def get_pwscf_structure(cell, pp_filenames=None):
lattice = cell.get_cell()
positions = cell.get_scaled_positions()
masses = cell.get_masses()
chemical_symbols = cell.get_chemical_symbols()
unique_symbols = []
atomic_species = []
for symbol, m in zip(chemical_symbols, masses):
if symbol not in unique_symbols:
unique_symbols.append(symbol)
atomic_species.append((symbol, m))
lines = ""
lines += ("! ibrav = 0, nat = %d, ntyp = %d\n" %
(len(positions), len(unique_symbols)))
lines += "CELL_PARAMETERS bohr\n"
lines += ((" %21.16f" * 3 + "\n") * 3) % tuple(lattice.ravel())
lines += "ATOMIC_SPECIES\n"
for symbol, mass in atomic_species:
if pp_filenames is None:
lines += " %2s %10.5f %s_PP_filename\n" % (symbol, mass, symbol)
else:
lines += " %2s %10.5f %s\n" % (symbol, mass, pp_filenames[symbol])
lines += "ATOMIC_POSITIONS crystal\n"
for i, (symbol, pos_line) in enumerate(zip(
chemical_symbols,
get_scaled_positions_lines(positions).split('\n'))):
lines += (" %2s " % symbol) + pos_line
if i < len(chemical_symbols) - 1:
lines += "\n"
return lines
def get_pwscf_structure(cell, pp_filenames=None):
lattice = cell.get_cell()
positions = cell.get_scaled_positions()
masses = cell.get_masses()
chemical_symbols = cell.get_chemical_symbols()
unique_symbols = []
atomic_species = []
for symbol, m in zip(chemical_symbols, masses):
if symbol not in unique_symbols:
unique_symbols.append(symbol)
atomic_species.append((symbol, m))
lines = ""
lines += ("! ibrav = 0, nat = %d, ntyp = %d\n" %
(len(positions), len(unique_symbols)))
lines += "CELL_PARAMETERS bohr\n"
lines += ((" %21.16f" * 3 + "\n") * 3) % tuple(lattice.ravel())
lines += "ATOMIC_SPECIES\n"
for symbol, mass in atomic_species:
if pp_filenames is None:
lines += " %2s %10.5f %s_PP_filename\n" % (symbol, mass, symbol)
else:
lines += " %2s %10.5f %s\n" % (symbol, mass,
pp_filenames[symbol])
lines += "ATOMIC_POSITIONS crystal\n"
for i, (symbol, pos_line) in enumerate(zip(
chemical_symbols,
get_scaled_positions_lines(positions).split('\n'))):
lines += (" %2s " % symbol) + pos_line
if i < len(chemical_symbols) - 1:
lines += "\n"
return lines
def get_elk_structure(cell, sp_filenames=None):
"""Return Elk structure in text."""
lattice = cell.get_cell()
(num_atoms, symbols, scaled_positions,
sort_list) = sort_positions_by_symbols(cell.get_chemical_symbols(),
cell.get_scaled_positions())
if sp_filenames is None:
spfnames = [s + ".in" for s in symbols]
else:
spfnames = sp_filenames
lines = ""
lines += "avec\n"
lines += ((" %21.16f" * 3 + "\n") * 3) % tuple(lattice.ravel())
lines += "atoms\n"
n_pos = 0
lines += " %d\n" % len(num_atoms)
for i, (n, s) in enumerate(zip(num_atoms, spfnames)):
lines += " '%s'\n" % s
lines += " %d\n" % n
lines += get_scaled_positions_lines(scaled_positions[n_pos:(n_pos +
n)])
if i < len(num_atoms) - 1:
lines += "\n"
n_pos += n
return lines
def get_elk_structure(cell, sp_filenames=None):
lattice = cell.get_cell()
(num_atoms,
symbols,
scaled_positions,
sort_list) = sort_positions_by_symbols(cell.get_chemical_symbols(),
cell.get_scaled_positions())
if sp_filenames is None:
spfnames = [s + ".in" for s in symbols]
else:
spfnames = sp_filenames
lines = ""
lines += "avec\n"
lines += ((" %21.16f" * 3 + "\n") * 3) % tuple(lattice.ravel())
lines += "atoms\n"
n_pos = 0
lines += " %d\n" % len(num_atoms)
for i, (n, s) in enumerate(zip(num_atoms, spfnames)):
lines += " \'%s\'\n" % s
lines += " %d\n" % n
lines += get_scaled_positions_lines(scaled_positions[n_pos:(n_pos + n)])
if i < len(num_atoms) - 1:
lines += "\n"
n_pos += n
return lines
def get_abinit_structure(cell):
znucl = []
numbers = cell.get_atomic_numbers()
for n in numbers:
if n not in znucl:
znucl.append(n)
typat = []
for n in numbers:
typat.append(znucl.index(n) + 1)
lines = ""
lines += "natom %d\n" % len(numbers)
lines += "typat\n"
lines += (" %d" * len(typat) + "\n") % tuple(typat)
lines += "ntypat %d\n" % len(znucl)
lines += ("znucl" + " %d" * len(znucl) + "\n") % tuple(znucl)
lines += "acell 1 1 1\n"
lines += "rprim\n"
lines += ((" % 20.16f" * 3 + "\n") * 3) % tuple(cell.get_cell().ravel())
lines += "xred\n"
lines += get_scaled_positions_lines(cell.get_scaled_positions())
return lines
def get_abinit_structure(cell):
znucl = []
numbers = cell.get_atomic_numbers()
for n in numbers:
if n not in znucl:
znucl.append(n)
typat = []
for n in numbers:
typat.append(znucl.index(n) + 1)
lines = ""
lines += "natom %d\n" % len(numbers)
lines += "typat\n"
lines += (" %d" * len(typat) + "\n") % tuple(typat)
lines += "ntypat %d\n" % len(znucl)
lines += ("znucl" + " %d" * len(znucl) + "\n") % tuple(znucl)
lines += "acell 1 1 1\n"
lines += "rprim\n"
lines += ((" % 20.16f" * 3 + "\n") * 3) % tuple(cell.get_cell().ravel())
lines += "xred\n"
lines += get_scaled_positions_lines(cell.get_scaled_positions())
return lines