def read_system(name): # Load system data dn = 'quickff.data.systems' if '/' in name: words = name.split('/') dn += '.%s' % ('.'.join(words[:-1])) name = words[-1] with path(dn, name) as fn: numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio( fn) fns_wpart = glob(os.path.join(os.path.dirname(fn), 'gaussian_mbis.h5')) # Try to load charges. charges = None if len(fns_wpart) > 0: with h5.File(fns_wpart[0], 'r') as f: charges = f['charges'][:] # Create system object. system = System(numbers, coords, charges=charges) system.detect_bonds() system.set_standard_masses() # Load ab initio data. ai = SecondOrderTaylor('ai', coords=system.pos.copy(), energy=energy, grad=grad, hess=hess, pbc=pbc) return system, ai
def read_system(name): fn = context.get_fn('systems/%s' %name) numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(fn) system = System(numbers, coords) system.detect_bonds() system.set_standard_masses() ai = SecondOrderTaylor('ai', coords=system.pos.copy(), energy=energy, grad=grad, hess=hess, pbc=pbc) return system, ai
def read_system(name): # Load system data. fn = context.get_fn(os.path.join('systems', name)) numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(fn) # Try to load charges. charges = None fns_wpart = glob(os.path.join(os.path.dirname(fn), 'gaussian_mbis.h5')) if len(fns_wpart) > 0: with h5.File(fns_wpart[0], 'r') as f: charges = f['charges'][:] # Create system object. system = System(numbers, coords, charges=charges) system.detect_bonds() system.set_standard_masses() # Load ab initio data. ai = SecondOrderTaylor('ai', coords=system.pos.copy(), energy=energy, grad=grad, hess=hess, pbc=pbc) return system, ai
def read_system(name): # Load system data. fn = context.get_fn(os.path.join('systems', name)) numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(fn) # Try to load charges. charges = None fns_wpart = glob(os.path.join(os.path.dirname(fn), 'gaussian_mbis.h5')) if len(fns_wpart) > 0: with h5.File(fns_wpart[0], 'r') as f: charges = f['charges'][:] # Create system object. system = System(numbers, coords, charges=charges) system.detect_bonds() system.set_standard_masses() # Load ab initio data. ai = SecondOrderTaylor('ai', coords=system.pos.copy(), energy=energy, grad=grad, hess=hess, pbc=pbc) return system, ai
def main(): args = parse_args() # Load system file if args.fn_sys.endswith('.fchk'): numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio( args.fn_sys, do_hess=False) system = System(numbers, coords, rvecs=None, charges=None, radii=None, masses=masses) system.detect_bonds() else: system = System.from_file(args.fn_sys) # Guess atom types if needed if args.ffatypes is not None: guess_ffatypes(system, args.ffatypes) ffatypes = [system.ffatypes[i] for i in system.ffatype_ids] # Load atomic charges fn_charges, _, path = args.charges.partition(':') if fn_charges.endswith('.h5'): with h5.File(fn_charges, 'r') as f: if not path in f: raise IOError( 'Given HDF5 file %s does not contain a dataset %s' % (fn_charges, path)) charges = f[path][:] radii = None if args.gaussian: path_radii = os.path.join(os.path.dirname(path), 'radii') if 'radii' in f[path]: radii = average(f['%s/radii' % path][:], ffatypes, fmt='dict') else: radii = average(get_ei_radii(system.numbers), ffatypes, fmt='dict') elif fn_charges.endswith('.chk'): sample = load_chk(fn_charges) if path in sample.keys(): charges = sample[path] else: raise IOError( 'Given CHK file %s does not contain a dataset with label %s' % (fn_charges, path)) radii = None if args.gaussian: if 'radii' in sample.keys(): radii = average(sample['radii'], ffatypes, fmt='dict') else: raise IOError( 'Invalid extension, fn_charges should be a HDF5 or a CHK file.') # Derive charge parameters if args.bci: constraints = {} if args.bci_constraints is not None: constraints = read_bci_constraints(args.bci_constraints) bcis = charges_to_bcis(charges, ffatypes, system.bonds, constraints=constraints, verbose=args.verbose) make_yaff_ei(args.fn_out, None, bcis=bcis, radii=radii) else: charges = average(charges, ffatypes, fmt='dict', verbose=args.verbose) make_yaff_ei(args.fn_out, charges, radii=radii)
def main(): options, args = parse() fn_sys, fn_in, path = args if fn_sys.endswith('.fchk'): numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio( fn_sys, do_hess=False) system = System(numbers, coords, rvecs=None, charges=None, radii=None, masses=masses) system.detect_bonds() else: system = System.from_file(fn_sys) if options.ffatypes is not None: guess_ffatypes(system, options.ffatypes) ffatypes = [system.ffatypes[i] for i in system.ffatype_ids] if fn_in.endswith('.h5'): h5 = h5py.File(fn_in) if not path in h5 or 'charges' not in h5[path]: raise IOError( 'Given HDF5 file %s does not contain dataset %s/charges' % (fn_in, path)) charges = h5['%s/charges' % path][:] radii = None if options.gaussian: if 'radii' in h5[path]: radii = average(h5['%s/radii' % path][:], ffatypes, fmt='dict') else: radii = average(get_ei_radii(system.numbers), ffatypes, fmt='dict') elif fn_in.endswith('.chk'): sample = load_chk(fn_in) if path in sample.keys(): charges = sample[path] else: raise IOError( 'Given CHK file %s does not contain dataset with label %s' % (fn_in, path)) radii = None if options.gaussian: if 'radii' in sample.keys(): radii = average(sample['radii'], ffatypes, fmt='dict') else: raise IOError( 'Invalid extension, fn_in should be a HDF5 or a CHK file.') if options.output is None: if path == '.': fn_out = 'pars_ei.txt' else: fn_out = 'pars_ei_%s.txt' % path.replace('/', '_') else: fn_out = options.output if options.bci: constraints = {} if options.bci_constraints is not None: constraints = read_bci_constraints(options.bci_constraints) bcis = charges_to_bcis(charges, ffatypes, system.bonds, constraints=constraints, verbose=options.verbose) make_yaff_ei(fn_out, None, bcis=bcis, radii=radii) else: charges = average(charges, ffatypes, fmt='dict', verbose=options.verbose) make_yaff_ei(fn_out, charges, radii=radii)
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 qff(args=None): if args is None: args = qff_parse_args() else: args = qff_parse_args(args) #define logger verbosity = None if args.silent: verbosity = 'silent' else: if args.very_verbose: verbosity = 'highest' elif args.verbose: verbosity = 'high' #get settings kwargs = { 'fn_traj': args.fn_traj, 'only_traj': args.only_traj, 'program_mode': args.program_mode, 'plot_traj': args.plot_traj, 'xyz_traj': args.xyz_traj, 'suffix': args.suffix, 'log_level': verbosity, 'log_file': args.logfile, 'ffatypes': args.ffatypes, 'ei': args.ei, 'ei_rcut': args.ei_rcut, 'vdw': args.vdw, 'vdw_rcut': args.vdw_rcut, 'covres': args.covres, } settings = Settings(fn=args.config_file, **kwargs) with log.section('INIT', 1, timer='Initializing'): log.dump('Initializing system') #read system and ab initio reference system = None energy = 0.0 grad = None hess = None pbc = None rvecs = None for fn in args.fn: 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 list(sample.keys()): energy = sample['energy'] if 'grad' in list(sample.keys()): grad = sample['grad'] elif 'gradient' in list(sample.keys()): grad = sample['gradient'] if 'hess' in list(sample.keys()): hess = sample['hess'] elif 'hessian' in list(sample.keys()): hess = sample['hessian'] if 'rvecs' in list(sample.keys()): pbc = [1, 1, 1] else: pbc = [0, 0, 0] if system is None: system = System.from_file(fn) else: if 'pos' in list(sample.keys()): system.pos = sample['pos'] elif 'coords' in list(sample.keys()): system.pos = sample['coords'] if 'rvecs' in list(sample.keys()): system.cell = Cell(sample['rvecs']) elif 'cell' in list(sample.keys()): system.cell = Cell(sample['cell']) if 'bonds' in list(sample.keys()): system.bonds = sample['bonds'] if 'ffatypes' in list(sample.keys()): system.ffatypes = sample['ffatypes'] if 'ffatype_ids' in list(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 settings.ffatypes is not None: set_ffatypes(system, settings.ffatypes) else: raise AssertionError('No atom types defined') if settings.do_hess_negfreq_proj: log.dump( 'Projecting negative frequencies out of the mass-weighted hessian.' ) with log.section('SYS', 3, 'Initializing'): hess = project_negative_freqs(hess, system.masses) #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 settings.ei is not None: if rvecs is None: if settings.ei_rcut is None: rcut = 50 * angstrom else: rcut = settings.ei_rcut ff = ForceField.generate(system, settings.ei, rcut=rcut) else: if settings.ei_rcut is None: rcut = 20 * angstrom else: rcut = settings.ei_rcut ff = ForceField.generate(system, settings.ei, rcut=rcut, alpha_scale=3.2, gcut_scale=1.5, smooth_ei=True) refs.append(YaffForceField('EI', ff)) if settings.vdw is not None: ff = ForceField.generate(system, settings.vdw, rcut=settings.vdw_rcut) refs.append(YaffForceField('vdW', ff)) if settings.covres is not None: ff = ForceField.generate(system, settings.covres) refs.append(YaffForceField('Cov res', ff)) #define quickff program assert settings.program_mode in allowed_programs, \ 'Given program mode %s not allowed. Choose one of %s' %( settings.program_mode, ', '.join([prog for prog in allowed_programs if not prog=='BaseProgram']) ) mode = program_modes[settings.program_mode] program = mode(system, ai, settings, ffrefs=refs) #run program program.run() return program