def test_xas_wflow_abatom_by_symbol(self):
wf_prim = get_wf_xas("O", self.structure, feff_input_set="XANES", edge="K",
use_primitive=True, user_tag_settings=self.user_tag_settings)
wf = get_wf_xas("O", self.structure, feff_input_set="XANES", edge="K",
use_primitive=False, user_tag_settings=self.user_tag_settings)
self.assertEqual(len(wf_prim.as_dict()["fws"]), 1)
self.assertEqual(len(wf.as_dict()["fws"]), 1)
def test_xanes_vs_exafs(self):
wf_xanes = get_wf_xas(self.absorbing_atom, self.structure, feff_input_set="XANES", edge="K",
user_tag_settings=self.user_tag_settings)
wf_exafs = get_wf_xas(self.absorbing_atom, self.structure, feff_input_set="EXAFS", edge="K")
self.assertEqual(wf_xanes.as_dict()["fws"][0]["spec"]['_tasks'][0]['feff_input_set']['@class'],
'MPXANESSet')
self.assertEqual(wf_exafs.as_dict()["fws"][0]["spec"]['_tasks'][0]['feff_input_set']['@class'],
'MPEXAFSSet')
def test_xas_wflow_abatom_by_idx(self):
if not FEFF_CMD:
# fake run
xmu_file_path = os.path.abspath(
os.path.join(module_dir, "../../test_files/xmu.dat"))
feff_bin = "cp {} .".format(xmu_file_path)
else:
feff_bin = FEFF_CMD
wf = get_wf_xas(self.absorbing_atom,
self.structure,
feff_input_set="XANES",
edge="K",
feff_cmd=feff_bin,
db_file=">>db_file<<",
use_primitive=False,
user_tag_settings=self.user_tag_settings)
self.assertEqual(len(wf.as_dict()["fws"]), 1)
self.lp.add_wf(wf)
# run
rapidfire(
self.lp,
fworker=FWorker(env={"db_file": os.path.join(db_dir, "db.json")}))
d = self.get_task_collection().find_one({"spectrum_type": "XANES"})
self._check_run(d)
def wf_Xanes_K_edge(structure, c=None):
c = c or {}
feff_cmd = c.get("FEFF_CMD", "feff_mpi")
db_file = c.get("DB_FILE", None)
metadata = c.get("METADATA", {})
absorbing_atom = c.get("ABSORBING_ATOM")
user_tag_settings = {
"RPATH": -1,
"SCF": "7 0 30 0.2 3",
"FMS": "9 0",
"LDOS": "-30.0 30.0 0.1",
"RECIPROCAL": "",
"EDGE": "K",
"COREHOLE": "RPA"
}
metadata.update({"absorbing_atom_idx": str(absorbing_atom)})
wf = get_wf_xas(absorbing_atom,
structure,
edge="K",
feff_cmd=feff_cmd,
db_file=db_file,
metadata=metadata,
user_tag_settings=user_tag_settings,
use_primitive=False)
return wf
def test_xas_wflow_abatom_by_idx(self):
if not FEFF_CMD:
# fake run
xmu_file_path = os.path.abspath(os.path.join(module_dir, "../../test_files/xmu.dat"))
feff_bin = "cp {} .".format(xmu_file_path)
else:
feff_bin = FEFF_CMD
wf = get_wf_xas(self.absorbing_atom, self.structure, feff_input_set="XANES", edge="K",
feff_cmd=feff_bin, db_file=">>db_file<<", use_primitive=False,
user_tag_settings=self.user_tag_settings)
self.assertEqual(len(wf.as_dict()["fws"]), 1)
self.lp.add_wf(wf)
# run
rapidfire(self.lp, fworker=FWorker(env={"db_file": os.path.join(db_dir, "db.json")}))
d = self.get_task_collection().find_one({"spectrum_type": "XANES"})
self._check_run(d)
def wf_Xanes_K_edge(structure, c=None):
c = c or {}
feff_cmd = c.get("FEFF_CMD", "feff_mpi")
db_file = c.get("DB_FILE", None)
metadata = c.get("METADATA", {})
absorbing_atom = c.get("ABSORBING_ATOM")
user_tag_settings = {"RPATH": -1,
"SCF": "7 0 30 0.2 3",
"FMS": "9 0",
"LDOS": "-30.0 30.0 0.1",
"RECIPROCAL": "",
"EDGE": "K",
"COREHOLE": "RPA"}
metadata.update({"absorbing_atom_idx": str(absorbing_atom)})
wf = get_wf_xas(absorbing_atom, structure, edge="K", feff_cmd=feff_cmd, db_file=db_file,
metadata=metadata, user_tag_settings=user_tag_settings, use_primitive=False)
return wf
