def _initialize_lammps(self, structure):
lmp = lammps.Lammps(units='metal',
style='full',
args=['-log', 'none', '-screen', 'none'])
lmp.system.add_pymatgen_structure(structure, self.elements)
lmp.thermo.add('my_ke', 'ke', 'all')
return lmp
def initiate_lmp(self, cs_springs):
"""
Initialises the system for the structure (read in from a lammps input file) with non-changing parameters implemented.
Args:
cs_springs (dict): The key is the atom label (str) and the value the spring values (list(float)).
Returns:
lmp (obj): Lammps system object with structure and specified commands implemented.
"""
lmp = lammps.Lammps(units='metal',
style='full',
args=['-log', 'none', '-screen', 'none'])
lmp.command('read_data {}'.format(self.file_name))
lmp.command('group cores type {}'.format(self.type_core()))
if len(self.bond_types) != 0:
lmp.command('group shells type {}'.format(self.type_shell()))
if cs_springs:
lmp.command('pair_style buck/coul/long/cs 10.0')
lmp.command('pair_coeff * * 0 1 0')
lmp.command('bond_style harmonic')
for bond in self.bond_types:
lmp.command(bond.bond_string())
else:
lmp.command('pair_style buck/coul/long 10.0')
lmp.command('pair_coeff * * 0 1 0')
lmp.command('kspace_style ewald 1e-6')
#setup for minimization
lmp.command('min_style cg')
return lmp
async def submit(self,
structure,
potential,
properties=None,
lammps_additional_commands=None):
properties = properties or {'stress', 'energy', 'forces'}
results = {}
lammps_additional_commands = lammps_additional_commands or ['run 0']
lmp = lammps.Lammps(units='metal',
style='full',
args=['-log', 'none', '-screen', 'none'])
elements, rotation_matrix = lmp.system.add_pymatgen_structure(
structure)
inv_rotation_matrix = np.linalg.inv(rotation_matrix)
lmp.thermo.add('my_ke', 'ke', 'all')
if 'initial_positions' in properties:
results['initial_positions'] = np.dot(lmp.system.positions.copy(),
inv_rotation_matrix)
lammps_files = write_potential_files(potential,
elements=elements,
unique_id=self.unique_id)
for filename, content in lammps_files.items():
with open(filename, 'w') as f:
f.write(content)
lammps_commands = write_potential(potential,
elements=elements,
unique_id=self.unique_id)
for command in lammps_commands:
lmp.command(command)
for command in lammps_additional_commands:
lmp.command(command)
# to handle non-orthogonal unit cells
if 'lattice' in properties:
lengths, angles_r = lmp.box.lengths_angles
angles = [math.degrees(_) for _ in angles_r]
results['lattice'] = pmg.Lattice.from_parameters(
*lengths, *angles).matrix
if 'positions' in properties:
results['positions'] = np.dot(lmp.system.positions.copy(),
inv_rotation_matrix)
if 'stress' in properties:
S = lmp.thermo.computes['thermo_press'].vector
results['stress'] = np.array([[S[0], S[3],
S[5]], [S[3], S[1], S[4]],
[S[5], S[4], S[2]]])
if 'energy' in properties:
results['energy'] = lmp.thermo.computes[
'thermo_pe'].scalar + lmp.thermo.computes['my_ke'].scalar
if 'forces' in properties:
results['forces'] = lmp.system.forces.copy()
if 'symbols' in properties:
results['symbols'] = [elements[i - 1] for i in lmp.system.types[0]]
if 'velocities' in properties:
results['velocities'] = np.dot(lmp.system.velocities.copy(),
inv_rotation_matrix)
if 'timesteps' in properties:
results['timesteps'] = lmp.time_step
# compatibility...
future = asyncio.Future()
future.set_result({'results': results})
return future