def write_input_files(self, at, label):
write_xyz(os.path.join(self.subdir, 'atoms.%d.xyz' % self.client_id), at)
# copy in parameter files
if self.param_files is not None:
for param_file in self.param_files:
param_file_basename = os.path.basename(param_file)
shutil.copyfile(param_file, os.path.join(self.subdir, param_file_basename))
def pack_atoms_to_xyz_str(at, label):
at.info['label'] = label
buffer = StringIO.StringIO()
write_xyz(buffer, at)
data = str(buffer)
buffer.close()
# preceed message by its length
data_length = ('%8d' % len(data)).encode('ascii')
data = data_length + data.encode('ascii')
return data
def from_ase(cls, atoms, *args: str):
"""Loading ASE Atoms object by using extXYZ as an intermediate data format."""
from io import StringIO
from ase.io.extxyz import write_xyz
with StringIO() as f:
write_xyz(f, atoms)
xyz_str = f.getvalue()
return cls.from_str(xyz_str, *args)
def write(filename, images, format=None, **kwargs):
"""Write Atoms object(s) to file.
filename: str
Name of the file to write to.
images: Atoms object or list of Atoms objects
A single Atoms object or a list of Atoms objects.
format: str
Used to specify the file-format. If not given, the
file-format will be taken from suffix of the filename.
The accepted output formats:
========================= ===========
format short name
========================= ===========
ASE pickle trajectory traj
ASE bundle trajectory bundle
CUBE file cube
XYZ-file xyz
VASP POSCAR/CONTCAR file vasp
ABINIT input file abinit
Protein Data Bank pdb
CIF-file cif
XCrySDen Structure File xsf
FHI-aims geometry file aims
gOpenMol .plt file plt
Python script py
Encapsulated Postscript eps
Portable Network Graphics png
Persistance of Vision pov
VTK XML Image Data vti
VTK XML Structured Grid vts
VTK XML Unstructured Grid vtu
TURBOMOLE coord file tmol
exciting exi
AtomEye configuration cfg
WIEN2k structure file struct
CASTEP cell file cell
DftbPlus input file dftb
ETSF etsf.nc
DFTBPlus GEN format gen
CMR db/cmr-file db
CMR db/cmr-file cmr
EON reactant.con file eon
Gromacs coordinates gro
GROMOS96 (only positions) g96
X3D x3d
X3DOM HTML html
Extended XYZ file extxyz
========================= ===========
The use of additional keywords is format specific.
The ``cube`` and ``plt`` formats accept (plt requires it) a ``data``
keyword, which can be used to write a 3D array to the file along
with the nuclei coordinates.
The ``vti``, ``vts`` and ``vtu`` formats are all specifically directed
for use with MayaVi, and the latter is designated for visualization of
the atoms whereas the two others are intended for volume data. Further,
it should be noted that the ``vti`` format is intended for orthogonal
unit cells as only the grid-spacing is stored, whereas the ``vts`` format
additionally stores the coordinates of each grid point, thus making it
useful for volume date in more general unit cells.
The ``eps``, ``png``, and ``pov`` formats are all graphics formats,
and accept the additional keywords:
rotation: str (default '')
The rotation angles, e.g. '45x,70y,90z'.
show_unit_cell: int (default 0)
Can be 0, 1, 2 to either not show, show, or show all of the unit cell.
radii: array or float (default 1.0)
An array of same length as the list of atoms indicating the sphere radii.
A single float specifies a uniform scaling of the default covalent radii.
bbox: 4 floats (default None)
Set the bounding box to (xll, yll, xur, yur) (lower left, upper right).
colors: array (default None)
An array of same length as the list of atoms, indicating the rgb color
code for each atom. Default is the jmol_colors of ase/data/colors.
scale: int (default 20)
Number of pixels per Angstrom.
For the ``pov`` graphics format, ``scale`` should not be specified.
The elements of the color array can additionally be strings, or 4
and 5 vectors for named colors, rgb + filter, and rgb + filter + transmit
specification. This format accepts the additional keywords:
``run_povray``, ``display``, ``pause``, ``transparent``,
``canvas_width``, ``canvas_height``, ``camera_dist``,
``image_plane``, ``camera_type``, ``point_lights``,
``area_light``, ``background``, ``textures``, ``celllinewidth``,
``bondlinewidth``, ``bondatoms``
The ``xyz`` format accepts a comment string using the ``comment`` keyword:
comment: str (default '')
Optional comment written on the second line of the file.
"""
if format is None:
if filename == '-':
format = 'xyz'
filename = sys.stdout
elif 'POSCAR' in filename or 'CONTCAR' in filename:
format = 'vasp'
elif 'OUTCAR' in filename:
format = 'vasp_out'
elif filename.endswith('etsf.nc'):
format = 'etsf'
elif filename.lower().endswith('.con'):
format = 'eon'
elif os.path.basename(filename) == 'coord':
format = 'tmol'
else:
suffix = filename.split('.')[-1]
format = {
'cell': 'castep_cell',
}.get(suffix, suffix) # XXX this does not make sense
# Maybe like this:
## format = {'traj': 'trajectory',
## 'nc': 'netcdf',
## 'exi': 'exciting',
## 'in': 'aims',
## 'tmol': 'turbomole',
## }.get(suffix, suffix)
if format in ['json', 'db']:
from ase.db import connect
connect(filename, format).write(images)
return
if format == 'castep_cell':
from ase.io.castep import write_cell
write_cell(filename, images, **kwargs)
return
if format == 'exi':
from ase.io.exciting import write_exciting
write_exciting(filename, images)
return
if format == 'cif':
from ase.io.cif import write_cif
write_cif(filename, images)
if format == 'xyz':
from ase.io.extxyz import write_xyz
write_xyz(filename,
images,
columns=['symbols', 'positions'],
write_info=False,
**kwargs)
return
if format == 'extxyz':
from ase.io.extxyz import write_xyz
write_xyz(filename, images, **kwargs)
return
if format == 'gen':
from ase.io.gen import write_gen
write_gen(filename, images)
return
elif format == 'in':
format = 'aims'
elif format == 'tmol':
from ase.io.turbomole import write_turbomole
write_turbomole(filename, images)
return
elif format == 'dftb':
from ase.io.dftb import write_dftb
write_dftb(filename, images)
return
elif format == 'struct':
from ase.io.wien2k import write_struct
write_struct(filename, images, **kwargs)
return
elif format == 'findsym':
from ase.io.findsym import write_findsym
write_findsym(filename, images)
return
elif format == 'etsf':
from ase.io.etsf import ETSFWriter
writer = ETSFWriter(filename)
if not isinstance(images, (list, tuple)):
images = [images]
writer.write_atoms(images[0])
writer.close()
return
elif format == 'cmr':
from ase.io.cmr_io import write_db
return write_db(filename, images, **kwargs)
elif format == 'eon':
from ase.io.eon import write_reactant_con
write_reactant_con(filename, images)
return
elif format == 'gro':
from ase.io.gromacs import write_gromacs
write_gromacs(filename, images)
return
elif format == 'g96':
from ase.io.gromos import write_gromos
write_gromos(filename, images)
return
elif format == 'html':
from ase.io.x3d import write_html
write_html(filename, images)
return
format = {
'traj': 'trajectory',
'nc': 'netcdf',
'bundle': 'bundletrajectory'
}.get(format, format)
name = 'write_' + format
if format in ['vti', 'vts', 'vtu']:
format = 'vtkxml'
if format is None:
format = filetype(filename)
try:
write = getattr(__import__('ase.io.%s' % format, {}, {}, [name]), name)
except ImportError:
raise TypeError('Unknown format: "%s".' % format)
write(filename, images, **kwargs)
def write(filename, images, format=None, **kwargs):
"""Write Atoms object(s) to file.
filename: str
Name of the file to write to.
images: Atoms object or list of Atoms objects
A single Atoms object or a list of Atoms objects.
format: str
Used to specify the file-format. If not given, the
file-format will be taken from suffix of the filename.
The accepted output formats:
========================= ===========
format short name
========================= ===========
ASE pickle trajectory traj
ASE bundle trajectory bundle
CUBE file cube
XYZ-file xyz
VASP POSCAR/CONTCAR file vasp
ABINIT input file abinit
Protein Data Bank pdb
CIF-file cif
XCrySDen Structure File xsf
FHI-aims geometry file aims
gOpenMol .plt file plt
Python script py
Encapsulated Postscript eps
Portable Network Graphics png
Persistance of Vision pov
VTK XML Image Data vti
VTK XML Structured Grid vts
VTK XML Unstructured Grid vtu
TURBOMOLE coord file tmol
exciting exi
AtomEye configuration cfg
WIEN2k structure file struct
CASTEP cell file cell
DftbPlus input file dftb
ETSF etsf.nc
DFTBPlus GEN format gen
CMR db/cmr-file db
CMR db/cmr-file cmr
EON reactant.con file eon
Gromacs coordinates gro
GROMOS96 (only positions) g96
X3D x3d
X3DOM HTML html
Extended XYZ file extxyz
========================= ===========
Many formats allow on open file-like object to be passed instead
of ``filename``. In this case the format cannot be auto-decected,
so the ``format`` argument should be explicitly given.
The use of additional keywords is format specific.
The ``cube`` and ``plt`` formats accept (plt requires it) a ``data``
keyword, which can be used to write a 3D array to the file along
with the nuclei coordinates.
The ``vti``, ``vts`` and ``vtu`` formats are all specifically directed
for use with MayaVi, and the latter is designated for visualization of
the atoms whereas the two others are intended for volume data. Further,
it should be noted that the ``vti`` format is intended for orthogonal
unit cells as only the grid-spacing is stored, whereas the ``vts`` format
additionally stores the coordinates of each grid point, thus making it
useful for volume date in more general unit cells.
The ``eps``, ``png``, and ``pov`` formats are all graphics formats,
and accept the additional keywords:
rotation: str (default '')
The rotation angles, e.g. '45x,70y,90z'.
show_unit_cell: int (default 0)
Can be 0, 1, 2 to either not show, show, or show all of the unit cell.
radii: array or float (default 1.0)
An array of same length as the list of atoms indicating the sphere radii.
A single float specifies a uniform scaling of the default covalent radii.
bbox: 4 floats (default None)
Set the bounding box to (xll, yll, xur, yur) (lower left, upper right).
colors: array (default None)
An array of same length as the list of atoms, indicating the rgb color
code for each atom. Default is the jmol_colors of ase/data/colors.
scale: int (default 20)
Number of pixels per Angstrom.
For the ``pov`` graphics format, ``scale`` should not be specified.
The elements of the color array can additionally be strings, or 4
and 5 vectors for named colors, rgb + filter, and rgb + filter + transmit
specification. This format accepts the additional keywords:
``run_povray``, ``display``, ``pause``, ``transparent``,
``canvas_width``, ``canvas_height``, ``camera_dist``,
``image_plane``, ``camera_type``, ``point_lights``,
``area_light``, ``background``, ``textures``, ``celllinewidth``,
``bondlinewidth``, ``bondatoms``
The ``xyz`` format accepts a comment string using the ``comment`` keyword:
comment: str (default '')
Optional comment written on the second line of the file.
"""
if format is None:
if filename == '-':
format = 'xyz'
filename = sys.stdout
elif 'POSCAR' in filename or 'CONTCAR' in filename:
format = 'vasp'
elif 'OUTCAR' in filename:
format = 'vasp_out'
elif filename.endswith('etsf.nc'):
format = 'etsf'
elif filename.lower().endswith('.con'):
format = 'eon'
elif os.path.basename(filename) == 'coord':
format = 'tmol'
else:
suffix = filename.split('.')[-1]
format = {'cell': 'castep_cell',
}.get(suffix, suffix) # XXX this does not make sense
# Maybe like this:
## format = {'traj': 'trajectory',
## 'nc': 'netcdf',
## 'exi': 'exciting',
## 'in': 'aims',
## 'tmol': 'turbomole',
## }.get(suffix, suffix)
if format in ['json', 'db']:
from ase.db import connect
connect(filename, format).write(images)
return
if format == 'castep_cell':
from ase.io.castep import write_cell
write_cell(filename, images, **kwargs)
return
if format == 'exi':
from ase.io.exciting import write_exciting
write_exciting(filename, images)
return
if format == 'cif':
from ase.io.cif import write_cif
write_cif(filename, images)
if format == 'xyz':
from ase.io.extxyz import write_xyz
write_xyz(filename, images, columns=['symbols', 'positions'],
write_info=False, write_results=False, **kwargs)
return
if format == 'extxyz':
from ase.io.extxyz import write_xyz
write_xyz(filename, images, **kwargs)
return
if format == 'gen':
from ase.io.gen import write_gen
write_gen(filename, images)
return
elif format == 'in':
format = 'aims'
elif format == 'tmol':
from ase.io.turbomole import write_turbomole
write_turbomole(filename, images)
return
elif format == 'dftb':
from ase.io.dftb import write_dftb
write_dftb(filename, images)
return
elif format == 'struct':
from ase.io.wien2k import write_struct
write_struct(filename, images, **kwargs)
return
elif format == 'findsym':
from ase.io.findsym import write_findsym
write_findsym(filename, images)
return
elif format == 'etsf':
from ase.io.etsf import ETSFWriter
writer = ETSFWriter(filename)
if not isinstance(images, (list, tuple)):
images = [images]
writer.write_atoms(images[0])
writer.close()
return
elif format == 'cmr':
from ase.io.cmr_io import write_db
return write_db(filename, images, **kwargs)
elif format == 'eon':
from ase.io.eon import write_reactant_con
write_reactant_con(filename, images)
return
elif format == 'gro':
from ase.io.gromacs import write_gromacs
write_gromacs(filename, images)
return
elif format == 'g96':
from ase.io.gromos import write_gromos
write_gromos(filename, images)
return
elif format == 'html':
from ase.io.x3d import write_html
write_html(filename, images)
return
format = {'traj': 'trajectory',
'nc': 'netcdf',
'bundle': 'bundletrajectory'
}.get(format, format)
name = 'write_' + format
if format in ['vti', 'vts', 'vtu']:
format = 'vtkxml'
elif format == 'trj':
name = 'write_trajectory'
format = 'pickletrajectory'
elif format is None:
format = filetype(filename)
try:
write = getattr(__import__('ase.io.%s' % format, {}, {}, [name]), name)
except ImportError:
raise TypeError('Unknown format: "%s".' % format)
write(filename, images, **kwargs)
print('(111)surface')
atoms_info += Atoms(numbers=[1],
positions=[(r2[0], r2[1], r2[2] - r_SiH)])
print("Symbols = {}".format(atoms_info.symbols))
print("natoms = {}".format(len(atoms_info)))
### Get cell info ###
# The input XYZ file is assumed to have the cell info
# at the last two lines
a1 = input_main["lattice"]["unit_vec"][0]
a2 = input_main["lattice"]["unit_vec"][1]
a3 = np.array([0.0, 0.0, slab_size + input_main["param"]["slab_margin"]])
atoms_info.set_cell(np.array([a1, a2, a3]))
comment = "Lattice= \"{} {} {} {} {} {} {} {} {}\" Properties=species:S:1:pos:R:3 pbc=\"T T T\"".format(
a1[0], a1[1], a1[2], a2[0], a2[1], a2[2], a3[0], a3[1], a3[2])
write_xyz(open(wfile_name + ".xyz", "w"), atoms_info, comment)
from ase.io import read, write
ase_union = read(wfile_name + ".xyz")
### CIF file ###
ase_union.write(wfile_name + '.cif', format='cif')
### Constraints ###
from ase.constraints import FixAtoms
z_atoms = atoms_info.get_positions()[:, 2]
ase_union.set_constraint(
FixAtoms(indices=np.where(z_atoms <= z_bottom_2nd[1])[0]))
### Quantum Espresso ###
from ase.calculators.espresso import Espresso
if os.path.isfile("neb_path.xyz"):
os.remove("neb_path.xyz")
images = []
print "shape of potential array", np.shape(potentials)
#print "Final image potentials:", potentials[-1,1:]
if np.shape(potentials)[0] > 1:
final_pots = (potentials)[-1,1:]
else:
final_pots = potentials[0][1:]
print final_pots, potentials
for potential, pos_file, force_file in zip(final_pots, positions, forces):
print pos_file, force_file, potential
ats = io.read(pos_file,index="-1")
alat = 14.35
ats.cell = np.array([[alat,0.0,0.0],[0.0,alat,0.0],[0.0,0.0,alat]])
ats.set_pbc(True)
forces = io.read(force_file,index="-1")
#if conversion required:
#forces *= units.Hartree/units.Bohr
#bit of a hack but the positions of the force images are the forces:
calc = Calculator(ats,potential,forces=forces.get_positions())
ats.set_calculator(calc)
forces = ats.get_forces()
ats.arrays['forces'] = forces
write_xyz("neb_path.xyz",ats, append=True)
images.append(ats)
calc_neb_barriers(prefix, images)
import os
import sys
import glob
import numpy as np
from ase import io
from ase.io.extxyz import write_xyz
prefix = sys.argv[1]
positions = glob.glob("{prefix}.pos_*xyz".format(prefix=prefix))
positions.sort(key=func)
func = lambda x: int(x.split("_")[1].split(".")[0])
if os.path.isfile("neb_restart.xyz"):
os.remove("neb_restart.xyz")
for pos_file in positions:
ats = io.read(pos_file, index="-1")
write_xyz("neb_restart.xyz", ats, append=True)
np.savetxt(prefix + "_fit.txt", np.array([Sfit, Efit]))
np.savetxt(prefix + "_lines.txt", np.vstack(lines))
fig.savefig(prefix + "_barrier.eps")
if __name__ == '__main__':
prefix = sys.argv[1]
job_dirs = glob.glob("{prefix}*".format(prefix=prefix))
job_dirs = filter(os.path.isdir, job_dirs)
func = lambda x: int(x.split("_")[1])
job_dirs.sort(key=func)
images = []
print "Removing old neb path"
if os.path.isfile("neb_path.xyz"):
os.remove("neb_path.xyz")
for job in job_dirs:
print "pulling ", job
with pushd(job) as ctx0:
try:
ats = io.read('OUTCAR', index='-1')
ats.arrays['forces'] = ats.get_forces()
except StopIteration:
print "Could not pull OUTCAR for:", job
else:
images.append(ats)
for image in images:
write_xyz("neb_path.xyz", image, append=True)
calc_neb_barriers(prefix, images)
def xdatcar_to_xyz(argv):
"""Convert XDATCAR file to xyz.
Each comment line begins with #.
After frame number is printed. If timestep is given, actual time is written; assumes fs.
First comment line contains ASE object info as well.
Result is written on stdout."""
#-------------------------------------------------------------------------------
# Argument parser
#-------------------------------------------------------------------------------
parser = argparse.ArgumentParser(description=__doc__)
# Positional arguments
parser.add_argument('filename',
default='XDATCAR',
type=str,
nargs='?',
help='input file. If not given XDATCAR is used;'
) # if NULL is given, stdin is used.')
# Optional args
parser.add_argument('--dt',
dest='dt',
type=float,
default=None,
help='timestep in femptosecon;')
parser.add_argument('--debug',
action='store_true',
dest='debug',
help='show debug informations.')
#-------------------------------------------------------------------------------
# Initialize and check variables
#-------------------------------------------------------------------------------
args = parser.parse_args(argv)
# Set up LOGGER
c_log = logging.getLogger(__name__)
# Adopted format: level - current function name - mess. Width is fixed as visual aid
std_format = '[%(levelname)5s - %(funcName)10s] %(message)s'
logging.basicConfig(format=std_format)
c_log.setLevel(logging.INFO)
# Set debug option
if args.debug: c_log.setLevel(logging.DEBUG)
c_log.debug(args)
# Set time variable properly
t_unit = "fs"
if args.dt is None:
args.dt = 1
t_unit = ""
#-------------------------------------------------------------------------------
# Load file and print xyz to stdout
#-------------------------------------------------------------------------------
# Load xdatcar as list of Atoms obj
# For some reason we need to put index=0 to load all of it, otherwise is just the first.
for t, frame in enumerate(read_vasp_xdatcar(args.filename, index=0)):
c_line = "# %.6f %s " % (t * args.dt, t_unit)
# If it's the first line, print first atoms object info
# Here we are assuming that since it's MD, cell and compositions are not changing.
if t == 0:
c_line += "%s %s" % (frame, frame.info)
write_xyz(sys.stdout, frame, append=True, comment=c_line)
