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https://github.com/pfloos/quack
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add SQLite database
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42
tests/create_database.py
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42
tests/create_database.py
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import sqlite3
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from molecule import Molecule
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from molecule import save_molecules_to_json, load_molecules_from_json
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from molecule import create_database, add_molecule_to_db
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molecules = [
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Molecule(
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name="H2O",
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multiplicity=1,
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geometry=[
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{"element": "O", "x": 0.000000, "y": 0.000000, "z": 0.117790},
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{"element": "H", "x": 0.000000, "y": 0.755453, "z": -0.471161},
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{"element": "H", "x": 0.000000, "y": -0.755453, "z": -0.471161}
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],
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energies={
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"RHF": {
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"cc-pvdz": -76.0267058009,
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"cc-pvtz": -76.0570239304,
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"cc-pvqz": -76.0646816616
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},
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}
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),
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]
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# Save molecules to JSON
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save_molecules_to_json(molecules, 'molecules.json')
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# Load molecules from JSON
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loaded_molecules = load_molecules_from_json('molecules.json')
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print(loaded_molecules)
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# Create a database and add molecules
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db_name = 'molecules.db'
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create_database(db_name)
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for molecule in molecules:
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add_molecule_to_db(db_name, molecule)
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86
tests/molecule.py
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86
tests/molecule.py
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import json
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import sqlite3
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class Molecule:
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def __init__(self, name, multiplicity, geometry, energies):
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self.name = name
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self.multiplicity = multiplicity
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self.geometry = geometry # List of tuples (atom, x, y, z)
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self.energies = energies # Dictionary of dictionaries: {method: {basis: energy}}
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def get_energy(self, method, basis):
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"""Retrieve energy for a specific method and basis set."""
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return self.energies.get(method, {}).get(basis, None)
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def to_dict(self):
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return {
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"name": self.name,
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"multiplicity": self.multiplicity,
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"geometry": self.geometry,
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"energies": self.energies,
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}
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@staticmethod
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def from_dict(data):
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return Molecule(
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name=data["name"],
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multiplicity=data["multiplicity"],
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geometry=data["geometry"],
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energies=data["energies"]
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)
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def save_molecules_to_json(molecules, filename):
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with open(filename, 'w') as f:
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json_data = [molecule.to_dict() for molecule in molecules]
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json.dump(json_data, f, indent=4)
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def load_molecules_from_json(filename):
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with open(filename, 'r') as f:
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json_data = json.load(f)
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return [Molecule.from_dict(data) for data in json_data]
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def create_database(db_name):
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conn = sqlite3.connect(db_name)
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cursor = conn.cursor()
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cursor.execute('''CREATE TABLE IF NOT EXISTS molecules
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(name TEXT, multiplicity INTEGER, geometry TEXT, energies TEXT)''')
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conn.commit()
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conn.close()
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def add_molecule_to_db(db_name, molecule):
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conn = sqlite3.connect(db_name)
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cursor = conn.cursor()
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geometry_str = json.dumps(molecule.geometry)
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energies_str = json.dumps(molecule.energies)
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cursor.execute("INSERT INTO molecules VALUES (?, ?, ?, ?)",
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(molecule.name, molecule.multiplicity, geometry_str, energies_str))
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conn.commit()
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conn.close()
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def get_molecules_from_db(db_name):
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conn = sqlite3.connect(db_name)
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cursor = conn.cursor()
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cursor.execute("SELECT name, multiplicity, geometry, energies FROM molecules")
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rows = cursor.fetchall()
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molecules = []
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for row in rows:
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name, multiplicity, geometry_str, energies_str = row
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geometry = json.loads(geometry_str)
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energies = json.loads(energies_str) # energies is a dictionary of dictionaries
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molecules.append(Molecule(name, multiplicity, geometry, energies))
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conn.close()
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return molecules
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def write_geometry_to_xyz(molecule, filename):
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with open(filename, 'w') as f:
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# First line: number of atoms
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f.write(f"{len(molecule.geometry)}\n")
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# Second line: empty comment line
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f.write("\n")
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# Remaining lines: atom positions
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for atom, x, y, z in molecule.geometry:
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f.write(f"{atom} {x:.6f} {y:.6f} {z:.6f}\n")
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@ -5,6 +5,9 @@ import subprocess
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import platform
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import platform
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from datetime import datetime
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from datetime import datetime
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from molecule import get_molecules_from_db
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current_date = datetime.now()
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current_date = datetime.now()
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quack_root = os.getenv('QUACK_ROOT')
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quack_root = os.getenv('QUACK_ROOT')
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@ -65,15 +68,6 @@ list_opt = [hf_opt, mp_opt, cc_opt, tda_opt, gf_opt, gw_opt, gt_opt, acfdt_opt,
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# ---
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# ---
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mol_multip = {
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"Ne": 1,
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"H2O": 1,
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}
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list_basis = ["cc-pvdz", "cc-pvtz", "cc-pvqz"]
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# ---
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class class_RHF:
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class class_RHF:
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def gen_input():
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def gen_input():
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work_path.mkdir(parents=True, exist_ok=True)
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work_path.mkdir(parents=True, exist_ok=True)
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print(f"Directory '{work_path}' created.\n")
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print(f"Directory '{work_path}' created.\n")
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for methd in ["RHF", "UHF", "GHF", "ROHF"]:
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for mol in molecules:
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work_methd = Path('{}/{}'.format(work_path, methd))
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mol_name = mol.name
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if not work_methd.exists():
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mol_mult = mol.multiplicity
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work_methd.mkdir(parents=True, exist_ok=True)
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print(f"Directory '{work_methd}' created.\n")
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class_methd = class_map.get(methd)
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# create input files
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for methd in list_methd:
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class_methd.gen_input()
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for mol in mol_multip:
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if methd not in mol.energies:
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print(f"Method {methd} does not exist for {mol_name}.")
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continue
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multip = mol_multip[mol]
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for bas, _ in mol.energies[methd].items():
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for bas in list_basis:
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work_methd = Path('{}/{}'.format(work_path, methd))
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if not work_methd.exists():
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work_methd.mkdir(parents=True, exist_ok=True)
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print(f"Directory '{work_methd}' created.\n")
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file_out = "{}/{}/{}_{}_{}.out".format(work_path, methd, mol, multip, bas)
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class_methd = class_map.get(methd)
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print(" testing {} for {}@{} (2S+1 = {})".format(methd, mol, bas, multip))
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# create input files
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class_methd.gen_input()
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file_out = "{}/{}/{}_{}_{}.out".format(work_path, methd, mol_name, mol_mult, bas)
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print(" testing {} for {}@{} (2S+1 = {})".format(methd, mol_name, bas, mol_mult))
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print(" file_out: {}".format(file_out))
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print(" file_out: {}".format(file_out))
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class_methd.run_job(file_out, mol, bas, multip)
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class_methd.run_job(file_out, mol_name, bas, mol_mult)
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print("\n")
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print("\n")
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print("\n\n")
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print("\n\n")
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@ -195,10 +195,10 @@ def main():
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print("\n\n\n")
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print("\n\n\n")
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db_name = 'molecules.db'
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molecules = get_molecules_from_db(db_name)
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list_methd = ["RHF", "UHF", "GHF", "ROHF"]
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main()
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main()
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