Cleaned up the imports, moved constants to separate file temporarily to

python/mrchem/CUBEparser.py

@@ -23,15 +23,13 @@
 # For information on the complete list of contributors to MRChem, see:
 # <https://mrchem.readthedocs.io/>
 #
-from .input_parser.plumbing import pyparsing as pp
+
 import os
 from json import dump
 
-BOHR_2_METER = 5.29177210903e-11
-"""Conversion from atomic units of length (Bohr) to meter (CODATA 2018)"""
-ANGSTROM_2_BOHR = 1e-10 / BOHR_2_METER
-#ANGSTROM_2_BOHR = 1.889725989
-"""Conversion factor from Angstrom to Bohr"""
+from .input_parser.plumbing import pyparsing as pp
+from.physical_constants import PhysicalConstants as PC
+
 
 def write_cube_dict(file_dict, world_unit):
     all_path_list = []
@@ -175,7 +173,7 @@ def count(s, l, t):
 
     # get cube origin data
     N_atoms = parsed_cube["NATOMS"]
-    origin = parsed_cube["ORIGIN"] if (world_unit == "bohr") else [p*ANGSTROM_2_BOHR for p in parsed_cube["ORIGIN"]]
+    origin = parsed_cube["ORIGIN"] if (world_unit == "bohr") else [p*PC.ANGSTROM_2_BOHR for p in parsed_cube["ORIGIN"]]
 
     # Set the amount of values depending on if the DSET_IDs were present or not
     if (len(parsed_cube["DSET_IDS"]) != 0):
@@ -200,9 +198,9 @@ def count(s, l, t):
     if (world_unit == "bohr"):
         Voxel_axes = [parsed_cube["XAXIS"]["VECTOR"], parsed_cube["YAXIS"]["VECTOR"], parsed_cube["ZAXIS"]["VECTOR"]]
     else:
-        X_voxel = [p*ANGSTROM_2_BOHR for p in parsed_cube["XAXIS"]["VECTOR"]]
-        Y_voxel = [p*ANGSTROM_2_BOHR for p in parsed_cube["YAXIS"]["VECTOR"]]
-        Z_voxel = [p*ANGSTROM_2_BOHR for p in parsed_cube["ZAXIS"]["VECTOR"]]
+        X_voxel = [p*PC.ANGSTROM_2_BOHR for p in parsed_cube["XAXIS"]["VECTOR"]]
+        Y_voxel = [p*PC.ANGSTROM_2_BOHR for p in parsed_cube["YAXIS"]["VECTOR"]]
+        Z_voxel = [p*PC.ANGSTROM_2_BOHR for p in parsed_cube["ZAXIS"]["VECTOR"]]
         Voxel_axes = [X_voxel, Y_voxel, Z_voxel]
 
     # get the atom coordinates
@@ -211,7 +209,7 @@ def count(s, l, t):
 
     Z_n = [atom["ATOMIC_NUMBER"] for atom in parsed_cube["GEOM"]]
     atom_charges = [atom["CHARGE"] for atom in parsed_cube["GEOM"]]
-    atom_coords = [atom["POSITION"] if (world_unit == "bohr") else [p*ANGSTROM_2_BOHR for p in atom["POSITION"]] for atom in parsed_cube["GEOM"]]
+    atom_coords = [atom["POSITION"] if (world_unit == "bohr") else [p*PC.ANGSTROM_2_BOHR for p in atom["POSITION"]] for atom in parsed_cube["GEOM"]]
 
     # construct the CUBE vector. Indexing is CUBE_vector[MO_ID][i*N_vals[1]*N_vals[2] + j*N_vals[2] + k] where i, j and k correspond to steps in the X, Y and Z voxel axes directions respectively.
     CUBE_vector = []

python/mrchem/api.py

@@ -25,8 +25,16 @@
 
 import math
 
-from .helpers import *
-from .CUBEparser import *
+from .helpers import (
+    write_scf_fock,
+    write_scf_guess,
+    write_scf_solver,
+    write_scf_properties,
+    write_scf_plot,
+    write_rsp_calc,
+    parse_wf_method
+)
+from .physical_constants import PhysicalConstants as PC
 from .periodictable import PeriodicTable as PT, PeriodicTableByZ as PT_Z
 from .validators import MoleculeValidator
 
@@ -35,7 +43,7 @@ def translate_input(user_dict):
     # get the origin in the desired units of measure
     origin = user_dict["world_origin"]
     if user_dict["world_unit"] == "angstrom":
-        origin = [ANGSTROM_2_BOHR * r for r in origin]
+        origin = [PC.ANGSTROM_2_BOHR * r for r in origin]
 
     # prepare bits and pieces
     mol_dict = write_molecule(user_dict, origin)

python/mrchem/helpers.py

@@ -23,13 +23,9 @@
 # <https://mrchem.readthedocs.io/>
 #
 
-from .CUBEparser import *
+from .physical_constants import PhysicalConstants as PC
+from .CUBEparser import write_cube_dict
 
-BOHR_2_METER = 5.29177210903e-11
-"""Conversion from atomic units of length (Bohr) to meter (CODATA 2018)"""
-ANGSTROM_2_BOHR = 1e-10 / BOHR_2_METER
-#ANGSTROM_2_BOHR = 1.889725989
-"""Conversion factor from Angstrom to Bohr"""
 # yapf: disable
 SHORTHAND_FUNCTIONALS = [
     'svwn3',
@@ -262,7 +258,7 @@ def write_scf_plot(user_dict):
         plot_dict["plotter"] = user_dict["Plotter"]
         if user_dict["world_unit"] == "angstrom":
             plot_dict["plotter"] = {
-                k: [ANGSTROM_2_BOHR * r for r in plot_dict["plotter"][k]]
+                k: [PC.ANGSTROM_2_BOHR * r for r in plot_dict["plotter"][k]]
                 for k in plot_dict["plotter"].keys()
             }
     return plot_dict

python/mrchem/physical_constants.py

@@ -0,0 +1,28 @@
+#
+# MRChem, a numerical real-space code for molecular electronic structure
+# calculations within the self-consistent field (SCF) approximations of quantum
+# chemistry (Hartree-Fock and Density Functional Theory).
+# Copyright (C) 2022 Stig Rune Jensen, Luca Frediani, Peter Wind and contributors.
+#
+# This file is part of MRChem.
+#
+# MRChem is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# MRChem is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with MRChem.  If not, see <https://www.gnu.org/licenses/>.
+#
+# For information on the complete list of contributors to MRChem, see:
+# <https://mrchem.readthedocs.io/>
+#
+
+class PhysicalConstants:
+    BOHR_2_METER = 5.29177210903e-11
+    ANGSTROM_2_BOHR = 1.0e-10 / BOHR_2_METER

python/mrchem/validators.py

@@ -27,7 +27,7 @@
 import itertools
 import re
 
-from .helpers import ANGSTROM_2_BOHR
+from .physical_constants import PhysicalConstants as PC
 from .periodictable import PeriodicTable, PeriodicTableByZ
 
 
@@ -127,7 +127,7 @@ def __init__(self, user_dict, origin):
             self.atomic_coords = self.ang2bohr_array(self.atomic_coords)
             self.cavity_coords = self.ang2bohr_array(self.cavity_coords)
             self.cavity_radii = self.ang2bohr_vector(self.cavity_radii)
-            self.cavity_width *= ANGSTROM_2_BOHR
+            self.cavity_width *= PC.ANGSTROM_2_BOHR
 
     def get_coords_in_program_syntax(self):
         """Convert nuclear coordinates from JSON syntax to program syntax."""
@@ -328,10 +328,10 @@ def euclidian_distance(a, b):
     def ang2bohr_array(coords):
         """Helper function. Convert List[List[float]] from angstrom to bohr."""
         return [
-            [c * ANGSTROM_2_BOHR for c in element] for element in coords
+            [c * PC.ANGSTROM_2_BOHR for c in element] for element in coords
         ]
 
     @staticmethod
     def ang2bohr_vector(vec):
         """Helper function. Convert List[float] from angstrom to bohr"""
-        return [el * ANGSTROM_2_BOHR for el in vec]
+        return [el * PC.ANGSTROM_2_BOHR for el in vec]