def setUp(self):
"""
1) Basic check for pymatgen configurations.
2) Setup all test workflow.
"""
super(TestNudgedElasticBandWorkflow, self).setUp()
# Structures used for test:
parent = PymatgenTest.get_structure("Li2O")
parent.remove_oxidation_states()
parent.make_supercell(2)
ep0, ep1 = get_endpoints_from_index(parent, [0, 1])
neb_dir = [os.path.join(module_dir, "..", "..", "test_files", "neb_wf", "4", "inputs", "{:02}",
"POSCAR").format(i) for i in range(5)]
self.structures = [Structure.from_file(n) for n in neb_dir]
# Run fake vasp
test_yaml = os.path.join(module_dir, "../../test_files/neb_wf/config/neb_unittest.yaml")
with open(test_yaml, 'r') as stream:
self.config = yaml.safe_load(stream)
# Use scratch directory as destination directory for testing
self.config["common_params"]["_fw_env"] = {"run_dest_root": self.scratch_dir}
# Config 1: The parent structure & two endpoint indexes provided; need relaxation first.
self.config_1 = copy.deepcopy(self.config)
self.config_1["common_params"]["is_optimized"] = False
self.config_1["common_params"]["wf_name"] = "NEB_test_1"
# Config 2: The parent structure & two endpoint indexes provided; no need to relax.
self.config_2 = copy.deepcopy(self.config)
del self.config_2["fireworks"][0]
self.config_2["common_params"]["is_optimized"] = True
self.config_2["common_params"]["wf_name"] = "NEB_test_2"
# Config 3: Two endpoints provided; need to relax two endpoints.
self.config_3 = copy.deepcopy(self.config)
del self.config_3["fireworks"][0]
self.config_3["common_params"]["is_optimized"] = False
self.config_3["common_params"]["wf_name"] = "NEB_test_3"
# Config 4: Two relaxed endpoints provided; no need to relax two endpoints.
self.config_4 = copy.deepcopy(self.config_3)
del self.config_4["fireworks"][0]
self.config_4["common_params"]["is_optimized"] = True
self.config_4["common_params"]["wf_name"] = "NEB_test_4"
# Config 5: All images including two endpoints are provided.
self.config_5 = copy.deepcopy(self.config)
del self.config_5["fireworks"][0: 2]
self.config_5["common_params"]["wf_name"] = "NEB_test_5"
self.wf_1 = wf_nudged_elastic_band([parent], parent, self.config_1)
self.wf_2 = wf_nudged_elastic_band([parent], parent, self.config_2)
self.wf_3 = wf_nudged_elastic_band([ep0, ep1], parent, self.config_3)
self.wf_4 = wf_nudged_elastic_band([ep0, ep1], parent, self.config_4)
self.wf_5 = wf_nudged_elastic_band(self.structures, parent, self.config_5)
# Workflow without the config file
self.wf_6 = wf_nudged_elastic_band(self.structures, parent)
def setUp(self):
"""
1) Basic check for pymatgen configurations.
2) Setup all test workflow.
"""
super(TestNudgedElasticBandWorkflow, self).setUp()
# Structures used for test:
parent = PymatgenTest.get_structure("Li2O")
parent.remove_oxidation_states()
parent.make_supercell(2)
ep0, ep1 = get_endpoints_from_index(parent, [0, 1])
neb_dir = [os.path.join(module_dir, "..", "..", "test_files", "neb_wf", "4", "inputs", "{:02}",
"POSCAR").format(i) for i in range(5)]
self.structures = [Structure.from_file(n) for n in neb_dir]
# Run fake vasp
test_yaml = os.path.join(module_dir, "../../test_files/neb_wf/config/neb_unittest.yaml")
with open(test_yaml, 'r') as stream:
self.config = yaml.safe_load(stream)
# Use scratch directory as destination directory for testing
self.config["common_params"]["_fw_env"] = {"run_dest_root": self.scratch_dir}
# Config 1: The parent structure & two endpoint indexes provided; need relaxation first.
self.config_1 = copy.deepcopy(self.config)
self.config_1["common_params"]["is_optimized"] = False
self.config_1["common_params"]["wf_name"] = "NEB_test_1"
# Config 2: The parent structure & two endpoint indexes provided; no need to relax.
self.config_2 = copy.deepcopy(self.config)
del self.config_2["fireworks"][0]
self.config_2["common_params"]["is_optimized"] = True
self.config_2["common_params"]["wf_name"] = "NEB_test_2"
# Config 3: Two endpoints provided; need to relax two endpoints.
self.config_3 = copy.deepcopy(self.config)
del self.config_3["fireworks"][0]
self.config_3["common_params"]["is_optimized"] = False
self.config_3["common_params"]["wf_name"] = "NEB_test_3"
# Config 4: Two relaxed endpoints provided; no need to relax two endpoints.
self.config_4 = copy.deepcopy(self.config_3)
del self.config_4["fireworks"][0]
self.config_4["common_params"]["is_optimized"] = True
self.config_4["common_params"]["wf_name"] = "NEB_test_4"
# Config 5: All images including two endpoints are provided.
self.config_5 = copy.deepcopy(self.config)
del self.config_5["fireworks"][0: 2]
self.config_5["common_params"]["wf_name"] = "NEB_test_5"
self.wf_1 = wf_nudged_elastic_band([parent], parent, self.config_1)
self.wf_2 = wf_nudged_elastic_band([parent], parent, self.config_2)
self.wf_3 = wf_nudged_elastic_band([ep0, ep1], parent, self.config_3)
self.wf_4 = wf_nudged_elastic_band([ep0, ep1], parent, self.config_4)
self.wf_5 = wf_nudged_elastic_band(self.structures, parent, self.config_5)
# Workflow without the config file
self.wf_6 = wf_nudged_elastic_band(self.structures, parent)
def test_get_endpoints_from_index(self):
endpoints = get_endpoints_from_index(structure=self.structure,
site_indices=[0, 1])
ep_0 = endpoints[0].as_dict()
ep_1 = endpoints[1].as_dict()
ep_0_expect = Structure.from_file(get_path("POSCAR_ep0",
dirname="io_files")).as_dict()
ep_1_expect = Structure.from_file(get_path("POSCAR_ep1",
dirname="io_files")).as_dict()
self.assertEqual(ep_0, ep_0_expect)
self.assertEqual(ep_1, ep_1_expect)
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)
def get_wf_neb_from_structure(structure, user_incar_settings=None, additional_spec=None,
user_kpoints_settings=None, additional_cust_args=None):
"""
Obtain the CI-NEB workflow staring with a parent structure. This works only under the single
vacancy diffusion mechanism.
Workflow: (parent relaxation) --> Endpoints relaxation --> NEB_1 --> NEB_2 --> ... --> NEB_r
(i) If parent is not relaxed: then parent relaxation--ep--neb(r)
(r rounds of NEB)
(ii) If parent is relaxed: ep--neb(r) (r rounds of NEB)
Args:
structure (Structure): The parent structure.
user_incar_settings([dict]): Additional user_incar_settings. Note that the order of the
list is set as: "parent", "ep_relax", "neb1", "neb2" etc., which contains
at least three elements. The first dict is for parent structure relaxation,
the second dict is for endpoints relaxation, and the rest are for NEB
calculations. For example, [{}, {}, {"IOPT": 7}, {"IOPT": 1}]. Besides,
user_incar_settings is used to determine how many NEB rounds will be. Default
is [{}, {}, {}].
additional_spec (dict): User spec settings to overwrite default_spec.
user_kpoints_settings ([dict]): Additional user_kpoints_settings, which contains at at
least three elements, which is similar to user_incar_settings. For example,
[{}, {}, {"grid_density": 100}] for the workflow from the parent structure
relaxation, then the endpoint relaxation followed by one-round NEB simulation.
Default values depend on the selected VaspInputSet.
additional_cust_args ([dict]): Optional parameters for RunVaspCustodian, same structure
with user_incar_settings and user_kpoints_settings.
Returns:
Workflow
"""
spec = _update_spec(additional_spec)
site_indices = spec["site_indices"]
is_optimized = spec["is_optimized"]
wf_name = spec["wf_name"]
endpoints = get_endpoints_from_index(structure, site_indices)
# Default settings for "parent", "ep0" and "ep1". If is_optimized is False, spec["ep0"] and
# spec["ep1"] will be updated after parent relaxation.
spec["parent"] = structure.as_dict()
spec["ep0"], spec["ep1"] = endpoints[0].as_dict(), endpoints[1].as_dict()
# Assume one round NEB if user_incar_settings not provided.
user_incar_settings = user_incar_settings or [{}, {}, {}]
neb_round = len(user_incar_settings[2:])
user_kpoints_settings = user_kpoints_settings or [{"grid_density": 1000}] * (neb_round + 2)
additional_cust_args = additional_cust_args or [{}] * (neb_round + 2)
for incar in user_incar_settings[2:]:
if incar.get("IMAGES"):
# If "incar_images" shows up, the number of images is pre-defined
spec["incar_images"] = incar["IMAGES"]
break
if is_optimized: # Start from endpoints
neb_fws, rlx_fws = [], []
# Get neb fireworks.
for n in range(neb_round):
fw = NEBFW(spec=spec, neb_label=str(n + 1), from_images=False,
user_incar_settings=user_incar_settings[n + 2],
user_kpoints_settings=user_kpoints_settings[n + 2],
additional_cust_args=additional_cust_args[n + 2])
neb_fws.append(fw)
# Get relax fireworks
for label in ["ep0", "ep1"]:
fw = NEBRelaxationFW(spec=spec, label=label,
user_incar_settings=user_incar_settings[1],
user_kpoints_settings=user_kpoints_settings[1],
additional_cust_args=additional_cust_args[1])
rlx_fws.append(fw)
# Build fireworks link
links = {rlx_fws[0]: [neb_fws[0]], rlx_fws[1]: [neb_fws[0]]}
else: # Start from parent structure
neb_fws, rlx_fws = [], []
# Get neb fireworks.
for n in range(neb_round):
fw = NEBFW(spec=spec, neb_label=str(n + 1), from_images=False,
user_incar_settings=user_incar_settings[n + 2],
user_kpoints_settings=user_kpoints_settings[n + 2],
additional_cust_args=additional_cust_args[n + 2])
neb_fws.append(fw)
# Get relaxation fireworks.
rlx_fws.append(NEBRelaxationFW(spec=spec, label="parent",
user_incar_settings=user_incar_settings[0],
user_kpoints_settings=user_kpoints_settings[0],
additional_cust_args=additional_cust_args[0]))
for i, label in enumerate(["ep0", "ep1"]):
fw = NEBRelaxationFW(spec=spec, label=label,
user_incar_settings=user_incar_settings[1],
user_kpoints_settings=user_kpoints_settings[1],
additional_cust_args=additional_cust_args[1])
rlx_fws.append(fw)
# Build fireworks link
links = {rlx_fws[0]: [rlx_fws[1], rlx_fws[2]],
rlx_fws[1]: [neb_fws[0]],
rlx_fws[2]: [neb_fws[0]]}
# Put all fireworks together with link
fws = rlx_fws + neb_fws
if neb_round >= 2:
for r in range(1, neb_round):
links[neb_fws[r - 1]] = [neb_fws[r]]
workflow = Workflow(fws, links_dict=links, name=wf_name)
return workflow