def write_lammps(filename, struct, symbolsbasename='lmp.struct.symbols'):
"""Write Structure object to lammps format. That file can be read in a
lammps input file by ``read_data``. Write file ``lmp.struct.symbols`` with
atom symbols.
Parameters
----------
filename : str
name of file to write
symbolsbasename : str, optional
file for atom symbols
struct : Structure
References
----------
ase.calculators.lammpsrun (ASE 3.8).
"""
dr = os.path.dirname(filename)
fn = os.path.join(dr, symbolsbasename)
common.file_write(fn, '\n'.join(struct.symbols))
common.file_write(filename, lammps.struct_str(struct))
def write_lammps(filename, struct, symbolsbasename='lmp.struct.symbols'):
"""Write Structure object to lammps format. That file can be read in a
lammps input file by ``read_data``. Write file ``lmp.struct.symbols`` with
atom symbols.
Parameters
----------
filename : str
name of file to write
symbolsbasename : str, optional
file for atom symbols
struct : Structure
References
----------
ase.calculators.lammpsrun (ASE 3.8).
"""
dr = os.path.dirname(filename)
fn = os.path.join(dr, symbolsbasename)
common.file_write(fn, '\n'.join(struct.symbols))
common.file_write(filename, lammps.struct_str(struct))
templates = [
batch.FileTemplate(basename=x)
for x in ['lmp.in', 'lmp.struct', 'lmp.struct.symbols']
]
# rs-AlN
st = crys.Structure(coords_frac=np.array([[0.0] * 3, [0.5] * 3]),
symbols=['Al', 'N'],
cryst_const=np.array([2.78] * 3 + [60] * 3))
params_lst = []
for target_press in np.linspace(-20, 20, 15): # GPa, bar in lammps
params_lst.append([
sql.SQLEntry(key='target_press', sqlval=target_press * 1e4),
sql.SQLEntry(key='struct', sqlval=lammps.struct_str(st)),
sql.SQLEntry(key='symbols', sqlval='\n'.join(st.symbols)),
])
calc = batch.ParameterStudy(
machines=local,
templates=templates,
params_lst=params_lst,
study_name='lammps_ev',
)
calc.write_input(sleep=0, backup=False, mode='w')
if not os.path.exists('calc'):
os.symlink('calc_local', 'calc')
common.system("cp -r potentials calc_local/")
scratch='/tmp',
filename='calc.templ/job.local',
home='/home/schmerler')
templates = [batch.FileTemplate(basename=x) for x in
['lmp.in', 'lmp.struct', 'lmp.struct.symbols']]
# rs-AlN
st = crys.Structure(coords_frac=np.array([[0.0]*3, [0.5]*3]),
symbols=['Al','N'],
cryst_const=np.array([2.78]*3 + [60]*3))
params_lst = []
for target_press in np.linspace(-20,20,15): # GPa, bar in lammps
params_lst.append([sql.SQLEntry(key='target_press', sqlval=target_press*1e4),
sql.SQLEntry(key='struct', sqlval=lammps.struct_str(st)),
sql.SQLEntry(key='symbols', sqlval='\n'.join(st.symbols)),
])
calc = batch.ParameterStudy(machines=local,
templates=templates,
params_lst=params_lst,
study_name='lammps_ev',
)
calc.write_input(sleep=0, backup=False, mode='w')
if not os.path.exists('calc'):
os.symlink('calc_local', 'calc')
common.system("cp -r potentials calc_local/")