def create_random_xyz_traj_to_write(request):
natoms, frames, comment, expected_cell, precision = request.param
a, b, c, alpha, beta, gamma = mt.h2abc_deg(expected_cell)
fmt_header = "# CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f %s"
comment = fmt_header % (a, b, c, alpha, beta, gamma, comment)
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms, frames, comment)
filedesc.seek(0)
masses = [Elements.mass(_am) for _am in atom_names]
cell_list = []
atoms_list = []
for _fr in xrange(frames):
cell = Cell(expected_cell)
atoms = Atoms(natoms)
atoms.q[:] = xyz[_fr * natoms * 3:(_fr + 1) * natoms * 3]
atoms.names = atom_names[_fr * natoms:(_fr + 1) * natoms]
atoms.m[:] = masses[_fr * natoms:(_fr + 1) * natoms]
atoms_list.append(atoms)
cell_list.append(cell)
return (filedesc, atoms_list, cell_list, comment, precision)
def print_instanton_geo(prefix, step, nbeads, natoms, names, q, pots, cell,
shift):
outfile = open(prefix + '_' + str(step) + '.ener', 'w')
print >> outfile, ('#Bead Energy (eV)')
for i in range(nbeads):
print >> outfile, (
str(i) + ' ' +
str(units.unit_to_user('energy', "electronvolt", pots[i] - shift)))
outfile.close()
# print_file("xyz", pos[0], cell, out, title='positions{angstrom}')
unit = 'angstrom'
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
outfile = open(prefix + '_' + str(step) + '.xyz', 'w')
for i in range(nbeads):
print >> outfile, natoms
# print >> outfile, (('CELL(abcABC): Traj: positions(%s) Bead: %i' %(unit,i) ))
print >> outfile, (
'CELL(abcABC): %f %f %f %f %f %f cell{atomic_unit} Traj: positions{%s} Bead: %i'
% (a, b, c, alpha, beta, gamma, unit, i))
# print >> outfile, ('#Potential (eV): ' + str(units.unit_to_user('energy', "electronvolt", pots[i] - shift)))
for j in range(natoms):
print >> outfile, names[j], \
str(units.unit_to_user('length', unit, q[i, 3 * j])), \
str(units.unit_to_user('length', unit, q[i, 3 * j + 1])), \
str(units.unit_to_user('length', unit, q[i, 3 * j + 2]))
outfile.close()
def print_pdb(atoms, cell, filedesc=sys.stdout, title=""):
"""Prints an atomic configuration into a pdb formatted file.
Also prints the cell parameters in standard pdb form. Note
that the angles are in degrees.
Args:
atoms: An atoms object giving the atom positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
title: An optional string of max. 70 characters.
"""
fmt_cryst = "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f%s%4i\n"
fmt_atom = "ATOM %5i %4s%1s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2i\n"
if title != "":
filedesc.write("TITLE %70s\n" % (title))
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
z = 1
filedesc.write(fmt_cryst %
(a, b, c, alpha, beta, gamma, " P 1 ", z))
natoms = atoms.natoms
qs = depstrip(atoms.q)
lab = depstrip(atoms.names)
for i in range(natoms):
data = (i + 1, lab[i], ' ', ' 1', ' ', 1, ' ', qs[3 * i],
qs[3 * i + 1], qs[3 * i + 2], 0.0, 0.0, ' ', 0)
filedesc.write(fmt_atom % data)
filedesc.write("END\n")
def print_xyz_path(beads, cell, filedesc=sys.stdout):
"""Prints all the bead configurations, into a xyz formatted file.
Prints all the replicas for each time step separately, rather than all at
once.
Args:
beads: A beads object giving the bead positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
"""
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
natoms = beads.natoms
nbeads = beads.nbeads
for j in range(nbeads):
filedesc.write(
"%d\n# bead: %d CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f \n"
% (natoms, j, a, b, c, alpha, beta, gamma)
)
for i in range(natoms):
qs = depstrip(beads.q)
lab = depstrip(beads.names)
filedesc.write("%8s %12.5e %12.5e %12.5e\n" % (lab[i], qs[j][3 * i], qs[j][3 * i + 1], qs[j][3 * i + 2]))
def print_xyz(atoms,
cell,
filedesc=sys.stdout,
title="",
cell_conv=1.0,
atoms_conv=1.0):
"""Prints an atomic configuration into an XYZ formatted file.
Args:
atoms: An atoms object giving the centroid positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
title: This gives a string to be appended to the comment line.
"""
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h * cell_conv)
natoms = atoms.natoms
fmt_header = "%d\n# CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f %s\n"
filedesc.write(fmt_header % (natoms, a, b, c, alpha, beta, gamma, title))
# direct access to avoid unnecessary slow-down
qs = dstrip(atoms.q) * atoms_conv
lab = dstrip(atoms.names)
for i in range(natoms):
filedesc.write("%8s %12.5e %12.5e %12.5e\n" %
(lab[i], qs[3 * i], qs[3 * i + 1], qs[3 * i + 2]))
def print_instanton_geo(prefix, step, nbeads, natoms, names, q, pots, cell, shift, output_maker):
outfile = output_maker.get_output(prefix + '_' + str(step) + '.ener', 'w')
print >> outfile, ('#Bead Energy (eV)')
for i in range(nbeads):
print >> outfile, (str(i) + ' ' + str(units.unit_to_user('energy', "electronvolt", pots[i] - shift)))
outfile.close()
# print_file("xyz", pos[0], cell, out, title='positions{angstrom}')
unit = 'angstrom'
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
outfile = output_maker.get_output(prefix + '_' + str(step) + '.xyz', 'w')
for i in range(nbeads):
print >> outfile, natoms
print >> outfile, ('CELL(abcABC): %f %f %f %f %f %f cell{atomic_unit} Traj: positions{%s} Bead: %i' % (a, b, c, alpha, beta, gamma, unit, i))
for j in range(natoms):
print >> outfile, names[j], \
str(units.unit_to_user('length', unit, q[i, 3 * j])), \
str(units.unit_to_user('length', unit, q[i, 3 * j + 1])), \
str(units.unit_to_user('length', unit, q[i, 3 * j + 2]))
outfile.close()
def print_xyz_path(beads,
cell,
filedesc=sys.stdout,
cell_conv=1.0,
atoms_conv=1.0):
"""Prints all the bead configurations into a XYZ formatted file.
Prints all the replicas for each time step separately, rather than all at
once.
Args:
beads: A beads object giving the bead positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
"""
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h * cell_conv)
fmt_header = "%d\n# bead: %d CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f \n"
natoms = beads.natoms
nbeads = beads.nbeads
for j in range(nbeads):
filedesc.write(fmt_header % (natoms, j, a, b, c, alpha, beta, gamma))
for i in range(natoms):
qs = dstrip(beads.q) * atoms_conv
lab = dstrip(beads.names)
filedesc.write(
"%8s %12.5e %12.5e %12.5e\n" %
(lab[i], qs[j][3 * i], qs[j][3 * i + 1], qs[j][3 * i + 2]))
def print_pdb(atoms, cell, filedesc = sys.stdout, title=""):
"""Prints the atom configurations, into a pdb formatted file.
Also prints the cell parameters in standard pdb form. Note
that the angles are in degrees.
Args:
atoms: An atoms object giving the atom positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
title: An optional string of max. 70 characters.
"""
if title != "" :
filedesc.write("TITLE %70s\n" % (title))
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
z = 1
filedesc.write("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f%s%4i\n" % (a, b, c, alpha, beta, gamma, " P 1 ", z))
natoms = atoms.natoms
qs = depstrip(atoms.q)
lab = depstrip(atoms.names)
for i in range(natoms):
filedesc.write("ATOM %5i %4s%1s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2i\n" % (i+1, lab[i], ' ', ' 1', ' ', 1, ' ', qs[3*i], qs[3*i+1], qs[3*i+2], 0.0, 0.0, ' ', 0))
filedesc.write("END\n")
def print_pdb_path(beads, cell, filedesc = sys.stdout):
"""Prints all the bead configurations, into a pdb formatted file.
Prints the ring polymer springs as well as the bead positions using the
CONECT command. Also prints the cell parameters in standard pdb form. Note
that the angles are in degrees.
Args:
beads: A beads object giving the bead positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
"""
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
z = 1 #What even is this parameter?
filedesc.write("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f%s%4i\n" % (a, b, c, alpha, beta, gamma, " P 1 ", z))
natoms = beads.natoms
nbeads = beads.nbeads
for j in range(nbeads):
for i in range(natoms):
qs = depstrip(beads.q)
lab = depstrip(beads.names)
filedesc.write("ATOM %5i %4s%1s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2i\n" % (j*natoms+i+1, lab[i],' ',' 1',' ',1,' ', qs[j][3*i], qs[j][3*i+1], qs[j][3*i+2],0.0,0.0,' ',0))
if nbeads > 1:
for i in range(natoms):
filedesc.write("CONECT%5i%5i\n" % (i+1, (nbeads-1)*natoms+i+1))
for j in range(nbeads-1):
for i in range(natoms):
filedesc.write("CONECT%5i%5i\n" % (j*natoms+i+1, (j+1)*natoms+i+1))
filedesc.write("END\n")
def print_json(atoms, cell, filedesc=sys.stdout, title="", cell_conv=1.0, atoms_conv=1.0):
"""Prints an atomic configuration into an XYZ formatted file.
Args:
atoms: An atoms object giving the centroid positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
title: This gives a string to be appended to the comment line.
"""
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h * cell_conv)
natoms = atoms.natoms
# direct access to avoid unnecessary slow-down
qs = dstrip(atoms.q) * atoms_conv
lab = dstrip(atoms.names)
data = {}
data['natoms'] = natoms
data['cell'] = [a, b, c, alpha, beta, gamma]
data['title'] = title
data['q'] = qs.tolist()
data['labels'] = lab.tolist()
filedesc.write(json.dumps(data))
filedesc.write(" \n")
def print_instanton_geo(prefix, step, nbeads, natoms, names, q, f, pots, cell,
shift, output_maker):
""" Alternative (but very useful) output of the instanton geometry and potential energy """
outfile = output_maker.get_output(prefix + "_" + str(step) + ".ener", "w")
print("#Bead Energy (eV)", file=outfile)
for i in range(nbeads):
print(
(str(i) + " " +
str(units.unit_to_user("energy", "electronvolt",
pots[i] - shift))),
file=outfile,
)
outfile.close_stream()
# print_file("xyz", pos[0], cell, out, title='positions{angstrom}')
unit = "angstrom"
unit2 = "atomic_unit"
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
outfile = output_maker.get_output(prefix + "_" + str(step) + ".xyz", "w")
outfile2 = output_maker.get_output(
prefix + "_forces_" + str(step) + ".xyz", "w")
for i in range(nbeads):
print(natoms, file=outfile)
print(natoms, file=outfile2)
print(
("CELL(abcABC): %f %f %f %f %f %f cell{atomic_unit} Traj: positions{%s} Bead: %i"
% (a, b, c, alpha, beta, gamma, unit, i)),
file=outfile,
)
print(
("CELL(abcABC): %f %f %f %f %f %f cell{atomic_unit} Traj: positions{%s} Bead: %i"
% (a, b, c, alpha, beta, gamma, unit2, i)),
file=outfile2,
)
# print >> outfile, ('#Potential (eV): ' + str(units.unit_to_user('energy', "electronvolt", pots[i] - shift)))
for j in range(natoms):
print(
names[j],
str(units.unit_to_user("length", unit, q[i, 3 * j])),
str(units.unit_to_user("length", unit, q[i, 3 * j + 1])),
str(units.unit_to_user("length", unit, q[i, 3 * j + 2])),
file=outfile,
)
for j in range(natoms):
print(
names[j],
str(units.unit_to_user("force", unit2, f[i, 3 * j])),
str(units.unit_to_user("force", unit2, f[i, 3 * j + 1])),
str(units.unit_to_user("force", unit2, f[i, 3 * j + 2])),
file=outfile2,
)
outfile.close_stream()
outfile2.close_stream()
def print_xyz(atoms, cell, filedesc=sys.stdout, title="", cell_conv=1.0, atoms_conv=1.0):
"""Prints an atomic configuration into an XYZ formatted file.
Args:
atoms: An atoms object giving the centroid positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
title: This gives a string to be appended to the comment line.
"""
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h * cell_conv)
natoms = atoms.natoms
fmt_header = "%d\n# CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f %s\n"
filedesc.write(fmt_header % (natoms, a, b, c, alpha, beta, gamma, title))
# direct access to avoid unnecessary slow-down
qs = dstrip(atoms.q) * atoms_conv
lab = dstrip(atoms.names)
for i in range(natoms):
filedesc.write("%8s %12.5e %12.5e %12.5e\n" % (lab[i], qs[3 * i], qs[3 * i + 1], qs[3 * i + 2]))
def print_json(atoms, cell, filedesc=sys.stdout, title=""):
"""Prints an atomic configuration into an XYZ formatted file.
Args:
atoms: An atoms object giving the centroid positions.
cell: A cell object giving the system box.
filedesc: An open writable file object. Defaults to standard output.
title: This gives a string to be appended to the comment line.
"""
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
natoms = atoms.natoms
# direct access to avoid unnecessary slow-down
qs = depstrip(atoms.q)
lab = depstrip(atoms.names)
filedesc.write(
json.dumps([
natoms, a, b, c, alpha, beta, gamma, title,
qs.tolist(),
lab.tolist()
]))
filedesc.write("\n")
def print_instanton_geo(prefix, step, nbeads, natoms, names, q, f, pots, cell, shift, output_maker):
outfile = output_maker.get_output(prefix + '_' + str(step) + '.ener', 'w')
print(('#Bead Energy (eV)'), file=outfile)
for i in range(nbeads):
print((str(i) + ' ' + str(units.unit_to_user('energy', "electronvolt", pots[i] - shift))), file=outfile)
outfile.close_stream()
# print_file("xyz", pos[0], cell, out, title='positions{angstrom}')
unit = 'angstrom'
unit2 = 'atomic_unit'
a, b, c, alpha, beta, gamma = mt.h2abc_deg(cell.h)
outfile = output_maker.get_output(prefix + '_' + str(step) + '.xyz', 'w')
outfile2 = output_maker.get_output(prefix + '_forces_' + str(step) + '.xyz', 'w')
for i in range(nbeads):
print(natoms, file=outfile)
print(natoms, file=outfile2)
print(('CELL(abcABC): %f %f %f %f %f %f cell{atomic_unit} Traj: positions{%s} Bead: %i' % (a, b, c, alpha, beta, gamma, unit, i)), file=outfile)
print(('CELL(abcABC): %f %f %f %f %f %f cell{atomic_unit} Traj: positions{%s} Bead: %i' % (a, b, c, alpha, beta, gamma, unit2, i)), file=outfile2)
# print >> outfile, ('#Potential (eV): ' + str(units.unit_to_user('energy', "electronvolt", pots[i] - shift)))
for j in range(natoms):
print(names[j], \
str(units.unit_to_user('length', unit, q[i, 3 * j])), \
str(units.unit_to_user('length', unit, q[i, 3 * j + 1])), \
str(units.unit_to_user('length', unit, q[i, 3 * j + 2])), file=outfile)
for j in range(natoms):
print(names[j], \
str(units.unit_to_user('force', unit2, f[i, 3 * j])), \
str(units.unit_to_user('force', unit2, f[i, 3 * j + 1])), \
str(units.unit_to_user('force', unit2, f[i, 3 * j + 2])), file=outfile2)
outfile.close_stream()
outfile2.close_stream()