def read_gromacs(filename):
""" From:
http://manual.gromacs.org/current/online/gro.html
C format
"%5d%5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"
python: starting from 0, including first excluding last
0:4 5:10 10:15 15:20 20:28 28:36 36:44 44:52 52:60 60:68
Import gromacs geometry type files (.gro).
Reads atom positions,
velocities(if present) and
simulation cell (if present)
"""
from ase.data import chemical_symbols
from ase import units
atoms = Atoms()
filed = open(filename, 'r')
lines = filed.readlines()
filed.close()
positions = []
gromacs_velocities = []
symbols = []
gromacs_residuenames = []
gromacs_atomtypes = []
for line in (lines[2:-1]):
#print line[0:5]+':'+line[5:11]+':'+line[11:15]+':'+line[15:20]
inp = line.split()
floatvect = float(line[20:28]) * 10.0, \
float(line[28:36]) * 10.0, \
float(line[36:44]) * 10.0
positions.append(floatvect)
try:
#velocities from nm/ps to ase units
floatvect = \
float(line[44:52]) * units.nm / (1000.0 * units.fs), \
float(line[52:60]) * units.nm / (1000.0 * units.fs), \
float(line[60:68]) * units.nm / (1000.0 * units.fs)
except:
floatvect = 0.0, 0.0, 0.0
gromacs_velocities.append(floatvect)
symbols.append(inp[1][0:2])
gromacs_residuenames.append(inp[0])
gromacs_atomtypes.append(inp[1])
line = lines[-1]
symbols_ok = []
for isymbol in symbols:
if isymbol in chemical_symbols:
#ok atom name
symbols_ok.append(isymbol)
else:
#not ok atom name
symbols_ok.append(isymbol[0])
atoms = Atoms(symbols_ok, positions)
atoms.set_velocities(gromacs_velocities)
if not atoms.has('residuenames'):
atoms.new_array('residuenames', gromacs_residuenames, str)
atoms.set_array('residuenames', gromacs_residuenames, str)
if not atoms.has('atomtypes'):
atoms.new_array('atomtypes', gromacs_atomtypes, str)
atoms.set_array('atomtypes', gromacs_atomtypes, str)
try:
line = lines[-1]
inp = line.split()
floatvect0 = \
float(inp[0]) * 10.0, \
float(inp[1]) * 10.0, \
float(inp[2]) * 10.0
try:
floatvect1 = \
float(inp[3]) * 10.0, \
float(inp[4]) * 10.0, \
float(inp[5]) * 10.0
floatvect2 = \
float(inp[6]) * 10.0, \
float(inp[7]) * 10.0, \
float(inp[8]) * 10.0
mycell = []
#gromacs manual (manual.gromacs.org/online/gro.html) says:
#v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
#
#v1(x) v2(y) v3(z) fv0[0 1 2] v1(x) v2(x) v3(x)
#v1(y) v1(z) v2(x) fv1[0 1 2] v1(y) v2(y) v3(y)
#v2(z) v3(x) v3(y) fv2[0 1 2] v1(z) v2(z) v3(z)
mycell += [[floatvect0[0], floatvect1[2], floatvect2[1]]]
mycell += [[floatvect1[0], floatvect0[1], floatvect2[2]]]
mycell += [[floatvect1[1], floatvect2[0], floatvect0[2]]]
atoms.set_cell(mycell)
atoms.set_pbc(True)
except:
mycell = []
#gromacs manual (manual.gromacs.org/online/gro.html) says:
#v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
mycell += [[floatvect0[0], 0.0, 0.0]]
mycell += [[0.0, floatvect0[1], 0.0]]
mycell += [[0.0, 0.0, floatvect0[2]]]
atoms.set_cell(floatvect0)
atoms.set_pbc(True)
except:
atoms.set_pbc(False)
return atoms
def read_gromacs(filename):
""" From:
http://manual.gromacs.org/current/online/gro.html
C format
"%5d%5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"
python: starting from 0, including first excluding last
0:4 5:10 10:15 15:20 20:28 28:36 36:44 44:52 52:60 60:68
Import gromacs geometry type files (.gro).
Reads atom positions,
velocities(if present) and
simulation cell (if present)
"""
from ase.data import chemical_symbols
from ase import units
atoms = Atoms()
filed = open(filename, "r")
lines = filed.readlines()
filed.close()
positions = []
gromacs_velocities = []
symbols = []
gromacs_residuenames = []
gromacs_atomtypes = []
for line in lines[2:-1]:
# print line[0:5]+':'+line[5:11]+':'+line[11:15]+':'+line[15:20]
inp = line.split()
floatvect = float(line[20:28]) * 10.0, float(line[28:36]) * 10.0, float(line[36:44]) * 10.0
positions.append(floatvect)
try:
# velocities from nm/ps to ase units
floatvect = (
float(line[44:52]) * units.nm / (1000.0 * units.fs),
float(line[52:60]) * units.nm / (1000.0 * units.fs),
float(line[60:68]) * units.nm / (1000.0 * units.fs),
)
except:
floatvect = 0.0, 0.0, 0.0
gromacs_velocities.append(floatvect)
symbols.append(inp[1][0:2])
gromacs_residuenames.append(inp[0])
gromacs_atomtypes.append(inp[1])
line = lines[-1]
symbols_ok = []
for isymbol in symbols:
if isymbol in chemical_symbols:
# ok atom name
symbols_ok.append(isymbol)
else:
# not ok atom name
symbols_ok.append(isymbol[0])
atoms = Atoms(symbols_ok, positions)
atoms.set_velocities(gromacs_velocities)
if not atoms.has("residuenames"):
atoms.new_array("residuenames", gromacs_residuenames, str)
atoms.set_array("residuenames", gromacs_residuenames, str)
if not atoms.has("atomtypes"):
atoms.new_array("atomtypes", gromacs_atomtypes, str)
atoms.set_array("atomtypes", gromacs_atomtypes, str)
try:
line = lines[-1]
inp = line.split()
floatvect0 = float(inp[0]) * 10.0, float(inp[1]) * 10.0, float(inp[2]) * 10.0
try:
floatvect1 = float(inp[3]) * 10.0, float(inp[4]) * 10.0, float(inp[5]) * 10.0
floatvect2 = float(inp[6]) * 10.0, float(inp[7]) * 10.0, float(inp[8]) * 10.0
mycell = []
# gromacs manual (manual.gromacs.org/online/gro.html) says:
# v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
#
# v1(x) v2(y) v3(z) fv0[0 1 2] v1(x) v2(x) v3(x)
# v1(y) v1(z) v2(x) fv1[0 1 2] v1(y) v2(y) v3(y)
# v2(z) v3(x) v3(y) fv2[0 1 2] v1(z) v2(z) v3(z)
mycell += [[floatvect0[0], floatvect1[2], floatvect2[1]]]
mycell += [[floatvect1[0], floatvect0[1], floatvect2[2]]]
mycell += [[floatvect1[1], floatvect2[0], floatvect0[2]]]
atoms.set_cell(mycell)
atoms.set_pbc(True)
print("9N")
except:
mycell = []
# gromacs manual (manual.gromacs.org/online/gro.html) says:
# v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
mycell += [[floatvect0[0], 0.0, 0.0]]
mycell += [[0.0, floatvect0[1], 0.0]]
mycell += [[0.0, 0.0, floatvect0[2]]]
atoms.set_cell(floatvect0)
atoms.set_pbc(True)
except:
atoms.set_pbc(False)
return atoms
def read_gromacs(filename):
""" From:
http://manual.gromacs.org/current/online/gro.html
C format
"%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"
python: starting from 0, including first excluding last
0:4 5:10 10:15 15:20 20:28 28:36 36:44 44:52 52:60 60:68
Import gromacs geometry type files (.gro).
Reads atom positions,
velocities(if present) and
simulation cell (if present)
"""
atoms = Atoms()
filed = open(filename, 'r')
lines = filed.readlines()
filed.close()
positions = []
gromacs_velocities = []
symbols = []
tags = []
gromacs_residuenumbers = []
gromacs_residuenames = []
gromacs_atomtypes = []
sym2tag = {}
tag = 0
for line in (lines[2:-1]):
# print(line[0:5]+':'+line[5:11]+':'+line[11:15]+':'+line[15:20])
# it is not a good idea to use the split method with gromacs input
# since the fields are defined by a fixed column number. Therefore,
# they may not be space between the fields
# inp = line.split()
floatvect = float(line[20:28]) * 10.0, \
float(line[28:36]) * 10.0, \
float(line[36:44]) * 10.0
positions.append(floatvect)
# read velocities
velocities = np.array([0.0, 0.0, 0.0])
vx = line[44:52].strip()
vy = line[52:60].strip()
vz = line[60:68].strip()
for iv, vxyz in enumerate([vx, vy, vz]):
if len(vxyz) > 0:
try:
velocities[iv] = float(vxyz)
except ValueError:
raise ValueError("can not convert velocity to float")
else:
velocities = None
if velocities is not None:
# velocities from nm/ps to ase units
velocities *= units.nm / (1000.0 * units.fs)
gromacs_velocities.append(velocities)
gromacs_residuenumbers.append(int(line[0:5]))
gromacs_residuenames.append(line[5:11].strip())
symbol_read = line[11:16].strip()[0:2]
if symbol_read not in sym2tag.keys():
sym2tag[symbol_read] = tag
tag += 1
tags.append(sym2tag[symbol_read])
if symbol_read in atomic_numbers:
symbols.append(symbol_read)
elif symbol_read[0] in atomic_numbers:
symbols.append(symbol_read[0])
elif symbol_read[-1] in atomic_numbers:
symbols.append(symbol_read[-1])
else:
# not an atomic symbol
# if we can not determine the symbol, we use
# the dummy symbol X
symbols.append("X")
gromacs_atomtypes.append(line[11:16].strip())
line = lines[-1]
atoms = Atoms(symbols, positions, tags=tags)
if len(gromacs_velocities) == len(atoms):
atoms.set_velocities(gromacs_velocities)
elif len(gromacs_velocities) != 0:
raise ValueError("Some atoms velocities were not specified!")
if not atoms.has('residuenumbers'):
atoms.new_array('residuenumbers', gromacs_residuenumbers, int)
atoms.set_array('residuenumbers', gromacs_residuenumbers, int)
if not atoms.has('residuenames'):
atoms.new_array('residuenames', gromacs_residuenames, str)
atoms.set_array('residuenames', gromacs_residuenames, str)
if not atoms.has('atomtypes'):
atoms.new_array('atomtypes', gromacs_atomtypes, str)
atoms.set_array('atomtypes', gromacs_atomtypes, str)
# determine PBC and unit cell
atoms.pbc = False
inp = lines[-1].split()
try:
grocell = list(map(float, inp))
except ValueError:
return atoms
if len(grocell) < 3:
return atoms
cell = np.diag(grocell[:3])
if len(grocell) >= 9:
cell.flat[[1, 2, 3, 5, 6, 7]] = grocell[3:9]
atoms.cell = cell * 10.
atoms.pbc = True
return atoms
def __init__(self, geometry=None, **kwargs) -> None:
if geometry == None:
atoms = Atoms(**kwargs)
elif type(geometry) == ase.atoms.Atoms:
atoms = geometry.copy()
elif Path(geometry).is_file():
if str(Path(geometry).parts[-1]) == "geometry.in.next_step":
atoms = ase.io.read(geometry, format="aims")
else:
try:
atoms = ase.io.read(geometry)
except Exception as excpt:
logger.error(str(excpt))
raise Exception(
"ASE was not able to recognize the file format, e.g., a non-standard cif-format."
)
elif Path(geometry).is_dir():
raise Exception(
"You specified a directory as input. The geometry must be a file."
)
else:
atoms = None
assert type(atoms) == ase.atoms.Atoms, "Atoms not read correctly."
# Get data from another Atoms object:
numbers = atoms.get_atomic_numbers()
positions = atoms.get_positions()
cell = atoms.get_cell()
celldisp = atoms.get_celldisp()
pbc = atoms.get_pbc()
constraint = [c.copy() for c in atoms.constraints]
masses = atoms.get_masses()
magmoms = None
charges = None
momenta = None
if atoms.has("initial_magmoms"):
magmoms = atoms.get_initial_magnetic_moments()
if atoms.has("initial_charges"):
charges = atoms.get_initial_charges()
if atoms.has("momenta"):
momenta = atoms.get_momenta()
self.arrays = {}
super().__init__(
numbers=numbers,
positions=positions,
cell=cell,
celldisp=celldisp,
pbc=pbc,
constraint=constraint,
masses=masses,
magmoms=magmoms,
charges=charges,
momenta=momenta,
)
self._is_1d = None
self._is_2d = None
self._is_3d = None
self._periodic_axes = None
self._check_lattice_vectors()
try:
self.sg = ase.spacegroup.get_spacegroup(self, symprec=1e-2)
except:
self.sg = ase.spacegroup.Spacegroup(1)
self.lattice = self.cell.get_bravais_lattice().crystal_family
def read_dlp4(f):
"""Read a DL_POLY_4 config/revcon file.
Typically used indirectly through read('filename', atoms, format='dlp4').
Can be unforgiven with custom chemical element names.
Please complain to [email protected] for bugs."""
line = f.readline()
line = f.readline().split()
levcfg = int(line[0])
imcon = int(line[1])
pbc = False
if imcon > 0:
pbc = True
cell = zeros((3, 3))
if pbc:
for j in range(3):
line = f.readline().split()
for i in range(3):
try:
cell[j, i] = float(line[i])
except ValueError:
raise RuntimeError("error reading cell")
symbols = []
positions = []
velocities = []
forces = []
line = f.readline()
while line:
symbol = line.split()[0]
if symbol in chemical_symbols:
symbols.append(symbol)
else:
ns = symbol[0]
if ns in chemical_symbols:
symbols.append(ns)
else:
ns = symbol[0:2]
if ns in chemical_symbols:
symbols.append(ns)
else:
symbols.append('X')
x, y, z = f.readline().split()[:3]
positions.append([float(x), float(y), float(z)])
if levcfg > 0:
vx, vy, vz = f.readline().split()[:3]
velocities.append([float(vx), float(vy), float(vz)])
if levcfg > 1:
fx, fy, fz = f.readline().split()[:3]
forces.append([float(fx), float(fy), float(fz)])
line = f.readline()
ats = Atoms(positions=positions,
symbols=symbols,
cell=cell,
pbc=pbc)
# XXX Fix this once atom labels are a thing.
if not ats.has('names'):
ats.new_array('names', symbols, str)
ats.set_array('names', symbols, str)
f.readline()
if levcfg > 0:
ats.set_velocities(velocities)
if levcfg > 1:
ats.set_calculator(SinglePointCalculator(ats, forces=forces))
return ats
def read_dlp4(f):
"""Read a DL_POLY_4 config/revcon file.
Typically used indirectly through read('filename', atoms, format='dlp4').
Can be unforgiven with custom chemical element names.
Please complain to [email protected] for bugs."""
line = f.readline()
line = f.readline().split()
levcfg = int(line[0])
imcon = int(line[1])
pbc = False
if imcon > 0:
pbc = True
cell = zeros((3, 3))
if pbc:
for j in range(3):
line = f.readline().split()
for i in range(3):
try:
cell[j, i] = float(line[i])
except ValueError:
raise RuntimeError("error reading cell")
symbols = []
positions = []
velocities = []
forces = []
line = f.readline()
while line:
symbol = line.split()[0]
if symbol in chemical_symbols:
symbols.append(symbol)
else:
ns = symbol[0]
if ns in chemical_symbols:
symbols.append(ns)
else:
ns = symbol[0:2]
if ns in chemical_symbols:
symbols.append(ns)
else:
symbols.append('X')
x, y, z = f.readline().split()[:3]
positions.append([float(x), float(y), float(z)])
if levcfg > 0:
vx, vy, vz = f.readline().split()[:3]
velocities.append([float(vx), float(vy), float(vz)])
if levcfg > 1:
fx, fy, fz = f.readline().split()[:3]
forces.append([float(fx), float(fy), float(fz)])
line = f.readline()
ats = Atoms(positions=positions, symbols=symbols, cell=cell, pbc=pbc)
# XXX Fix this once atom labels are a thing.
if not ats.has('names'):
ats.new_array('names', symbols, str)
ats.set_array('names', symbols, str)
f.readline()
if levcfg > 0:
ats.set_velocities(velocities)
if levcfg > 1:
ats.set_calculator(SinglePointCalculator(ats, forces=forces))
return ats
def read_gromacs(filename):
""" From:
http://manual.gromacs.org/current/online/gro.html
C format
"%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"
python: starting from 0, including first excluding last
0:4 5:10 10:15 15:20 20:28 28:36 36:44 44:52 52:60 60:68
Import gromacs geometry type files (.gro).
Reads atom positions,
velocities(if present) and
simulation cell (if present)
"""
from ase.data import atomic_numbers
from ase import units
atoms = Atoms()
filed = open(filename, 'r')
lines = filed.readlines()
filed.close()
positions = []
gromacs_velocities = []
symbols = []
tags = []
gromacs_residuenumbers = []
gromacs_residuenames = []
gromacs_atomtypes = []
sym2tag = {}
tag = 0
for line in (lines[2:-1]):
#print line[0:5]+':'+line[5:11]+':'+line[11:15]+':'+line[15:20]
# it is not a good idea to use the split method with gromacs input
# since the fields are defined by a fixed column number. Therefore,
# they may not be space between the fields
#inp = line.split()
floatvect = float(line[20:28]) * 10.0, \
float(line[28:36]) * 10.0, \
float(line[36:44]) * 10.0
positions.append(floatvect)
# read velocities
velocities = np.array([0.0, 0.0, 0.0])
vx = line[44:52].strip()
vy = line[52:60].strip()
vz = line[60:68].strip()
for iv, vxyz in enumerate([vx, vy, vz]):
if len(vxyz) > 0:
try:
velocities[iv] = float(vxyz)
except ValueError:
raise ValueError("can not convert velocity to float")
else:
velocities = None
if velocities is not None:
# velocities from nm/ps to ase units
velocities *= units.nm / (1000.0 * units.fs)
gromacs_velocities.append(velocities)
gromacs_residuenumbers.append(int(line[0:5]))
gromacs_residuenames.append(line[5:11].strip())
symbol_read = line[11:16].strip()[0:2]
if symbol_read not in sym2tag.keys():
sym2tag[symbol_read] = tag
tag += 1
tags.append(sym2tag[symbol_read])
if symbol_read in atomic_numbers:
symbols.append(symbol_read)
elif symbol_read[0] in atomic_numbers:
symbols.append(symbol_read[0])
elif symbol_read[-1] in atomic_numbers:
symbols.append(symbol_read[-1])
else:
# not an atomic symbol
# if we can not determine the symbol, we use
# the dummy symbol X
symbols.append("X")
gromacs_atomtypes.append(line[11:16].strip())
line = lines[-1]
atoms = Atoms(symbols, positions, tags=tags)
if len(gromacs_velocities) == len(atoms):
atoms.set_velocities(gromacs_velocities)
elif len(gromacs_velocities) != 0:
raise ValueError("Some atoms velocities were not specified!")
if not atoms.has('residuenumbers'):
atoms.new_array('residuenumbers', gromacs_residuenumbers, int)
atoms.set_array('residuenumbers', gromacs_residuenumbers, int)
if not atoms.has('residuenames'):
atoms.new_array('residuenames', gromacs_residuenames, str)
atoms.set_array('residuenames', gromacs_residuenames, str)
if not atoms.has('atomtypes'):
atoms.new_array('atomtypes', gromacs_atomtypes, str)
atoms.set_array('atomtypes', gromacs_atomtypes, str)
try:
line = lines[-1]
inp = line.split()
floatvect0 = \
float(inp[0]) * 10.0, \
float(inp[1]) * 10.0, \
float(inp[2]) * 10.0
try:
floatvect1 = \
float(inp[3]) * 10.0, \
float(inp[4]) * 10.0, \
float(inp[5]) * 10.0
floatvect2 = \
float(inp[6]) * 10.0, \
float(inp[7]) * 10.0, \
float(inp[8]) * 10.0
mycell = []
#gromacs manual (manual.gromacs.org/online/gro.html) says:
#v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
#
#v1(x) v2(y) v3(z) fv0[0 1 2] v1(x) v2(x) v3(x)
#v1(y) v1(z) v2(x) fv1[0 1 2] v1(y) v2(y) v3(y)
#v2(z) v3(x) v3(y) fv2[0 1 2] v1(z) v2(z) v3(z)
mycell += [[floatvect0[0], floatvect1[2], floatvect2[1]]]
mycell += [[floatvect1[0], floatvect0[1], floatvect2[2]]]
mycell += [[floatvect1[1], floatvect2[0], floatvect0[2]]]
atoms.set_cell(mycell)
atoms.set_pbc(True)
except:
mycell = []
#gromacs manual (manual.gromacs.org/online/gro.html) says:
#v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
mycell += [[floatvect0[0], 0.0, 0.0]]
mycell += [[0.0, floatvect0[1], 0.0]]
mycell += [[0.0, 0.0, floatvect0[2]]]
atoms.set_cell(floatvect0)
atoms.set_pbc(True)
except:
atoms.set_pbc(False)
return atoms
