add SQLite database

tests/create_database.py

@@ -0,0 +1,42 @@
+
+import sqlite3
+
+from molecule import Molecule
+from molecule import save_molecules_to_json, load_molecules_from_json
+from molecule import create_database, add_molecule_to_db
+
+
+
+molecules = [
+    Molecule(
+        name="H2O",
+        multiplicity=1,
+        geometry=[
+            {"element": "O", "x": 0.000000, "y": 0.000000, "z": 0.117790},
+            {"element": "H", "x": 0.000000, "y": 0.755453, "z": -0.471161},
+            {"element": "H", "x": 0.000000, "y": -0.755453, "z": -0.471161}
+        ],
+        energies={
+            "RHF": {
+                "cc-pvdz": -76.0267058009, 
+                "cc-pvtz": -76.0570239304, 
+                "cc-pvqz": -76.0646816616
+            },
+        }
+    ),
+]
+
+
+# Save molecules to JSON
+save_molecules_to_json(molecules, 'molecules.json')
+
+# Load molecules from JSON
+loaded_molecules = load_molecules_from_json('molecules.json')
+print(loaded_molecules)
+
+# Create a database and add molecules
+db_name = 'molecules.db'
+create_database(db_name)
+for molecule in molecules:
+    add_molecule_to_db(db_name, molecule)
+

tests/molecule.py

@@ -0,0 +1,86 @@
+
+import json
+import sqlite3
+
+class Molecule:
+    def __init__(self, name, multiplicity, geometry, energies):
+        self.name = name
+        self.multiplicity = multiplicity
+        self.geometry = geometry  # List of tuples (atom, x, y, z)
+        self.energies = energies  # Dictionary of dictionaries: {method: {basis: energy}}
+
+    def get_energy(self, method, basis):
+        """Retrieve energy for a specific method and basis set."""
+        return self.energies.get(method, {}).get(basis, None)
+
+    def to_dict(self):
+        return {
+            "name": self.name,
+            "multiplicity": self.multiplicity,
+            "geometry": self.geometry,
+            "energies": self.energies,
+        }
+
+    @staticmethod
+    def from_dict(data):
+        return Molecule(
+            name=data["name"],
+            multiplicity=data["multiplicity"],
+            geometry=data["geometry"],
+            energies=data["energies"]
+        )
+
+def save_molecules_to_json(molecules, filename):
+    with open(filename, 'w') as f:
+        json_data = [molecule.to_dict() for molecule in molecules]
+        json.dump(json_data, f, indent=4)
+
+def load_molecules_from_json(filename):
+    with open(filename, 'r') as f:
+        json_data = json.load(f)
+        return [Molecule.from_dict(data) for data in json_data]
+
+
+def create_database(db_name):
+    conn = sqlite3.connect(db_name)
+    cursor = conn.cursor()
+    cursor.execute('''CREATE TABLE IF NOT EXISTS molecules
+                      (name TEXT, multiplicity INTEGER, geometry TEXT, energies TEXT)''')
+    conn.commit()
+    conn.close()
+
+def add_molecule_to_db(db_name, molecule):
+    conn = sqlite3.connect(db_name)
+    cursor = conn.cursor()
+    geometry_str = json.dumps(molecule.geometry)
+    energies_str = json.dumps(molecule.energies)
+    cursor.execute("INSERT INTO molecules VALUES (?, ?, ?, ?)",
+                   (molecule.name, molecule.multiplicity, geometry_str, energies_str))
+    conn.commit()
+    conn.close()
+
+def get_molecules_from_db(db_name):
+    conn = sqlite3.connect(db_name)
+    cursor = conn.cursor()
+    cursor.execute("SELECT name, multiplicity, geometry, energies FROM molecules")
+    rows = cursor.fetchall()
+    molecules = []
+    for row in rows:
+        name, multiplicity, geometry_str, energies_str = row
+        geometry = json.loads(geometry_str)
+        energies = json.loads(energies_str)  # energies is a dictionary of dictionaries
+        molecules.append(Molecule(name, multiplicity, geometry, energies))
+    conn.close()
+    return molecules
+
+def write_geometry_to_xyz(molecule, filename):
+    with open(filename, 'w') as f:
+        # First line: number of atoms
+        f.write(f"{len(molecule.geometry)}\n")
+        # Second line: empty comment line
+        f.write("\n")
+        # Remaining lines: atom positions
+        for atom, x, y, z in molecule.geometry:
+            f.write(f"{atom} {x:.6f} {y:.6f} {z:.6f}\n")
+
+

tests/test_hf.py

@@ -5,6 +5,9 @@ import subprocess
 import platform
 from datetime import datetime
 
+from molecule import get_molecules_from_db
+
+
 current_date = datetime.now()
 
 quack_root = os.getenv('QUACK_ROOT')
@@ -65,15 +68,6 @@ list_opt = [hf_opt, mp_opt, cc_opt, tda_opt, gf_opt, gw_opt, gt_opt, acfdt_opt,
 
 # ---
 
-mol_multip = {
-    "Ne": 1,
-    "H2O": 1,
-}
-
-list_basis = ["cc-pvdz", "cc-pvtz", "cc-pvqz"]
-
-# ---
-
 class class_RHF:
 
     def gen_input():
@@ -163,7 +157,19 @@ def main():
         work_path.mkdir(parents=True, exist_ok=True)
         print(f"Directory '{work_path}' created.\n")
 
-    for methd in ["RHF", "UHF", "GHF", "ROHF"]:
+    for mol in molecules:
+
+        mol_name = mol.name
+        mol_mult = mol.multiplicity
+
+
+        for methd in list_methd:
+
+            if methd not in mol.energies:
+                print(f"Method {methd} does not exist for {mol_name}.")
+                continue
+
+            for bas, _ in mol.energies[methd].items():
 
                 work_methd = Path('{}/{}'.format(work_path, methd))
                 if not work_methd.exists():
@@ -175,18 +181,12 @@ def main():
                 # create input files
                 class_methd.gen_input()
         
-        for mol in mol_multip:
+                file_out = "{}/{}/{}_{}_{}.out".format(work_path, methd, mol_name, mol_mult, bas)
 
-            multip = mol_multip[mol]
+                print(" testing {} for {}@{} (2S+1 = {})".format(methd, mol_name, bas, mol_mult))
-
-            for bas in list_basis:
-
-                file_out = "{}/{}/{}_{}_{}.out".format(work_path, methd, mol, multip, bas)
-
-                print(" testing {} for {}@{} (2S+1 = {})".format(methd, mol, bas, multip))
                 print(" file_out: {}".format(file_out))
 
-                class_methd.run_job(file_out, mol, bas, multip)
+                class_methd.run_job(file_out, mol_name, bas, mol_mult)
 
                 print("\n")
             print("\n\n")
@@ -195,10 +195,10 @@ def main():
         print("\n\n\n")
         
 
+db_name = 'molecules.db'
+molecules = get_molecules_from_db(db_name)
+
+list_methd = ["RHF", "UHF", "GHF", "ROHF"]
+
 main()
 
-
-
-
-
-