def wrapper_test(): try: init() fun_methylene() finally: finish() remove_plams_dir()
# Default imports from qmworks import Settings, templates, run, rdkitTools from noodles import gather # User Defined imports from math import sqrt from qmworks.packages.SCM import dftb from qmworks.components import PES_scan, select_max import plams # ========== ============= plams.init() hartree2kcal = 627.5095 startvalue = {'C': 2.1, 'N': 1.9, 'O': 1.8} settings = Settings() settings.specific.dftb.dftb.scc.mixing = 0.15 settings.specific.dftb.dftb.scc.iterations = 200 settings.specific.dftb.geometry.iterations = 200 settings.specific.dftb.geometry.converge = "rad=0.002" def calc_reactant(name): smiles = {'C': '[CH2]=', 'N': '[NH]=', 'O': 'O='}[name[0]] +\ {'N': '[NH+]', 'O': '[O+]', 'S': '[S+]'}[name[1]] +\ {'C': '[CH2-]', 'N': '[NH-]', 'O': '[O-]'}[name[2]] mol = rdkitTools.smiles2plams(smiles) mol.properties.smiles = smiles return dftb(templates.geometry.overlay(settings),