def _reload(self):
pr = Project(path=self._job_project_path)
self._job = pr.load(self._job_name)
self._job.interactive_open()
self._job.interactive_initialize_interface()
self._job.calc_static()
self._job.run(run_again=True)
def _initialize(self, ref_job_full_path, structure):
loc = self.get_graph_location()
name = loc + '_job'
project_path, ref_job_path = split(ref_job_full_path)
pr = Project(path=project_path)
ref_job = pr.load(ref_job_path)
job = ref_job.copy_to(project=pr,
new_job_name=name,
input_only=True,
new_database_entry=True)
if structure is not None:
job.structure = structure
if isinstance(job, GenericInteractive):
job.interactive_open()
if isinstance(job, LammpsInteractive) and self._fast_lammps_mode:
# Note: This might be done by default at some point in LammpsInteractive, and could then be removed here
job.interactive_flush_frequency = 10**10
job.interactive_write_frequency = 10**10
self._disable_lmp_output = True
job.calc_static()
job.run(run_again=True)
# TODO: Running is fine for Lammps, but wasteful for DFT codes! Get the much cheaper interface
# initialization working -- right now it throws a (passive) TypeError due to database issues
else:
raise TypeError('Job of class {} is not compatible.'.format(
ref_job.__class__))
self._job = job
self._job_name = name
self._job_project_path = project_path
def command_line(argv):
"""
Parse the command line arguments.
Args:
argv: Command line arguments
"""
input_path = None
output_path = None
try:
opts, args = getopt.getopt(argv, "i:o:h",
["input_path=", "output_path=", "help"])
except getopt.GetoptError:
print(
'python -m pyiron.base.job.reloadfile -i <inputpath> -o <outputpath>'
)
sys.exit()
else:
for opt, arg in opts:
if opt in ("-i", "--input_path"):
input_path = os.path.abspath(arg)
if opt in ("-o", "--output_path"):
output_path = os.path.abspath(arg)
with h5py.File(input_path, 'r') as f:
job_name = list(f.keys())[0]
project_path = os.path.join(os.path.abspath('.'), job_name + '.h5')
shutil.copy(input_path, project_path)
file = os.path.basename(project_path)
job_name = os.path.splitext(file)[0]
db_project_path = s.top_path(project_path)
project = os.path.dirname(project_path)
db_project = (project + '/').replace(db_project_path, '')
job_reload = Project(project).load_from_jobpath(job_id=None,
db_entry={
'id': 1000,
'status': '',
'chemicalformula':
'',
'job': job_name,
'subjob':
'/' + job_name,
'projectpath':
db_project_path,
'project':
db_project,
'hamilton': '',
'hamversion': '',
'parentid': None,
'masterid': None
},
convert_to_object=True)
job_reload.status.initialized = True
job_reload.server.run_mode.modal = True
job_reload.run()
shutil.copy(project_path, output_path)
sys.exit()
def command_line(argv):
"""
Parse the command line arguments.
Args:
argv: Command line arguments
"""
input_path = None
output_path = None
try:
opts, args = getopt.getopt(argv, "i:o:h",
["input_path=", "output_path=", "help"])
except getopt.GetoptError:
print(
"python -m pyiron.base.job.reloadfile -i <inputpath> -o <outputpath>"
)
sys.exit()
else:
for opt, arg in opts:
if opt in ("-i", "--input_path"):
input_path = os.path.abspath(arg)
if opt in ("-o", "--output_path"):
output_path = os.path.abspath(arg)
with h5py.File(input_path, "r") as f:
job_name = list(f.keys())[0]
project_path = os.path.join(os.path.abspath("."), job_name + ".h5")
shutil.copy(input_path, project_path)
file = os.path.basename(project_path)
job_name = os.path.splitext(file)[0]
db_project_path = s.top_path(project_path)
project = os.path.dirname(project_path)
db_project = (project + "/").replace(db_project_path, "")
job_reload = Project(project).load_from_jobpath(
job_id=None,
db_entry={
"id": 1000,
"status": "",
"chemicalformula": "",
"job": job_name,
"subjob": "/" + job_name,
"projectpath": db_project_path,
"project": db_project,
"hamilton": "",
"hamversion": "",
"parentid": None,
"masterid": None,
},
convert_to_object=True,
)
job_reload.status.initialized = True
job_reload.server.run_mode.modal = True
job_reload.run()
shutil.copy(project_path, output_path)
sys.exit()
import sys
from pyiron import Project, __version__
pr = Project("tests/static/backwards/")
for job in pr.iter_jobs(recursive=True, convert_to_object=False):
if job.name == "sphinx":
job = job.to_object()
job.run()
print("job {} loaded from {}".format(job.id, sys.argv[0]))
def tearDownClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
project = Project(os.path.join(cls.execution_path, "test_project"))
project.remove_jobs_silently(recursive=True)
project.remove(enable=True)
def setUpClass(cls):
cls.execution_path = os.path.dirname(os.path.abspath(__file__))
# print(cls.execution_path)
cls.project = Project(os.path.join(cls.execution_path, "test_project"))
import sys
from pyiron import Project, __version__
pr = Project(
"tests/static/backwards/V{}".format(__version__).replace(".", "_")
)
structure = pr.create_ase_bulk("Al")
job = pr.create_job(pr.job_type.Sphinx, "sphinx")
job.structure = structure
job.save()
print("job {} saved from {}".format(job.id, sys.argv[0]))