handle wildcard case while loading the element

Author: enjyashraf18

atomdb/datasets/slater/run.py

@@ -26,12 +26,9 @@
 # from importlib_resources import files
 from atomdb.utils import DEFAULT_DATAPATH
 from scipy.special import factorial
-import tables as pt
 from dataclasses import dataclass, field
 from typing import Optional, Dict
 
-
-
 __all__ = ["AtomicDensity", "load_slater_wfn", "run"]
 
 
@@ -1198,6 +1195,8 @@ def run(elem, charge, mult, nexc, dataset, datapath):
 
 
 
+
+
     # Conceptual-DFT properties (WIP)
     ip = -mo_e_up[np.sum(occs_up) - 1]  # - energy of HOMO
     # ea = -mo_e_dn[np.sum(occs_dn)] if np.sum(occs_dn) < np.sum(occs_up) else None  # - LUMO energy

atomdb/migration/datasets/datasets_data.py

@@ -1,3 +1,7 @@
+"""
+running this file will recreate datasets_data.h5, that will lead to create an empty datasets folder once again
+"""
+
 from importlib_resources import files
 import tables as pt
 

atomdb/migration/periodic/elements_data.py

@@ -14,6 +14,20 @@
 hdf5_file = files("atomdb.data").joinpath("elements_data.h5")
 
 
+PROPERTY_NAME_MAP = {
+    "atmass": "atmass",
+    "cov_radius": "cov_radius",
+    "vdw_radius": "vdw_radius",
+    "at_radius": "at_radius",
+    "polarizability": "polarizability",
+    "dispersion_c6": "dispersion_c6",
+    "dispersion": "dispersion_c6",
+    "elem": "symbol",
+    "atnum": "atnum",
+    "name": "name",
+}
+
+
 # Properties of each element in the HDF5 file.
 PROPERTY_CONFIGS = [
     {
@@ -347,6 +361,21 @@ def write_data_info_to_hdf5(data_info_list):
         property_info_table.flush()
 
 
+
+def map_element_symbol(ELEMENTS_H5FILE):
+    element_symbol_map = {}
+    for element_group in ELEMENTS_H5FILE.root.Elements:
+        symbol = element_group.symbol[0]['value'].decode('utf-8').strip()
+        atnum = element_group.atnum[0]['value']
+        name = element_group.name[0]['value'].decode('utf-8').strip()
+        element_symbol_map[symbol] = (atnum, name)
+
+    return element_symbol_map
+
+
+
+
+
 if __name__ == "__main__":
     # Read the elements data from the CSV file
     data, unique_headers, sources_data, units_data = read_elements_data_csv(elements_data_csv)