def test_read_struct():
struct = Atoms(
'H4', pbc=[True, True, True],
cell=[[4.00759, 0.0, 0.0],
[-2.003795, 3.47067475, 0.0],
[3.06349683e-16, 5.30613216e-16, 5.00307]],
positions=[[-2.003795e-05, 2.31379473, 0.875437189],
[2.00381504, 1.15688001, 4.12763281],
[2.00381504, 1.15688001, 3.37697219],
[-2.003795e-05, 2.31379473, 1.62609781]],
)
struct.info = {'dataset': 'deltatest', 'kpoints': np.array([28, 28, 20]),
'identifier': 'deltatest_H_1.00',
'unique_id': '4cf83e2f89c795fb7eaf9662e77542c1'}
ase.io.write('tmp.xyz', struct)
C -1.15405 2.86652 -1.26699
C -5.53758 3.70936 0.63504
C -7.28250 4.71303 -3.82016
""")
f.close()
a = ase.io.read('structure.xyz')
os.unlink('structure.xyz')
# read xyz with / in key value
f = open('slash.xyz', 'w')
f.write("""4
key1=a key2=a/b
Mg -4.25650 3.79180 -2.54123
C -1.15405 2.86652 -1.26699
C -5.53758 3.70936 0.63504
C -7.28250 4.71303 -3.82016
""")
f.close()
a = ase.io.read('slash.xyz')
assert a.info['key1'] == r'a'
assert a.info['key2'] == r'a/b'
os.unlink('slash.xyz')
struct = Atoms('H4', pbc=[True, True, True],
cell=[[4.00759, 0.0, 0.0], [-2.003795, 3.47067475, 0.0], [3.06349683e-16, 5.30613216e-16, 5.00307]], positions=[[-2.003795e-05, 2.31379473, 0.875437189], [2.00381504, 1.15688001, 4.12763281], [2.00381504, 1.15688001, 3.37697219], [-2.003795e-05, 2.31379473, 1.62609781]])
struct.info = {'key_value_pairs': {'dataset': 'deltatest', 'kpoints': np.array([28, 28, 20]), 'identifier': 'deltatest_H_1.00'}, 'unique_id': '4cf83e2f89c795fb7eaf9662e77542c1'}
ase.io.write('tmp.xyz', struct)
os.unlink('tmp.xyz')
assert a.info['key3'] == r'a@b'
assert a.info['key4'] == r'a@b'
os.unlink('slash.xyz')
struct = Atoms('H4',
pbc=[True, True, True],
cell=[[4.00759, 0.0, 0.0], [-2.003795, 3.47067475, 0.0],
[3.06349683e-16, 5.30613216e-16, 5.00307]],
positions=[[-2.003795e-05, 2.31379473, 0.875437189],
[2.00381504, 1.15688001, 4.12763281],
[2.00381504, 1.15688001, 3.37697219],
[-2.003795e-05, 2.31379473, 1.62609781]])
struct.info = {
'key_value_pairs': {
'dataset': 'deltatest',
'kpoints': np.array([28, 28, 20]),
'identifier': 'deltatest_H_1.00'
},
'unique_id': '4cf83e2f89c795fb7eaf9662e77542c1'
}
ase.io.write('tmp.xyz', struct)
os.unlink('tmp.xyz')
# Complex properties line. Keys and values that break with a regex parser.
# see https://gitlab.com/ase/ase/issues/53 for more info
complex_xyz_string = (
' ' # start with a separator
'str=astring '
'quot="quoted value" '
u'quote_special="a_to_Z_$%%^&*\xfc\u2615" '
def read_lammps_dump(fileobj, index=-1):
"""Method which reads a LAMMPS dump file."""
if isinstance(fileobj, str):
f = paropen(fileobj)
else:
f = fileobj
# load everything into memory
lines = f.readlines()
natoms = 0
images = []
while len(lines) > natoms:
line = lines.pop(0)
if 'ITEM: TIMESTEP' in line:
natoms = 0
lo = []
hi = []
tilt = []
#id = [] ; types = []
positions = None
velocities = None
forces = None
quaternions = None
charges = None
if 'ITEM: NUMBER OF ATOMS' in line:
line = lines.pop(0)
natoms = int(line.split()[0])
if 'ITEM: BOX BOUNDS' in line:
# save labels behind "ITEM: BOX BOUNDS" in triclinic case (>=lammps-7Jul09)
tilt_items = line.split()[3:]
for i in range(3):
line = lines.pop(0)
fields = line.split()
lo.append(float(fields[0]))
hi.append(float(fields[1]))
if (len(fields) >= 3):
tilt.append(float(fields[2]))
# determine cell tilt (triclinic case!)
if (len(tilt) >= 3):
# for >=lammps-7Jul09 use labels behind "ITEM: BOX BOUNDS" to assign tilt (vector) elements ...
if (len(tilt_items) >= 3):
xy = tilt[tilt_items.index('xy')]
xz = tilt[tilt_items.index('xz')]
yz = tilt[tilt_items.index('yz')]
# ... otherwise assume default order in 3rd column (if the latter was present)
else:
xy = tilt[0]
xz = tilt[1]
yz = tilt[2]
else:
xy = xz = yz = 0
xhilo = (hi[0] - lo[0]) - abs(xy) - abs(xz)
yhilo = (hi[1] - lo[1]) - abs(yz)
zhilo = (hi[2] - lo[2])
celldispx = lo[0] - min(0, xy) - min(0, xz)
celldispy = lo[1] - min(0, yz)
celldispz = lo[2]
cell = [[xhilo, 0, 0], [xy, yhilo, 0], [xz, yz, zhilo]]
celldisp = [[celldispx, celldispy, celldispz]]
if 'ITEM: ATOMS' in line:
atom_attributes = {}
for (i, x) in enumerate(line.split()[2:]):
atom_attributes[x] = i
positions = np.zeros((natoms, 3)) * np.nan
types = np.empty(natoms, dtype=int)
if 'vx' in atom_attributes:
velocities = np.zeros((natoms, 3)) * np.nan
if 'fx' in atom_attributes:
forces = np.zeros((natoms, 3)) * np.nan
if 'c_q[1]' in atom_attributes:
quaternions = np.zeros((natoms, 4)) * np.nan
if 'q' in atom_attributes:
charges = np.zeros(natoms)
def get_values(fields, keys):
return [float(fields[atom_attributes[key]]) for key in keys]
for n in range(natoms):
line = lines.pop(0)
fields = line.split()
id = int(fields[atom_attributes['id']])
#id.append( int(fields[atom_attributes['id']]) )
types[id - 1] = int(fields[atom_attributes['type']])
try:
positions[id - 1] = get_values(fields, ['x', 'y', 'z'])
except:
print id, positions.shape, n_atoms, line
raise
if velocities != None:
velocities[id - 1] = get_values(fields, ['vx', 'vy', 'vz'])
if forces != None:
forces[id - 1] = get_values(fields, ['fx', 'fy', 'fz'])
if quaternions != None:
quaternions[id - 1] = get_values(
fields, ['c_q[1]', 'c_q[2]', 'c_q[3]', 'c_q[4]'])
if charges != None:
charges[id - 1] = get_values(fields, 'q')[0]
#if len(quaternions):
# images.append(Quaternions(symbols=types,
# positions=positions,
# cell=cell, celldisp=celldisp,
# quaternions=quaternions, info=info))
atoms = Atoms(symbols=types, positions=positions, cell=cell)
if velocities != None:
atoms.set_velocities(velocities)
if charges != None:
atoms.set_charges(charges)
info = dict(celldisp=celldisp)
if forces != None:
info['forces'] = forces
atoms.info = info
images.append(atoms)
return images[index]
def read_lammps_dump(fileobj, index=-1):
"""Method which reads a LAMMPS dump file."""
if isinstance(fileobj, str):
f = paropen(fileobj)
else:
f = fileobj
# load everything into memory
lines = f.readlines()
natoms = 0
images = []
while len(lines) > natoms:
line = lines.pop(0)
if 'ITEM: TIMESTEP' in line:
natoms = 0
lo = [] ; hi = [] ; tilt = []
#id = [] ; types = []
positions = None
velocities = None
forces = None
quaternions = None
charges = None
if 'ITEM: NUMBER OF ATOMS' in line:
line = lines.pop(0)
natoms = int(line.split()[0])
if 'ITEM: BOX BOUNDS' in line:
# save labels behind "ITEM: BOX BOUNDS" in triclinic case (>=lammps-7Jul09)
tilt_items = line.split()[3:]
for i in range(3):
line = lines.pop(0)
fields = line.split()
lo.append(float(fields[0]))
hi.append(float(fields[1]))
if (len(fields) >= 3):
tilt.append(float(fields[2]))
# determine cell tilt (triclinic case!)
if (len(tilt) >= 3):
# for >=lammps-7Jul09 use labels behind "ITEM: BOX BOUNDS" to assign tilt (vector) elements ...
if (len(tilt_items) >= 3):
xy = tilt[tilt_items.index('xy')]
xz = tilt[tilt_items.index('xz')]
yz = tilt[tilt_items.index('yz')]
# ... otherwise assume default order in 3rd column (if the latter was present)
else:
xy = tilt[0]
xz = tilt[1]
yz = tilt[2]
else:
xy = xz = yz = 0
xhilo = (hi[0] - lo[0]) - abs(xy) - abs(xz)
yhilo = (hi[1] - lo[1]) - abs(yz)
zhilo = (hi[2] - lo[2])
celldispx = lo[0] - min(0, xy) - min(0, xz)
celldispy = lo[1] - min(0, yz)
celldispz = lo[2]
cell = [[xhilo,0,0],[xy,yhilo,0],[xz,yz,zhilo]]
celldisp = [[celldispx, celldispy, celldispz]]
if 'ITEM: ATOMS' in line:
atom_attributes = {}
for (i, x) in enumerate(line.split()[2:]):
atom_attributes[x] = i
positions = np.zeros((natoms, 3))*np.nan
types = np.empty(natoms, dtype=int)
if 'vx' in atom_attributes:
velocities = np.zeros((natoms, 3))*np.nan
if 'fx' in atom_attributes:
forces = np.zeros((natoms, 3))*np.nan
if 'c_q[1]' in atom_attributes:
quaternions = np.zeros((natoms, 4))*np.nan
if 'q' in atom_attributes:
charges = np.zeros(natoms)
def get_values(fields, keys):
return [float(fields[atom_attributes[key]]) for key in keys]
for n in range(natoms):
line = lines.pop(0)
fields = line.split()
id = int(fields[atom_attributes['id']])
#id.append( int(fields[atom_attributes['id']]) )
types[id-1] = int(fields[atom_attributes['type']])
try:
positions[id-1] = get_values(fields, ['x', 'y', 'z'])
except:
print id, positions.shape, n_atoms, line
raise
if velocities != None:
velocities[id-1] = get_values(fields, ['vx', 'vy', 'vz'])
if forces != None:
forces[id-1] = get_values(fields, ['fx', 'fy', 'fz'])
if quaternions != None:
quaternions[id-1] = get_values(fields, ['c_q[1]', 'c_q[2]', 'c_q[3]', 'c_q[4]'])
if charges != None:
charges[id-1] = get_values(fields, 'q')[0]
#if len(quaternions):
# images.append(Quaternions(symbols=types,
# positions=positions,
# cell=cell, celldisp=celldisp,
# quaternions=quaternions, info=info))
atoms = Atoms(symbols=types, positions=positions, cell=cell)
if velocities != None:
atoms.set_velocities(velocities)
if charges != None:
atoms.set_charges(charges)
info = dict(celldisp=celldisp)
if forces != None:
info['forces'] = forces
atoms.info = info
images.append(atoms)
return images[index]