def main(): options, fns = parse() #define logger if options.silent: log.set_level('silent') else: if options.very_verbose: log.set_level('highest') elif options.verbose: log.set_level('high') if options.logfile is not None and isinstance(options.logfile, str): log.write_to_file(options.logfile) with log.section('QFF', 1, timer='Initializing'): log.dump('Initializing system') #read system and ab initio reference system = None energy = 0.0 grad = None hess = None rvecs = None for fn in fns: if fn.endswith('.fchk') or fn.endswith('.xml'): numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio( fn) if system is None: system = System(numbers, coords, rvecs=rvecs, charges=None, radii=None, masses=masses) else: system.pos = coords.copy() system.cell = Cell(rvecs) system.numbers = numbers.copy() if masses is not None: system.masses = masses.copy() system._init_derived() elif fn.endswith('.chk'): sample = load_chk(fn) if 'energy' in sample.keys(): energy = sample['energy'] if 'grad' in sample.keys(): grad = sample['grad'] elif 'gradient' in sample.keys(): grad = sample['gradient'] if 'hess' in sample.keys(): hess = sample['hess'] elif 'hessian' in sample.keys(): hess = sample['hessian'] if system is None: system = System.from_file(fn) else: if 'pos' in sample.keys(): system.pos = sample['pos'] elif 'coords' in sample.keys(): system.pos = sample['coords'] if 'rvecs' in sample.keys(): system.cell = Cell(sample['rvecs']) elif 'cell' in sample.keys(): system.cell = Cell(sample['cell']) if 'bonds' in sample.keys(): system.bonds = sample['bonds'] if 'ffatypes' in sample.keys(): system.ffatypes = sample['ffatypes'] if 'ffatype_ids' in sample.keys(): system.ffatype_ids = sample['ffatype_ids'] system._init_derived() else: raise NotImplementedError('File format for %s not supported' % fn) assert system is not None, 'No system could be defined from input' assert grad is not None, 'No ab initio gradient found in input' assert hess is not None, 'No ab initio hessian found in input' #complete the system information if system.bonds is None: system.detect_bonds() if system.masses is None: system.set_standard_masses() if system.ffatypes is None: if options.ffatypes in ['low', 'medium', 'high', 'highest']: guess_ffatypes(system, options.ffatypes) elif options.ffatypes is not None: raise NotImplementedError( 'Guessing atom types from %s not implemented' % options.ffatypes) else: raise AssertionError('No atom types defined') #construct ab initio reference ai = SecondOrderTaylor('ai', coords=system.pos.copy(), energy=energy, grad=grad, hess=hess, pbc=pbc) #detect a priori defined contributions to the force field refs = [] if options.ei is not None: if rvecs is None: ff = ForceField.generate(system, options.ei, rcut=50 * angstrom) else: ff = ForceField.generate(system, options.ei, rcut=20 * angstrom, alpha_scale=3.2, gcut_scale=1.5, smooth_ei=True) refs.append(YaffForceField('EI', ff)) if options.vdw is not None: ff = ForceField.generate(system, options.vdw, rcut=20 * angstrom) refs.append(YaffForceField('vdW', ff)) if options.covres is not None: ff = ForceField.generate(system, options.covres) refs.append(YaffForceField('Cov res', ff)) #define quickff program assert options.program_mode in allowed_programs, \ 'Given program mode %s not allowed. Choose one of %s' %( options.program_mode, ', '.join([prog for prog in allowed_programs if not prog=='BaseProgram']) ) mode = program_modes[options.program_mode] only_traj = 'PT_ALL' if options.only_traj is not None: only_traj = options.only_traj.split(',') program = mode(system, ai, ffrefs=refs, fn_traj=options.fn_traj, only_traj=only_traj, plot_traj=options.ener_traj, xyz_traj=options.xyz_traj, suffix=options.suffix) #run program program.run()
def _set_log(self): log.set_level(self.log_level) f = self.log_file if f is not None and (isinstance(f, str) or isinstance(f, IOBase)): log.write_to_file(f)
def _set_log(self): log.set_level(self.log_level) f = self.log_file if f is not None and (isinstance(f, str) or isinstance(f, IOBase)): log.write_to_file(f)