remove old periodic dependency in promolecule

Author: enjyashraf18

atomdb/datasets/gaussian/h5file_creator.py

@@ -3,14 +3,15 @@
 from importlib_resources import files
 import tables as pt
 from dataclasses import asdict
-from atomdb.datasets.gaussian.run import NPOINTS
+# from atomdb.datasets.gaussian.run import NPOINTS
 from atomdb.periodic_test import element_symbol_map, ElementAttr
 
 
 # Suppresses NaturalNameWarning warnings from PyTables.
 warnings.filterwarnings("ignore", category=pt.NaturalNameWarning)
 
 max_norba = 41
+NPOINTS = 1000
 
 GAUSSIAN_PROPERTY_CONFIGS = [
     {

atomdb/datasets/hci/h5file_creator.py

@@ -3,14 +3,15 @@
 from importlib_resources import files
 import tables as pt
 from dataclasses import asdict
-from atomdb.datasets.hci.run import NPOINTS
+# from atomdb.datasets.hci.run import NPOINTS
 from atomdb.periodic_test import element_symbol_map, ElementAttr
 
 
 # Suppresses NaturalNameWarning warnings from PyTables.
 warnings.filterwarnings("ignore", category=pt.NaturalNameWarning)
 
 max_norba = 56
+NPOINTS = 1000
 
 HCI_PROPERTY_CONFIGS = [
     {

atomdb/datasets/slater/h5file_creator.py

@@ -3,14 +3,15 @@
 from importlib_resources import files
 import tables as pt
 from dataclasses import asdict
-from atomdb.datasets.slater.run import NPOINTS
+# from atomdb.datasets.slater.run import NPOINTS
 from atomdb.periodic_test import element_symbol_map, ElementAttr
 
 
 # Suppresses NaturalNameWarning warnings from PyTables.
 warnings.filterwarnings("ignore", category=pt.NaturalNameWarning)
 
 max_norba = 56
+NPOINTS = 1000
 
 SLATER_PROPERTY_CONFIGS = [
     {

atomdb/datasets/uhf_augccpvdz/h5file_creator.py

@@ -3,14 +3,15 @@
 from importlib_resources import files
 import tables as pt
 from dataclasses import asdict
-from atomdb.datasets.uhf_augccpvdz.run import NPOINTS
+# from atomdb.datasets.uhf_augccpvdz.run import NPOINTS
 from atomdb.periodic_test import element_symbol_map, ElementAttr
 
 
 # Suppresses NaturalNameWarning warnings from PyTables.
 warnings.filterwarnings("ignore", category=pt.NaturalNameWarning)
 
 max_norba = 100  # needs to be calculated
+NPOINTS = 1000
 
 UHF_AUGCCPVDZ_PROPERTY_CONFIGS = [
     {

atomdb/periodic_test.py

@@ -9,6 +9,7 @@
     "PROPERTY_NAME_MAP",
     "get_scalar_data",
     "element_symbol_map",
+    "atnum_to_symbol",
     "ElementAttr",
 ]
 
@@ -106,3 +107,5 @@ def map_element_symbol():
 
 
 element_symbol_map = map_element_symbol()
+atnum_to_symbol = {atnum[0]: elem for elem, atnum in element_symbol_map.items()}
+print(atnum_to_symbol)

atomdb/promolecule.py

@@ -24,7 +24,8 @@
 import numpy as np
 from scipy.optimize import linprog
 
-from atomdb.periodic import element_number, element_symbol
+# from atomdb.periodic import element_number, element_symbol
+from atomdb.periodic_test import element_symbol_map, atnum_to_symbol, ElementAttr
 from atomdb.species import load
 from atomdb.utils import DEFAULT_DATAPATH, DEFAULT_DATASET, DEFAULT_REMOTE, MULTIPLICITIES
 
@@ -582,8 +583,8 @@ def make_promolecule(
     if isinstance(atnums, (Integral, str)):
         atnums = [atnums]
     # Get atomic symbols/numbers from inputs
-    atnums = [element_number(atom) for atom in atnums]
-    atoms = [element_symbol(atom) for atom in atnums]
+    atnums = [element_symbol_map[atom][ElementAttr.atnum] if isinstance(atom, str) else atom for atom in atnums]
+    atoms = [atnum_to_symbol[atom] if isinstance(atom, Integral) else atom for atom in atnums]
 
     # Handle default charge parameters
     if charges is None: