def write_structure(self, cwd, file_name="structure_wrapper.sx"):
structure_file_name = "structure.sx"
iw = InputWriter()
iw.structure = self.structure
iw.write_structure(file_name=structure_file_name, cwd=cwd)
with open(os.path.join(cwd, file_name), "w") as f:
f.writelines(["structure { include <" + structure_file_name + ">; }"])
def _start_process(
self,
structure,
executable,
maxDist=5,
ionic_steps=1000,
ionic_energy_tolerance=1.0e-3,
ionic_force_tolerance=1.0e-2,
max_step_length=1.0e-1,
soft_mode_damping=1,
selective_dynamics=False,
ssa=False,
):
if selective_dynamics:
input_writer_obj = InputWriter()
input_writer_obj.structure = structure
if ssa:
input_writer_obj.structure.set_initial_magnetic_moments(len(structure)*[None])
input_writer_obj.write_structure(
file_name="structure.sx",
cwd=self.working_directory,
structure_str=None,
symmetry_enabled=True,
keep_angstrom=True,
)
self._write_input(
working_directory=self.working_directory,
maxDist=maxDist,
ionic_steps=ionic_steps,
ionic_energy_tolerance=ionic_energy_tolerance,
ionic_force_tolerance=ionic_force_tolerance,
max_step_length=max_step_length,
soft_mode_damping=soft_mode_damping,
selective_dynamics=selective_dynamics,
)
shell = os.name == "nt"
try:
with open(
posixpath.join(self.working_directory, "out.txt"), mode="w"
) as f_out:
with open(
posixpath.join(self.working_directory, "error.txt"), mode="w"
) as f_err:
self._process = subprocess.Popen(
[executable],
cwd=self.working_directory,
shell=shell,
stdout=f_out,
stderr=f_err,
universal_newlines=True,
)
except subprocess.CalledProcessError as e:
raise ValueError("run_job.py crashed")
while not self._interactive_pipes_initialized(self.working_directory):
time.sleep(1)
self._interactive_initialize_interface()