def test():
at = ase.io.read(input, format="lammps-data", units="metal")
expected_output = [
'8',
'Lattice="102.3776 0.0 0.0 0.0 102.3776 0.0 0.0 0.0 102.3776" Properties=species:S:1:pos:R:3:bonds:S:1:masses:R:1:mol-id:I:1:Z:I:1:angles:S:1:momenta:R:3:type:I:1:id:I:1:travel:I:3 pbc="T T T"',
'H -7.06540129 -0.47737244 -51.10245267 1(1) 56.00000001 1 1 _ -0.00730459 -0.00103203 0.00505674 1 1 2 -1 6',
'H -8.12378444 -1.33406959 47.65830228 2(1) 56.00000001 1 1 0-2(1) 0.00439485 -0.00032011 0.00778011 1 2 2 -1 5',
'H -12.09052522 -3.23153540 47.36343710 3(1) 56.00000001 1 1 1-3(1) -0.00200271 0.00070515 0.00555628 1 3 2 -1 5',
'H -8.32722450 -4.84131620 45.60905541 _ 56.00000001 1 1 _ 0.00662811 -0.00000681 0.00498875 1 4 2 -1 5',
'H -5.38796182 49.52463522 30.05486271 5(1) 56.00000001 2 1 _ 0.00624468 -0.00952675 0.00127261 1 5 6 -7 -2',
'H -8.49500759 -49.36329713 32.58892582 6(1) 56.00000001 2 1 4-6(1) 0.00213880 0.00803380 0.00415973 1 6 6 -6 -2',
'H -9.75442821 49.86975598 36.36228789 7(1) 56.00000001 2 1 5-7(1) 0.00307596 -0.00467567 0.01149316 1 7 6 -7 -2',
'H -5.57124378 47.66022553 38.84723587 _ 56.00000001 2 1 _ 0.00428003 0.00338636 0.00417005 1 8 6 -7 -2',
''
]
buf = StringIO()
ase.io.write(buf,
at,
format="extxyz",
columns=[
"symbols", "positions", "bonds", "masses", "mol-id",
"numbers", "angles", "momenta", "type", "id", "travel"
],
write_info=False)
lines = [line.strip() for line in buf.getvalue().split("\n")]
assert lines == expected_output
def test_lammpsdata_read(datadir):
import ase.io
from ase.utils import StringIO
lammps_data_path = datadir / 'lammpsdata_input.data'
lammps_data = ase.io.read(lammps_data_path, format="lammps-data",
units="metal")
expected_output_path = datadir / 'lammpsdata_expected_output.xyz'
with open(expected_output_path) as f:
expected_output = f.read().splitlines()
buf = StringIO()
ase.io.write(buf, lammps_data, format="extxyz",
columns=["symbols",
"positions",
"bonds",
"masses",
"mol-id",
"numbers",
"angles",
"momenta",
"type",
"id",
"travel"],
write_info=False)
lines = [line.strip() for line in buf.getvalue().split("\n")]
assert lines == expected_output
def read_nwchem_output(filename):
"""Method to read geometry from a nwchem output."""
f = filename
if isinstance(filename, basestring):
f = open(filename)
lines = f.readlines()
i = 0
while i < len(lines):
if lines[i].find('XYZ format geometry') >= 0:
natoms = int(lines[i + 2].split()[0])
string = ''
for j in range(2, natoms + 4):
xyzstring = lines[i + j]
symbol = xyzstring.split()[0].strip()
# replace bq ghost with X: MDTMP can we do better?
if symbol.startswith('bq'):
xyzstring = xyzstring.replace(symbol, 'X')
string += xyzstring
atoms = read(StringIO(string), format='xyz')
i += natoms + 4
else:
i += 1
if isinstance(filename, basestring):
f.close()
return atoms
def read_nwchem(filename):
"""Method to read geometry from an NWChem input file."""
f = filename
if isinstance(filename, basestring):
f = open(filename)
lines = f.readlines()
# Find geometry region of input file.
stopline = 0
for index, line in enumerate(lines):
if line.startswith('geometry'):
startline = index + 1
stopline = -1
elif (line.startswith('end') and stopline == -1):
stopline = index
# Format and send to read_xyz.
xyz_text = '%i\n' % (stopline - startline)
xyz_text += ' geometry\n'
for line in lines[startline:stopline]:
xyz_text += line
atoms = read(StringIO(xyz_text), format='xyz')
atoms.set_cell((0., 0., 0.)) # no unit cell defined
if type(filename) == str:
f.close()
return atoms
def test_lammpsdata_write(datadir):
import ase.io
from ase.utils import StringIO
lammps_data_path = datadir / 'lammpsdata_input.data'
lammps_data = ase.io.read(lammps_data_path,
format="lammps-data",
units="metal")
expected_output_path = datadir / 'lammpsdata_expected_output.data'
with open(expected_output_path) as f:
expected_output = f.read().splitlines()
buf = StringIO()
ase.io.write(buf, lammps_data, format="lammps-data", atom_style="full")
lines = [line.strip() for line in buf.getvalue().split("\n")]
assert lines == expected_output
def __str__(self):
# Write PAW setup information in order of appearance:
ids = set()
s = ''
for id in self.id_a:
if id in ids:
continue
ids.add(id)
setup = self.setups[id]
output = StringIO()
setup.print_info(functools.partial(print, file=output))
txt = output.getvalue()
basis_descr = setup.get_basis_description()
basis_descr = basis_descr.replace('\n ', '\n ')
s += txt + ' ' + basis_descr + '\n\n'
s += 'Reference energy: %.6f\n' % (self.Eref * units.Hartree)
return s
input = StringIO(
"""LAMMPS data file via write_data, version 29 Mar 2019, timestep = 1000000
8 atoms
1 atom types
6 bonds
1 bond types
4 angles
1 angle types
-5.1188800000000001e+01 5.1188800000000001e+01 xlo xhi
-5.1188800000000001e+01 5.1188800000000001e+01 ylo yhi
-5.1188800000000001e+01 5.1188800000000001e+01 zlo zhi
Masses
1 56
Atoms
1 1 1 0.0 -7.0654012878945753e+00 -4.7737244253442213e-01 -5.1102452666801824e+01 2 -1 6
2 1 1 0.0 -8.1237844371679362e+00 -1.3340695922796841e+00 4.7658302278206179e+01 2 -1 5
3 1 1 0.0 -1.2090525219882498e+01 -3.2315354021627760e+00 4.7363437099502839e+01 2 -1 5
4 1 1 0.0 -8.3272244953257601e+00 -4.8413162043515321e+00 4.5609055410298623e+01 2 -1 5
5 2 1 0.0 -5.3879618209198750e+00 4.9524635221072280e+01 3.0054862714858366e+01 6 -7 -2
6 2 1 0.0 -8.4950075933508273e+00 -4.9363297129348325e+01 3.2588925816534982e+01 6 -6 -2
7 2 1 0.0 -9.7544282093133940e+00 4.9869755980935565e+01 3.6362287886934432e+01 6 -7 -2
8 2 1 0.0 -5.5712437770663756e+00 4.7660225526197003e+01 3.8847235874270240e+01 6 -7 -2
Velocities
1 -1.2812627962466232e-02 -1.8102422526771818e-03 8.8697845357364469e-03
2 7.7087896348612683e-03 -5.6149199730983867e-04 1.3646724560472424e-02
3 -3.5128553734623657e-03 1.2368758037550581e-03 9.7460093657088121e-03
4 1.1626059392751346e-02 -1.1942908859710665e-05 8.7505240354339674e-03
5 1.0953500823880464e-02 -1.6710422557096375e-02 2.2322216388444985e-03
6 3.7515599452757294e-03 1.4091708517087744e-02 7.2963916249300454e-03
7 5.3953961772651359e-03 -8.2013715102925017e-03 2.0159609509813853e-02
8 7.5074008407567160e-03 5.9398495239242483e-03 7.3144909044607909e-03
Bonds
1 1 1 2
2 1 2 3
3 1 3 4
4 1 5 6
5 1 6 7
6 1 7 8
Angles
1 1 1 2 3
2 1 2 3 4
3 1 5 6 7
4 1 6 7 8
""")
def test(self):
input = StringIO(
"""LAMMPS data file via write_data, version 29 Mar 2019, timestep = 1000000
8 atoms
1 atom types
6 bonds
1 bond types
4 angles
1 angle types
-5.1188800000000001e+01 5.1188800000000001e+01 xlo xhi
-5.1188800000000001e+01 5.1188800000000001e+01 ylo yhi
-5.1188800000000001e+01 5.1188800000000001e+01 zlo zhi
Masses
1 56
Atoms
1 1 1 0.0 -7.0654012878945753e+00 -4.7737244253442213e-01 -5.1102452666801824e+01 2 -1 6
2 1 1 0.0 -8.1237844371679362e+00 -1.3340695922796841e+00 4.7658302278206179e+01 2 -1 5
3 1 1 0.0 -1.2090525219882498e+01 -3.2315354021627760e+00 4.7363437099502839e+01 2 -1 5
4 1 1 0.0 -8.3272244953257601e+00 -4.8413162043515321e+00 4.5609055410298623e+01 2 -1 5
5 2 1 0.0 -5.3879618209198750e+00 4.9524635221072280e+01 3.0054862714858366e+01 6 -7 -2
6 2 1 0.0 -8.4950075933508273e+00 -4.9363297129348325e+01 3.2588925816534982e+01 6 -6 -2
7 2 1 0.0 -9.7544282093133940e+00 4.9869755980935565e+01 3.6362287886934432e+01 6 -7 -2
8 2 1 0.0 -5.5712437770663756e+00 4.7660225526197003e+01 3.8847235874270240e+01 6 -7 -2
Velocities
1 -1.2812627962466232e-02 -1.8102422526771818e-03 8.8697845357364469e-03
2 7.7087896348612683e-03 -5.6149199730983867e-04 1.3646724560472424e-02
3 -3.5128553734623657e-03 1.2368758037550581e-03 9.7460093657088121e-03
4 1.1626059392751346e-02 -1.1942908859710665e-05 8.7505240354339674e-03
5 1.0953500823880464e-02 -1.6710422557096375e-02 2.2322216388444985e-03
6 3.7515599452757294e-03 1.4091708517087744e-02 7.2963916249300454e-03
7 5.3953961772651359e-03 -8.2013715102925017e-03 2.0159609509813853e-02
8 7.5074008407567160e-03 5.9398495239242483e-03 7.3144909044607909e-03
Bonds
1 1 1 2
2 1 2 3
3 1 3 4
4 1 5 6
5 1 6 7
6 1 7 8
Angles
1 1 1 2 3
2 1 2 3 4
3 1 5 6 7
4 1 6 7 8
""")
at = ase.io.read(input, format="lammps-data", units="metal")
expected_output = [
'8',
'Lattice="102.3776 0.0 0.0 0.0 102.3776 0.0 0.0 0.0 102.3776" Properties=species:S:1:pos:R:3:bonds:S:1:masses:R:1:mol-id:I:1:Z:I:1:angles:S:1:momenta:R:3:type:I:1:id:I:1:travel:I:3 pbc="T T T"',
'H -7.06540129 -0.47737244 -51.10245267 1(1) 56.00000001 1 1 _ -0.00730459 -0.00103203 0.00505674 1 1 2 -1 6',
'H -8.12378444 -1.33406959 47.65830228 2(1) 56.00000001 1 1 0-2(1) 0.00439485 -0.00032011 0.00778011 1 2 2 -1 5',
'H -12.09052522 -3.23153540 47.36343710 3(1) 56.00000001 1 1 1-3(1) -0.00200271 0.00070515 0.00555628 1 3 2 -1 5',
'H -8.32722450 -4.84131620 45.60905541 _ 56.00000001 1 1 _ 0.00662811 -0.00000681 0.00498875 1 4 2 -1 5',
'H -5.38796182 49.52463522 30.05486271 5(1) 56.00000001 2 1 _ 0.00624468 -0.00952675 0.00127261 1 5 6 -7 -2',
'H -8.49500759 -49.36329713 32.58892582 6(1) 56.00000001 2 1 4-6(1) 0.00213880 0.00803380 0.00415973 1 6 6 -6 -2',
'H -9.75442821 49.86975598 36.36228789 7(1) 56.00000001 2 1 5-7(1) 0.00307596 -0.00467567 0.01149316 1 7 6 -7 -2',
'H -5.57124378 47.66022553 38.84723587 _ 56.00000001 2 1 _ 0.00428003 0.00338636 0.00417005 1 8 6 -7 -2',
''
]
buf = StringIO()
ase.io.write(buf,
at,
format="extxyz",
columns=[
"symbols", "positions", "bonds", "masses", "mol-id",
"numbers", "angles", "momenta", "type", "id", "travel"
],
write_info=False)
lines = [line.strip() for line in buf.getvalue().split("\n")]
self.assertEqual(lines, expected_output)
5 1 6 7
6 1 7 8
Angles
1 1 1 2 3
2 1 2 3 4
3 1 5 6 7
4 1 6 7 8
""")
at = ase.io.read(input, format="lammps-data")
expected_output = ['8', 'Lattice="102.3776 0.0 0.0 0.0 102.3776 0.0 0.0 0.0 102.3776" Properties=species:S:1:pos:R:3:bonds:S:1:masses:R:1:mol-id:I:1:Z:I:1:angles:S:1:momenta:R:3:type:I:1:id:I:1:travel:I:3 pbc="T T T"', 'H -7.06540129 -0.47737244 -51.10245267 1(1) 56.00000000 1 1 _ -0.71750717 -0.10137357 0.49670793 1 1 2 -1 6', 'H -8.12378444 -1.33406959 47.65830228 2(1) 56.00000000 1 1 0-2(1) 0.43169222 -0.03144355 0.76421658 1 2 2 -1 5', 'H -12.09052522 -3.23153540 47.36343710 3(1) 56.00000000 1 1 1-3(1) -0.19671990 0.06926505 0.54577652 1 3 2 -1 5', 'H -8.32722450 -4.84131620 45.60905541 _ 56.00000000 1 1 _ 0.65105933 -0.00066880 0.49002935 1 4 2 -1 5', 'H -5.38796182 49.52463522 30.05486271 5(1) 56.00000000 2 1 _ 0.61339605 -0.93578366 0.12500441 1 5 6 -7 -2', 'H -8.49500759 -49.36329713 32.58892582 6(1) 56.00000000 2 1 4-6(1) 0.21008736 0.78913568 0.40859793 1 6 6 -6 -2', 'H -9.75442821 49.86975598 36.36228789 7(1) 56.00000000 2 1 5-7(1) 0.30214219 -0.45927680 1.12893813 1 7 6 -7 -2', 'H -5.57124378 47.66022553 38.84723587 _ 56.00000000 2 1 _ 0.42041445 0.33263157 0.40961149 1 8 6 -7 -2', '']
buf = StringIO()
ase.io.write(buf, at, format="extxyz",
columns=["symbols",
"positions",
"bonds",
"masses",
"mol-id",
"numbers",
"angles",
"momenta",
"type",
"id",
"travel"],
write_info=False)
lines = [line.strip() for line in buf.getvalue().split("\n")]
