def test_get_endpoint_dist(self):
ep0 = Structure.from_file(get_path("POSCAR_ep0", dirname="io_files"))
ep1 = Structure.from_file(get_path("POSCAR_ep1", dirname="io_files"))
distances = get_endpoint_dist(ep0, ep1)
self.assertAlmostEqual(max(distances), 6.3461081051543893, 7)
self.assertEqual(min(distances), 0.0)
def run_task(self, fw_spec):
label = self["label"]
assert label in ["parent", "ep0", "ep1"] or "neb" in label, "Unknown label!"
d_img = float(self.get("d_img", 0.7)) # Angstrom
wf_name = fw_spec["wf_name"]
src_dir = os.path.abspath(".")
dest_dir = os.path.join(fw_spec["_fw_env"]["run_dest_root"], wf_name, label)
shutil.copytree(src_dir, dest_dir)
# Update fw_spec based on the type of calculations.
if "neb" in label:
# Update all relaxed images.
subs = glob.glob("[0-2][0-9]")
nimages = len(subs)
concar_list = ["{:02}/CONTCAR".format(i) for i in range(nimages)[1:-1]]
images = [Structure.from_file(contcar) for contcar in concar_list]
# Update the two ending "images".
images.insert(0, Structure.from_file("00/POSCAR"))
images.append(Structure.from_file("{:02}/POSCAR".format(nimages - 1)))
images = [s.as_dict() for s in images]
neb = fw_spec.get("neb")
neb.append(images)
update_spec = {"neb": neb, "_queueadapter": {"nnodes": str(len(images) - 2),
"nodes": str(len(images) - 2)}}
# Use neb walltime if it is in fw_spec
if fw_spec["neb_walltime"] is not None:
update_spec["_queueadapter"].update({"walltime": fw_spec.get("neb_walltime")})
elif label in ["ep0", "ep1"]:
# Update relaxed endpoint structures.
file = glob.glob("CONTCAR*")[0]
ep = Structure.from_file(file, False) # One endpoint
if fw_spec.get("incar_images"): # "incar_images": pre-defined image number.
update_spec = {label: ep.as_dict(),
"_queueadapter": {"nnodes": fw_spec["incar_images"],
"nodes": fw_spec["incar_images"]}}
else:
# Calculate number of images if "IMAGES" tag is not provided.
index = int(label[-1])
ep_1_dict = fw_spec.get("ep{}".format(1 - index)) # Another endpoint
try:
ep_1 = Structure.from_dict(ep_1_dict)
except:
ep_1 = ep_1_dict
max_dist = max(get_endpoint_dist(ep, ep_1))
nimages = round(max_dist / d_img) or 1
update_spec = {label: ep, "_queueadapter": {"nnodes": int(nimages),
"nodes": int(nimages)}}
# Use neb walltime if it is in fw_spec
if fw_spec["neb_walltime"] is not None:
update_spec["_queueadapter"].update({"walltime": fw_spec.get("neb_walltime")})
else: # label == "parent"
f = glob.glob("CONTCAR*")[0]
s = Structure.from_file(f, False)
ep0, ep1 = get_endpoints_from_index(s, fw_spec["site_indices"])
update_spec = {"parent": s.as_dict(), "ep0": ep0.as_dict(), "ep1": ep1.as_dict()}
# Clear current directory.
for d in os.listdir(src_dir):
try:
os.remove(os.path.join(src_dir, d))
except:
shutil.rmtree(os.path.join(src_dir, d))
return FWAction(update_spec=update_spec)
def run_task(self, fw_spec):
label = self["label"]
assert label in ["parent", "ep0", "ep1"
] or "neb" in label, "Unknown label!"
d_img = float(self.get("d_img", 0.7)) # Angstrom
wf_name = fw_spec["wf_name"]
src_dir = os.path.abspath(".")
dest_dir = os.path.join(fw_spec["_fw_env"]["run_dest_root"], wf_name,
label)
shutil.copytree(src_dir, dest_dir)
# Update fw_spec based on the type of calculations.
if "neb" in label:
# Update all relaxed images.
subs = glob.glob("[0-2][0-9]")
nimages = len(subs)
concar_list = [
"{:02}/CONTCAR".format(i) for i in range(nimages)[1:-1]
]
images = [Structure.from_file(contcar) for contcar in concar_list]
# Update the two ending "images".
images.insert(0, Structure.from_file("00/POSCAR"))
images.append(
Structure.from_file("{:02}/POSCAR".format(nimages - 1)))
images = [s.as_dict() for s in images]
neb = fw_spec.get("neb")
neb.append(images)
update_spec = {
"neb": neb,
"_queueadapter": {
"nnodes": str(len(images) - 2),
"nodes": str(len(images) - 2)
}
}
# Use neb walltime if it is in fw_spec
if fw_spec["neb_walltime"] is not None:
update_spec["_queueadapter"].update(
{"walltime": fw_spec.get("neb_walltime")})
elif label in ["ep0", "ep1"]:
# Update relaxed endpoint structures.
file = glob.glob("CONTCAR*")[0]
ep = Structure.from_file(file, False) # One endpoint
if fw_spec.get("incar_images"
): # "incar_images": pre-defined image number.
update_spec = {
label: ep.as_dict(),
"_queueadapter": {
"nnodes": fw_spec["incar_images"],
"nodes": fw_spec["incar_images"]
}
}
else:
# Calculate number of images if "IMAGES" tag is not provided.
index = int(label[-1])
ep_1_dict = fw_spec.get(
"ep{}".format(1 - index)) # Another endpoint
try:
ep_1 = Structure.from_dict(ep_1_dict)
except:
ep_1 = ep_1_dict
max_dist = max(get_endpoint_dist(ep, ep_1))
nimages = round(max_dist / d_img) or 1
update_spec = {
label: ep,
"_queueadapter": {
"nnodes": int(nimages),
"nodes": int(nimages)
}
}
# Use neb walltime if it is in fw_spec
if fw_spec["neb_walltime"] is not None:
update_spec["_queueadapter"].update(
{"walltime": fw_spec.get("neb_walltime")})
else: # label == "parent"
f = glob.glob("CONTCAR*")[0]
s = Structure.from_file(f, False)
ep0, ep1 = get_endpoints_from_index(s, fw_spec["site_indices"])
update_spec = {
"parent": s.as_dict(),
"ep0": ep0.as_dict(),
"ep1": ep1.as_dict()
}
# Clear current directory.
for d in os.listdir(src_dir):
try:
os.remove(os.path.join(src_dir, d))
except:
shutil.rmtree(os.path.join(src_dir, d))
return FWAction(update_spec=update_spec)
