def test_box(self, ethane):
import gsd
import gsd.hoomd
lengths = [2.0, 3.0, 4.0]
ethane.box = Box(lengths=[2.0, 3.0, 4.0])
ethane.save(filename="ethane.gsd", forcefield_name="oplsaa")
with gsd.hoomd.open("ethane.gsd", mode="rb") as f:
frame = f[0]
box_from_gsd = frame.configuration.box.astype(float)
(lx, ly, lz) = ethane.box.lengths
lx *= 10
ly *= 10
lz *= 10
assert np.array_equal(box_from_gsd[:3], [lx, ly, lz])
assert not np.any(box_from_gsd[3:])
ethane.periodicity = (True, True, True)
ethane.save(filename="ethane-periodicity.gsd",
forcefield_name="oplsaa")
with gsd.hoomd.open("ethane-periodicity.gsd", mode="rb") as f:
frame = f[0]
box_from_gsd_periodic = frame.configuration.box.astype(float)
assert np.array_equal(box_from_gsd, box_from_gsd_periodic)
box = Box(lengths=np.array([2.0, 2.0, 2.0]), angles=[92, 104, 119])
# check that providing a box to save overwrites compound.box
ethane.save(filename="triclinic-box.gsd",
forcefield_name="oplsaa",
box=box)
with gsd.hoomd.open("triclinic-box.gsd", mode="rb") as f:
frame = f[0]
lx, ly, lz, xy, xz, yz = frame.configuration.box
a = lx
b = np.sqrt(ly**2 + xy**2)
c = np.sqrt(lz**2 + xz**2 + yz**2)
assert np.isclose(np.cos(np.radians(92)),
(xy * xz + ly * yz) / (b * c))
assert np.isclose(np.cos(np.radians(104)), xz / c)
assert np.isclose(np.cos(np.radians(119)), xy / b)
def test_fill_region_box(self, h2o):
mybox = Box(lengths=[4, 4, 4], angles=[90.0, 90.0, 90.0])
filled = mb.fill_region(h2o,
n_compounds=50,
region=mybox,
bounds=[[0, 0, 0, 4, 4, 4]])
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
assert np.min(filled.xyz[:, 0]) >= 0
assert np.max(filled.xyz[:, 2]) <= 4
def test_fill_box_compound_ratio(self, h2o, ethane):
filled = mb.fill_box(
compound=[h2o, ethane],
density=800,
compound_ratio=[2, 1],
box=Box([2, 2, 2]),
)
n_ethane = len([c for c in filled.children if c.name == "Ethane"])
n_water = len([c for c in filled.children if c.name == "H2O"])
assert n_water / n_ethane == 2
def test_fill_region(self, h2o):
filled = mb.fill_region(
h2o,
n_compounds=50,
region=Box(lengths=[2, 3, 3], angles=[90.0, 90.0, 90.0]),
bounds=[[3, 2, 2, 5, 5, 5]],
)
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
assert np.min(filled.xyz[:, 0]) >= 3
assert np.min(filled.xyz[:, 1]) >= 2
assert np.min(filled.xyz[:, 2]) >= 2
assert np.max(filled.xyz[:, 0]) <= 5
assert np.max(filled.xyz[:, 1]) <= 5
assert np.max(filled.xyz[:, 2]) <= 5
def test_fill_region_multiple_bounds(self, ethane, h2o):
box1 = Box.from_mins_maxs_angles(mins=[2, 2, 2],
maxs=[4, 4, 4],
angles=[90.0, 90.0, 90.0])
box2 = mb.Box.from_mins_maxs_angles(mins=[4, 2, 2],
maxs=[6, 4, 4],
angles=[90.0, 90.0, 90.0])
filled = mb.fill_region(
compound=[ethane, h2o],
n_compounds=[2, 2],
region=[box1, box2],
bounds=[[2, 2, 2, 4, 4, 4], [4, 2, 2, 6, 4, 4]],
)
assert filled.n_particles == 2 * 8 + 2 * 3
assert filled.n_bonds == 2 * 7 + 2 * 2
assert np.max(filled.xyz[:16, 0]) < 4
assert np.min(filled.xyz[16:, 0]) > 4
def visualize(compound, show_bonds=True, show_ports=True, box=None,
verbose=False):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
if not box:
boundingbox = compound.boundingbox
if not any(boundingbox.lengths):
boundingbox.lengths = np.ones(3) / 10
longest_side = boundingbox.lengths.max()
center = (boundingbox.maxs + boundingbox.mins) / 2
mins = np.array([dim - longest_side/2 for dim in center])
maxs = np.array([dim + longest_side/2 for dim in center])
box = Box(mins=mins, maxs=maxs)
ax.set_xlim([box.mins[0] - 0.125, box.maxs[0] + 0.125])
ax.set_ylim([box.mins[1] - 0.125, box.maxs[1] + 0.125])
ax.set_zlim([box.mins[2] - 0.125, box.maxs[2] + 0.125])
volume = np.linalg.norm(box.lengths)
colors = {'C': 'cyan', 'H': 'white', 'O': 'red', 'Si': 'yellow',
'Unk': 'gray', 'OS': 'red', 'F': 'magenta'}
size = {'C': 1250/volume, 'H': 400/volume, 'O': 1300/volume,
'Si': 2000/volume, 'Unk': 1250/volume, 'OS': 1300/volume,
'F': 1000/volume}
n_particles = compound._n_particles(include_ports=show_ports)
for i, particle in enumerate(compound.particles(include_ports=show_ports)):
if verbose:
print('Rendering particle {} of {}'.format(i+1, n_particles))
pos = particle.pos
if particle.port_particle:
ax.scatter(pos[0], pos[1], pos[2], c='white', s=50/volume,
edgecolors='black')
else:
name = particle.name
name = ''.join([j for j in name if not j.isdigit()])
if name not in colors:
name = 'Unk'
ax.scatter(pos[0], pos[1], pos[2], c=colors[name],
s=size[name], edgecolors='black', alpha=0.8)
if show_bonds:
for bond in compound.bonds():
ax.plot(*np.stack((bond[0].pos, bond[1].pos), axis=1), color='black',
alpha=0.75, marker='o', markersize=1/volume, linewidth=1.0)
plt.show()
def test_units(self, ethane):
import gsd
import gsd.hoomd
ref_distance = 3.5
ref_energy = 0.066
ref_mass = 12.011
box = Box(lengths=[2.0, 3.0, 4.0], angles=[90.0, 90.0, 90.0])
ethane.save(
filename="ethane.gsd",
forcefield_name="oplsaa",
ref_distance=ref_distance,
ref_energy=ref_energy,
ref_mass=ref_mass,
box=box,
)
with gsd.hoomd.open("ethane.gsd", mode="rb") as f:
frame = f[0]
box_from_gsd = frame.configuration.box.astype(float)
assert np.array_equal(
np.round(box_from_gsd[:3], decimals=5),
np.round(np.asarray(box.lengths) * 10 / ref_distance, 5),
)
mass_dict = {"C": 12.011, "H": 1.008}
masses = frame.particles.mass.astype(float)
for mass, p in zip(masses, ethane.particles()):
assert round(mass, 3) == round(mass_dict[p.name] / ref_mass, 3)
charge_dict = {"C": -0.18, "H": 0.06}
charges = frame.particles.charge.astype(float)
e0 = 2.396452e-4
charge_factor = (4.0 * np.pi * e0 * ref_distance * ref_energy)**0.5
for charge, particle in zip(charges, ethane.particles()):
reduced_charge = charge_dict[particle.name] / charge_factor
assert round(charge, 3) == round(reduced_charge, 3)
positions = frame.particles.position.astype(float)
shift = positions[0] - (ethane[0].pos * 10 / ref_distance)
shifted_xyz = (ethane.xyz * 10 / ref_distance) + shift
assert np.array_equal(np.round(positions, decimals=4),
np.round(shifted_xyz, decimals=4))
def test_write_temp_file(self, h2o):
cwd = os.getcwd(
) # Must keep track of the temp dir that pytest creates
filled = mb.fill_box(h2o,
n_compounds=10,
box=Box([4, 4, 4]),
temp_file="temp_file1.pdb")
region = mb.fill_region(
h2o,
10,
[[2, 2, 2, 4, 4, 4]],
temp_file="temp_file2.pdb",
bounds=[[2, 2, 2, 4, 4, 4]],
)
solvated = mb.solvate(filled,
h2o,
10,
box=[4, 4, 4],
temp_file="temp_file3.pdb")
assert os.path.isfile(os.path.join(cwd, "temp_file1.pdb"))
assert os.path.isfile(os.path.join(cwd, "temp_file2.pdb"))
assert os.path.isfile(os.path.join(cwd, "temp_file3.pdb"))
def _proto_to_mb(proto):
"""Given compound_pb2.Compound, create mb.Compound.
Parameters
----------
proto: compound_pb2.Compound()
"""
if proto.element.symbol == "":
elem = None
else:
elem = ele.element_from_symbol(proto.element.symbol)
lengths = [proto.periodicity.x, proto.periodicity.y, proto.periodicity.z]
if np.all(np.array(lengths) != 0):
box = Box(lengths)
else:
box = None
return Compound(
name=proto.name,
pos=[proto.pos.x, proto.pos.y, proto.pos.z],
charge=proto.charge,
box=box,
element=elem,
)
def write_lammpsdata(structure, filename, atom_style='full'):
"""Output a LAMMPS data file.
Outputs a LAMMPS data file in the 'full' atom style format. Assumes use
of 'real' units. See http://lammps.sandia.gov/doc/atom_style.html for
more information on atom styles.
Parameters
----------
structure : parmed.Structure
ParmEd structure object
filename : str
Path of the output file
atom_style: str
Defines the style of atoms to be saved in a LAMMPS data file. The following atom
styles are currently supported: 'full', 'atomic', 'charge', 'molecular'
see http://lammps.sandia.gov/doc/atom_style.html for more
information on atom styles.
Notes
-----
See http://lammps.sandia.gov/doc/2001/data_format.html for a full description
of the LAMMPS data format. Currently the following sections are supported (in
addition to the header): *Masses*, *Nonbond Coeffs*, *Bond Coeffs*, *Angle
Coeffs*, *Dihedral Coeffs*, *Atoms*, *Bonds*, *Angles*, *Dihedrals*
"""
if atom_style not in ['atomic', 'charge', 'molecular', 'full']:
raise ValueError('Atom style "{}" is invalid or is not currently supported'.format(atom_style))
xyz = np.array([[atom.xx,atom.xy,atom.xz] for atom in structure.atoms])
forcefield = True
if structure[0].type == '':
forcefield = False
box = Box(lengths=np.array([structure.box[0], structure.box[1], structure.box[2]]))
if forcefield:
types = [atom.type for atom in structure.atoms]
else:
types = [atom.name for atom in structure.atoms]
unique_types = list(set(types))
unique_types.sort(key=natural_sort)
charges = [atom.charge for atom in structure.atoms]
bonds = [[bond.atom1.idx+1, bond.atom2.idx+1] for bond in structure.bonds]
angles = [[angle.atom1.idx+1,
angle.atom2.idx+1,
angle.atom3.idx+1] for angle in structure.angles]
dihedrals = [[dihedral.atom1.idx+1,
dihedral.atom2.idx+1,
dihedral.atom3.idx+1,
dihedral.atom4.idx+1] for dihedral in structure.rb_torsions]
if bonds:
if len(structure.bond_types) == 0:
bond_types = np.ones(len(bonds),dtype=int)
else:
unique_bond_types = dict(enumerate(set([(round(bond.type.k,3),
round(bond.type.req,3)) for bond in structure.bonds])))
unique_bond_types = OrderedDict([(y,x+1) for x,y in unique_bond_types.items()])
bond_types = [unique_bond_types[(round(bond.type.k,3),
round(bond.type.req,3))] for bond in structure.bonds]
if angles:
unique_angle_types = dict(enumerate(set([(round(angle.type.k,3),
round(angle.type.theteq,3)) for angle in structure.angles])))
unique_angle_types = OrderedDict([(y,x+1) for x,y in unique_angle_types.items()])
angle_types = [unique_angle_types[(round(angle.type.k,3),
round(angle.type.theteq,3))] for angle in structure.angles]
if dihedrals:
unique_dihedral_types = dict(enumerate(set([(round(dihedral.type.c0,3),
round(dihedral.type.c1,3),
round(dihedral.type.c2,3),
round(dihedral.type.c3,3),
round(dihedral.type.c4,3),
round(dihedral.type.c5,3),
round(dihedral.type.scee,1),
round(dihedral.type.scnb,1)) for dihedral in structure.rb_torsions])))
unique_dihedral_types = OrderedDict([(y,x+1) for x,y in unique_dihedral_types.items()])
dihedral_types = [unique_dihedral_types[(round(dihedral.type.c0,3),
round(dihedral.type.c1,3),
round(dihedral.type.c2,3),
round(dihedral.type.c3,3),
round(dihedral.type.c4,3),
round(dihedral.type.c5,3),
round(dihedral.type.scee,1),
round(dihedral.type.scnb,1))] for dihedral in structure.rb_torsions]
with open(filename, 'w') as data:
data.write(filename+' - created by mBuild\n\n')
data.write('{:d} atoms\n'.format(len(structure.atoms)))
if atom_style in ['full', 'molecular']:
data.write('{:d} bonds\n'.format(len(bonds)))
data.write('{:d} angles\n'.format(len(angles)))
data.write('{:d} dihedrals\n\n'.format(len(dihedrals)))
data.write('{:d} atom types\n'.format(len(set(types))))
if atom_style in ['full', 'molecular']:
if bonds:
data.write('{:d} bond types\n'.format(len(set(bond_types))))
if angles:
data.write('{:d} angle types\n'.format(len(set(angle_types))))
if dihedrals:
data.write('{:d} dihedral types\n'.format(len(set(dihedral_types))))
data.write('\n')
# Box data
for i,dim in enumerate(['x','y','z']):
data.write('{0:.6f} {1:.6f} {2}lo {2}hi\n'.format(box.mins[i],box.maxs[i],dim))
# Mass data
masses = [atom.mass for atom in structure.atoms]
mass_dict = dict([(unique_types.index(atom_type)+1,mass) for atom_type,mass in zip(types,masses)])
data.write('\nMasses\n\n')
for atom_type,mass in mass_dict.items():
data.write('{:d}\t{:.6f}\t# {}\n'.format(atom_type,mass,unique_types[atom_type-1]))
if forcefield:
# Pair coefficients
epsilons = [atom.epsilon for atom in structure.atoms]
sigmas = [atom.sigma for atom in structure.atoms]
epsilon_dict = dict([(unique_types.index(atom_type)+1,epsilon) for atom_type,epsilon in zip(types,epsilons)])
sigma_dict = dict([(unique_types.index(atom_type)+1,sigma) for atom_type,sigma in zip(types,sigmas)])
data.write('\nPair Coeffs # lj\n\n')
for idx,epsilon in epsilon_dict.items():
data.write('{}\t{:.5f}\t{:.5f}\n'.format(idx,epsilon,sigma_dict[idx]))
# Bond coefficients
if bonds:
data.write('\nBond Coeffs # harmonic\n\n')
for params,idx in unique_bond_types.items():
data.write('{}\t{}\t{}\n'.format(idx,*params))
# Angle coefficients
if angles:
data.write('\nAngle Coeffs # harmonic\n\n')
for params,idx in unique_angle_types.items():
data.write('{}\t{}\t{:.5f}\n'.format(idx,*params))
# Dihedral coefficients
if dihedrals:
data.write('\nDihedral Coeffs # opls\n\n')
for params,idx in unique_dihedral_types.items():
opls_coeffs = RB_to_OPLS(params[0],
params[1],
params[2],
params[3],
params[4],
params[5])
data.write('{}\t{:.5f}\t{:.5f}\t{:.5f}\t{:.5f}\n'.format(idx,*opls_coeffs))
# Atom data
data.write('\nAtoms\n\n')
if atom_style == 'atomic':
atom_line = '{index:d}\t{type_index:d}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif atom_style == 'charge':
atom_line = '{index:d}\t{type_index:d}\t{charge:.6f}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif atom_style == 'molecular':
atom_line = '{index:d}\t{zero:d}\t{type_index:d}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif atom_style == 'full':
atom_line ='{index:d}\t{zero:d}\t{type_index:d}\t{charge:.6f}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
for i,coords in enumerate(xyz):
data.write(atom_line.format(
index=i+1,type_index=unique_types.index(types[i])+1,
zero=0,charge=charges[i],
x=coords[0],y=coords[1],z=coords[2]))
if atom_style in ['full', 'molecular']:
# Bond data
if bonds:
data.write('\nBonds\n\n')
for i,bond in enumerate(bonds):
data.write('{:d}\t{:d}\t{:d}\t{:d}\n'.format(
i+1,bond_types[i],bond[0],bond[1]))
# Angle data
if angles:
data.write('\nAngles\n\n')
for i,angle in enumerate(angles):
data.write('{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n'.format(
i+1,angle_types[i],angle[0],angle[1],angle[2]))
# Dihedral data
if dihedrals:
data.write('\nDihedrals\n\n')
for i,dihedral in enumerate(dihedrals):
data.write('{:d}\t{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n'.format(
i+1,dihedral_types[i],dihedral[0],
dihedral[1],dihedral[2],dihedral[3]))
def test_save_box(self, ethane):
box = Box(lengths=[2.0, 2.0, 2.0], angles=[90.0, 90.0, 90.0])
ethane.save(filename="ethane-box.gsd",
forcefield_name="oplsaa",
box=box)
def test_fill_box_density_n_compounds(self, h2o):
filled = mb.fill_box(h2o,
density=100,
box=Box([3.1042931, 3.1042931, 3.1042931]))
assert filled.n_particles == 300
def test_box_no_bound(self, ethane):
box1 = Box(lengths=[2, 2, 2], angles=[90.0, 90.0, 90.0])
mb.fill_region(compound=[ethane],
n_compounds=[2],
region=box1,
bounds=None)
def test_fill_box(self, h2o):
filled = mb.fill_box(h2o, n_compounds=50, box=Box([2, 2, 2]))
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
assert np.array_equal(filled.box.lengths, [2, 2, 2])
assert np.array_equal(filled.box.angles, (90, 90, 90))
def test_save_triclinic_box_(self, ethane):
box = Box(lengths=np.array([2.0, 2.0, 2.0]), angles=[60, 70, 80])
ethane.save(filename="triclinic-box.gsd",
forcefield_name="oplsaa",
box=box)
def write_lammpsdata(structure, filename, atom_style='full'):
"""Output a LAMMPS data file.
Outputs a LAMMPS data file in the 'full' atom style format. Assumes use
of 'real' units. See http://lammps.sandia.gov/doc/atom_style.html for
more information on atom styles.
Parameters
----------
structure : parmed.Structure
ParmEd structure object
filename : str
Path of the output file
atom_style: str
Defines the style of atoms to be saved in a LAMMPS data file. The following atom
styles are currently supported: 'full', 'atomic', 'charge', 'molecular'
see http://lammps.sandia.gov/doc/atom_style.html for more
information on atom styles.
Notes
-----
See http://lammps.sandia.gov/doc/2001/data_format.html for a full description
of the LAMMPS data format. Currently the following sections are supported (in
addition to the header): *Masses*, *Nonbond Coeffs*, *Bond Coeffs*, *Angle
Coeffs*, *Dihedral Coeffs*, *Atoms*, *Bonds*, *Angles*, *Dihedrals*
Some of this function has beed adopted from `mdtraj`'s support of the LAMMPSTRJ
trajectory format. See https://github.com/mdtraj/mdtraj/blob/master/mdtraj/formats/lammpstrj.py for details.
"""
if atom_style not in ['atomic', 'charge', 'molecular', 'full']:
raise ValueError('Atom style "{}" is invalid or is not currently supported'.format(atom_style))
xyz = np.array([[atom.xx,atom.xy,atom.xz] for atom in structure.atoms])
forcefield = True
if structure[0].type == '':
forcefield = False
# Internally use nm
box = Box(lengths=np.array([0.1 * val for val in structure.box[0:3]]),
angles=structure.box[3:6])
if forcefield:
types = [atom.type for atom in structure.atoms]
else:
types = [atom.name for atom in structure.atoms]
unique_types = list(set(types))
unique_types.sort(key=natural_sort)
charges = [atom.charge for atom in structure.atoms]
bonds = [[bond.atom1.idx+1, bond.atom2.idx+1] for bond in structure.bonds]
angles = [[angle.atom1.idx+1,
angle.atom2.idx+1,
angle.atom3.idx+1] for angle in structure.angles]
dihedrals = [[dihedral.atom1.idx+1,
dihedral.atom2.idx+1,
dihedral.atom3.idx+1,
dihedral.atom4.idx+1] for dihedral in structure.rb_torsions]
if bonds:
if len(structure.bond_types) == 0:
bond_types = np.ones(len(bonds),dtype=int)
else:
unique_bond_types = dict(enumerate(set([(round(bond.type.k,3),
round(bond.type.req,3)) for bond in structure.bonds])))
unique_bond_types = OrderedDict([(y,x+1) for x,y in unique_bond_types.items()])
bond_types = [unique_bond_types[(round(bond.type.k,3),
round(bond.type.req,3))] for bond in structure.bonds]
if angles:
unique_angle_types = dict(enumerate(set([(round(angle.type.k,3),
round(angle.type.theteq,3)) for angle in structure.angles])))
unique_angle_types = OrderedDict([(y,x+1) for x,y in unique_angle_types.items()])
angle_types = [unique_angle_types[(round(angle.type.k,3),
round(angle.type.theteq,3))] for angle in structure.angles]
if dihedrals:
unique_dihedral_types = dict(enumerate(set([(round(dihedral.type.c0,3),
round(dihedral.type.c1,3),
round(dihedral.type.c2,3),
round(dihedral.type.c3,3),
round(dihedral.type.c4,3),
round(dihedral.type.c5,3),
round(dihedral.type.scee,1),
round(dihedral.type.scnb,1)) for dihedral in structure.rb_torsions])))
unique_dihedral_types = OrderedDict([(y,x+1) for x,y in unique_dihedral_types.items()])
dihedral_types = [unique_dihedral_types[(round(dihedral.type.c0,3),
round(dihedral.type.c1,3),
round(dihedral.type.c2,3),
round(dihedral.type.c3,3),
round(dihedral.type.c4,3),
round(dihedral.type.c5,3),
round(dihedral.type.scee,1),
round(dihedral.type.scnb,1))] for dihedral in structure.rb_torsions]
with open(filename, 'w') as data:
data.write(filename+' - created by mBuild\n\n')
data.write('{:d} atoms\n'.format(len(structure.atoms)))
if atom_style in ['full', 'molecular']:
data.write('{:d} bonds\n'.format(len(bonds)))
data.write('{:d} angles\n'.format(len(angles)))
data.write('{:d} dihedrals\n\n'.format(len(dihedrals)))
data.write('{:d} atom types\n'.format(len(set(types))))
if atom_style in ['full', 'molecular']:
if bonds:
data.write('{:d} bond types\n'.format(len(set(bond_types))))
if angles:
data.write('{:d} angle types\n'.format(len(set(angle_types))))
if dihedrals:
data.write('{:d} dihedral types\n'.format(len(set(dihedral_types))))
data.write('\n')
# Box data
if np.allclose(box.angles, np.array([90, 90, 90])):
for i,dim in enumerate(['x','y','z']):
data.write('{0:.6f} {1:.6f} {2}lo {2}hi\n'.format(
10.0 * box.mins[i],
10.0 * box.maxs[i],
dim))
else:
a, b, c = 10.0 * box.lengths
alpha, beta, gamma = np.radians(box.angles)
lx = a
xy = b * np.cos(gamma)
xz = c * np.cos(beta)
ly = np.sqrt(b**2 - xy**2)
yz = (b*c*np.cos(alpha) - xy*xz) / ly
lz = np.sqrt(c**2 - xz**2 - yz**2)
xlo, ylo, zlo = 10.0 * box.mins
xhi = xlo + lx
yhi = ylo + ly
zhi = zlo + lz
xlo_bound = xlo + np.min([0.0, xy, xz, xy+xz])
xhi_bound = xhi + np.max([0.0, xy, xz, xy+xz])
ylo_bound = ylo + np.min([0.0, yz])
yhi_bound = yhi + np.max([0.0, yz])
zlo_bound = zlo
zhi_bound = zhi
data.write('{0} {1} {2}\n'.format(xlo_bound, xhi_bound, xy))
data.write('{0} {1} {2}\n'.format(ylo_bound, yhi_bound, xz))
data.write('{0} {1} {2}\n'.format(zlo_bound, zhi_bound, yz))
# Mass data
masses = [atom.mass for atom in structure.atoms]
mass_dict = dict([(unique_types.index(atom_type)+1,mass) for atom_type,mass in zip(types,masses)])
data.write('\nMasses\n\n')
for atom_type,mass in mass_dict.items():
data.write('{:d}\t{:.6f}\t# {}\n'.format(atom_type,mass,unique_types[atom_type-1]))
if forcefield:
# Pair coefficients
epsilons = [atom.epsilon for atom in structure.atoms]
sigmas = [atom.sigma for atom in structure.atoms]
epsilon_dict = dict([(unique_types.index(atom_type)+1,epsilon) for atom_type,epsilon in zip(types,epsilons)])
sigma_dict = dict([(unique_types.index(atom_type)+1,sigma) for atom_type,sigma in zip(types,sigmas)])
data.write('\nPair Coeffs # lj\n\n')
for idx,epsilon in epsilon_dict.items():
data.write('{}\t{:.5f}\t{:.5f}\n'.format(idx,epsilon,sigma_dict[idx]))
# Bond coefficients
if bonds:
data.write('\nBond Coeffs # harmonic\n\n')
for params,idx in unique_bond_types.items():
data.write('{}\t{}\t{}\n'.format(idx,*params))
# Angle coefficients
if angles:
data.write('\nAngle Coeffs # harmonic\n\n')
for params,idx in unique_angle_types.items():
data.write('{}\t{}\t{:.5f}\n'.format(idx,*params))
# Dihedral coefficients
if dihedrals:
data.write('\nDihedral Coeffs # opls\n\n')
for params,idx in unique_dihedral_types.items():
opls_coeffs = RB_to_OPLS(params[0],
params[1],
params[2],
params[3],
params[4],
params[5])
data.write('{}\t{:.5f}\t{:.5f}\t{:.5f}\t{:.5f}\n'.format(idx,*opls_coeffs))
# Atom data
data.write('\nAtoms\n\n')
if atom_style == 'atomic':
atom_line = '{index:d}\t{type_index:d}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif atom_style == 'charge':
atom_line = '{index:d}\t{type_index:d}\t{charge:.6f}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif atom_style == 'molecular':
atom_line = '{index:d}\t{zero:d}\t{type_index:d}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif atom_style == 'full':
atom_line ='{index:d}\t{zero:d}\t{type_index:d}\t{charge:.6f}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
for i,coords in enumerate(xyz):
data.write(atom_line.format(
index=i+1,type_index=unique_types.index(types[i])+1,
zero=0,charge=charges[i],
x=coords[0],y=coords[1],z=coords[2]))
if atom_style in ['full', 'molecular']:
# Bond data
if bonds:
data.write('\nBonds\n\n')
for i,bond in enumerate(bonds):
data.write('{:d}\t{:d}\t{:d}\t{:d}\n'.format(
i+1,bond_types[i],bond[0],bond[1]))
# Angle data
if angles:
data.write('\nAngles\n\n')
for i,angle in enumerate(angles):
data.write('{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n'.format(
i+1,angle_types[i],angle[0],angle[1],angle[2]))
# Dihedral data
if dihedrals:
data.write('\nDihedrals\n\n')
for i,dihedral in enumerate(dihedrals):
data.write('{:d}\t{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n'.format(
i+1,dihedral_types[i],dihedral[0],
dihedral[1],dihedral[2],dihedral[3]))
def __init__(self, tile, n_tiles, name=None):
super(TiledCompound, self).__init__()
n_tiles = np.asarray(n_tiles)
periodicity = np.asarray(tile.periodicity)
if not np.all(n_tiles > 0):
raise ValueError("Number of tiles must be positive.")
if tile.box is None:
tile.box = tile.get_boundingbox()
# Check that the tile is periodic in the requested dimensions.
if not np.all(np.logical_or((n_tiles == 1), periodicity)):
raise ValueError(
"Tile not periodic in at least one of the specified dimensions."
)
if name is None:
name = tile.name + "-".join(str(d) for d in n_tiles)
self.name = name
self.periodicity = tile.periodicity
self.box = Box(np.array(tile.box.lengths) * n_tiles,
angles=tile.box.angles)
if all(n_tiles == 1):
self._add_tile(tile, (0, 0, 0))
self._hoist_ports(tile)
return # Don't waste time copying and checking bonds.
# For every tile, assign temporary ID's to particles which are internal
# to that tile. E.g., when replicating a tile with 1800 particles, every
# tile will contain particles with ID's from 0-1799. These ID's are used
# below to fix bonds crossing periodic boundary conditions where a new
# tile has been placed.
for idx, particle in enumerate(tile.particles(include_ports=True)):
particle.index = idx
# Replicate and place periodic tiles.
# -----------------------------------
for ijk in it.product(*[range(i) for i in n_tiles]):
new_tile = clone(tile)
new_tile.translate(np.multiply(ijk, np.asarray(tile.box.lengths)))
self._add_tile(new_tile, ijk)
self._hoist_ports(new_tile)
# Fix bonds across periodic boundaries.
# -------------------------------------
# Cutoff for long bonds is half the shortest periodic distance.
threshold_calc = [np.inf, np.inf, np.inf]
for i, truthy in enumerate(tile.periodicity):
if truthy:
threshold_calc[i] = tile.box.lengths[i]
else:
continue
dist_thresh = np.min(threshold_calc) / 2
# Create the bounds for the periodicKDtree, non-periodic dimensions are 0
bounds = [0, 0, 0]
length_array = np.asarray(tile.box.lengths)
for i, dim in enumerate(bounds):
if tile.periodicity[i]:
bounds[i] = self.box.lengths[i]
else:
continue
# Bonds that were periodic in the original tile.
periodic_bonds = set()
for particle1, particle2 in tile.bonds():
if np.linalg.norm(particle1.pos - particle2.pos) > dist_thresh:
periodic_bonds.add((particle1.index, particle2.index))
# Build a periodic kdtree of all particle positions.
self.particle_kdtree = PeriodicCKDTree(data=self.xyz, bounds=bounds)
all_particles = np.asarray(list(self.particles(include_ports=False)))
# Store bonds to remove/add since we'll be iterating over all bonds.
bonds_to_remove = set()
bonds_to_add = set()
for particle1, particle2 in self.bonds():
if (
particle1.index,
particle2.index,
) not in periodic_bonds and (
particle2.index,
particle1.index,
) not in periodic_bonds:
continue
dist = self.min_periodic_distance(particle1.pos, particle2.pos)
if dist > dist_thresh:
bonds_to_remove.add((particle1, particle2))
image2 = self._find_particle_image(particle1, particle2,
all_particles)
image1 = self._find_particle_image(particle2, particle1,
all_particles)
if (image2, particle1) not in bonds_to_add:
bonds_to_add.add((particle1, image2))
if (image1, particle2) not in bonds_to_add:
bonds_to_add.add((particle2, image1))
for bond in bonds_to_remove:
self.remove_bond(bond)
for bond in bonds_to_add:
self.add_bond(bond)
# Clean up temporary data.
for particle in self._particles(include_ports=True):
particle.index = None
del self.particle_kdtree
def write_lammpsdata(structure, filename, atom_style='full',
unit_style='real',
detect_forcefield_style=True, nbfix_in_data_file=True,
use_urey_bradleys=False,
use_rb_torsions=True, use_dihedrals=False):
"""Output a LAMMPS data file.
Outputs a LAMMPS data file in the 'full' atom style format. Default units are
'real' units. See http://lammps.sandia.gov/doc/atom_style.html for
more information on atom styles.
Parameters
----------
structure : parmed.Structure
ParmEd structure object
filename : str
Path of the output file
atom_style: str
Defines the style of atoms to be saved in a LAMMPS data file. The following atom
styles are currently supported: 'full', 'atomic', 'charge', 'molecular'
see http://lammps.sandia.gov/doc/atom_style.html for more
information on atom styles.
unit_style: str
Defines to unit style to be save in a LAMMPS data file. Defaults to 'real' units.
Current styles are supported: 'real', 'lj'
see https://lammps.sandia.gov/doc/99/units.html for more information
on unit styles
detect_forcefield_style: boolean
If True, format lammpsdata parameters based on the contents of
the parmed Structure
use_urey_bradleys: boolean
If True, will treat angles as CHARMM-style angles with urey bradley terms
while looking for `structure.urey_bradleys`
use_rb_torsions:
If True, will treat dihedrals OPLS-style torsions while looking for
`structure.rb_torsions`
use_dihedrals:
If True, will treat dihedrals as CHARMM-style dihedrals while looking for
`structure.dihedrals`
Notes
-----
See http://lammps.sandia.gov/doc/2001/data_format.html for a full description
of the LAMMPS data format. Currently the following sections are supported (in
addition to the header): *Masses*, *Nonbond Coeffs*, *Bond Coeffs*, *Angle
Coeffs*, *Dihedral Coeffs*, *Atoms*, *Bonds*, *Angles*, *Dihedrals*, *Impropers*
OPLS and CHARMM forcefield styles are supported, AMBER forcefield styles are NOT
Some of this function has beed adopted from `mdtraj`'s support of the LAMMPSTRJ
trajectory format. See https://github.com/mdtraj/mdtraj/blob/master/mdtraj/formats/lammpstrj.py for details.
"""
if atom_style not in ['atomic', 'charge', 'molecular', 'full']:
raise ValueError('Atom style "{}" is invalid or is not currently supported'.format(atom_style))
# Check if structure is paramterized
if unit_style == 'lj':
if any([atom.sigma for atom in structure.atoms]) is None:
raise ValueError('LJ units specified but one or more atoms has undefined LJ parameters.')
xyz = np.array([[atom.xx,atom.xy,atom.xz] for atom in structure.atoms])
forcefield = True
if structure[0].type == '':
forcefield = False
"""
Note:
-----
unique_types : a sorted list of unique atomtypes for all atoms in the structure.
Defined by:
atomtype : atom.type
unique_bond_types: an enumarated OrderedDict of unique bond types for all bonds in the structure.
Defined by bond parameters and component atomtypes, in order:
k : bond.type.k
req : bond.type.req
atomtypes : sorted((bond.atom1.type, bond.atom2.type))
unique_angle_types: an enumerated OrderedDict of unique angle types for all angles in the structure.
Defined by angle parameters and component atomtypes, in order:
k : angle.type.k
theteq : angle.type.theteq
vertex atomtype: angle.atom2.type
atomtypes: sorted((bond.atom1.type, bond.atom3.type))
unique_dihedral_types: an enumerated OrderedDict of unique dihedrals type for all dihedrals in the structure.
Defined by dihedral parameters and component atomtypes, in order:
c0 : dihedral.type.c0
c1 : dihedral.type.c1
c2 : dihedral.type.c2
c3 : dihedral.type.c3
c4 : dihedral.type.c4
c5 : dihedral.type.c5
scee : dihedral.type.scee
scnb : dihedral.type.scnb
atomtype 1 : dihedral.atom1.type
atomtype 2 : dihedral.atom2.type
atomtype 3 : dihedral.atom3.type
atomtype 4 : dihedral.atom4.type
"""
if forcefield:
types = [atom.type for atom in structure.atoms]
else:
types = [atom.name for atom in structure.atoms]
unique_types = list(set(types))
unique_types.sort(key=natural_sort)
charges = np.array([atom.charge for atom in structure.atoms])
# Convert coordinates to LJ units
if unit_style == 'lj':
# Get sigma, mass, and epsilon conversions by finding maximum of each
sigma_conversion_factor = np.max([atom.sigma for atom in structure.atoms])
epsilon_conversion_factor = np.max([atom.epsilon for atom in structure.atoms])
mass_conversion_factor = np.max([atom.mass for atom in structure.atoms])
xyz = xyz / sigma_conversion_factor
charges = (charges*1.6021e-19) / np.sqrt(4*np.pi*(sigma_conversion_factor*1e-10)*
(epsilon_conversion_factor*4184)*epsilon_0)
charges[np.isinf(charges)] = 0
# TODO: FIX CHARGE UNIT CONVERSION
else:
sigma_conversion_factor = 1
epsilon_conversion_factor = 1
mass_conversion_factor = 1
# Internally use nm
box = Box(lengths=np.array([0.1 * val for val in structure.box[0:3]]),
angles=structure.box[3:6])
# Divide by conversion factor
box.maxs /= sigma_conversion_factor
# Lammps syntax depends on the functional form
# Infer functional form based on the properties of the structure
if detect_forcefield_style:
# Check angles
if len(structure.urey_bradleys) > 0 :
print("Urey bradley terms detected, will use angle_style charmm")
use_urey_bradleys = True
else:
print("No urey bradley terms detected, will use angle_style harmonic")
use_urey_bradleys = False
# Check dihedrals
if len(structure.rb_torsions) > 0:
print("RB Torsions detected, will use dihedral_style opls")
use_rb_torsions = True
else:
use_rb_torsions = False
if len(structure.dihedrals) > 0:
print("Charmm dihedrals detected, will use dihedral_style charmm")
use_dihedrals = True
else:
use_dihedrals = False
if use_rb_torsions and use_dihedrals:
raise ValueError("Multiple dihedral styles detected, check your "
"Forcefield XML and structure")
# Check impropers
for dihedral in structure.dihedrals:
if dihedral.improper:
raise ValueError("Amber-style impropers are currently not supported")
bonds = [[bond.atom1.idx+1, bond.atom2.idx+1] for bond in structure.bonds]
angles = [[angle.atom1.idx+1,
angle.atom2.idx+1,
angle.atom3.idx+1] for angle in structure.angles]
if use_rb_torsions:
dihedrals = [[dihedral.atom1.idx+1,
dihedral.atom2.idx+1,
dihedral.atom3.idx+1,
dihedral.atom4.idx+1] for dihedral in structure.rb_torsions]
elif use_dihedrals:
dihedrals = [[dihedral.atom1.idx+1,
dihedral.atom2.idx+1,
dihedral.atom3.idx+1,
dihedral.atom4.idx+1] for dihedral in structure.dihedrals]
else:
dihedrals = []
impropers = [[improper.atom1.idx+1,
improper.atom2.idx+1,
improper.atom3.idx+1,
improper.atom4.idx+1] for improper in structure.impropers]
if bonds :
if len(structure.bond_types) == 0:
bond_types = np.ones(len(bonds),dtype=int)
else:
bond_types, unique_bond_types = _get_bond_types(structure,
bonds, sigma_conversion_factor,
epsilon_conversion_factor)
if angles:
angle_types, unique_angle_types = _get_angle_types(structure,
use_urey_bradleys, sigma_conversion_factor,
epsilon_conversion_factor)
if dihedrals:
dihedral_types, unique_dihedral_types = _get_dihedral_types(
structure, use_rb_torsions, use_dihedrals,
epsilon_conversion_factor)
if impropers:
improper_types, unique_improper_types = _get_impropers(structure,
epsilon_conversion_factor)
with open(filename, 'w') as data:
data.write(filename+' - created by mBuild; units = {}\n\n'.format(
unit_style))
data.write('{:d} atoms\n'.format(len(structure.atoms)))
if atom_style in ['full', 'molecular']:
data.write('{:d} bonds\n'.format(len(bonds)))
data.write('{:d} angles\n'.format(len(angles)))
data.write('{:d} dihedrals\n'.format(len(dihedrals)))
data.write('{:d} impropers\n\n'.format(len(impropers)))
data.write('{:d} atom types\n'.format(len(set(types))))
if atom_style in ['full', 'molecular']:
if bonds:
data.write('{:d} bond types\n'.format(len(set(bond_types))))
if angles:
data.write('{:d} angle types\n'.format(len(set(angle_types))))
if dihedrals:
data.write('{:d} dihedral types\n'.format(len(set(dihedral_types))))
if impropers:
data.write('{:d} improper types\n'.format(len(set(improper_types))))
data.write('\n')
# Box data
if np.allclose(box.angles, np.array([90, 90, 90])):
for i,dim in enumerate(['x','y','z']):
data.write('{0:.6f} {1:.6f} {2}lo {2}hi\n'.format(
10.0 * box.mins[i],
10.0 * box.maxs[i],
dim))
else:
a, b, c = 10.0 * box.lengths
alpha, beta, gamma = np.radians(box.angles)
lx = a
xy = b * np.cos(gamma)
xz = c * np.cos(beta)
ly = np.sqrt(b**2 - xy**2)
yz = (b*c*np.cos(alpha) - xy*xz) / ly
lz = np.sqrt(c**2 - xz**2 - yz**2)
xlo, ylo, zlo = 10.0 * box.mins
xhi = xlo + lx
yhi = ylo + ly
zhi = zlo + lz
xlo_bound = xlo + np.min([0.0, xy, xz, xy+xz])
xhi_bound = xhi + np.max([0.0, xy, xz, xy+xz])
ylo_bound = ylo + np.min([0.0, yz])
yhi_bound = yhi + np.max([0.0, yz])
zlo_bound = zlo
zhi_bound = zhi
data.write('{0:.6f} {1:.6f} xlo xhi\n'.format(
xlo_bound, xhi_bound))
data.write('{0:.6f} {1:.6f} ylo yhi\n'.format(
ylo_bound, yhi_bound))
data.write('{0:.6f} {1:.6f} zlo zhi\n'.format(
zlo_bound, zhi_bound))
data.write('{0:.6f} {1:.6f} {2:6f} xy xz yz\n'.format(
xy, xz, yz))
# Mass data
masses = np.array([atom.mass for atom in structure.atoms]) / mass_conversion_factor
mass_dict = dict([(unique_types.index(atom_type)+1,mass) for atom_type,mass in zip(types,masses)])
data.write('\nMasses\n\n')
for atom_type,mass in mass_dict.items():
data.write('{:d}\t{:.6f}\t# {}\n'.format(atom_type,mass,unique_types[atom_type-1]))
if forcefield:
epsilons = np.array([atom.epsilon for atom in structure.atoms]) / epsilon_conversion_factor
sigmas = np.array([atom.sigma for atom in structure.atoms]) / sigma_conversion_factor
forcefields = [atom.type for atom in structure.atoms]
epsilon_dict = dict([(unique_types.index(atom_type)+1,epsilon) for atom_type,epsilon in zip(types,epsilons)])
sigma_dict = dict([(unique_types.index(atom_type)+1,sigma) for atom_type,sigma in zip(types,sigmas)])
forcefield_dict = dict([(unique_types.index(atom_type)+1,forcefield) for atom_type,forcefield in zip(types,forcefields)])
# Modified cross-interactions
if structure.has_NBFIX():
params = ParameterSet.from_structure(structure)
# Sort keys (maybe they should be sorted in ParmEd)
new_nbfix_types = OrderedDict()
for key, val in params.nbfix_types.items():
sorted_key = tuple(sorted(key))
if sorted_key in new_nbfix_types:
warn('Sorted key matches an existing key')
if new_nbfix_types[sorted_key]:
warn('nbfixes are not symmetric, overwriting old nbfix')
new_nbfix_types[sorted_key] = params.nbfix_types[key]
params.nbfix_types = new_nbfix_types
warn('Explicitly writing cross interactions using mixing rule: {}'.format(
structure.combining_rule))
coeffs = OrderedDict()
for combo in it.combinations_with_replacement(unique_types, 2):
# Attempt to find pair coeffis in nbfixes
if combo in params.nbfix_types:
type1 = unique_types.index(combo[0])+1
type2 = unique_types.index(combo[1])+1
rmin = params.nbfix_types[combo][0] # Angstrom OR lj units
epsilon = params.nbfix_types[combo][1] # kcal OR lj units
sigma = rmin/2**(1/6)
coeffs[(type1, type2)] = (round(sigma, 8), round(epsilon, 8))
else:
type1 = unique_types.index(combo[0]) + 1
type2 = unique_types.index(combo[1]) + 1
# Might not be necessary to be this explicit
if type1 == type2:
sigma = sigma_dict[type1]
epsilon = epsilon_dict[type1]
else:
if structure.combining_rule == 'lorentz':
sigma = (sigma_dict[type1]+sigma_dict[type2])*0.5
elif structure.combining_rule == 'geometric':
sigma = (sigma_dict[type1]*sigma_dict[type2])**0.5
else:
raise ValueError('Only lorentz and geometric combining rules are supported')
epsilon = (epsilon_dict[type1]*epsilon_dict[type2])**0.5
coeffs[(type1, type2)] = (round(sigma, 8), round(epsilon, 8))
if nbfix_in_data_file:
data.write('\nPairIJ Coeffs # modified lj\n')
data.write('# type1 type2 \tepsilon (kcal/mol) \tsigma (Angstrom)\n')
for (type1, type2), (sigma, epsilon) in coeffs.items():
data.write('{0} \t{1} \t{2} \t\t{3}\t\t# {4}\t{5}\n'.format(
type1, type2, epsilon, sigma, forcefield_dict[type1], forcefield_dict[type2]))
else:
data.write('\nPair Coeffs # lj\n\n')
for idx,epsilon in epsilon_dict.items():
data.write('{}\t{:.5f}\t{:.5f}\n'.format(idx,epsilon,sigma_dict[idx]))
print('Copy these commands into your input script:\n')
print('# type1 type2 \tepsilon (kcal/mol) \tsigma (Angstrom)\n')
for (type1, type2), (sigma, epsilon) in coeffs.items():
print('pair_coeff\t{0} \t{1} \t{2} \t\t{3} \t\t# {4} \t{5}'.format(
type1, type2, epsilon, sigma,forcefield_dict[type1],forcefield_dict[type2]))
# Pair coefficients
else:
data.write('\nPair Coeffs # lj \n')
if unit_style == 'real':
data.write('#\tepsilon (kcal/mol)\t\tsigma (Angstrom)\n')
elif unit_style == 'lj':
data.write('#\treduced_epsilon \t\treduced_sigma \n')
for idx,epsilon in epsilon_dict.items():
data.write('{}\t{:.5f}\t\t{:.5f}\t\t# {}\n'.format(idx,epsilon,sigma_dict[idx],forcefield_dict[idx]))
# Bond coefficients
if bonds:
data.write('\nBond Coeffs # harmonic\n')
if unit_style == 'real':
data.write('#\tk(kcal/mol/angstrom^2)\t\treq(angstrom)\n')
elif unit_style == 'lj':
data.write('#\treduced_k\t\treduced_req\n')
for params,idx in unique_bond_types.items():
data.write('{}\t{}\t\t{}\t\t# {}\t{}\n'.format(idx,params[0],params[1],params[2][0],params[2][1]))
# Angle coefficients
if angles:
if use_urey_bradleys:
data.write('\nAngle Coeffs # charmm\n')
data.write('#\tk(kcal/mol/rad^2)\t\ttheteq(deg)\tk(kcal/mol/angstrom^2)\treq(angstrom)\n')
for params,idx in unique_angle_types.items():
data.write('{}\t{}\t{:.5f}\t{:.5f}\t{:.5f}\n'.format(idx,*params))
else:
data.write('\nAngle Coeffs # harmonic\n')
data.write('#\treduced_k\t\ttheteq(deg)\n')
for params,idx in unique_angle_types.items():
data.write('{}\t{}\t\t{:.5f}\t# {}\t{}\t{}\n'.format(idx,params[0],params[1],
params[3][0],params[2],params[3][1]))
# Dihedral coefficients
if dihedrals:
if use_rb_torsions:
data.write('\nDihedral Coeffs # opls\n')
if unit_style == 'real':
data.write('#\tf1(kcal/mol)\tf2(kcal/mol)\tf3(kcal/mol)\tf4(kcal/mol)\n')
elif unit_style == 'lj':
data.write('#\tf1\tf2\tf3\tf4 (all lj reduced units)\n')
for params,idx in unique_dihedral_types.items():
opls_coeffs = RB_to_OPLS(params[0],
params[1],
params[2],
params[3],
params[4],
params[5])
data.write('{}\t{:.5f}\t{:.5f}\t\t{:.5f}\t\t{:.5f}\t# {}\t{}\t{}\t{}\n'.format(idx,opls_coeffs[0],
opls_coeffs[1],
opls_coeffs[2],
opls_coeffs[3],
params[8],params[9],
params[10],params[11]))
elif use_dihedrals:
data.write('\nDihedral Coeffs # charmm\n')
data.write('#k, n, phi, weight\n')
for params, idx in unique_dihedral_types.items():
data.write('{}\t{:.5f}\t{:d}\t{:d}\t{:.5f}\t# {}\t{}\t{}\t{}\n'.format(idx, params[0],
params[1], params[2],
params[3], params[6],
params[7], params[8], params[9]))
# Improper coefficients
if impropers:
data.write('\nImproper Coeffs # harmonic\n')
data.write('#k, phi\n')
for params,idx in unique_improper_types.items():
data.write('{}\t{:.5f}\t{:.5f}\t# {}\t{}\t{}\t{}\n'.format(idx, params[0],
params[1], params[2],
params[3], params[4],
params[5]))
# Atom data
data.write('\nAtoms\n\n')
if atom_style == 'atomic':
atom_line = '{index:d}\t{type_index:d}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif atom_style == 'charge':
if unit_style == 'real':
atom_line = '{index:d}\t{type_index:d}\t{charge:.6f}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif unit_style == 'lj':
atom_line = '{index:d}\t{type_index:d}\t{charge:.4ef}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif atom_style == 'molecular':
atom_line = '{index:d}\t{zero:d}\t{type_index:d}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif atom_style == 'full':
if unit_style == 'real':
atom_line ='{index:d}\t{zero:d}\t{type_index:d}\t{charge:.6f}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
elif unit_style == 'lj':
atom_line ='{index:d}\t{zero:d}\t{type_index:d}\t{charge:.4e}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n'
for i,coords in enumerate(xyz):
data.write(atom_line.format(
index=i+1,type_index=unique_types.index(types[i])+1,
zero=structure.atoms[i].residue.idx,charge=charges[i],
x=coords[0],y=coords[1],z=coords[2]))
if atom_style in ['full', 'molecular']:
# Bond data
if bonds:
data.write('\nBonds\n\n')
for i,bond in enumerate(bonds):
data.write('{:d}\t{:d}\t{:d}\t{:d}\n'.format(
i+1,bond_types[i],bond[0],bond[1]))
# Angle data
if angles:
data.write('\nAngles\n\n')
for i,angle in enumerate(angles):
data.write('{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n'.format(
i+1,angle_types[i],angle[0],angle[1],angle[2]))
# Dihedral data
if dihedrals:
data.write('\nDihedrals\n\n')
for i,dihedral in enumerate(dihedrals):
data.write('{:d}\t{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n'.format(
i+1,dihedral_types[i],dihedral[0],
dihedral[1],dihedral[2],dihedral[3]))
# Dihedral data
if impropers:
data.write('\nImpropers\n\n')
for i,improper in enumerate(impropers):
data.write('{:d}\t{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n'.format(
i+1,improper_types[i],improper[2],
improper[1],improper[0],improper[3]))
def write_lammpsdata(
structure,
filename,
atom_style="full",
unit_style="real",
mins=None,
maxs=None,
pair_coeff_label=None,
detect_forcefield_style=True,
nbfix_in_data_file=True,
use_urey_bradleys=False,
use_rb_torsions=True,
use_dihedrals=False,
zero_dihedral_weighting_factor=False,
moleculeID_offset=1,
):
"""Output a LAMMPS data file.
Outputs a LAMMPS data file in the 'full' atom style format. Default units
are 'real' units. See http://lammps.sandia.gov/doc/atom_style.html for
more information on atom styles.
Parameters
----------
structure : parmed.Structure
ParmEd structure object
filename : str
Path of the output file
atom_style: str
Defines the style of atoms to be saved in a LAMMPS data file. The
following atom styles are currently supported:
'full', 'atomic', 'charge', 'molecular'
see http://lammps.sandia.gov/doc/atom_style.html for more information
on atom styles.
unit_style: str
Defines to unit style to be save in a LAMMPS data file. Defaults to
'real' units. Current styles are supported: 'real', 'lj'
see https://lammps.sandia.gov/doc/99/units.html for more information
on unit styles
mins : list
minimum box dimension in x, y, z directions
maxs : list
maximum box dimension in x, y, z directions
pair_coeff_label : str
Provide a custom label to the pair_coeffs section in the lammps data
file. Defaults to None, which means a suitable default will be chosen.
detect_forcefield_style: boolean
If True, format lammpsdata parameters based on the contents of
the parmed Structure
use_urey_bradleys: boolean
If True, will treat angles as CHARMM-style angles with urey bradley
terms while looking for `structure.urey_bradleys`
use_rb_torsions:
If True, will treat dihedrals OPLS-style torsions while looking for
`structure.rb_torsions`
use_dihedrals:
If True, will treat dihedrals as CHARMM-style dihedrals while looking
for `structure.dihedrals`
zero_dihedral_weighting_factor:
If True, will set weighting parameter to zero in CHARMM-style dihedrals.
This should be True if the CHARMM dihedral style is used in non-CHARMM forcefields.
moleculeID_offset : int , optional, default=1
Since LAMMPS treats the MoleculeID as an additional set of information
to identify what molecule an atom belongs to, this currently
behaves as a residue id. This value needs to start at 1 to be
considered a real molecule.
Notes
-----
See http://lammps.sandia.gov/doc/2001/data_format.html for a full
description of the LAMMPS data format. Currently the following sections are
supported (in addition to the header): *Masses*, *Nonbond Coeffs*,
*Bond Coeffs*, *Angle Coeffs*, *Dihedral Coeffs*, *Atoms*, *Bonds*,
*Angles*, *Dihedrals*, *Impropers*
OPLS and CHARMM forcefield styles are supported, AMBER forcefield styles
are NOT
Some of this function has beed adopted from `mdtraj`'s support of the
LAMMPSTRJ trajectory format. See
https://github.com/mdtraj/mdtraj/blob/master/mdtraj/formats/lammpstrj.py
for details.
unique_types : a sorted list of unique atomtypes for all atoms in the
structure where atomtype = atom.type.
unique_bond_types: an enumarated OrderedDict of unique bond types for all
bonds in the structure.
Defined by bond parameters and component atomtypes, in order:
--- k : bond.type.k
--- req : bond.type.req
--- atomtypes : sorted((bond.atom1.type, bond.atom2.type))
unique_angle_types: an enumerated OrderedDict of unique angle types for all
angles in the structure.
Defined by angle parameters and component atomtypes, in order:
--- k : angle.type.k
--- theteq : angle.type.theteq
--- vertex atomtype: angle.atom2.type
--- atomtypes: sorted((bond.atom1.type, bond.atom3.type))
unique_dihedral_types: an enumerated OrderedDict of unique dihedrals type
for all dihedrals in the structure.
Defined by dihedral parameters and component atomtypes, in order:
--- c0 : dihedral.type.c0
--- c1 : dihedral.type.c1
--- c2 : dihedral.type.c2
--- c3 : dihedral.type.c3
--- c4 : dihedral.type.c4
--- c5 : dihedral.type.c5
--- scee : dihedral.type.scee
--- scnb : dihedral.type.scnb
--- atomtype 1 : dihedral.atom1.type
--- atomtype 2 : dihedral.atom2.type
--- atomtype 3 : dihedral.atom3.type
--- atomtype 4 : dihedral.atom4.type
"""
# copy structure so the input structure isn't modified in-place
structure = structure.copy(cls=Structure, split_dihedrals=True)
if atom_style not in ["atomic", "charge", "molecular", "full"]:
raise ValueError(
'Atom style "{atom_style}" is invalid or is not currently supported'
)
# Check if structure is paramterized
if unit_style == "lj":
if any([atom.sigma for atom in structure.atoms]) is None:
raise ValueError(
"LJ units specified but one or more atoms has undefined LJ "
"parameters.")
xyz = np.array([[atom.xx, atom.xy, atom.xz] for atom in structure.atoms])
forcefield = True
if structure[0].type == "":
forcefield = False
if forcefield:
types = [atom.type for atom in structure.atoms]
else:
types = [atom.name for atom in structure.atoms]
unique_types = list(set(types))
unique_types.sort(key=natural_sort)
charges = np.array([atom.charge for atom in structure.atoms])
# Convert coordinates to LJ units
if unit_style == "lj":
# Get sigma, mass, and epsilon conversions by finding maximum of each
sigma_conversion_factor = np.max([a.sigma for a in structure.atoms])
epsilon_conversion_factor = np.max(
[a.epsilon for a in structure.atoms])
mass_conversion_factor = np.max([a.mass for a in structure.atoms])
xyz = xyz / sigma_conversion_factor
charges = (charges * 1.6021e-19) / np.sqrt(
4 * np.pi * (sigma_conversion_factor * 1e-10) *
(epsilon_conversion_factor * 4184) * epsilon_0)
charges[np.isinf(charges)] = 0
else:
sigma_conversion_factor = 1
epsilon_conversion_factor = 1
mass_conversion_factor = 1
# lammps does not require the box to be centered at any a specific origin
# min and max dimensions are therefore needed to write the file in a
# consistent way the parmed structure only stores the box length. It is
# not rigorous to assume bounds are 0 to L or -L/2 to L/2
# NOTE: 0 to L is current default, mins and maxs should be passed by user
if _check_minsmaxs(mins, maxs):
box = Box.from_mins_maxs_angles(mins=mins,
maxs=maxs,
angles=structure.box[3:6])
else:
# Internally use nm
box = Box(
lengths=np.array([0.1 * val for val in structure.box[0:3]]),
angles=structure.box[3:6],
)
warn(
"Explicit box bounds (i.e., mins and maxs) were not provided. Box "
"bounds are assumed to be min = 0 and max = length in each "
"direction. This may not produce a system with the expected "
"spatial location and may cause non-periodic systems to fail. "
"Bounds can be defined explicitly by passing the them to the "
"write_lammpsdata function or by passing box info to the save "
"function.")
# Divide by conversion factor
Lx = box.Lx * (1 / sigma_conversion_factor)
Ly = box.Ly * (1 / sigma_conversion_factor)
Lz = box.Lz * (1 / sigma_conversion_factor)
box = Box(lengths=(Lx, Ly, Lz), angles=box.angles)
# Lammps syntax depends on the functional form
# Infer functional form based on the properties of the structure
if detect_forcefield_style:
# Check angles
if len(structure.urey_bradleys) > 0:
print("Urey bradley terms detected, will use angle_style charmm")
use_urey_bradleys = True
else:
print(
"No urey bradley terms detected, will use angle_style harmonic"
)
use_urey_bradleys = False
# Check dihedrals
if len(structure.rb_torsions) > 0:
print("RB Torsions detected, will use dihedral_style opls")
use_rb_torsions = True
else:
use_rb_torsions = False
if len([d for d in structure.dihedrals if not d.improper]) > 0:
print("Charmm dihedrals detected, will use dihedral_style charmm")
use_dihedrals = True
else:
use_dihedrals = False
if use_rb_torsions and use_dihedrals:
raise ValueError("Multiple dihedral styles detected, check your "
"Forcefield XML and structure")
bonds = [[b.atom1.idx + 1, b.atom2.idx + 1] for b in structure.bonds]
angles = [[angle.atom1.idx + 1, angle.atom2.idx + 1, angle.atom3.idx + 1]
for angle in structure.angles]
if use_rb_torsions:
dihedrals = [[
d.atom1.idx + 1, d.atom2.idx + 1, d.atom3.idx + 1, d.atom4.idx + 1
] for d in structure.rb_torsions]
elif use_dihedrals:
dihedrals = [[
d.atom1.idx + 1, d.atom2.idx + 1, d.atom3.idx + 1, d.atom4.idx + 1
] for d in structure.dihedrals if not d.improper]
else:
dihedrals = []
impropers = [[
i.atom1.idx + 1, i.atom2.idx + 1, i.atom3.idx + 1, i.atom4.idx + 1
] for i in structure.impropers]
imp_dihedrals = [[
d.atom1.idx + 1, d.atom2.idx + 1, d.atom3.idx + 1, d.atom4.idx + 1
] for d in structure.dihedrals if d.improper]
if impropers and imp_dihedrals:
raise ValueError("Use of multiple improper styles is not supported")
if bonds:
if len(structure.bond_types) == 0:
bond_types = np.ones(len(bonds), dtype=int)
else:
bond_types, unique_bond_types = _get_bond_types(
structure,
bonds,
sigma_conversion_factor,
epsilon_conversion_factor,
)
if angles:
angle_types, unique_angle_types = _get_angle_types(
structure,
use_urey_bradleys,
sigma_conversion_factor,
epsilon_conversion_factor,
)
if imp_dihedrals:
(
imp_dihedral_types,
unique_imp_dihedral_types,
) = _get_improper_dihedral_types(structure, epsilon_conversion_factor)
if dihedrals:
dihedral_types, unique_dihedral_types = _get_dihedral_types(
structure,
use_rb_torsions,
use_dihedrals,
epsilon_conversion_factor,
zero_dihedral_weighting_factor,
)
if impropers:
improper_types, unique_improper_types = _get_impropers(
structure, epsilon_conversion_factor)
with open(filename, "w") as data:
data.write(f"{filename} - created by mBuild; units = {unit_style}\n\n")
data.write("{:d} atoms\n".format(len(structure.atoms)))
if atom_style in ["full", "molecular"]:
data.write("{:d} bonds\n".format(len(bonds)))
data.write("{:d} angles\n".format(len(angles)))
data.write("{:d} dihedrals\n".format(len(dihedrals)))
data.write("{:d} impropers\n\n".format(
len(impropers) + len(imp_dihedrals)))
data.write("{:d} atom types\n".format(len(set(types))))
if atom_style in ["full", "molecular"]:
if bonds:
data.write("{:d} bond types\n".format(len(set(bond_types))))
if angles:
data.write("{:d} angle types\n".format(len(set(angle_types))))
if dihedrals:
data.write("{:d} dihedral types\n".format(
len(set(dihedral_types))))
if impropers:
data.write("{:d} improper types\n".format(
len(set(improper_types))))
elif imp_dihedrals:
data.write("{:d} improper types\n".format(
len(set(imp_dihedral_types))))
data.write("\n")
# Box data
# NOTE: Needs better logic handling maxs and mins of a bounding box
# NOTE: JBG, "this should be a method/attribute of Compound?"
if np.allclose(box.angles, 90.0, atol=1e-5) and (mins is None):
for i, dim in enumerate(["x", "y", "z"]):
data.write("{0:.6f} {1:.6f} {2}lo {2}hi\n".format(
0.0, 10.0 * box.lengths[i], dim))
# NOTE:
# currently non-orthogonal bounding box translates
# Compound such that mins are new origin
else:
a = 10.0 * box.Lx
b = 10.0 * box.Ly
c = 10.0 * box.Lz
alpha, beta, gamma = np.radians(box.angles)
xy = box.xy
xz = box.xz
yz = box.yz
# NOTE: using (0,0,0) as origin
xlo, ylo, zlo = (0.0, 0.0, 0.0)
xhi = xlo + a
yhi = ylo + b
zhi = zlo + c
xlo_bound = xlo + np.min([0.0, xy, xz, xy + xz])
xhi_bound = xhi + np.max([0.0, xy, xz, xy + xz])
ylo_bound = ylo + np.min([0.0, yz])
yhi_bound = yhi + np.max([0.0, yz])
zlo_bound = zlo
zhi_bound = zhi
data.write("{0:.6f} {1:.6f} xlo xhi\n".format(
xlo_bound, xhi_bound))
data.write("{0:.6f} {1:.6f} ylo yhi\n".format(
ylo_bound, yhi_bound))
data.write("{0:.6f} {1:.6f} zlo zhi\n".format(
zlo_bound, zhi_bound))
data.write("{0:.6f} {1:.6f} {2:6f} xy xz yz\n".format(xy, xz, yz))
# Mass data
if not forcefield:
masses = (np.array([atom.mass for atom in structure.atoms]) /
mass_conversion_factor)
else:
tmp_masses = list()
for atom in structure.atoms:
# handle case where atomtype does not contain a mass
try:
tmp_masses.append(atom.atom_type.mass)
except AttributeError:
warn(
f"No mass or defined atomtype for atom: {atom}. Using atom mass of {atom.mass / mass_conversion_factor}"
)
tmp_masses.append(atom.mass)
masses = np.asarray(tmp_masses) / mass_conversion_factor
mass_dict = dict([(unique_types.index(atom_type) + 1, mass)
for atom_type, mass in zip(types, masses)])
data.write("\nMasses\n\n")
for atom_type, mass in sorted(mass_dict.items()):
data.write("{:d}\t{:.6f}\t# {}\n".format(
atom_type, mass, unique_types[atom_type - 1]))
if forcefield:
epsilons = (np.array([atom.epsilon for atom in structure.atoms]) /
epsilon_conversion_factor)
sigmas = (np.array([atom.sigma for atom in structure.atoms]) /
sigma_conversion_factor)
forcefields = [atom.type for atom in structure.atoms]
epsilon_dict = dict([
(unique_types.index(atom_type) + 1, epsilon)
for atom_type, epsilon in zip(types, epsilons)
])
sigma_dict = dict([(unique_types.index(atom_type) + 1, sigma)
for atom_type, sigma in zip(types, sigmas)])
forcefield_dict = dict([
(unique_types.index(atom_type) + 1, forcefield)
for atom_type, forcefield in zip(types, forcefields)
])
# Modified cross-interactions
if structure.has_NBFIX():
params = ParameterSet.from_structure(structure)
# Sort keys (maybe they should be sorted in ParmEd)
new_nbfix_types = OrderedDict()
for key in params.nbfix_types.keys():
sorted_key = tuple(sorted(key))
if sorted_key in new_nbfix_types:
warn("Sorted key matches an existing key")
if new_nbfix_types[sorted_key]:
warn("nbfixes are not symmetric, overwriting old "
"nbfix")
new_nbfix_types[sorted_key] = params.nbfix_types[key]
params.nbfix_types = new_nbfix_types
warn(
"Explicitly writing cross interactions using mixing rule: "
"{}".format(structure.combining_rule))
coeffs = OrderedDict()
for combo in it.combinations_with_replacement(unique_types, 2):
# Attempt to find pair coeffis in nbfixes
if combo in params.nbfix_types:
type1 = unique_types.index(combo[0]) + 1
type2 = unique_types.index(combo[1]) + 1
epsilon = params.nbfix_types[combo][
0] # kcal OR lj units
rmin = params.nbfix_types[combo][
1] # Angstrom OR lj units
sigma = rmin / 2**(1 / 6)
coeffs[(type1, type2)] = (
round(sigma, 8),
round(epsilon, 8),
)
else:
type1 = unique_types.index(combo[0]) + 1
type2 = unique_types.index(combo[1]) + 1
# Might not be necessary to be this explicit
if type1 == type2:
sigma = sigma_dict[type1]
epsilon = epsilon_dict[type1]
else:
if structure.combining_rule == "lorentz":
sigma = (sigma_dict[type1] +
sigma_dict[type2]) * 0.5
elif structure.combining_rule == "geometric":
sigma = (sigma_dict[type1] *
sigma_dict[type2])**0.5
else:
raise ValueError(
"Only lorentz and geometric combining "
"rules are supported")
epsilon = (epsilon_dict[type1] *
epsilon_dict[type2])**0.5
coeffs[(type1, type2)] = (
round(sigma, 8),
round(epsilon, 8),
)
if nbfix_in_data_file:
if pair_coeff_label:
data.write(
"\nPairIJ Coeffs # {}\n".format(pair_coeff_label))
else:
data.write("\nPairIJ Coeffs # modified lj\n")
data.write(
"# type1 type2\tepsilon (kcal/mol)\tsigma (Angstrom)\n"
)
for (type1, type2), (sigma, epsilon) in coeffs.items():
data.write(
"{0} \t{1} \t{2} \t\t{3}\t\t# {4}\t{5}\n".format(
type1,
type2,
epsilon,
sigma,
forcefield_dict[type1],
forcefield_dict[type2],
))
else:
if pair_coeff_label:
data.write(
"\nPair Coeffs # {}\n".format(pair_coeff_label))
else:
data.write("\nPair Coeffs # lj\n")
for idx, epsilon in sorted(epsilon_dict.items()):
data.write("{}\t{:.5f}\t{:.5f}\n".format(
idx, epsilon, sigma_dict[idx]))
print("Copy these commands into your input script:\n")
print(
"# type1 type2\tepsilon (kcal/mol)\tsigma (Angstrom)\n"
)
for (type1, type2), (sigma, epsilon) in coeffs.items():
print(
"pair_coeff\t{0} \t{1} \t{2} \t\t{3} \t\t# {4} \t{5}"
.format(
type1,
type2,
epsilon,
sigma,
forcefield_dict[type1],
forcefield_dict[type2],
))
# Pair coefficients
else:
if pair_coeff_label:
data.write("\nPair Coeffs # {}\n".format(pair_coeff_label))
else:
data.write("\nPair Coeffs # lj\n")
if unit_style == "real":
data.write("#\tepsilon (kcal/mol)\t\tsigma (Angstrom)\n")
elif unit_style == "lj":
data.write("#\treduced_epsilon \t\treduced_sigma \n")
for idx, epsilon in sorted(epsilon_dict.items()):
data.write("{}\t{:.5f}\t\t{:.5f}\t\t# {}\n".format(
idx, epsilon, sigma_dict[idx], forcefield_dict[idx]))
# Bond coefficients
if bonds:
data.write("\nBond Coeffs # harmonic\n")
if unit_style == "real":
data.write("#\tk(kcal/mol/angstrom^2)\t\treq(angstrom)\n")
elif unit_style == "lj":
data.write("#\treduced_k\t\treduced_req\n")
sorted_bond_types = {
k: v
for k, v in sorted(unique_bond_types.items(),
key=lambda item: item[1])
}
for params, idx in sorted_bond_types.items():
data.write("{}\t{}\t\t{}\t\t# {}\t{}\n".format(
idx,
params[0],
params[1],
params[2][0],
params[2][1],
))
# Angle coefficients
if angles:
sorted_angle_types = {
k: v
for k, v in sorted(unique_angle_types.items(),
key=lambda item: item[1])
}
if use_urey_bradleys:
data.write("\nAngle Coeffs # charmm\n")
data.write(
"#\tk(kcal/mol/rad^2)\t\ttheteq(deg)\tk(kcal/mol/angstrom^2)\treq(angstrom)\n"
)
for params, idx in sorted_angle_types.items():
data.write("{}\t{}\t{:.5f}\t{:.5f}\t{:.5f}\n".format(
idx, *params))
else:
data.write("\nAngle Coeffs # harmonic\n")
data.write("#\treduced_k\t\ttheteq(deg)\n")
for params, idx in sorted_angle_types.items():
data.write("{}\t{}\t\t{:.5f}\t# {}\t{}\t{}\n".format(
idx,
params[0],
params[1],
params[3][0],
params[2],
params[3][1],
))
# Dihedral coefficients
if dihedrals:
sorted_dihedral_types = {
k: v
for k, v in sorted(unique_dihedral_types.items(),
key=lambda item: item[1])
}
if use_rb_torsions:
data.write("\nDihedral Coeffs # opls\n")
if unit_style == "real":
data.write(
"#\tf1(kcal/mol)\tf2(kcal/mol)\tf3(kcal/mol)\tf4(kcal/mol)\n"
)
elif unit_style == "lj":
data.write(
"#\tf1\tf2\tf3\tf4 (all lj reduced units)\n")
for params, idx in sorted_dihedral_types.items():
opls_coeffs = RB_to_OPLS(
params[0],
params[1],
params[2],
params[3],
params[4],
params[5],
error_if_outside_tolerance=False,
)
data.write(
"{}\t{:.5f}\t{:.5f}\t\t{:.5f}\t\t{:.5f}\t# {}\t{}\t{}\t{}\n"
.format(
idx,
opls_coeffs[1],
opls_coeffs[2],
opls_coeffs[3],
opls_coeffs[4],
params[8],
params[9],
params[10],
params[11],
))
elif use_dihedrals:
data.write("\nDihedral Coeffs # charmm\n")
data.write("#k, n, phi, weight\n")
for params, idx in sorted_dihedral_types.items():
data.write(
"{}\t{:.5f}\t{:d}\t{:d}\t{:.5f}\t# {}\t{}\t{}\t{}\n"
.format(
idx,
params[0],
params[1],
params[2],
params[3],
params[6],
params[7],
params[8],
params[9],
))
# Improper coefficients
if impropers:
sorted_improper_types = {
k: v
for k, v in sorted(unique_improper_types.items(),
key=lambda item: item[1])
}
data.write("\nImproper Coeffs # harmonic\n")
data.write("#k, phi\n")
for params, idx in sorted_improper_types.items():
data.write("{}\t{:.5f}\t{:.5f}\t# {}\t{}\t{}\t{}\n".format(
idx,
params[0],
params[1],
params[2],
params[3],
params[4],
params[5],
))
elif imp_dihedrals:
# Improper dihedral coefficients
sorted_imp_dihedral_types = {
k: v
for k, v in sorted(
unique_imp_dihedral_types.items(),
key=lambda item: item[1],
)
}
data.write("\nImproper Coeffs # cvff\n")
data.write("#K, d, n\n")
for params, idx in sorted_imp_dihedral_types.items():
data.write(
"{}\t{:.5f}\t{:d}\t{:d}\t# {}\t{}\t{}\t{}\n".format(
idx,
params[0],
params[1],
params[2],
params[5],
params[6],
params[7],
params[8],
))
# Atom data
data.write("\nAtoms # {}\n\n".format(atom_style))
if atom_style == "atomic":
atom_line = "{index:d}\t{type_index:d}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n"
elif atom_style == "charge":
if unit_style == "real":
atom_line = "{index:d}\t{type_index:d}\t{charge:.6f}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n"
elif unit_style == "lj":
atom_line = "{index:d}\t{type_index:d}\t{charge:.4ef}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n"
elif atom_style == "molecular":
atom_line = "{index:d}\t{zero:d}\t{type_index:d}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n"
elif atom_style == "full":
if unit_style == "real":
atom_line = "{index:d}\t{zero:d}\t{type_index:d}\t{charge:.6f}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n"
elif unit_style == "lj":
atom_line = "{index:d}\t{zero:d}\t{type_index:d}\t{charge:.4e}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n"
for i, coords in enumerate(xyz):
data.write(
atom_line.format(
index=i + 1,
type_index=unique_types.index(types[i]) + 1,
zero=structure.atoms[i].residue.idx + moleculeID_offset,
charge=charges[i],
x=coords[0],
y=coords[1],
z=coords[2],
))
if atom_style in ["full", "molecular"]:
# Bond data
if bonds:
data.write("\nBonds\n\n")
for i, bond in enumerate(bonds):
data.write("{:d}\t{:d}\t{:d}\t{:d}\n".format(
i + 1, bond_types[i], bond[0], bond[1]))
# Angle data
if angles:
data.write("\nAngles\n\n")
for i, angle in enumerate(angles):
data.write("{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n".format(
i + 1, angle_types[i], angle[0], angle[1], angle[2]))
# Dihedral data
if dihedrals:
data.write("\nDihedrals\n\n")
for i, dihedral in enumerate(dihedrals):
data.write("{:d}\t{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n".format(
i + 1,
dihedral_types[i],
dihedral[0],
dihedral[1],
dihedral[2],
dihedral[3],
))
# Dihedral data
if impropers:
data.write("\nImpropers\n\n")
for i, improper in enumerate(impropers):
data.write("{:d}\t{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n".format(
i + 1,
improper_types[i],
improper[2],
improper[1],
improper[0],
improper[3],
))
elif imp_dihedrals:
data.write("\nImpropers\n\n")
for i, improper in enumerate(imp_dihedrals):
# The atoms are written central-atom third in LAMMPS data file.
# This is correct for AMBER impropers even though
# LAMMPS documentation implies central-atom-first.
data.write("{:d}\t{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n".format(
i + 1,
imp_dihedral_types[i],
improper[0],
improper[1],
improper[2],
improper[3],
))