def calculate(self, atoms):
"""Total Turbomole energy is calculated (to file 'energy'
also forces are calculated (to file 'gradient')
"""
self.positions = atoms.get_positions().copy()
self.cell = atoms.get_cell().copy()
self.pbc = atoms.get_pbc().copy()
#write current coordinates to file 'coord' for Turbomole
write_turbomole('coord', atoms)
#Turbomole energy calculation
os.system('rm -f output.energy.dummy; \
' + self.tm_program_energy + '> output.energy.dummy')
#check that the energy run converged
if os.path.isfile('dscf_problem'):
print 'Turbomole scf energy calculation did not converge'
print 'issue command t2x -c > last.xyz'
print 'and check geometry last.xyz and job.xxx or statistics'
raise RuntimeError, \
'Please run Turbomole define and come thereafter back'
self.read_energy()
#Turbomole atomic forces calculation
#killing the previous gradient file because
#turbomole gradients are affected by the previous values
os.system('rm -f gradient; rm -f output.forces.dummy; \
' + self.tm_program_forces + '> output.forces.dummy')
self.read_forces(atoms)
self.converged = True
def set_atoms(self, atoms):
if self.atoms == atoms:
return
# performs an update of the atoms
Calculator.set_atoms(self, atoms)
write_turbomole('coord', atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
def set_atoms(self, atoms):
if self.atoms == atoms:
return
# performs an update of the atoms
super(Turbomole, self).set_atoms(atoms)
write_turbomole('coord', atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
def set_atoms(self, atoms):
if self.atoms == atoms:
return
# performs an update of the atoms
Calculator.set_atoms(self, atoms)
write_turbomole("coord", atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
def set_atoms(self, atoms):
if self.atoms == atoms:
if (self.updated and os.path.isfile('coord')):
self.updated = False
a = read_turbomole().get_positions()
if np.allclose(a,atoms.get_positions(), rtol=0, atol=1e-13):
return
else:
return
# performs an update of the atoms
write_turbomole('coord', atoms)
Calculator.set_atoms(self, atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
def set_atoms(self, atoms):
if self.atoms == atoms:
if (self.updated and os.path.isfile('coord')):
self.updated = False
a = read_turbomole().get_positions()
if np.allclose(a, atoms.get_positions(), rtol=0, atol=1e-13):
return
else:
return
# performs an update of the atoms
write_turbomole('coord', atoms)
Calculator.set_atoms(self, atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
def set_atoms(self, atoms):
if self.atoms == atoms:
return
# performs an update of the atoms
Calculator.set_atoms(self, atoms)
#
# We may reside in a clean directory,
# Write 'control' and auxiliary files:
#
self.store2files(TURBOMOLE_INPUT_FILES)
write_turbomole('coord', atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
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)