def write_pdb(fileobj, images):
"""Write images to PDB-file.
The format is assumed to follow the description given in
http://www.wwpdb.org/documentation/format32/sect9.html."""
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if not isinstance(images, (list, tuple)):
images = [images]
if images[0].get_pbc().any():
from ase.lattice.spacegroup.cell import cell_to_cellpar
cellpar = cell_to_cellpar( images[0].get_cell())
# ignoring Z-value, using P1 since we have all atoms defined explicitly
format = 'CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1\n'
fileobj.write(format % (cellpar[0], cellpar[1], cellpar[2], cellpar[3], cellpar[4], cellpar[5]))
# 1234567 123 6789012345678901 89 67 456789012345678901234567 890
format = 'ATOM %5d %4s MOL 1 %8.3f%8.3f%8.3f 1.00 0.00 %2s \n'
# RasMol complains if the atom index exceeds 100000. There might
# be a limit of 5 digit numbers in this field.
MAXNUM = 100000
symbols = images[0].get_chemical_symbols()
natoms = len(symbols)
for n,atoms in enumerate(images):
fileobj.write('MODEL '+str(n+1)+'\n')
p = atoms.get_positions()
for a in range(natoms):
x, y, z = p[a]
fileobj.write(format % (a % MAXNUM, symbols[a], x, y, z, symbols[a].rjust(2)))
fileobj.write('ENDMDL\n')
def write_pdb(fileobj, images):
"""Write images to PDB-file.
The format is assumed to follow the description given in
http://www.wwpdb.org/documentation/format32/sect9.html."""
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if not isinstance(images, (list, tuple)):
images = [images]
if images[0].get_pbc().any():
from ase.lattice.spacegroup.cell import cell_to_cellpar
cellpar = cell_to_cellpar( images[0].get_cell())
# ignoring Z-value, using P1 since we have all atoms defined explicitly
format = 'CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1\n'
fileobj.write(format % (cellpar[0], cellpar[1], cellpar[2], cellpar[3], cellpar[4], cellpar[5]))
# 1234567 123 6789012345678901 89 67 456789012345678901234567 890
format = 'ATOM %5d %4s MOL 1 %8.3f%8.3f%8.3f 1.00 0.00 %2s \n'
# RasMol complains if the atom index exceeds 100000. There might
# be a limit of 5 digit numbers in this field.
MAXNUM = 100000
symbols = images[0].get_chemical_symbols()
natoms = len(symbols)
for n,atoms in enumerate(images):
fileobj.write('MODEL '+str(n+1)+'\n')
p = atoms.get_positions()
for a in range(natoms):
x, y, z = p[a]
fileobj.write(format % (a % MAXNUM, symbols[a], x, y, z, symbols[a].rjust(2)))
fileobj.write('ENDMDL\n')
def get_string(self, significant_figures=6, write_info=False):
"""
Returns a string to be written as a Res file.
Args:
significant_figures (int): No. of significant figures to
output all quantities. Defaults to 6.
write_info (bool): if True, format TITL line using key-value pairs
from atoms.info in addition to attributes stored in Res object
Returns:
String representation of Res.
"""
# Title line
if write_info:
info = self.atoms.info.copy()
for attribute in ['name', 'pressure', 'energy',
'spacegroup', 'times_found']:
if getattr(self, attribute) and attribute not in info:
info[attribute] = getattr(self, attribute)
lines = ['TITL ' + ' '.join(['{0}={1}'.format(k, v)
for (k, v) in info.items()])]
else:
lines = ['TITL ' + self.print_title()]
# Cell
abc_ang = cell_to_cellpar(self.atoms.get_cell())
fmt = '{{0:.{0}f}}'.format(significant_figures)
cell = ' '.join([fmt.format(a) for a in abc_ang])
lines.append('CELL 1.0 ' + cell)
# Latt
lines.append('LATT -1')
# Atoms
symbols = self.atoms.get_chemical_symbols()
species_types = []
for symbol in symbols:
if symbol not in species_types:
species_types.append(symbol)
lines.append('SFAC ' + ' '.join(species_types))
fmt = '{{0}} {{1}} {{2:.{0}f}} {{3:.{0}f}} {{4:.{0}f}} 1.0'
fmtstr = fmt.format(significant_figures)
for symbol, coords in zip(symbols, self.atoms_.get_positions()):
lines.append(
fmtstr.format(symbol,
species_types.index(symbol) + 1,
coords[0],
coords[1],
coords[2]))
lines.append('END')
return '\n'.join(lines)
def export_to_vft(self, fname=None):
#f = open(fname, "wb")
import ase.data
import StringIO
import numpy as np
import ase.lattice.spacegroup.cell as cell
def shrink_list(nums):
start = nums[0]
end = nums[0]
output = ""
step = 1
for i in range(1, len(nums)):
if nums[i] == start + step:
end = nums[i]
step += 1
else:
end = nums[i - 1]
if start == end:
output += ("" if output == "" else ",") + str(start)
else:
output += ("" if output == "" else
",") + str(start) + ":" + str(end)
start = nums[i]
end = nums[i]
step = 1
if (i == len(nums) - 1):
if start == end:
output += ("" if output == "" else ",") + str(start)
else:
output += ("" if output == "" else
",") + str(start) + ":" + str(end)
return output
output = StringIO.StringIO()
output.write("# STRUCTURE BLOCK\n")
#atom 0,2,4 radius 1.0 name N
for t in range(len(self.ordering)):
w_ids = shrink_list(self.ordering[t])
at_num = self.struct.get_ase().get_atomic_numbers()[
self.ordering[t][0]]
w_radius = ase.data.vdw.vdw_radii[at_num]
w_name = ase.data.chemical_symbols[at_num]
if np.isnan(w_radius):
w_radius = ase.data.covalent_radii[at_num]
output.write(
"atom {0} radius {1} name {2} atomicnumber {3}\n".format(
w_ids, w_radius, w_name, t))
output.write("# TIMESTEP BLOCKS\n")
for i in range(len(self.pos)):
w_cell = " ".join([
"{0:.8f}".format(ap)
for ap in cell.cell_to_cellpar(self.cells[i])
])
output.write("timestep\n")
output.write("pbc {0}\n".format(w_cell))
for kind_order in self.ordering:
for o in kind_order:
ordered_pos = self.pos[i][o]
a_pos = " ".join(
["{0:.8f}".format(ap) for ap in ordered_pos])
output.write("{0}\n".format(a_pos))
try:
if not fname == None:
f = open(fname, 'wb')
f.write(output.getvalue())
f.close()
else:
return output.getvalue()
except:
return None
finally:
output.close()
def write_reactant_con(fileobj, images):
"""Writes structure to EON reactant.con file
Multiple snapshots are not allowed."""
if isinstance(fileobj, str):
f = paropen(fileobj, 'w')
else:
f = fileobj
if isinstance(images, Atoms):
atoms = images
elif len(images) == 1:
atoms = images[0]
else:
raise ValueError('Can only write one configuration to EON '
'reactant.con file')
out = []
out.append(atoms.info.get('comment', 'Generated by ASE'))
out.append('0.0000 TIME') # ??
a, b, c, alpha, beta, gamma = cell_to_cellpar(atoms.cell)
out.append('%-10.6f %-10.6f %-10.6f' % (a, b, c))
out.append('%-10.6f %-10.6f %-10.6f' % (alpha, beta, gamma))
out.append('0 0') # ??
out.append('0 0 0') # ??
symbols = atoms.get_chemical_symbols()
massdict = dict(zip(symbols, atoms.get_masses()))
atomtypes = sorted(massdict.keys())
atommasses = [massdict[at] for at in atomtypes]
natoms = [symbols.count(at) for at in atomtypes]
ntypes = len(atomtypes)
out.append(str(ntypes))
out.append(' '.join([str(n) for n in natoms]))
out.append(' '.join([str(n) for n in atommasses]))
for n in range(ntypes):
out.append(atomtypes[n])
out.append('Coordinates of Component %d' % (n + 1))
indices = [i for i, at in enumerate(symbols) if at == atomtypes[n]]
a = atoms[indices]
coords = a.positions
for c in a.constraints:
if not isinstance(c, FixAtoms):
warn('Only FixAtoms constraints are supported by con files. '
'Dropping %r', c)
continue
if c.index.dtype.kind == 'b':
fixed = np.array(c.index, dtype=int)
else:
fixed = np.zeros((natoms[n], ), dtype=int)
for i in c.index:
fixed[i] = 1
for i, (xyz, fix) in enumerate(zip(coords, fixed)):
out.append('%10.5f %10.5f %10.5f %d %d' %
(tuple(xyz) + (fix, i)))
f.write('\n'.join(out))
if isinstance(fileobj, str):
f.close()
def write(self, atoms=None, frame=None, arrays=None, time=None):
"""
Write the atoms to the file.
If the atoms argument is not given, the atoms object specified
when creating the trajectory object is used.
"""
self._open()
self._call_observers(self.pre_observers)
if atoms is None:
atoms = self.atoms
if hasattr(atoms, 'interpolate'):
# seems to be a NEB
neb = atoms
assert not neb.parallel
try:
neb.get_energies_and_forces(all=True)
except AttributeError:
pass
for image in neb.images:
self.write(image)
return
if not self.has_header:
self._define_file_structure(atoms)
else:
if len(atoms) != self.n_atoms:
raise ValueError('Bad number of atoms!')
if frame is None:
i = self.frame
else:
i = frame
# Number can be per file variable
numbers = self._get_variable(self._numbers_var)
if numbers.dimensions[0] == self._frame_dim:
numbers[i] = atoms.get_atomic_numbers()
else:
if np.any(numbers != atoms.get_atomic_numbers()):
raise ValueError('Atomic numbers do not match!')
self._get_variable(self._positions_var)[i] = atoms.get_positions()
if atoms.has('momenta'):
self._add_velocities()
self._get_variable(self._velocities_var)[i] = \
atoms.get_momenta() / atoms.get_masses().reshape(-1, 1)
a, b, c, alpha, beta, gamma = cell_to_cellpar(atoms.get_cell())
cell_lengths = np.array([a, b, c]) * atoms.pbc
self._get_variable(self._cell_lengths_var)[i] = cell_lengths
self._get_variable(self._cell_angles_var)[i] = [alpha, beta, gamma]
if arrays is not None:
for array in arrays:
data = atoms.get_array(array)
if array in self.extra_per_file_vars:
# This field exists but is per file data. Check that the
# data remains consistent.
if np.any(self._get_variable(array) != data):
raise ValueError('Trying to write Atoms object with '
'incompatible data for the {} '
'array.'.format(array))
else:
self._add_array(atoms, array, data.dtype, data.shape)
self._get_variable(array)[i] = data
if time is not None:
self._add_time()
self._get_variable(self._time_var)[i] = time
self._call_observers(self.post_observers)
self.frame += 1
self._close()
def write(self, atoms=None, frame=None, arrays=None, time=None):
"""
Write the atoms to the file.
If the atoms argument is not given, the atoms object specified
when creating the trajectory object is used.
"""
self._open()
self._call_observers(self.pre_observers)
if atoms is None:
atoms = self.atoms
if hasattr(atoms, 'interpolate'):
# seems to be a NEB
neb = atoms
assert not neb.parallel
try:
neb.get_energies_and_forces(all=True)
except AttributeError:
pass
for image in neb.images:
self.write(image)
return
if not self.has_header:
self._write_header(atoms)
else:
if len(atoms) != self.n_atoms:
raise ValueError('Bad number of atoms!')
if self.frame > 0:
if (atoms.numbers != self.numbers).any():
raise ValueError('Bad atomic numbers!')
else:
self.numbers = atoms.get_atomic_numbers()
self._get_variable(self._numbers_var)[:] = \
atoms.get_atomic_numbers()
if frame is None:
i = self.frame
else:
i = frame
self._get_variable(self._positions_var)[i] = atoms.get_positions()
if atoms.has('momenta'):
self._add_velocities()
self._get_variable(self._velocities_var)[i] = \
atoms.get_momenta() / atoms.get_masses().reshape(-1, 1)
a, b, c, alpha, beta, gamma = cell_to_cellpar(atoms.get_cell())
cell_lengths = np.array([a, b, c]) * atoms.pbc
self._get_variable(self._cell_lengths_var)[i] = cell_lengths
self._get_variable(self._cell_angles_var)[i] = [alpha, beta, gamma]
if arrays is not None:
for array in arrays:
data = atoms.get_array(array)
self._add_array(atoms, array, data.dtype, data.shape)
self._get_variable(array)[i] = data
if time is not None:
self._get_variable(self._time_var)[i] = time
self._call_observers(self.post_observers)
self.frame += 1
self._close()
def write(self, atoms=None, frame=None, arrays=None, time=None):
"""
Write the atoms to the file.
If the atoms argument is not given, the atoms object specified
when creating the trajectory object is used.
"""
self._open()
self._call_observers(self.pre_observers)
if atoms is None:
atoms = self.atoms
if hasattr(atoms, 'interpolate'):
# seems to be a NEB
neb = atoms
assert not neb.parallel
try:
neb.get_energies_and_forces(all=True)
except AttributeError:
pass
for image in neb.images:
self.write(image)
return
if not self.has_header:
self._write_header(atoms)
else:
if len(atoms) != self.n_atoms:
raise ValueError('Bad number of atoms!')
if self.frame > 0:
if (atoms.numbers != self.numbers).any():
raise ValueError('Bad atomic numbers!')
else:
self.numbers = atoms.get_atomic_numbers()
self._get_variable(self._numbers_var)[:] = \
atoms.get_atomic_numbers()
if frame is None:
i = self.frame
else:
i = frame
self._get_variable(self._positions_var)[i] = atoms.get_positions()
if atoms.has('momenta'):
self._add_velocities()
self._get_variable(self._velocities_var)[i] = \
atoms.get_momenta() / atoms.get_masses().reshape(-1, 1)
a, b, c, alpha, beta, gamma = cell_to_cellpar(atoms.get_cell())
cell_lengths = np.array([a, b, c]) * atoms.pbc
self._get_variable(self._cell_lengths_var)[i] = cell_lengths
self._get_variable(self._cell_angles_var)[i] = [alpha, beta, gamma]
if arrays is not None:
for array in arrays:
data = atoms.get_array(array)
self._add_array(atoms, array, data.dtype, data.shape)
self._get_variable(array)[i] = data
if time is not None:
self._get_variable(self._time_var)[i] = time
self._call_observers(self.post_observers)
self.frame += 1
self._close()
def write_reactant_con(fileobj, images):
"""Writes structure to EON reactant.con file
Multiple snapshots are not allowed."""
if isinstance(fileobj, str):
f = paropen(fileobj, "w")
else:
f = fileobj
if isinstance(images, Atoms):
atoms = images
elif len(images) == 1:
atoms = images[0]
else:
raise ValueError("Can only write one configuration to EON " "reactant.con file")
out = []
out.append(atoms.info.get("comment", "Generated by ASE"))
out.append("0.0000 TIME") # ??
a, b, c, alpha, beta, gamma = cell_to_cellpar(atoms.cell)
out.append("%-10.6f %-10.6f %-10.6f" % (a, b, c))
out.append("%-10.6f %-10.6f %-10.6f" % (gamma, beta, alpha))
out.append("0 0") # ??
out.append("0 0 0") # ??
symbols = atoms.get_chemical_symbols()
massdict = dict(list(zip(symbols, atoms.get_masses())))
atomtypes = sorted(massdict.keys())
atommasses = [massdict[at] for at in atomtypes]
natoms = [symbols.count(at) for at in atomtypes]
ntypes = len(atomtypes)
out.append(str(ntypes))
out.append(" ".join([str(n) for n in natoms]))
out.append(" ".join([str(n) for n in atommasses]))
atom_id = 0
for n in range(ntypes):
fixed = np.array([False] * len(atoms))
out.append(atomtypes[n])
out.append("Coordinates of Component %d" % (n + 1))
indices = [i for i, at in enumerate(symbols) if at == atomtypes[n]]
a = atoms[indices]
coords = a.positions
for c in a.constraints:
if not isinstance(c, FixAtoms):
warn("Only FixAtoms constraints are supported by con files. " "Dropping %r", c)
continue
if c.index.dtype.kind == "b":
fixed = np.array(c.index, dtype=int)
else:
fixed = np.zeros((natoms[n],), dtype=int)
for i in c.index:
fixed[i] = 1
for xyz, fix in zip(coords, fixed):
out.append("%22.17f %22.17f %22.17f %d %4d" % (tuple(xyz) + (fix, atom_id)))
atom_id += 1
f.write("\n".join(out))
f.write("\n")
if isinstance(fileobj, str):
f.close()