def __init__(self, filename):
from Scientific.IO.NetCDF import NetCDFFile
self.nc = NetCDFFile(filename, 'w')
self.nc.file_format = 'ETSF Nanoquanta'
self.nc.file_format_version = np.array([3.3], dtype=np.float32)
self.nc.Conventions = 'http://www.etsf.eu/fileformats/'
self.nc.history = 'File generated by ASE'
def read_dacapo(filename):
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
vars = nc.variables
cell = vars['UnitCell'][-1]
try:
magmoms = vars['InitialAtomicMagneticMoment'][:]
except KeyError:
magmoms = None
try:
tags = vars['AtomTags'][:]
except KeyError:
tags = None
atoms = Atoms(scaled_positions=vars['DynamicAtomPositions'][-1],
symbols=[(a + b).strip()
for a, b in vars['DynamicAtomSpecies'][:]],
cell=cell,
magmoms=magmoms,
tags=tags,
pbc=True)
try:
energy = vars['TotalEnergy'][-1]
force = vars['DynamicAtomForces'][-1]
except KeyError:
energy = None
force = None
calc = SinglePointCalculator(atoms, energy=energy,
forces=force) ### Fixme magmoms
atoms.set_calculator(calc)
return atoms
class Reader:
def __init__(self, filename, comm):
self.nc = NetCDFFile(filename)
def dimension(self, name):
return self.nc.dimensions[name]
def __getitem__(self, name):
value = getattr(self.nc, name)
if isinstance(value, str):
try:
value = eval(value)
except (SyntaxError, NameError):
pass
return value
else:
return value[0]
def has_array(self, name):
return name in self.nc.variables
def get(self, name, *indices):
var = self.nc.variables[name]
if var.shape == ():
return var.getValue()
else:
if var.dimensions[-1] == 'two':
x = var[indices]
array = np.empty(x.shape[:-1], complex)
array.real = x[..., 0]
array.imag = x[..., 1]
return array
else:
return var[indices]
def get_reference(self, name, *indices):
return NetCDFReference(self.nc.variables[name], indices)
def close(self):
self.nc.close()
def filetype(filename):
"""Try to guess the type of the file."""
if os.path.isdir(filename):
# Potentially a BundleTrajectory
if BundleTrajectory.is_bundle(filename):
return 'bundle'
elif os.path.normpath(filename) == 'states':
return 'eon'
else:
raise IOError('Directory: ' + filename)
if filename.startswith('pg://'):
return 'postgresql'
fileobj = open(filename, 'rU')
s3 = fileobj.read(3)
if len(s3) == 0:
raise IOError('Empty file: ' + filename)
if s3.startswith('{"'):
return 'json'
if filename.endswith('.db'):
return 'db'
if filename.lower().endswith('.cmr'):
return 'cmr'
if is_tarfile(filename):
return 'gpw'
if s3 == 'CDF':
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
if 'number_of_dynamic_atoms' in nc.dimensions:
return 'dacapo'
history = nc.history
if history == 'GPAW restart file':
return 'gpw-nc'
if history == 'ASE trajectory':
return 'nc'
if history == 'Dacapo':
return 'dacapo'
if hasattr(nc, 'file_format') and nc.file_format.startswith('ETSF'):
return 'etsf'
raise IOError('Unknown netCDF file!')
if is_zipfile(filename):
return 'vnl'
fileobj.seek(0)
lines = fileobj.readlines(1000)
if lines[0].startswith('PickleTrajectory'):
return 'traj'
if (lines[1].startswith('OUTER LOOP:')
or filename.lower().endswith('.cube')):
return 'cube'
if ' ___ ___ ___ _ _ _ \n' in lines:
return 'gpaw-text'
if (' &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n'
in lines[:90]):
return 'dacapo-text'
for line in lines:
if line[0] != '#':
word = line.strip()
if word in ['ANIMSTEPS', 'CRYSTAL', 'SLAB', 'POLYMER', 'MOLECULE']:
return 'xsf'
filename_v = os.path.basename(filename)
if 'POSCAR' in filename_v or 'CONTCAR' in filename_v:
return 'vasp'
if 'OUTCAR' in filename_v:
return 'vasp_out'
if filename.lower().endswith('.exi'):
return 'exi'
if filename.lower().endswith('.mol'):
return 'mol'
if filename.lower().endswith('.pdb'):
return 'pdb'
if filename.lower().endswith('.cif'):
return 'cif'
if filename.lower().endswith('.struct'):
return 'struct'
if filename.lower().endswith('.struct_out'):
return 'struct_out'
fileobj.seek(0)
while True:
line = fileobj.readline()
if not line:
break
if 'Invoking FHI-aims ...' in line:
return 'aims_out'
if 'atom' in line:
data = line.split()
try:
Atoms(symbols=[data[4]],
positions=[[
float(data[1]),
float(data[2]),
float(data[3])
]])
return 'aims'
except:
pass
if filename.lower().endswith('.in'):
fileobj.seek(0)
while True:
line = fileobj.readline()
if not line:
break
if ('&system' in line) or ('&SYSTEM' in line):
return 'esp_in'
return 'aims'
if filename.lower().endswith('.cfg'):
return 'cfg'
if os.path.split(filename)[1] == 'atoms.dat':
return 'iwm'
if filename.endswith('I_info'):
return 'Cmdft'
if lines[0].startswith('$coord') or os.path.basename(filename) == 'coord':
return 'tmol'
if (lines[0].startswith('$grad')
or os.path.basename(filename) == 'gradient'):
return 'tmol-gradient'
if lines[0].startswith('Geometry'):
return 'dftb'
if filename.lower().endswith('.geom'):
return 'castep_geom'
if filename.lower().endswith('.castep'):
return 'castep'
if filename.lower().endswith('.cell'):
return 'castep_cell'
if s3 == '<?x':
from ase.io.vtkxml import probe_vtkxml
xmltype = probe_vtkxml(filename)
if xmltype == 'ImageData':
return 'vti'
elif xmltype == 'StructuredGrid':
return 'vts'
elif xmltype == 'UnstructuredGrid':
return 'vtu'
elif xmltype is not None:
raise IOError('Unknown VTK XML file!')
if filename.lower().endswith('.sdf'):
return 'sdf'
if filename.lower().endswith('.gen'):
return 'gen'
if filename.lower().endswith('.con'):
return 'eon'
if 'ITEM: TIMESTEP\n' in lines:
return 'lammps'
if filename.lower().endswith('.gro'):
return 'gromacs'
if filename.lower().endswith('.log'):
return 'gaussian_out'
if filename.lower().endswith('.com'):
return 'gaussian'
if filename.lower().endswith('.g96'):
return 'gromos'
if filename.lower().endswith('.out'):
return 'esp_out'
if filename.endswith('.nw'):
return 'nw'
return 'xyz'
def read_netcdf(filename, index=-1):
nc = NetCDFFile(filename)
dims = nc.dimensions
vars = nc.variables
positions = vars['CartesianPositions']
numbers = vars['AtomicNumbers'][:]
pbc = vars['BoundaryConditions'][:]
cell = vars['UnitCell']
tags = vars['Tags'][:]
if not tags.any():
tags = None
magmoms = vars['MagneticMoments'][:]
if not magmoms.any():
magmoms = None
nimages = positions.shape[0]
attach_calculator = False
if 'PotentialEnergy' in vars:
energy = vars['PotentialEnergy']
attach_calculator = True
else:
energy = nimages * [None]
if 'CartesianForces' in vars:
forces = vars['CartesianForces']
attach_calculator = True
else:
forces = nimages * [None]
if 'Stress' in vars:
stress = vars['Stress']
attach_calculator = True
else:
stress = nimages * [None]
if isinstance(index, int):
indices = [index]
else:
indices = range(nimages)[index]
images = []
for i in indices:
atoms = Atoms(positions=positions[i],
numbers=numbers,
cell=cell[i],
pbc=pbc,
tags=tags,
magmoms=magmoms)
if attach_calculator:
calc = SinglePointCalculator(atoms,
energy=energy[i],
forces=forces[i],
stress=stress[i]) # Fixme magmoms
atoms.set_calculator(calc)
images.append(atoms)
if isinstance(index, int):
return images[0]
else:
return images
def saveNetcdf(fileName,data):
# NetCDF package
try:
from ase.io.pupynere import NetCDFFile
except ImportError:
print "ase.io.pupynere not installed on this computer."
# get input data shape
nx,ny,nz = data.shape
print 'data type '+str(data.dtype)
# open file
f = NetCDFFile(fileName,'w')
# create netcdf dimensions
f.createDimension('x',nx)
f.createDimension('y',ny)
f.createDimension('z',nz)
rho = f.createVariable('rho','d',('x','y','z'))
rho[:] = np.ones((nx,ny,nz))
E = f.createVariable('E','d',('x','y','z'))
E[:] = np.zeros((nx,ny,nz))
rho_vx = f.createVariable('rho_vx','d',('x','y','z'))
rho_vx[:] = data
rho_vy = f.createVariable('rho_vy','d',('x','y','z'))
rho_vy[:] = np.zeros((nx,ny,nz))
rho_vz = f.createVariable('rho_vz','d',('x','y','z'))
rho_vz[:] = np.zeros((nx,ny,nz))
Bx = f.createVariable('Bx','d',('x','y','z'))
Bx[:] = np.zeros((nx,ny,nz))
By = f.createVariable('By','d',('x','y','z'))
By[:] = np.zeros((nx,ny,nz))
Bz = f.createVariable('Bz','d',('x','y','z'))
Bz[:] = np.zeros((nx,ny,nz))
f.sync()
f.close()
def saveNetcdf(fileName, data):
# NetCDF package
try:
from ase.io.pupynere import NetCDFFile
except ImportError:
print "ase.io.pupynere not installed on this computer."
# get input data shape
nx, ny, nz = data.shape
print 'data type ' + str(data.dtype)
# open file
f = NetCDFFile(fileName, 'w')
# create netcdf dimensions
f.createDimension('x', nx)
f.createDimension('y', ny)
f.createDimension('z', nz)
rho = f.createVariable('rho', 'd', ('x', 'y', 'z'))
rho[:] = np.ones((nx, ny, nz))
E = f.createVariable('E', 'd', ('x', 'y', 'z'))
E[:] = np.zeros((nx, ny, nz))
rho_vx = f.createVariable('rho_vx', 'd', ('x', 'y', 'z'))
rho_vx[:] = data
rho_vy = f.createVariable('rho_vy', 'd', ('x', 'y', 'z'))
rho_vy[:] = np.zeros((nx, ny, nz))
rho_vz = f.createVariable('rho_vz', 'd', ('x', 'y', 'z'))
rho_vz[:] = np.zeros((nx, ny, nz))
Bx = f.createVariable('Bx', 'd', ('x', 'y', 'z'))
Bx[:] = np.zeros((nx, ny, nz))
By = f.createVariable('By', 'd', ('x', 'y', 'z'))
By[:] = np.zeros((nx, ny, nz))
Bz = f.createVariable('Bz', 'd', ('x', 'y', 'z'))
Bz[:] = np.zeros((nx, ny, nz))
f.sync()
f.close()
def __init__(self, filename, comm):
self.nc = NetCDFFile(filename)
import numpy as np
from ase.io.pupynere import NetCDFFile
# Write array
a1 = np.random.rand(5, 5)
a2 = a1 * 2 - 5
nc = NetCDFFile('test.nc', 'w')
nc.createDimension('dimx', a1.shape[0])
nc.createDimension('dimy', a1.shape[1])
nc.createVariable('matrix1', 'd', ('dimx', 'dimy'))[:] = a1
nc.createVariable('matrix2', 'd', ('dimx', 'dimy'))[:] = a2
nc.sync()
nc.close()
# Read array
nc = NetCDFFile('test.nc', 'r')
b1 = nc.variables['matrix1'][:]
b2 = nc.variables['matrix2'][:]
assert np.all(a1 == b1) and np.all(a2 == b2)
def filetype(filename):
"""Try to guess the type of the file."""
if os.path.isdir(filename):
# Potentially a BundleTrajectory
if BundleTrajectory.is_bundle(filename):
return 'bundle'
else:
raise IOError('Directory: ' + filename)
fileobj = open(filename)
s3 = fileobj.read(3)
if len(s3) == 0:
raise IOError('Empty file: ' + filename)
if is_tarfile(filename):
return 'gpw'
if s3 == 'CDF':
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
if 'number_of_dynamic_atoms' in nc.dimensions:
return 'dacapo'
history = nc.history
if history == 'GPAW restart file':
return 'gpw-nc'
if history == 'ASE trajectory':
return 'nc'
if history == 'Dacapo':
return 'dacapo'
if hasattr(nc, 'file_format') and nc.file_format.startswith('ETSF'):
return 'etsf'
raise IOError('Unknown netCDF file!')
if is_zipfile(filename):
return 'vnl'
fileobj.seek(0)
lines = fileobj.readlines(1000)
if lines[0].startswith('PickleTrajectory'):
return 'traj'
if lines[1].startswith('OUTER LOOP:') or filename.lower().endswith(
'.cube'):
return 'cube'
if ' ___ ___ ___ _ _ _ \n' in lines:
return 'gpaw-text'
if (' &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n'
in lines[:90]):
return 'dacapo-text'
for line in lines:
if line[0] != '#':
word = line.strip()
if word in ['ANIMSTEPS', 'CRYSTAL', 'SLAB', 'POLYMER', 'MOLECULE']:
return 'xsf'
filename_v = basename(filename)
if 'POSCAR' in filename_v or 'CONTCAR' in filename_v:
return 'vasp'
if 'OUTCAR' in filename_v:
return 'vasp_out'
if filename.lower().endswith('.exi'):
return 'exi'
if filename.lower().endswith('.mol'):
return 'mol'
if filename.lower().endswith('.pdb'):
return 'pdb'
if filename.lower().endswith('.cif'):
return 'cif'
if filename.lower().endswith('.struct'):
return 'struct'
if filename.lower().endswith('.in'):
return 'aims'
if filename.lower().endswith('.out'):
return 'aims_out'
if filename.lower().endswith('.cfg'):
return 'cfg'
if os.path.split(filename)[1] == 'atoms.dat':
return 'iwm'
if filename.endswith('I_info'):
return 'Cmdft'
if lines[0].startswith('$coord'):
return 'tmol'
if lines[0].startswith('Geometry'):
return 'dftb'
if s3 == '<?x':
from ase.io.vtkxml import probe_vtkxml
xmltype = probe_vtkxml(filename)
if xmltype == 'ImageData':
return 'vti'
elif xmltype == 'StructuredGrid':
return 'vts'
elif xmltype == 'UnstructuredGrid':
return 'vtu'
elif xmltype is not None:
raise IOError('Unknown VTK XML file!')
if filename.lower().endswith('.sdf'):
return 'sdf'
return 'xyz'
def __init__(self, filename):
self.nc = NetCDFFile(filename, 'r')
class ETSFWriter:
def __init__(self, filename):
from Scientific.IO.NetCDF import NetCDFFile
self.nc = NetCDFFile(filename, 'w')
self.nc.file_format = 'ETSF Nanoquanta'
self.nc.file_format_version = np.array([3.3], dtype=np.float32)
self.nc.Conventions = 'http://www.etsf.eu/fileformats/'
self.nc.history = 'File generated by ASE'
def write_atoms(self, atoms):
specie_a = np.empty(len(atoms), np.int32)
nspecies = 0
species = {}
numbers = []
for a, Z in enumerate(atoms.get_atomic_numbers()):
if Z not in species:
species[Z] = nspecies
nspecies += 1
numbers.append(Z)
specie_a[a] = species[Z]
dimensions = [
('character_string_length', 80),
('number_of_atoms', len(atoms)),
('number_of_atom_species', nspecies),
('number_of_cartesian_directions', 3),
('number_of_reduced_dimensions', 3),
('number_of_vectors', 3)]
for name, size in dimensions:
self.nc.createDimension(name, size)
var = self.add_variable
var('primitive_vectors',
('number_of_vectors', 'number_of_cartesian_directions'),
atoms.cell / Bohr, units='atomic units')
var('atom_species', ('number_of_atoms',), specie_a + 1)
var('reduced_atom_positions',
('number_of_atoms', 'number_of_reduced_dimensions'),
atoms.get_scaled_positions())
var('atomic_numbers', ('number_of_atom_species',),
np.array(numbers, dtype=float))
def close(self):
self.nc.close()
def add_variable(self, name, dims, data=None, **kwargs):
if data is None:
char = 'd'
else:
if isinstance(data, np.ndarray):
char = data.dtype.char
elif isinstance(data, float):
char = 'd'
elif isinstance(data, int):
char = 'i'
else:
char = 'c'
var = self.nc.createVariable(name, char, dims)
for attr, value in kwargs.items():
setattr(var, attr, value)
if data is not None:
if len(dims) == 0:
var.assignValue(data)
else:
if char == 'c':
if len(dims) == 1:
var[:len(data)] = data
else:
for i, x in enumerate(data):
var[i, :len(x)] = x
else:
var[:] = data
return var
