def get_constraint(constraint_idx): """ Map constraints from QE output to FixAtoms or FixCartesian constraint """ if not np.any(constraint_idx): return None a = [a for a, c in enumerate(constraint_idx) if np.all(c is not None)] mask = [[(ic + 1) % 2 for ic in c] for c in constraint_idx if np.all(c is not None)] if np.all(np.array(mask)) == 1: constraint = FixAtoms(a) else: constraint = FixCartesian(a, mask) return constraint
def _read_xyz_frame(lines, natoms, properties_parser=key_val_str_to_dict, nvec=0): # comment line line = next(lines).strip() if nvec > 0: info = {'comment': line} else: info = properties_parser(line) if line else {} pbc = None if 'pbc' in info: pbc = info['pbc'] del info['pbc'] elif 'Lattice' in info: # default pbc for extxyz file containing Lattice # is True in all directions pbc = [True, True, True] elif nvec > 0: # cell information given as pseudo-Atoms pbc = [False, False, False] cell = None if 'Lattice' in info: # NB: ASE cell is transpose of extended XYZ lattice cell = info['Lattice'].T del info['Lattice'] elif nvec > 0: # cell information given as pseudo-Atoms cell = np.zeros((3, 3)) if 'Properties' not in info: # Default set of properties is atomic symbols and positions only info['Properties'] = 'species:S:1:pos:R:3' properties, names, dtype, convs = parse_properties(info['Properties']) del info['Properties'] data = [] for ln in range(natoms): try: line = next(lines) except StopIteration: raise XYZError( 'ase.io.extxyz: Frame has {} atoms, expected {}'.format( len(data), natoms)) vals = line.split() row = tuple([conv(val) for conv, val in zip(convs, vals)]) data.append(row) try: data = np.array(data, dtype) except TypeError: raise XYZError('Badly formatted data ' 'or end of file reached before end of frame') # Read VEC entries if present if nvec > 0: for ln in range(nvec): try: line = next(lines) except StopIteration: raise XYZError( 'ase.io.adfxyz: Frame has {} cell vectors, expected {}'. format(len(cell), nvec)) entry = line.split() if not entry[0].startswith('VEC'): raise XYZError('Expected cell vector, got {}'.format(entry[0])) try: n = int(entry[0][3:]) if n != ln + 1: raise XYZError('Expected VEC{}, got VEC{}'.format( ln + 1, n)) except: raise XYZError('Expected VEC{}, got VEC{}'.format( ln + 1, entry[0][3:])) cell[ln] = np.array([float(x) for x in entry[1:]]) pbc[ln] = True if nvec != pbc.count(True): raise XYZError('Problem with number of cell vectors') pbc = tuple(pbc) arrays = {} for name in names: ase_name, cols = properties[name] if cols == 1: value = data[name] else: value = np.vstack([data[name + str(c)] for c in range(cols)]).T arrays[ase_name] = value symbols = None if 'symbols' in arrays: symbols = [s.capitalize() for s in arrays['symbols']] del arrays['symbols'] numbers = None duplicate_numbers = None if 'numbers' in arrays: if symbols is None: numbers = arrays['numbers'] else: duplicate_numbers = arrays['numbers'] del arrays['numbers'] charges = None if 'charges' in arrays: charges = arrays['charges'] del arrays['charges'] positions = None if 'positions' in arrays: positions = arrays['positions'] del arrays['positions'] atoms = Atoms(symbols=symbols, positions=positions, numbers=numbers, charges=charges, cell=cell, pbc=pbc, info=info) # Read and set constraints if 'move_mask' in arrays: if properties['move_mask'][1] == 3: atoms.set_constraint([ FixCartesian(a, mask=arrays['move_mask'][a, :]) for a in range(natoms) ]) elif properties['move_mask'][1] == 1: atoms.set_constraint(FixAtoms(mask=~arrays['move_mask'])) else: raise XYZError('Not implemented constraint') del arrays['move_mask'] for name, array in arrays.items(): atoms.new_array(name, array) if duplicate_numbers is not None: atoms.set_atomic_numbers(duplicate_numbers) # Load results of previous calculations into SinglePointCalculator results = {} for key in list(atoms.info.keys()): if key in all_properties: results[key] = atoms.info[key] # special case for stress- convert to Voigt 6-element form if key.startswith('stress') and results[key].shape == (3, 3): stress = results[key] stress = np.array([ stress[0, 0], stress[1, 1], stress[2, 2], stress[1, 2], stress[0, 2], stress[0, 1] ]) results[key] = stress for key in list(atoms.arrays.keys()): if key in all_properties: results[key] = atoms.arrays[key] if results != {}: calculator = SinglePointCalculator(atoms, **results) atoms.set_calculator(calculator) return atoms
def read_aims_output(filename, index=-1): """Import FHI-aims output files with all data available, i.e. relaxations, MD information, force information etc etc etc.""" from ase import Atoms, Atom from ase.calculators.singlepoint import SinglePointCalculator from ase.units import Ang, fs from ase.constraints import FixAtoms, FixCartesian molecular_dynamics = False fd = open(filename, 'r') cell = [] images = [] fix = [] fix_cart = [] f = None pbc = False found_aims_calculator = False v_unit = Ang / (1000.0 * fs) while True: line = fd.readline() if not line: break # if "List of parameters used to initialize the calculator:" in line: # fd.readline() # calc = read_aims_calculator(fd) # calc.out = filename # found_aims_calculator = True if "| Number of atoms :" in line: inp = line.split() n_atoms = int(inp[5]) if "| Unit cell:" in line: if not pbc: pbc = True for i in range(3): inp = fd.readline().split() cell.append([inp[1], inp[2], inp[3]]) if "Found relaxation constraint for atom" in line: xyz = [0, 0, 0] ind = int(line.split()[5][:-1]) - 1 if "All coordinates fixed" in line: if ind not in fix: fix.append(ind) if "coordinate fixed" in line: coord = line.split()[6] if coord == 'x': xyz[0] = 1 elif coord == 'y': xyz[1] = 1 elif coord == 'z': xyz[2] = 1 keep = True for n, c in enumerate(fix_cart): if ind == c.a: keep = False if keep: fix_cart.append(FixCartesian(ind, xyz)) else: fix_cart[n].mask[xyz.index(1)] = 0 if "Atomic structure:" in line and not molecular_dynamics: fd.readline() atoms = Atoms() for i in range(n_atoms): inp = fd.readline().split() atoms.append(Atom(inp[3], (inp[4], inp[5], inp[6]))) if "Complete information for previous time-step:" in line: molecular_dynamics = True if "Updated atomic structure:" in line and not molecular_dynamics: fd.readline() atoms = Atoms() velocities = [] for i in range(n_atoms): inp = fd.readline().split() if 'lattice_vector' in inp[0]: cell = [] for i in range(3): cell += [[float(inp[1]), float(inp[2]), float(inp[3])]] inp = fd.readline().split() atoms.set_cell(cell) inp = fd.readline().split() atoms.append(Atom(inp[4], (inp[1], inp[2], inp[3]))) if molecular_dynamics: inp = fd.readline().split() if "Atomic structure (and velocities)" in line: fd.readline() atoms = Atoms() velocities = [] for i in range(n_atoms): inp = fd.readline().split() atoms.append(Atom(inp[4], (inp[1], inp[2], inp[3]))) inp = fd.readline().split() velocities += [[ float(inp[1]) * v_unit, float(inp[2]) * v_unit, float(inp[3]) * v_unit ]] atoms.set_velocities(velocities) if len(fix): atoms.set_constraint([FixAtoms(indices=fix)] + fix_cart) else: atoms.set_constraint(fix_cart) images.append(atoms) if "Total atomic forces" in line: f = [] for i in range(n_atoms): inp = fd.readline().split() f.append([float(inp[2]), float(inp[3]), float(inp[4])]) if not found_aims_calculator: e = images[-1].get_potential_energy() images[-1].set_calculator( SinglePointCalculator(atoms, energy=e, forces=f)) e = None f = None if "Total energy corrected" in line: e = float(line.split()[5]) if pbc: atoms.set_cell(cell) atoms.pbc = True if not found_aims_calculator: atoms.set_calculator(SinglePointCalculator(atoms, energy=e)) if not molecular_dynamics: if len(fix): atoms.set_constraint([FixAtoms(indices=fix)] + fix_cart) else: atoms.set_constraint(fix_cart) images.append(atoms) e = None # if found_aims_calculator: # calc.set_results(images[-1]) # images[-1].set_calculator(calc) fd.close() if molecular_dynamics: images = images[1:] # return requested images, code borrowed from ase/io/trajectory.py if isinstance(index, int): return images[index] else: step = index.step or 1 if step > 0: start = index.start or 0 if start < 0: start += len(images) stop = index.stop or len(images) if stop < 0: stop += len(images) else: if index.start is None: start = len(images) - 1 else: start = index.start if start < 0: start += len(images) if index.stop is None: stop = -1 else: stop = index.stop if stop < 0: stop += len(images) return [images[i] for i in range(start, stop, step)]
def read_aims(filename): """Import FHI-aims geometry type files. Reads unitcell, atom positions and constraints from a geometry.in file. """ from ase import Atoms from ase.constraints import FixAtoms, FixCartesian import numpy as np atoms = Atoms() fd = open(filename, 'r') lines = fd.readlines() fd.close() positions = [] cell = [] symbols = [] magmoms = [] fix = [] fix_cart = [] xyz = np.array([0, 0, 0]) i = -1 n_periodic = -1 periodic = np.array([False, False, False]) cart_positions, scaled_positions = False, False for n, line in enumerate(lines): inp = line.split() if inp == []: continue if inp[0] == 'atom': cart_positions = True if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) floatvect = float(inp[1]), float(inp[2]), float(inp[3]) positions.append(floatvect) symbols.append(inp[-1]) i += 1 xyz = np.array([0, 0, 0]) if inp[0] == 'atom_frac': scaled_positions = True if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) floatvect = float(inp[1]), float(inp[2]), float(inp[3]) positions.append(floatvect) symbols.append(inp[-1]) i += 1 xyz = np.array([0, 0, 0]) elif inp[0] == 'lattice_vector': floatvect = float(inp[1]), float(inp[2]), float(inp[3]) cell.append(floatvect) n_periodic = n_periodic + 1 periodic[n_periodic] = True elif inp[0] == 'initial_moment': magmoms.append(float(inp[1])) if inp[0] == 'constrain_relaxation': if inp[1] == '.true.': fix.append(i) elif inp[1] == 'x': xyz[0] = 1 elif inp[1] == 'y': xyz[1] = 1 elif inp[1] == 'z': xyz[2] = 1 if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) if cart_positions and scaled_positions: raise Exception("Can't specify atom positions with mixture of " 'Cartesian and fractional coordinates') elif scaled_positions and periodic.any(): atoms = Atoms(symbols, scaled_positions=positions, cell=cell, pbc=periodic) else: atoms = Atoms(symbols, positions) if len(magmoms) > 0: atoms.set_initial_magnetic_moments(magmoms) if periodic.any(): atoms.set_cell(cell) atoms.set_pbc(periodic) if len(fix): atoms.set_constraint([FixAtoms(indices=fix)] + fix_cart) else: atoms.set_constraint(fix_cart) return atoms
def read_aims(filename, apply_constraints=True): """Import FHI-aims geometry type files. Reads unitcell, atom positions and constraints from a geometry.in file. If geometric constraint (symmetry parameters) are in the file include that information in atoms.info["symmetry_block"] """ from ase import Atoms from ase.constraints import ( FixAtoms, FixCartesian, FixScaledParametricRelations, FixCartesianParametricRelations, ) import numpy as np atoms = Atoms() with open(filename, "r") as fd: lines = fd.readlines() positions = [] cell = [] symbols = [] velocities = [] magmoms = [] symmetry_block = [] charges = [] fix = [] fix_cart = [] xyz = np.array([0, 0, 0]) i = -1 n_periodic = -1 periodic = np.array([False, False, False]) cart_positions, scaled_positions = False, False for line in lines: inp = line.split() if inp == []: continue if inp[0] == "atom": cart_positions = True if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) floatvect = float(inp[1]), float(inp[2]), float(inp[3]) positions.append(floatvect) magmoms.append(0.0) charges.append(0.0) symbols.append(inp[-1]) i += 1 xyz = np.array([0, 0, 0]) elif inp[0] == "atom_frac": scaled_positions = True if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) floatvect = float(inp[1]), float(inp[2]), float(inp[3]) positions.append(floatvect) magmoms.append(0.0) symbols.append(inp[-1]) i += 1 xyz = np.array([0, 0, 0]) elif inp[0] == "lattice_vector": floatvect = float(inp[1]), float(inp[2]), float(inp[3]) cell.append(floatvect) n_periodic = n_periodic + 1 periodic[n_periodic] = True elif inp[0] == "initial_moment": magmoms[-1] = float(inp[1]) elif inp[0] == "initial_charge": charges[-1] = float(inp[1]) elif inp[0] == "constrain_relaxation": if inp[1] == ".true.": fix.append(i) elif inp[1] == "x": xyz[0] = 1 elif inp[1] == "y": xyz[1] = 1 elif inp[1] == "z": xyz[2] = 1 elif inp[0] == "velocity": floatvect = [v_unit * float(l) for l in inp[1:4]] velocities.append(floatvect) elif inp[0] in [ "symmetry_n_params", "symmetry_params", "symmetry_lv", "symmetry_frac", ]: symmetry_block.append(" ".join(inp)) if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) if cart_positions and scaled_positions: raise Exception("Can't specify atom positions with mixture of " "Cartesian and fractional coordinates") elif scaled_positions and periodic.any(): atoms = Atoms(symbols, scaled_positions=positions, cell=cell, pbc=periodic) else: atoms = Atoms(symbols, positions) if len(velocities) > 0: if len(velocities) != len(positions): raise Exception( "Number of positions and velocities have to coincide.") atoms.set_velocities(velocities) fix_params = [] if len(symmetry_block) > 5: params = symmetry_block[1].split()[1:] lattice_expressions = [] lattice_params = [] atomic_expressions = [] atomic_params = [] n_lat_param = int(symmetry_block[0].split(" ")[2]) lattice_params = params[:n_lat_param] atomic_params = params[n_lat_param:] for ll, line in enumerate(symmetry_block[2:]): expression = " ".join(line.split(" ")[1:]) if ll < 3: lattice_expressions += expression.split(",") else: atomic_expressions += expression.split(",") fix_params.append( FixCartesianParametricRelations.from_expressions( list(range(3)), lattice_params, lattice_expressions, use_cell=True, )) fix_params.append( FixScaledParametricRelations.from_expressions( list(range(len(atoms))), atomic_params, atomic_expressions)) if any(magmoms): atoms.set_initial_magnetic_moments(magmoms) if any(charges): atoms.set_initial_charges(charges) if periodic.any(): atoms.set_cell(cell) atoms.set_pbc(periodic) if len(fix): atoms.set_constraint([FixAtoms(indices=fix)] + fix_cart + fix_params) else: atoms.set_constraint(fix_cart + fix_params) if fix_params and apply_constraints: atoms.set_positions(atoms.get_positions()) return atoms
def read_aims_output(filename, index=-1): """Import FHI-aims output files with all data available, i.e. relaxations, MD information, force information etc etc etc.""" from ase import Atoms, Atom from ase.calculators.singlepoint import SinglePointCalculator from ase.constraints import FixAtoms, FixCartesian molecular_dynamics = False fd = open(filename, "r") cell = [] images = [] fix = [] fix_cart = [] f = None pbc = False found_aims_calculator = False stress = None for line in fd: # if "List of parameters used to initialize the calculator:" in line: # next(fd) # calc = read_aims_calculator(fd) # calc.out = filename # found_aims_calculator = True if "| Number of atoms :" in line: inp = line.split() n_atoms = int(inp[5]) if "| Unit cell:" in line: if not pbc: pbc = True for i in range(3): inp = next(fd).split() cell.append([inp[1], inp[2], inp[3]]) if "Found relaxation constraint for atom" in line: xyz = [0, 0, 0] ind = int(line.split()[5][:-1]) - 1 if "All coordinates fixed" in line: if ind not in fix: fix.append(ind) if "coordinate fixed" in line: coord = line.split()[6] if coord == "x": xyz[0] = 1 elif coord == "y": xyz[1] = 1 elif coord == "z": xyz[2] = 1 keep = True for n, c in enumerate(fix_cart): if ind == c.a: keep = False if keep: fix_cart.append(FixCartesian(ind, xyz)) else: fix_cart[n].mask[xyz.index(1)] = 0 if "Atomic structure:" in line and not molecular_dynamics: next(fd) atoms = Atoms() for _ in range(n_atoms): inp = next(fd).split() atoms.append(Atom(inp[3], (inp[4], inp[5], inp[6]))) if "Complete information for previous time-step:" in line: molecular_dynamics = True if "Updated atomic structure:" in line and not molecular_dynamics: atoms = _parse_atoms(fd, n_atoms=n_atoms) elif "Atomic structure (and velocities)" in line: next(fd) atoms = Atoms() velocities = [] for i in range(n_atoms): inp = next(fd).split() atoms.append(Atom(inp[4], (inp[1], inp[2], inp[3]))) inp = next(fd).split() floatvect = [v_unit * float(l) for l in inp[1:4]] velocities.append(floatvect) atoms.set_velocities(velocities) if len(fix): atoms.set_constraint([FixAtoms(indices=fix)] + fix_cart) else: atoms.set_constraint(fix_cart) images.append(atoms) # if we enter here, the SocketIO/PIMD Wrapper was used elif ("Atomic structure that " "was used in the preceding time step of the wrapper") in line: # parse atoms and add calculator information, i.e., the energies # and forces that were already collected atoms = _parse_atoms(fd, n_atoms=n_atoms) results = images[-1].calc.results atoms.calc = SinglePointCalculator(atoms, **results) # replace last image with updated atoms images[-1] = atoms # make sure `atoms` does not point to `images[-1` later on atoms = atoms.copy() # FlK: add analytical stress and replace stress=None if "Analytical stress tensor - Symmetrized" in line: # scroll to significant lines for _ in range(4): next(fd) stress = [] for _ in range(3): inp = next(fd) stress.append([float(i) for i in inp.split()[2:5]]) if "Total atomic forces" in line: f = [] for i in range(n_atoms): inp = next(fd).split() # FlK: use inp[-3:] instead of inp[1:4] to make sure this works # when atom number is not preceded by a space. f.append([float(i) for i in inp[-3:]]) if not found_aims_calculator: e = images[-1].get_potential_energy() # FlK: Add the stress if it has been computed if stress is None: calc = SinglePointCalculator(atoms, energy=e, forces=f) else: calc = SinglePointCalculator(atoms, energy=e, forces=f, stress=stress) images[-1].calc = calc e = None f = None if "Total energy corrected" in line: e = float(line.split()[5]) if pbc: atoms.set_cell(cell) atoms.pbc = True if not found_aims_calculator: atoms.calc = SinglePointCalculator(atoms, energy=e) if not molecular_dynamics: if len(fix): atoms.set_constraint([FixAtoms(indices=fix)] + fix_cart) else: atoms.set_constraint(fix_cart) images.append(atoms) e = None # if found_aims_calculator: # calc.set_results(images[-1]) # images[-1].calc = calc # FlK: add stress per atom if "Per atom stress (eV) used for heat flux calculation" in line: # scroll to boundary next(l for l in fd if "-------------" in l) stresses = [] for l in [next(fd) for _ in range(n_atoms)]: # Read stresses xx, yy, zz, xy, xz, yz = [float(d) for d in l.split()[2:8]] stresses.append([[xx, xy, xz], [xy, yy, yz], [xz, yz, zz]]) if not found_aims_calculator: e = images[-1].get_potential_energy() f = images[-1].get_forces() stress = images[-1].get_stress(voigt=False) calc = SinglePointCalculator(atoms, energy=e, forces=f, stress=stress, stresses=stresses) images[-1].calc = calc fd.close() if molecular_dynamics: images = images[1:] # return requested images, code borrowed from ase/io/trajectory.py if isinstance(index, int): return images[index] else: step = index.step or 1 if step > 0: start = index.start or 0 if start < 0: start += len(images) stop = index.stop or len(images) if stop < 0: stop += len(images) else: if index.start is None: start = len(images) - 1 else: start = index.start if start < 0: start += len(images) if index.stop is None: stop = -1 else: stop = index.stop if stop < 0: stop += len(images) return [images[i] for i in range(start, stop, step)]
def read_aims(filename): """Import FHI-aims geometry type files. Reads unitcell, atom positions and constraints from a geometry.in file. """ from ase import Atoms from ase.constraints import FixAtoms, FixCartesian import numpy as np atoms = Atoms() fd = open(filename, 'r') lines = fd.readlines() fd.close() positions = [] cell = [] symbols = [] fix = [] fix_cart = [] xyz = np.array([0, 0, 0]) i = -1 n_periodic = -1 periodic = np.array([False, False, False]) for n, line in enumerate(lines): inp = line.split() if inp == []: continue if inp[0] == 'atom': if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) floatvect = float(inp[1]), float(inp[2]), float(inp[3]) positions.append(floatvect) symbols.append(inp[-1]) i += 1 xyz = np.array([0, 0, 0]) elif inp[0] == 'lattice_vector': floatvect = float(inp[1]), float(inp[2]), float(inp[3]) cell.append(floatvect) n_periodic = n_periodic + 1 periodic[n_periodic] = True if inp[0] == 'constrain_relaxation': if inp[1] == '.true.': fix.append(i) elif inp[1] == 'x': xyz[0] = 1 elif inp[1] == 'y': xyz[1] = 1 elif inp[1] == 'z': xyz[2] = 1 if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) atoms = Atoms(symbols, positions) if periodic.all(): atoms.set_cell(cell) atoms.set_pbc(periodic) if len(fix): atoms.set_constraint([FixAtoms(indices=fix)] + fix_cart) else: atoms.set_constraint(fix_cart) return atoms
a = bulk('Si') a.info['val_1'] = 42.0 a.info['val_2'] = 42.0 # was np.float but that's the same. Can remove a.info['val_3'] = np.int64(42) a.write('tmp.xyz') with open('tmp.xyz', 'r') as fd: comment_line = fd.readlines()[1] assert "val_1=42.0" in comment_line and "val_2=42.0" in comment_line and "val_3=42" in comment_line b = ase.io.read('tmp.xyz') assert abs(b.info['val_1'] - 42.0) < 1e-6 assert abs(b.info['val_2'] - 42.0) < 1e-6 assert abs(b.info['val_3'] - 42) == 0 @pytest.mark.parametrize('constraint', [FixAtoms(indices=(0, 2)), FixCartesian(1, mask=(1, 0, 1)), [FixCartesian(0), FixCartesian(2)]]) def test_constraints(constraint): atoms = molecule('H2O') atoms.set_constraint(constraint) columns = ['symbols', 'positions', 'move_mask'] ase.io.write('tmp.xyz', atoms, columns=columns) atoms2 = ase.io.read('tmp.xyz') assert not compare_atoms(atoms, atoms2) constraint2 = atoms2.constraints cls = type(constraint) if cls == FixAtoms: assert len(constraint2) == 1
def sf_calc(bulk, n_steps, z_offset, p0=None, p1=None, relax_from_configs=None): global bulk_energy p0 = np.array(p0) p1 = np.array(p1) E0 = bulk_energy surf_unrelaxed = np.zeros((n_steps, n_steps), dtype=(float, 3)) surf_relaxed = np.zeros((n_steps, n_steps), dtype=(float, 3)) path_unrelaxed = [] path_relaxed = [] sf = bulk.copy() pos = sf.get_positions() pos[:, 2] += z_offset sf.set_positions(pos) pos = sf.get_scaled_positions() pos -= np.floor(pos) sf.set_scaled_positions(pos) if p0 is not None and p1 is not None: # paths # unrelaxed for i in range(n_steps): print "start path unrelaxed step", i sys.stdout.flush() p = p0 + (p1 - p0) * i / float(n_steps - 1) sf_cur = sf.copy() sf_cur.arrays['move_mask_3'] = np.zeros((len(sf_cur), 3), dtype=int) sf_cur.arrays['move_mask_3'][:, 2] = 1 sf_cur.set_calculator(model.calculator) cell = sf_cur.get_cell() cell[2, :] += cell[0, :] * p[0] + cell[1, :] * p[1] sf_cur.set_cell(cell) E = (sf_cur.get_potential_energy() - E0) / np.linalg.norm( np.cross(cell[0, :], cell[1, :])) path_unrelaxed.append((i / float(n_steps - 1), p[0], p[1], E)) # relaxed sf_cur = sf.copy() sf_cur.arrays['move_mask_3'] = np.zeros((len(sf_cur), 3), dtype=int) sf_cur.arrays['move_mask_3'][:, 2] = 1 sf_cur.set_calculator(model.calculator) dp = (p1 - p0) / float(n_steps - 1) p = p0.copy() cell = sf_cur.get_cell() cell[2, :] += cell[0, :] * p[0] + cell[1, :] * p[1] sf_cur.set_cell(cell) relax_from_configs_i = 0 for i in range(n_steps): print "start path relaxed step", i sys.stdout.flush() if model.name == 'CASTEP_file': sf_cur.calc.fix_all_cell = False sf_cur.set_constraint( [FixCartesian(j, [1, 1, 0]) for j in range(len(sf_cur))]) sf_cur.calc.cell_constraints = ["0 0 1", "0 0 0"] sf_cur.calc._old_atoms = None if debug: ase.io.write(file_unrelaxed, sf_cur, "extxyz") file_unrelaxed.flush() try: sf_cur.set_cell( relax_from_configs[relax_from_configs_i].get_cell(), False) sf_cur.set_positions( relax_from_configs[relax_from_configs_i].get_positions()) print "got sf_cur from 'relax_from_configs'" sys.stdout.flush() except: pass sf_cur_rel = relax_atoms_cell( sf_cur, tol=tol, method='cg_n', max_steps=500, traj_file=None, mask=[False, False, True, False, False, False]) relax_from_configs_i += 1 if debug: ase.io.write(file_relaxed, sf_cur, "extxyz") file_relaxed.flush() print "done relaxation" sys.stdout.flush() E = (sf_cur.get_potential_energy() - E0) / np.linalg.norm( np.cross(cell[0, :], cell[1, :])) path_relaxed.append((i / float(n_steps - 1), p[0], p[1], E)) cell = sf_cur.get_cell() cell[2, :] += cell[0, :] * dp[0] + cell[1, :] * dp[1] sf_cur.set_cell(cell) p += dp return (path_unrelaxed, path_relaxed) else: # surfaces # unrelaxed j_doffset = sf.get_cell()[1, :] * (1.0 / float(n_steps - 1)) for i in range(n_steps): x_i = float(i) / float(n_steps - 1) sf_cur = sf.copy() sf_cur.arrays['move_mask_3'] = np.zeros((len(sf_cur), 3), dtype=int) sf_cur.arrays['move_mask_3'][:, 2] = 1 sf_cur.set_calculator(model.calculator) cell = sf_cur.get_cell() cell[2, :] += cell[0, :] * x_i sf_cur.set_cell(cell) for j in range(n_steps - i): x_j = float(j) / float(n_steps - 1) print(i, j, x_i, x_j) if debug: ase.io.write(file_unrelaxed, sf_cur, "extxyz") file_unrelaxed.flush() E = (sf_cur.get_potential_energy() - E0) / np.linalg.norm( np.cross(cell[0, :], cell[1, :])) surf_unrelaxed[i, j] = (x_i, x_j, E) if i + j != n_steps - 1: surf_unrelaxed[n_steps - j - 1, n_steps - i - 1] = (1.0 - x_j, 1.0 - x_i, E) cell = sf_cur.get_cell() cell[2, :] += j_doffset sf_cur.set_cell(cell, scale_atoms=False) # relaxed relax_from_configs_i = 0 j_doffset = sf.get_cell()[1, :] * (1.0 / float(n_steps - 1)) for i in range(n_steps): x_i = float(i) / float(n_steps - 1) sf_cur = sf.copy() # set constraints # cs = [] # for i_at in range(len(bulk)): # cs.append(FixCartesian(i_at, mask=[0,0,1])) # sf_cur.set_constraint(cs) sf_cur.arrays['move_mask_3'] = np.zeros((len(sf_cur), 3), dtype=int) sf_cur.arrays['move_mask_3'][:, 2] = 1 sf_cur.set_calculator(model.calculator) cell = sf_cur.get_cell() cell[2, :] += cell[0, :] * x_i sf_cur.set_cell(cell) for j in range(n_steps - i): x_j = float(j) / float(n_steps - 1) print(i, j, x_i, x_j) try: sf_cur.set_cell( relax_from_configs[relax_from_configs_i].get_cell(), False) sf_cur.set_positions( relax_from_configs[relax_from_configs_i].get_positions( )) except: pass sf_cur_rel = relax_atoms_cell( sf_cur, tol=tol, method='cg_n', max_steps=500, traj_file=None, mask=[False, False, True, False, False, False]) relax_from_configs_i += 1 if debug: ase.io.write(file_relaxed, sf_cur_rel, "extxyz") file_relaxed.flush() E = (sf_cur_rel.get_potential_energy() - E0) / np.linalg.norm( np.cross(cell[0, :], cell[1, :])) surf_relaxed[i, j] = (x_i, x_j, E) if i + j != n_steps - 1: surf_relaxed[n_steps - j - 1, n_steps - i - 1] = (1.0 - x_j, 1.0 - x_i, E) cell = sf_cur.get_cell() cell[2, :] += j_doffset sf_cur.set_cell(cell, scale_atoms=False) return (surf_unrelaxed, surf_relaxed)
def read_aims(filename): """Import FHI-aims geometry type files. Reads unitcell, atom positions and constraints from a geometry.in file. """ from ase import Atoms from ase.constraints import FixAtoms, FixCartesian import numpy as np atoms = Atoms() fd = open(filename, "r") lines = fd.readlines() fd.close() positions = [] cell = [] symbols = [] velocities = [] magmoms = [] fix = [] fix_cart = [] xyz = np.array([0, 0, 0]) i = -1 n_periodic = -1 periodic = np.array([False, False, False]) cart_positions, scaled_positions = False, False for n, line in enumerate(lines): inp = line.split() if inp == []: continue if inp[0] == "atom": cart_positions = True if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) floatvect = float(inp[1]), float(inp[2]), float(inp[3]) positions.append(floatvect) symbols.append(inp[-1]) i += 1 xyz = np.array([0, 0, 0]) elif inp[0] == "atom_frac": scaled_positions = True if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) floatvect = float(inp[1]), float(inp[2]), float(inp[3]) positions.append(floatvect) symbols.append(inp[-1]) i += 1 xyz = np.array([0, 0, 0]) elif inp[0] == "lattice_vector": floatvect = float(inp[1]), float(inp[2]), float(inp[3]) cell.append(floatvect) n_periodic = n_periodic + 1 periodic[n_periodic] = True elif inp[0] == "initial_moment": magmoms.append(float(inp[1])) elif inp[0] == "constrain_relaxation": if inp[1] == ".true.": fix.append(i) elif inp[1] == "x": xyz[0] = 1 elif inp[1] == "y": xyz[1] = 1 elif inp[1] == "z": xyz[2] = 1 elif inp[0] == "velocity": floatvect = [v_unit * float(l) for l in inp[1:4]] velocities.append(floatvect) if xyz.all(): fix.append(i) elif xyz.any(): fix_cart.append(FixCartesian(i, xyz)) if cart_positions and scaled_positions: raise Exception("Can't specify atom positions with mixture of " "Cartesian and fractional coordinates") elif scaled_positions and periodic.any(): atoms = Atoms(symbols, scaled_positions=positions, cell=cell, pbc=periodic) else: atoms = Atoms(symbols, positions) if len(velocities) > 0: if len(velocities) != len(positions): raise Exception( "Number of positions and velocities have to coincide.") atoms.set_velocities(velocities) if len(magmoms) > 0: atoms.set_initial_magnetic_moments(magmoms) if periodic.any(): atoms.set_cell(cell) atoms.set_pbc(periodic) if len(fix): atoms.set_constraint([FixAtoms(indices=fix)] + fix_cart) else: atoms.set_constraint(fix_cart) return atoms