def test_image_num(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
test_file_dir = os.path.join(module_dir, "..", "..", "..", "test_files",
"path_finder")
start_s = Poscar.from_file(os.path.join(test_file_dir, 'LFP_POSCAR_s')).structure
end_s = Poscar.from_file(os.path.join(test_file_dir, 'LFP_POSCAR_e')).structure
mid_s = start_s.interpolate(end_s, nimages=2,
interpolate_lattices=False)[1]
chg = Chgcar.from_file(os.path.join(test_file_dir, 'LFP_CHGCAR.gz'))
moving_cation_specie = Element('Li')
relax_sites = []
for site_i, site in enumerate(start_s.sites):
if site.specie == moving_cation_specie:
relax_sites.append(site_i)
pf = NEBPathfinder(start_s, end_s, relax_sites=relax_sites,
v=ChgcarPotential(chg).get_v(), n_images=(8 * 3))
images = []
for i, image in enumerate(pf.images):
if i % 3 == 0:
images.append(image)
self.assertEqual(len(images), 9)
pf_mid = NEBPathfinder(start_s, end_s, relax_sites=relax_sites,
v=ChgcarPotential(chg).get_v(), n_images=10, mid_struct=mid_s)
moving_site = relax_sites[0]
dists = [s1.sites[moving_site].distance(s2.sites[moving_site])
for s1, s2 in zip(pf.images[:-1], pf.images[1:])]
# check that all the small distances are about equal
self.assertTrue(abs(min(dists)-max(dists))/mean(dists) < 0.02)
def find_path(self, end_structure, images, sites=[], charge=None):
from pymatgen.analysis.path_finder import NEBPathfinder
from pymatgen.analysis.path_finder import FreeVolumePotential
from pymatgen.analysis.path_finder import ChgcarPotential
init_struct = self.poscar.structure
final_struct = end_structure
if charge is None:
dim = [50, 50, 120]
v = FreeVolumePotential(final_struct, dim)
obj = NEBPathfinder(init_struct,
final_struct,
sites,
v.get_v(),
n_images=images)
obj.interpolate()
new_path = obj.images
else:
v = ChgcarPotential(charge)
obj = NEBPathfinder(init_struct,
final_struct, [80, 81, 82],
v.get_v(),
n_images=images)
obj.interpolate()
new_path = obj.images
joblist = []
for index, item in enumerate(new_path):
filepath = os.path.join(self.foldname, '{0:02d}'.format(index))
joblist.append(easyjob(item, filepath))
return joblist
def _get_pathfinder_from_hop(self, migration_path, n_images=20):
# get migration pathfinder objects which contains the paths
ipos = migration_path.isite.frac_coords
epos = migration_path.esite.frac_coords
mpos = migration_path.esite.frac_coords
start_struct = self.base_aeccar.structure.copy()
end_struct = self.base_aeccar.structure.copy()
mid_struct = self.base_aeccar.structure.copy()
# the moving ion is always inserted on the zero index
start_struct.insert(0,
self.migrating_specie,
ipos,
properties=dict(magmom=0))
end_struct.insert(0,
self.migrating_specie,
epos,
properties=dict(magmom=0))
mid_struct.insert(0,
self.migrating_specie,
mpos,
properties=dict(magmom=0))
chgpot = ChgcarPotential(self.base_aeccar, normalize=False)
npf = NEBPathfinder(
start_struct,
end_struct,
relax_sites=[0],
v=chgpot.get_v(),
n_images=n_images,
mid_struct=mid_struct,
)
return npf
def test_image_num(self):
os.path.dirname(os.path.abspath(__file__))
test_file_dir = os.path.join(PymatgenTest.TEST_FILES_DIR,
"path_finder")
start_s = Poscar.from_file(os.path.join(test_file_dir,
"LFP_POSCAR_s")).structure
end_s = Poscar.from_file(os.path.join(test_file_dir,
"LFP_POSCAR_e")).structure
chg = Chgcar.from_file(os.path.join(test_file_dir, "LFP_CHGCAR.gz"))
moving_cation_specie = Element("Li")
relax_sites = []
for site_i, site in enumerate(start_s.sites):
if site.specie == moving_cation_specie:
relax_sites.append(site_i)
pf = NEBPathfinder(
start_s,
end_s,
relax_sites=relax_sites,
v=ChgcarPotential(chg).get_v(),
n_images=(8 * 3),
)
images = []
for i, image in enumerate(pf.images):
if i % 3 == 0:
images.append(image)
self.assertEqual(len(images), 9)
moving_site = relax_sites[0]
dists = [
s1.sites[moving_site].distance(s2.sites[moving_site])
for s1, s2 in zip(pf.images[:-1], pf.images[1:])
]
# check that all the small distances are about equal
self.assertTrue(abs(min(dists) - max(dists)) / mean(dists) < 0.02)
def test_image_num(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
test_file_dir = os.path.join(module_dir, "..", "..", "..",
"test_files", "path_finder")
start_s = Poscar.from_file(os.path.join(test_file_dir,
'LFP_POSCAR_s')).structure
end_s = Poscar.from_file(os.path.join(test_file_dir,
'LFP_POSCAR_e')).structure
chg = Chgcar.from_file(os.path.join(test_file_dir, 'LFP_CHGCAR.gz'))
moving_cation_specie = Element('Li')
relax_sites = []
for site_i, site in enumerate(start_s.sites):
if site.specie == moving_cation_specie:
relax_sites.append(site_i)
pf = NEBPathfinder(start_s,
end_s,
relax_sites=relax_sites,
v=ChgcarPotential(chg).get_v(),
n_images=(8 * 3))
images = []
for i, image in enumerate(pf.images):
if i % 3 == 0:
images.append(image)
self.assertEqual(len(images), 9)
def neb(directory,
nimages=7,
functional=("pbe", {}),
is_metal=False,
is_migration=False):
"""
Set up the NEB calculation from the initial and final structures.
Args:
directory (str): Directory in which the transition calculations should be
set up.
functional (tuple): Tuple with the functional choices. The first element
contains a string that indicates the functional used ("pbe", "hse", ...),
whereas the second element contains a dictionary that allows the user
to specify the various functional tags.
nimages (int): Number of images to use in the NEB calculation.
is_metal (bool): Flag that indicates the material being studied is a
metal, which changes the smearing from Gaussian to second order
Methfessel-Paxton of 0.2 eV.
is_migration (bool): Flag that indicates that the transition is a migration
of an atom in the structure.
Returns:
None
"""
directory = os.path.abspath(directory)
# Extract the optimized initial and final geometries
initial_dir = os.path.join(directory, "initial")
final_dir = os.path.join(directory, "final")
try:
# Check to see if the initial final_cathode structure is present
initial_structure = Cathode.from_file(
os.path.join(initial_dir,
"final_cathode.json")).as_ordered_structure()
except FileNotFoundError:
# In case the required json file is not present, check to see if
# there is VASP output which can be used
initial_structure = Structure.from_file(
os.path.join(initial_dir, "CONTCAR"))
# Add the magnetic configuration to the initial structure
initial_out = Outcar(os.path.join(initial_dir, "OUTCAR"))
initial_magmom = [site["tot"] for site in initial_out.magnetization]
try:
initial_structure.add_site_property("magmom", initial_magmom)
except ValueError:
if len(initial_magmom) == 0:
print("No magnetic moments found in OUTCAR file. Setting "
"magnetic moments to zero.")
initial_magmom = [0] * len(initial_structure)
initial_structure.add_site_property("magmom", initial_magmom)
else:
raise ValueError("Number of magnetic moments in OUTCAR file "
"do not match the number of sites!")
except BaseException:
raise FileNotFoundError("Could not find required structure "
"information in " + initial_dir + ".")
try:
final_structure = Structure.from_file(
os.path.join(final_dir, "CONTCAR"))
except FileNotFoundError:
final_structure = Cathode.from_file(
os.path.join(final_dir,
"final_cathode.json")).as_ordered_structure()
# In case the transition is a migration
if is_migration:
# Set up the static potential for the Pathfinder from the host charge
# density
host_charge_density = Chgcar.from_file(os.path.join(directory, "host"))
host_potential = ChgcarPotential(host_charge_density)
migration_site_index = find_migrating_ion(initial_structure,
final_structure)
neb_path = NEBPathfinder(start_struct=initial_structure,
end_struct=final_structure,
relax_sites=migration_site_index,
v=host_potential)
images = neb_path.images
neb_path.plot_images("neb.vasp")
# In case an "middle image" has been provided via which to interpolate
elif os.path.exists(os.path.join(directory, "middle")):
print("Found a 'middle' directory in the NEB directory. Interpolating "
"via middle geometry.")
# Load the middle image
middle_structure = Structure.from_file(
os.path.join(directory, "middle", "CONTCAR"))
# Perform an interpolation via this image
images_1 = initial_structure.interpolate(
end_structure=middle_structure,
nimages=int((nimages + 1) / 2),
interpolate_lattices=True)
images_2 = middle_structure.interpolate(end_structure=final_structure,
nimages=int((nimages) / 2 + 1),
interpolate_lattices=True)
images = images_1[:-1] + images_2
else:
# Linearly interpolate the initial and final structures
images = initial_structure.interpolate(end_structure=final_structure,
nimages=nimages + 1,
interpolate_lattices=True)
# TODO Add functionality for NEB calculations with changing lattices
user_incar_settings = {}
# Set up the functional
if functional[0] != "pbe":
functional_config = _load_yaml_config(functional[0] + "Set")
functional_config["INCAR"].update(functional[1])
user_incar_settings.update(functional_config["INCAR"])
# Add the standard Methfessel-Paxton smearing for metals
if is_metal:
user_incar_settings.update({"ISMEAR": 2, "SIGMA": 0.2})
neb_calculation = PybatNEBSet(images,
potcar_functional=DFT_FUNCTIONAL,
user_incar_settings=user_incar_settings)
# Set up the NEB calculation
neb_calculation.write_input(directory)
# Make a file to visualize the transition
neb_calculation.visualize_transition(
os.path.join(directory, "transition.cif"))
def run_task(self, fw_spec):
n_images = self["n_images"]
end_points_combo = self["end_points_combo"]
# checks if format of end_points_combo is correct and if so
# get two desired end_points indexes for end point structures
try:
combo = end_points_combo.split("+")
if len(combo) == 2:
c = [int(combo[0]), int(combo[1])]
else:
raise ValueError(
"NEBPathfinder requires exactly two end points")
except:
raise ValueError("{} end_points_combo input is incorrect".format(
str(end_points_combo)))
# get the database connection
db_file = env_chk(self["db_file"], fw_spec)
mmdb = VaspCalcDb.from_db_file(db_file, admin=True)
mmdb.collection = mmdb.db["approx_neb"]
wf_uuid = self["approx_neb_wf_uuid"]
# get end_points and task_id of host from approx_neb collection
approx_neb_doc = mmdb.collection.find_one({"wf_uuid": wf_uuid}, {
"end_points": 1,
"host.task_id": 1,
"_id": 0
})
end_points = approx_neb_doc["end_points"]
task_id = approx_neb_doc["host"]["task_id"]
# get potential gradient, v, from host chgcar
mmdb.collection = mmdb.db["tasks"]
host_chgcar = mmdb.get_chgcar(task_id)
v_chgcar = ChgcarPotential(host_chgcar)
host_v = v_chgcar.get_v()
# get start and end point structures from end_points
start_struct = Structure.from_dict(
end_points[c[0]]["output"]["structure"])
end_struct = Structure.from_dict(
end_points[c[1]]["output"]["structure"])
# checks if inserted site indexes match
inserted_site_indexes = end_points[c[0]]["inserted_site_indexes"]
if inserted_site_indexes != end_points[c[1]]["inserted_site_indexes"]:
raise ValueError(
"Inserted site indexes of end point structures must match for NEBPathfinder"
)
# applies NEBPathFinder to interpolate and get images to store in
# pathfinder_output.
neb_pf = NEBPathfinder(
start_struct,
end_struct,
relax_sites=inserted_site_indexes,
v=host_v,
n_images=n_images + 1,
)
# note NEBPathfinder currently returns n_images+1 images (rather than n_images)
# and the first and last images generated are very similar to the end points
# provided so they are discarded
pathfinder_output = {
"images":
[structure.as_dict() for structure in neb_pf.images[1:-1]],
"relax_site_indexes": inserted_site_indexes,
}
# stores images generated by NEBPathFinder in approx_neb collection
# pathfinder field which is a nested dictionary using
# end_points_combo as a key.
mmdb.collection = mmdb.db["approx_neb"]
pf_subdoc = mmdb.collection.find_one({"wf_uuid": wf_uuid}, {
"pathfinder": 1,
"_id": 0
})
if "pathfinder" not in pf_subdoc.keys():
pf_subdoc = {}
else:
pf_subdoc = pf_subdoc["pathfinder"]
pf_subdoc.update({end_points_combo: pathfinder_output})
mmdb.collection.update_one(
{"wf_uuid": wf_uuid},
{
"$set": {
"pathfinder": pf_subdoc,
"last_updated": datetime.utcnow()
}
},
)
return FWAction(
stored_data={
"wf_uuid": wf_uuid,
"end_points_combo": c,
"pathfinder": pathfinder_output,
})