
+    48: "Cd",
+    49: "In",
+    50: "Sn",
+    51: "Sb",
+    52: "Te",
+    53: "I",
+    54: "Xe",
+    55: "Cs",
+    56: "Ba",
+    57: "La",
+    58: "Ce",
+    59: "Pr",
+    60: "Nd",
+    61: "Pm",
+    62: "Sm",
+    63: "Eu",
+    64: "Gd",
+    65: "Tb",
+    66: "Dy",
+    67: "Ho",
+    68: "Er",
+    69: "Tm",
+    70: "Yb",
+    71: "Lu",
+    72: "Hf",
+    73: "Ta",
+    74: "W",
+    75: "Re",
+    76: "Os",
+    77: "Ir",
+    78: "Pt",
+    79: "Au",
+    80: "Hg",
+    81: "Tl",
+    82: "Pb",
+    83: "Bi",
+    84: "Po",
+    85: "At",
+    86: "Rn",
+    87: "Fr",
+    88: "Ra",
+    89: "Ac",
+    90: "Th",
+    91: "Pa",
+    92: "U",
+    93: "Np",
+    94: "Pu",
+    95: "Am",
+    96: "Cm",
+    97: "Bk",
+    98: "Cf",
+    99: "Es",
+    100: "Fm",
+    101: "Md",
+    102: "No",
+    103: "Lr",
+    104: "Rf",
+    105: "Db",
+    106: "Sg",
+    107: "Bh",
+    108: "Hs",
+    109: "Mt",
+    110: "Ds",
+    111: "Rg",
+    112: "Cn",
+    113: "Nh",
+    114: "Fl",
+    115: "Mc",
+    116: "Lv",
+    117: "Ts",
+    118: "Og",
+}
+PSE_NUMBERS: dict[str, int] = {k.lower(): v for v, k in PSE.items()}
+PSE_SYMBOLS: dict[int, str] = {v: k.lower() for v, k in PSE.items()}
+
+BOHR2AA = (
+    0.529177210544  # taken from https://physics.nist.gov/cgi-bin/cuu/Value?bohrrada0
+)
+AA2BOHR = 1 / BOHR2AA
diff --git a/src/mindlessgen/data/parameters.py b/src/mindlessgen/data/parameters.py
@@ -0,0 +1,226 @@
+"""
+This module contains the parameters for the mindlessgen package.
+"""
+
+MAX_ELEM = 86
+
+# Covalent radii (taken from Pyykko and Atsumi, Chem. Eur. J. 15, 2009, 188-197)
+# Values for metals decreased by 10%
+# D3 covalent radii used to construct the coordination number
+COV_RADII_PYYKKO = [
+    0.32,
+    0.46,  # H, He
+    1.20,
+    0.94,
+    0.77,
+    0.75,
+    0.71,
+    0.63,
+    0.64,
+    0.67,  # Li-Ne
+    1.40,
+    1.25,
+    1.13,
+    1.04,
+    1.10,
+    1.02,
+    0.99,
+    0.96,  # Na-Ar
+    1.76,
+    1.54,  # K, Ca
+    1.33,
+    1.22,
+    1.21,
+    1.10,
+    1.07,  # Sc-
+    1.04,
+    1.00,
+    0.99,
+    1.01,
+    1.09,  # -Zn
+    1.12,
+    1.09,
+    1.15,
+    1.10,
+    1.14,
+    1.17,  # Ga-Kr
+    1.89,
+    1.67,  # Rb, Sr
+    1.47,
+    1.39,
+    1.32,
+    1.24,
+    1.15,  # Y-
+    1.13,
+    1.13,
+    1.08,
+    1.15,
+    1.23,  # -Cd
+    1.28,
+    1.26,
+    1.26,
+    1.23,
+    1.32,
+    1.31,  # In-Xe
+    2.09,
+    1.76,  # Cs, Ba
+    1.62,
+    1.47,
+    1.58,
+    1.57,
+    1.56,
+    1.55,
+    1.51,  # La-Eu
+    1.52,
+    1.51,
+    1.50,
+    1.49,
+    1.49,
+    1.48,
+    1.53,  # Gd-Yb
+    1.46,
+    1.37,
+    1.31,
+    1.23,
+    1.18,  # Lu-
+    1.16,
+    1.11,
+    1.12,
+    1.13,
+    1.32,  # -Hg
+    1.30,
+    1.30,
+    1.36,
+    1.31,
+    1.38,
+    1.42,  # Tl-Rn
+    2.01,
+    1.81,  # Fr, Ra
+    1.67,
+    1.58,
+    1.52,
+    1.53,
+    1.54,
+    1.55,
+    1.49,  # Ac-Am
+    1.49,
+    1.51,
+    1.51,
+    1.48,
+    1.50,
+    1.56,
+    1.58,  # Cm-No
+    1.45,
+    1.41,
+    1.34,
+    1.29,
+    1.27,  # Lr-
+    1.21,
+    1.16,
+    1.15,
+    1.09,
+    1.22,  # -Cn
+    1.36,
+    1.43,
+    1.46,
+    1.58,
+    1.48,
+    1.57,  # Nh-Og
+]
+
+COV_RADII_MLMGEN = [
+    0.42666663,
+    0.6133333,
+    1.59999996,
+    1.25333325,
+    1.02666658,
+    0.99999994,
+    0.94666658,
+    0.83999994,
+    0.85333326,
+    0.8933333,
+    1.86666651,
+    1.66666656,
+    1.50666656,
+    1.38666653,
+    1.4666666,
+    1.35999989,
+    1.31999993,
+    1.27999989,
+    2.3466665,
+    2.05333315,
+    1.77333328,
+    1.6266666,
+    1.61333328,
+    1.4666666,
+    1.42666664,
+    1.38666653,
+    1.33333325,
+    1.31999993,
+    1.34666657,
+    1.45333329,
+    1.49333325,
+    1.45333329,
+    1.53333321,
+    1.4666666,
+    1.51999988,
+    1.55999984,
+    2.51999982,
+    2.22666647,
+    1.95999991,
+    1.8533332,
+    1.75999996,
+    1.65333324,
+    1.53333321,
+    1.50666656,
+    1.50666656,
+    1.43999997,
+    1.53333321,
+    1.63999992,
+    1.70666652,
+    1.67999988,
+    1.67999988,
+    1.63999992,
+    1.75999996,
+    1.74666648,
+    2.78666637,
+    2.3466665,
+    2.15999987,
+    1.95999991,
+    2.10666659,
+    2.09333327,
+    2.07999979,
+    2.06666647,
+    2.01333319,
+    2.02666651,
+    2.01333319,
+    1.99999987,
+    1.98666655,
+    1.98666655,
+    1.97333324,
+    2.03999983,
+    1.94666659,
+    1.82666656,
+    1.74666648,
+    1.63999992,
+    1.57333316,
+    1.54666652,
+    1.47999992,
+    1.49333325,
+    1.50666656,
+    1.75999996,
+    1.73333316,
+    1.73333316,
+    1.81333324,
+    1.74666648,
+    1.83999988,
+    1.89333316,
+    2.67999982,
+    2.41333311,
+    2.22666647,
+    2.10666659,
+    2.02666651,
+    2.03999983,
+    2.05333315,
+    2.06666647,
+]