Source code for pymatgen.analysis.diffusion.aimd.clustering
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
@@ -166,7 +165,7 @@ Source code for pymatgen.analysis.diffusion.aimd.clustering
iterations: Number of iterations thus far.
"""
if iterations > self.max_iterations:
- warnings.warn("Max iterations %d reached!" % self.max_iterations)
+ warnings.warn(f"Max iterations {self.max_iterations} reached!")
return True
if old_centroids is None:
return False
@@ -242,7 +241,7 @@ Source code for pymatgen.analysis.diffusion.aimd.clustering
iterations: Number of iterations thus far.
"""
if iterations > self.max_iterations:
- warnings.warn("Max iterations %d reached!" % self.max_iterations)
+ warnings.warn(f"Max iterations {self.max_iterations} reached!")
return True
if old_centroids is None:
return False
@@ -295,7 +294,7 @@ Source code for pymatgen.analysis.diffusion.aimd.clustering
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html
index d1c1b30d..d436d038 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.aimd.pathway — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.aimd.pathway — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.aimd.pathway
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.aimd.pathway
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
@@ -232,9 +231,9 @@ Source code for pymatgen.analysis.diffusion.aimd.pathway
if nc < nions:
raise ValueError(
- "The number of clusters ({}) is smaller than that of "
- "mobile ions ({})! Please try to decrease either "
- "'p_ratio' or 'd_cut' values!".format(nc, nions)
+ f"The number of clusters ({nc}) is smaller than that of "
+ f"mobile ions ({nions})! Please try to decrease either "
+ "'p_ratio' or 'd_cut' values!"
)
# For each low-energy site (cluster centroid), its coordinates are obtained
@@ -287,21 +286,22 @@ Source code for pymatgen.analysis.diffusion.aimd.pathway
f.write(" 1.00 \n")
for i in range(3):
- f.write(" {0} {1} {2} \n".format(*self.structure.lattice.matrix[i, :]))
+ v = self.structure.lattice.matrix[i, :]
+ f.write(f" {v[0]} {v[1]} {v[2]} \n")
f.write(" " + " ".join(symbols) + "\n")
f.write(" " + " ".join(natoms) + "\n")
f.write("direct\n")
for fcoord in init_fcoords:
- f.write(" {0:.8f} {1:.8f} {2:.8f} \n".format(*fcoord))
+ f.write(" {:.8f} {:.8f} {:.8f} \n".format(*fcoord)) # pylint: disable=C0209
f.write(" \n")
- f.write(" {0} {1} {2} \n".format(*self.lens))
+ f.write(" {} {} {} \n".format(*self.lens)) # pylint: disable=C0209
for i in range(self.lens[2]):
for j in range(self.lens[1]):
for k in range(self.lens[0]):
- f.write(" {0:.10e} ".format(self.Pr[k, j, i] * VolinAu))
+ f.write(f" {(self.Pr[k, j, i] * VolinAu):.10e} ")
if count % 5 == 0:
f.write("\n")
count += 1
@@ -414,7 +414,7 @@ Source code for pymatgen.analysis.diffusion.aimd.pathway
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html
index 764dd192..ed2cd7f9 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.aimd.rdf — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.aimd.rdf — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.aimd.rdf
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.aimd.rdf
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
@@ -299,7 +298,7 @@ Source code for pymatgen.analysis.diffusion.aimd.rdf
label="Peaks",
)
- plt.xlabel("$r$ ($\\rm\AA$)")
+ plt.xlabel("$r$ ($\\rm\\AA$)")
plt.ylabel("$g(r)$")
plt.legend(loc="upper right", fontsize=36)
plt.xlim(xlim[0], xlim[1])
@@ -326,7 +325,7 @@ Source code for pymatgen.analysis.diffusion.aimd.rdf
f.write("\n")
for r, gr in zip(self.interval, self.rdf):
- f.write(delimiter.join(["%s" % v for v in [r, gr]]))
+ f.write(delimiter.join([str(v) for v in [r, gr]]))
f.write("\n")
@@ -491,8 +490,8 @@ Source code for pymatgen.analysis.diffusion.aimd.rdf
& (self.distances[index] > 1e-8)
)
- density = sum([self.density[index][i] for i in species])
- natoms = sum([self.natoms[index][i] for i in ref_species])
+ density = sum(self.density[index][i] for i in species)
+ natoms = sum(self.natoms[index][i] for i in ref_species)
distances = self.distances[index][indices]
counts = self._dist_to_counts(distances)
rdf_temp = counts / density / self.volumes / natoms
@@ -518,7 +517,7 @@ Source code for pymatgen.analysis.diffusion.aimd.rdf
all_rdf = self.get_rdf(ref_species, species, is_average=False)[1]
if isinstance(species, str):
species = [species]
- density = [sum([i[j] for j in species]) for i in self.density]
+ density = [sum(i[j] for j in species) for i in self.density]
cn = [np.cumsum(rdf * density[i] * 4.0 * np.pi * self.r ** 2 * self.dr) for i, rdf in enumerate(all_rdf)]
if is_average:
cn = np.mean(cn, axis=0)
@@ -555,7 +554,7 @@ Source code for pymatgen.analysis.diffusion.aimd.rdf
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html
index 55de69da..74b80bb7 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.aimd.tests.test_clustering — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.aimd.tests.test_clustering — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.aimd.tests.test_clustering
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.aimd.tests.test_clustering
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
@@ -128,7 +127,7 @@ Source code for pymatgen.analysis.diffusion.aimd.tests.test_clustering
<
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_pathway.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_pathway.html
index e8e1010d..45b2b67e 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_pathway.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_pathway.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.aimd.tests.test_pathway — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.aimd.tests.test_pathway — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.aimd.tests.test_pathway
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.aimd.tests.test_pathway
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
__author__ = "Iek-Heng Chu"
@@ -89,7 +88,7 @@ Source code for pymatgen.analysis.diffusion.aimd.tests.test_pathway
[docs] def test_probability_classmethod(self):
file = os.path.join(tests_dir, "cNa3PS4_pda.json")
- data = json.load(open(file, "r"))
+ data = json.load(open(file))
diff_analyzer = DiffusionAnalyzer.from_dict(data)
# ProbabilityDensityAnalysis object
@@ -103,7 +102,7 @@ Source code for pymatgen.analysis.diffusion.aimd.tests.test_pathway
[docs] def test_generate_stable_sites(self):
file = os.path.join(tests_dir, "cNa3PS4_pda.json")
- data = json.load(open(file, "r"))
+ data = json.load(open(file))
diff_analyzer = DiffusionAnalyzer.from_dict(data)
# ProbabilityDensityAnalysis object
@@ -141,7 +140,7 @@ Source code for pymatgen.analysis.diffusion.aimd.tests.test_pathway
[docs] def test_site_occupancy_classmethod(self):
file = os.path.join(tests_dir, "cNa3PS4_pda.json")
- data = json.load(open(file, "r"))
+ data = json.load(open(file))
diff_analyzer = DiffusionAnalyzer.from_dict(data)
structure = diff_analyzer.structure
@@ -176,7 +175,7 @@ Source code for pymatgen.analysis.diffusion.aimd.tests.test_pathway
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_rdf.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_rdf.html
index a275133f..f5549ab6 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_rdf.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_rdf.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.aimd.tests.test_rdf — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.aimd.tests.test_rdf — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.aimd.tests.test_rdf
@@ -111,7 +111,7 @@ Source code for pymatgen.analysis.diffusion.aimd.tests.test_rdf
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_van_hove.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_van_hove.html
index dbf619ef..b60f2098 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_van_hove.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_van_hove.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.aimd.tests.test_van_hove — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.aimd.tests.test_van_hove — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.aimd.tests.test_van_hove
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.aimd.tests.test_van_hove
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
from pymatgen.core import Structure, Lattice
@@ -257,7 +256,7 @@ Source code for pymatgen.analysis.diffusion.aimd.tests.test_van_hove
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/van_hove.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/van_hove.html
index 0e905d26..3097aa22 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/aimd/van_hove.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/aimd/van_hove.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.aimd.van_hove — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.aimd.van_hove — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.aimd.van_hove
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.aimd.van_hove
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
@@ -266,7 +265,7 @@ Source code for pymatgen.analysis.diffusion.aimd.van_hove
grt = self.gsrt.copy()
vmax = 1.0
cb_ticks = [0, 1]
- cb_label = "4$\pi r^2G_s$($t$,$r$)"
+ cb_label = r"4$\pi r^2G_s$($t$,$r$)"
y = np.arange(np.shape(grt)[1]) * self.interval[-1] / float(len(self.interval) - 1)
x = np.arange(np.shape(grt)[0]) * self.timeskip
@@ -282,7 +281,7 @@ Source code for pymatgen.analysis.diffusion.aimd.van_hove
plt.pcolor(X, Y, grt, cmap="jet", vmin=grt.min(), vmax=vmax)
plt.xlabel("Time (ps)", size=labelsize)
- plt.ylabel("$r$ ($\AA$)", size=labelsize)
+ plt.ylabel(r"$r$ ($\AA$)", size=labelsize)
plt.axis([x.min(), x.max(), y.min(), y.max()])
cbar = plt.colorbar(ticks=cb_ticks)
@@ -317,7 +316,7 @@ Source code for pymatgen.analysis.diffusion.aimd.van_hove
ylim = [-0.005, 4.0]
elif mode == "self":
grt = self.gsrt.copy()
- ylabel = "4$\pi r^2G_s$($t$,$r$)"
+ ylabel = r"4$\pi r^2G_s$($t$,$r$)"
ylim = [-0.005, 1.0]
plt = pretty_plot(12, 8)
@@ -592,7 +591,7 @@ Source code for pymatgen.analysis.diffusion.aimd.van_hove
"""
if df is None:
df = self.get_df(func=EvolutionAnalyzer.rdf, pair=pair)
- x_label, cb_label = "$r$ ({}-{}) ($\\rm\AA$)".format(*pair), "$g(r)$"
+ x_label, cb_label = f"$r$ ({pair[0]}-{pair[1]}) ($\\rm\\AA$)", "$g(r)$"
p = self.plot_evolution_from_data(df=df, x_label=x_label, cb_label=cb_label, cmap=cmap)
return p
@@ -619,7 +618,7 @@ Source code for pymatgen.analysis.diffusion.aimd.van_hove
if df is None:
df = self.get_df(func=EvolutionAnalyzer.atom_dist, specie=specie, direction=direction)
x_label, cb_label = (
- "Atomic distribution along {} ".format(direction),
+ f"Atomic distribution along {direction}",
"Probability",
)
p = self.plot_evolution_from_data(df=df, x_label=x_label, cb_label=cb_label, cmap=cmap)
@@ -642,7 +641,7 @@ Source code for pymatgen.analysis.diffusion.aimd.van_hove
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/analyzer.html b/docs/_modules/pymatgen/analysis/diffusion/analyzer.html
index da70277e..f5a44a73 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/analyzer.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/analyzer.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.analyzer — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.analyzer — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.analyzer
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.analyzer
-# coding: utf-8
-# Copyright (c) Pymatgen Development Team.
+# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
@@ -513,7 +512,7 @@ Source code for pymatgen.analysis.diffusion.analyzer
plt.plot(plot_dt, rms[:, 0], label="RMS")
plt.plot(plot_dt, rms[:, 1], label="max")
plt.legend(loc="best")
- plt.xlabel("Timestep ({})".format(unit))
+ plt.xlabel(f"Timestep ({unit})")
plt.ylabel("normalized distance")
plt.tight_layout()
return plt
@@ -549,7 +548,7 @@ Source code for pymatgen.analysis.diffusion.analyzer
elif mode == "sites":
for i, site in enumerate(self.structure):
sd = self.sq_disp_ions[i, :]
- plt.plot(plot_dt, sd, label="%s - %d" % (site.specie.__str__(), i))
+ plt.plot(plot_dt, sd, label=f"{str(site.specie)} - {i}")
plt.legend(loc=2, prop={"size": 20})
elif mode == "mscd":
plt.plot(plot_dt, self.mscd, "r")
@@ -562,7 +561,7 @@ Source code for pymatgen.analysis.diffusion.analyzer
plt.plot(plot_dt, self.msd_components[:, 2], "b")
plt.legend(["Overall", "a", "b", "c"], loc=2, prop={"size": 20})
- plt.xlabel("Timestep ({})".format(unit))
+ plt.xlabel(f"Timestep ({unit})")
if mode == "mscd":
plt.ylabel("MSCD ($\\AA^2$)")
else:
@@ -601,7 +600,7 @@ Source code for pymatgen.analysis.diffusion.analyzer
f.write(delimiter.join(["t", "MSD", "MSD_a", "MSD_b", "MSD_c", "MSCD"]))
f.write("\n")
for dt, msd, msdc, mscd in zip(self.dt, self.msd, self.msd_components, self.mscd):
- f.write(delimiter.join(["%s" % v for v in [dt, msd] + list(msdc) + [mscd]]))
+ f.write(delimiter.join([str(v) for v in [dt, msd] + list(msdc) + [mscd]]))
f.write("\n")
[docs] @classmethod
@@ -968,7 +967,7 @@ Source code for pymatgen.analysis.diffusion.analyzer
plt.text(
0.6,
0.85,
- "E$_a$ = {:.0f} meV".format(Ea * 1000),
+ f"E$_a$ = {(Ea * 1000):.0f} meV",
fontsize=30,
transform=plt.axes().transAxes,
)
@@ -994,7 +993,7 @@ Source code for pymatgen.analysis.diffusion.analyzer
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/neb/full_path_mapper.html b/docs/_modules/pymatgen/analysis/diffusion/neb/full_path_mapper.html
index 829219e2..d53a3e65 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/neb/full_path_mapper.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/neb/full_path_mapper.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.neb.full_path_mapper — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.neb.full_path_mapper — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.neb.full_path_mapper
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.neb.full_path_mapper
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
Migraiton Graph Analysis
@@ -348,7 +347,7 @@ Source code for pymatgen.analysis.diffusion.neb.full_path_mapper
edge["ipos_cart"] = np.dot(i_site.frac_coords, self.only_sites.lattice.matrix)
edge["epos_cart"] = np.dot(e_site.frac_coords, self.only_sites.lattice.matrix)
- edge["hop"] = MigrationHop(i_site, e_site, self.symm_structure)
+ edge["hop"] = MigrationHop(i_site, e_site, self.symm_structure, symprec=self.symprec)
def _populate_edges_with_migration_hops(self):
"""
@@ -408,7 +407,7 @@ Source code for pymatgen.analysis.diffusion.neb.full_path_mapper
cost_val = np.prod([v[ik] for ik in cost_keys])
self.add_data_to_similar_edges(k, {"cost": cost_val})
-[docs] def get_path(self, max_val=100000):
+[docs] def get_path(self, max_val=100000, flip_hops=True):
"""
obtain a pathway through the material using hops that are in the current graph
Basic idea:
@@ -417,6 +416,10 @@ Source code for pymatgen.analysis.diffusion.neb.full_path_mapper
or any other neighboring UC not containing p1.
Args:
max_val: Filter the graph by a cost
+ flip_hops: If true, hops in paths returned will be flipped so
+ isites and esites match to form a coherent path.
+ If false, hops will retain their original orientation
+ from the migration graph.
Returns:
Generator for List of Dicts:
Each dict contains the information of a hop
@@ -471,7 +474,10 @@ Source code for pymatgen.analysis.diffusion.neb.full_path_mapper
found_ += 1
if found_ != 1:
raise RuntimeError("More than one edge matched in original graph.")
- yield u, path_hops
+ if flip_hops is True: # flip hops in path to form coherent pathway
+ yield u, order_path(path_hops, u)
+ else:
+ yield u, path_hops
[docs] def get_summary_dict(self, added_keys: List[str] = None) -> dict:
"""
@@ -685,12 +691,7 @@ Source code for pymatgen.analysis.diffusion.neb.full_path_mapper
isym = self.symm_structure.wyckoff_symbols[migration_hop.iindex]
esym = self.symm_structure.wyckoff_symbols[migration_hop.eindex]
mask_out.write_file(
- "{}_{}_{}_tot({:0.2f}).vasp".format(
- mask_file_seedname,
- isym,
- esym,
- mask_out.data[self.potential_data_key].sum(),
- )
+ f"{mask_file_seedname}_{isym}_{esym}_tot({mask_out.data[self.potential_data_key].sum():.2f}).vasp"
)
return (
@@ -783,14 +784,15 @@ Source code for pymatgen.analysis.diffusion.neb.full_path_mapper
return vv + step / 2.0
-[docs]def get_hop_site_sequence(hop_list: List[Dict], start_u: Union[int, str]) -> List:
+[docs]def get_hop_site_sequence(hop_list: List[Dict], start_u: Union[int, str], key: str = None) -> List:
"""
- Read in a list of hop dictionaries and print the sequence of sites.
+ Read in a list of hop dictionaries and print the sequence of sites (and relevant property values if any).
Args:
hop_list: a list of the data on a sequence of hops
start_u: the site index of the starting sites
+ key (optional): property to track in a hop (e.g.: "hop_distance")
Returns:
- String representation of the hop sequence
+ String representation of the hop sequence (and property values if any)
"""
hops = iter(hop_list)
ihop = next(hops)
@@ -806,9 +808,73 @@ Source code for pymatgen.analysis.diffusion.neb.full_path_mapper
site_seq.append(ihop["iindex"])
else:
raise RuntimeError("The sequence of sites for the path is invalid.")
+
+ if key is not None:
+ key_seq = []
+ hops = iter(hop_list)
+ for ihop in hops:
+ key_seq.append(ihop[key])
+ return [site_seq, key_seq]
+
return site_seq
+[docs]def order_path(hop_list: List[Dict], start_u: Union[int, str]) -> List[Dict]:
+ """
+ Takes a list of hop dictionaries and flips hops (switches isite and esite)
+ as needed to form a coherent path / sequence of sites according to
+ get_hop_site_sequence().
+ For example if hop_list = [{iindex:0, eindex:1, etc.}, {iindex:0, eindex:1, etc.}]
+ then the output is [{iindex:0, eindex:1, etc.}, {iindex:1, eindex:0, etc.}] so that
+ the following hop iindex matches the previous hop's eindex.
+ Args:
+ hop_list: a list of the data on a sequence of hops
+ start_u: the site index of the starting sites
+ Returns:
+ a list of the data on a sequence of hops with hops in coherent orientation
+ """
+ seq = get_hop_site_sequence(hop_list, start_u)
+
+ ordered_path = []
+ for n, hop in zip(seq[:-1], hop_list):
+ if n == hop["iindex"]: # don't flip hop
+ ordered_path.append(hop)
+ else:
+ # create flipped hop
+ fh = MigrationHop(
+ isite=hop["hop"].esite,
+ esite=hop["hop"].isite,
+ symm_structure=hop["hop"].symm_structure,
+ host_symm_struct=None,
+ symprec=hop["hop"].symprec,
+ )
+ # must manually set iindex and eindex
+ fh.iindex = hop["hop"].eindex
+ fh.eindex = hop["hop"].iindex
+ fhd = {
+ "to_jimage": tuple(-1 * i for i in hop["to_jimage"]),
+ "ipos": fh.isite.frac_coords,
+ "epos": fh.esite.frac_coords,
+ "ipos_cart": fh.isite.coords,
+ "epos_cart": fh.esite.coords,
+ "hop": fh,
+ "hop_label": hop["hop_label"],
+ "iindex": hop["eindex"],
+ "eindex": hop["iindex"],
+ "hop_distance": fh.length,
+ }
+ # flip any data that is in a list to match flipped hop orientation
+ for k in hop.keys():
+ if k not in fhd.keys():
+ if isinstance(hop[k], list):
+ fhd[k] = hop[k][::-1]
+ else:
+ fhd[k] = hop[k]
+ ordered_path.append(fhd)
+
+ return ordered_path
+
+
"""
Note the current pathway algorithm no longer needs supercells but the following
functions might still be useful for other applications
@@ -925,7 +991,7 @@ Source code for pymatgen.analysis.diffusion.neb.full_path_mapper
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/neb/io.html b/docs/_modules/pymatgen/analysis/diffusion/neb/io.html
index 9c1d7f35..055d2248 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/neb/io.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/neb/io.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.neb.io — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.neb.io — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.neb.io
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.neb.io
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
@@ -217,7 +216,7 @@ Source code for pymatgen.analysis.diffusion.neb.io
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/neb/pathfinder.html b/docs/_modules/pymatgen/analysis/diffusion/neb/pathfinder.html
index d79c5772..05dbb278 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/neb/pathfinder.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/neb/pathfinder.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.neb.pathfinder — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.neb.pathfinder — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.neb.pathfinder
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.neb.pathfinder
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
@@ -75,7 +74,6 @@ Source code for pymatgen.analysis.diffusion.neb.pathfinder
# TODO: (1) ipython notebook example files, unittests
from pymatgen.symmetry.structure import SymmetrizedStructure
-
from pymatgen.analysis.diffusion.utils.supercells import (
get_sc_fromstruct,
get_start_end_structures,
@@ -349,6 +347,7 @@ Source code for pymatgen.analysis.diffusion.neb.pathfinder
isite: Site,
esite: Site,
symm_structure: SymmetrizedStructure,
+ host_symm_struct: SymmetrizedStructure = None,
symprec: float = 0.001,
):
"""
@@ -356,6 +355,7 @@ Source code for pymatgen.analysis.diffusion.neb.pathfinder
isite: Initial site
esite: End site
symm_structure: SymmetrizedStructure
+ host_symm_struct: SymmetrizedStructure of the host structure, used to for its spacegroup
symprec: used to determine equivalence
"""
self.isite = isite
@@ -365,7 +365,11 @@ Source code for pymatgen.analysis.diffusion.neb.pathfinder
self.symm_structure = symm_structure
self.symprec = symprec
self.msite = PeriodicSite(esite.specie, (isite.frac_coords + esite.frac_coords) / 2, esite.lattice)
- sg = self.symm_structure.spacegroup
+ if host_symm_struct:
+ self.host_symm_structure = host_symm_struct
+ sg = self.host_symm_structure.spacegroup
+ else:
+ sg = self.symm_structure.spacegroup
for i, sites in enumerate(self.symm_structure.equivalent_sites):
if sg.are_symmetrically_equivalent([isite], [sites[0]]):
self.iindex = i
@@ -398,24 +402,15 @@ Source code for pymatgen.analysis.diffusion.neb.pathfinder
raise RuntimeError(f"No symmetrically equivalent site was found for {esite}")
def __repr__(self):
+ ifc = self.isite.frac_coords
+ efc = self.esite.frac_coords
return (
- "Path of %.4f A from %s [%.3f, %.3f, %.3f] "
- "(ind: %d, Wyckoff: %s) to %s [%.3f, %.3f, %.3f] (ind: %d, Wyckoff: %s)"
- % (
- self.length,
- self.isite.specie,
- self.isite.frac_coords[0],
- self.isite.frac_coords[1],
- self.isite.frac_coords[2],
- self.iindex,
- self.symm_structure.wyckoff_symbols[self.iindex],
- self.esite.specie,
- self.esite.frac_coords[0],
- self.esite.frac_coords[1],
- self.esite.frac_coords[2],
- self.eindex,
- self.symm_structure.wyckoff_symbols[self.eindex],
- )
+ f"Path of {self.length:.4f} A from {self.isite.specie} "
+ f"[{ifc[0]:.3f}, {ifc[1]:.3f}, {ifc[2]:.3f}] "
+ f"(ind: {self.iindex}, Wyckoff: {self.symm_structure.wyckoff_symbols[self.iindex]}) "
+ f"to {self.esite.specie} "
+ f"[{efc[0]:.3f}, {efc[1]:.3f}, {efc[2]:.3f}] "
+ f"(ind: {self.eindex}, Wyckoff: {self.symm_structure.wyckoff_symbols[self.eindex]})"
)
@property
@@ -493,9 +488,12 @@ Source code for pymatgen.analysis.diffusion.neb.pathfinder
if site.specie != self.isite.specie:
other_sites.append(site)
else:
- if not vac_mode or (self.isite.distance(site) <= 1e-8 or self.esite.distance(site) <= 1e-8):
+ if self.isite.distance(site) <= 1e-8 or self.esite.distance(site) <= 1e-8:
+ migrating_specie_sites.append(site)
continue
- migrating_specie_sites.append(site)
+
+ if vac_mode:
+ other_sites.append(site)
return migrating_specie_sites, other_sites
[docs] def get_sc_structures(
@@ -522,7 +520,10 @@ Source code for pymatgen.analysis.diffusion.neb.pathfinder
"""
migrating_specie_sites, other_sites = self._split_migrating_and_other_sites(vac_mode)
- base_struct = Structure.from_sites(other_sites)
+ if vac_mode:
+ base_struct = Structure.from_sites(other_sites + migrating_specie_sites)
+ else:
+ base_struct = Structure.from_sites(other_sites)
sc_mat = get_sc_fromstruct(
base_struct=base_struct,
min_atoms=min_atoms,
@@ -676,7 +677,7 @@ Source code for pymatgen.analysis.diffusion.neb.pathfinder
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/neb/periodic_dijkstra.html b/docs/_modules/pymatgen/analysis/diffusion/neb/periodic_dijkstra.html
index b134cdc1..8ad92bc4 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/neb/periodic_dijkstra.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/neb/periodic_dijkstra.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.neb.periodic_dijkstra — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.neb.periodic_dijkstra — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.neb.periodic_dijkstra
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.neb.periodic_dijkstra
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
Dijkstra's path search on a graph where the nodes are on a periodic graph
@@ -97,11 +96,11 @@ Source code for pymatgen.analysis.diffusion.neb.periodic_dijkstra
p_graph = copy_dict(dict(G.adjacency()))
# Make sure all the to_jimages are pointing in the correct direction
- for u in p_graph.keys():
- for v in p_graph[u].keys():
- for k, d in p_graph[u][v].items():
+ for u, value1 in p_graph.items():
+ for v, value2 in value1.items():
+ for k, d in value2.items():
if u > v:
- p_graph[u][v][k]["to_jimage"] = tuple(np.multiply(-1, d["to_jimage"]))
+ d["to_jimage"] = tuple(np.multiply(-1, d["to_jimage"]))
return p_graph
@@ -136,7 +135,7 @@ Source code for pymatgen.analysis.diffusion.neb.periodic_dijkstra
# use a default dict since we don't know how far out to search
best_ans = defaultdict(lambda: math.inf) # type: ignore
- path_parent = dict() # the parent of the current node in the optimal path
+ path_parent = {} # the parent of the current node in the optimal path
pq = [] # type: ignore
for isource in sources:
heapq.heappush(pq, (0, (isource, (0, 0, 0))))
@@ -227,7 +226,7 @@ Source code for pymatgen.analysis.diffusion.neb.periodic_dijkstra
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_full_path_mapper.html b/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_full_path_mapper.html
index 38a2115f..cfd974a4 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_full_path_mapper.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_full_path_mapper.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
import os
import unittest
@@ -64,6 +63,7 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper<
MigrationGraph,
MigrationHop,
get_hop_site_sequence,
+ order_path,
)
from pymatgen.analysis.diffusion.neb.periodic_dijkstra import _get_adjacency_with_images
@@ -213,26 +213,63 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper<
[docs] def test_get_path(self):
self.fpm_li.assign_cost_to_graph() # use 'hop_distance'
- paths = [*self.fpm_li.get_path()]
+ paths = [*self.fpm_li.get_path(flip_hops=False)]
p_strings = {"->".join(map(str, get_hop_site_sequence(ipath, start_u=u))) for u, ipath in paths}
self.assertIn("5->7->5", p_strings)
# convert each pathway to a string representation
- paths = [*self.fpm_li.get_path(max_val=2.0)]
+ paths = [*self.fpm_li.get_path(max_val=2.0, flip_hops=False)]
p_strings = {"->".join(map(str, get_hop_site_sequence(ipath, start_u=u))) for u, ipath in paths}
# After checking trimming the graph more hops are needed for the same path
self.assertIn("5->3->7->2->5", p_strings)
self.fpm_mg.assign_cost_to_graph() # use 'hop_distance'
- paths = [*self.fpm_mg.get_path()]
+ paths = [*self.fpm_mg.get_path(flip_hops=False)]
p_strings = {"->".join(map(str, get_hop_site_sequence(ipath, start_u=u))) for u, ipath in paths}
self.assertIn("1->0->1", p_strings)
+[docs] def test_get_key_in_path(self):
+ self.fpm_li.assign_cost_to_graph() # use 'hop_distance'
+ paths = [*self.fpm_li.get_path(flip_hops=False)]
+ hop_seq_info = [get_hop_site_sequence(ipath, start_u=u, key="hop_distance") for u, ipath in paths]
+
+ hop_distances = {}
+ for u, ipath in paths:
+ hop_distances[u] = []
+ for hop in ipath:
+ hop_distances[u].append(hop["hop_distance"])
+
+ # Check that the right key and respective values were pulled
+ for u, distances in hop_distances.items():
+ self.assertEqual(distances, hop_seq_info[u][1])
+ print(distances, hop_seq_info[u][1])
+
[docs] def test_not_matching_first(self):
structure = Structure.from_file(f"{dir_path}/pathfinder_files/Li6MnO4.json")
fpm_lmo = MigrationGraph.with_distance(structure, "Li", max_distance=4)
for u, v, d in fpm_lmo.m_graph.graph.edges(data=True):
- self.assertIn(d["hop"].eindex, {0, 1})
+ self.assertIn(d["hop"].eindex, {0, 1})
+
+[docs] def test_order_path(self):
+ # add list data to migration graph - to test if list data is flipped
+ for n, hop_d in self.fpm_li.unique_hops.items():
+ data = {"data": [hop_d["iindex"], hop_d["eindex"]]}
+ self.fpm_li.add_data_to_similar_edges(n, data, hop_d["hop"])
+
+ self.fpm_li.assign_cost_to_graph() # use 'hop_distance'
+
+ for n, hop_list in [*self.fpm_li.get_path(flip_hops=False)]:
+ ordered = order_path(hop_list, n)
+
+ # check if isites and esites are oriented to form a coherent path
+ for h1, h2 in zip(ordered[:-1], ordered[1:]):
+ self.assertEqual(h1["eindex"], h2["iindex"])
+
+ # if hop was flipped, check list data was flipped too
+ for h, ord_h in zip(hop_list, ordered):
+ if h["iindex"] != ord_h["iindex"]: # check only if hop was flipped
+ self.assertEqual(h["data"][0], ord_h["data"][-1])
+ self.assertEqual(h["data"][-1], ord_h["data"][0])
[docs]class ChargeBarrierGraphTest(unittest.TestCase):
@@ -289,7 +326,7 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper<
"""
self.cbg.populate_edges_with_chg_density_info()
length_vs_chg = list(
- sorted([(d["hop"].length, d["chg_total"]) for u, v, d in self.cbg.m_graph.graph.edges(data=True)])
+ sorted((d["hop"].length, d["chg_total"]) for u, v, d in self.cbg.m_graph.graph.edges(data=True))
)
prv = None
for length, chg in length_vs_chg:
@@ -326,7 +363,7 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper<
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_io.html b/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_io.html
index 0d52a240..54031889 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_io.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_io.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.neb.tests.test_io — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.neb.tests.test_io — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.neb.tests.test_io
@@ -48,9 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.neb.tests.test_io
-# coding: utf-8
-
-from pymatgen.core import Structure
+from pymatgen.core import Structure
from pymatgen.analysis.diffusion.neb.io import (
MVLCINEBEndPointSet,
MVLCINEBSet,
@@ -79,26 +77,27 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_io
[docs] def test_incar(self):
m = MVLCINEBEndPointSet(self.endpoint)
incar_string = m.incar.get_string(sort_keys=True, pretty=True)
- incar_expect = """ALGO = Fast
-EDIFF = 5e-05
-EDIFFG = -0.02
-ENCUT = 520
-IBRION = 2
-ICHARG = 1
-ISIF = 2
-ISMEAR = 0
-ISPIN = 2
-ISYM = 0
-LCHARG = False
-LORBIT = 11
-LREAL = Auto
-LWAVE = False
-MAGMOM = 35*0.6
-NELM = 200
-NELMIN = 4
-NSW = 99
-PREC = Accurate
-SIGMA = 0.05"""
+ incar_expect = """ALGO = Fast
+EDIFF = 5e-05
+EDIFFG = -0.02
+ENCUT = 520
+IBRION = 2
+ICHARG = 1
+ISIF = 2
+ISMEAR = 0
+ISPIN = 2
+ISYM = 0
+LCHARG = False
+LMAXMIX = 4
+LORBIT = 11
+LREAL = Auto
+LWAVE = False
+MAGMOM = 35*0.6
+NELM = 200
+NELMIN = 4
+NSW = 99
+PREC = Accurate
+SIGMA = 0.05"""
self.assertEqual(incar_string, incar_expect)
[docs] def test_incar_user_setting(self):
@@ -122,6 +121,7 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_io
ISPIN = 2
ISYM = 0
LCHARG = False
+LMAXMIX = 4
LORBIT = 11
LREAL = Auto
LWAVE = False
@@ -159,6 +159,7 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_io
ISYM = 0
LCHARG = False
LCLIMB = True
+LMAXMIX = 4
LORBIT = 0
LREAL = Auto
LWAVE = False
@@ -176,34 +177,34 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_io
user_incar_settings = {"IOPT": 3, "EDIFFG": -0.05, "NPAR": 4, "ISIF": 3}
m = MVLCINEBSet(self.structures, user_incar_settings=user_incar_settings)
incar_string = m.incar.get_string(sort_keys=True, pretty=True)
- incar_expect = """ALGO = Fast
-EDIFF = 5e-05
-EDIFFG = -0.05
-ENCUT = 520
-IBRION = 3
-ICHAIN = 0
-ICHARG = 1
-IMAGES = 1
-IOPT = 3
-ISIF = 3
-ISMEAR = 0
-ISPIN = 2
-ISYM = 0
-LCHARG = False
-LCLIMB = True
-LORBIT = 0
-LREAL = Auto
-LWAVE = False
-MAGMOM = 35*0.6
-NELM = 200
-NELMIN = 6
-NPAR = 4
-NSW = 200
-POTIM = 0
-PREC = Accurate
-SIGMA = 0.05
-SPRING = -5"""
-
+ incar_expect = """ALGO = Fast
+EDIFF = 5e-05
+EDIFFG = -0.05
+ENCUT = 520
+IBRION = 3
+ICHAIN = 0
+ICHARG = 1
+IMAGES = 1
+IOPT = 3
+ISIF = 3
+ISMEAR = 0
+ISPIN = 2
+ISYM = 0
+LCHARG = False
+LCLIMB = True
+LMAXMIX = 4
+LORBIT = 0
+LREAL = Auto
+LWAVE = False
+MAGMOM = 35*0.6
+NELM = 200
+NELMIN = 6
+NPAR = 4
+NSW = 200
+POTIM = 0
+PREC = Accurate
+SIGMA = 0.05
+SPRING = -5"""
self.assertEqual(incar_string.strip(), incar_expect.strip())
@@ -253,7 +254,7 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_io
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_pathfinder.html b/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_pathfinder.html
index 8cd76436..ce134cd4 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_pathfinder.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/neb/tests/test_pathfinder.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.neb.tests.test_pathfinder — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.neb.tests.test_pathfinder — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.neb.tests.test_pathfinder
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.neb.tests.test_pathfinder
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
import glob
import os
@@ -58,6 +57,7 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_pathfinder
import numpy as np
from pymatgen.core import PeriodicSite
from pymatgen.core import Structure
+from pymatgen.core import Composition
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.testing import PymatgenTest
@@ -267,7 +267,14 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_pathfinder
start, end, b_sc = self.m_hop.get_sc_structures(vac_mode=False)
start_site = next(filter(lambda x: x.species_string == "Li", start.sites))
end_site = next(filter(lambda x: x.species_string == "Li", end.sites))
- self.assertAlmostEqual(start_site.distance(end_site), dist_ref, 3)
+ assert start.composition == end.composition == Composition("Li1 Fe24 P24 O96")
+ assert b_sc.composition == Composition("Fe24 P24 O96")
+ self.assertAlmostEqual(start_site.distance(end_site), dist_ref, 3)
+
+[docs] def test_get_sc_structures_vacmode(self):
+ start, end, b_sc = self.m_hop.get_sc_structures(vac_mode=True)
+ assert start.composition == end.composition == Composition("Li23 Fe24 P24 O96")
+ assert b_sc.composition == Composition("Li24 Fe24 P24 O96")
if __name__ == "__main__":
@@ -290,7 +297,7 @@ Source code for pymatgen.analysis.diffusion.neb.tests.test_pathfinder
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/tests/test_analyzer.html b/docs/_modules/pymatgen/analysis/diffusion/tests/test_analyzer.html
index bf059893..f7234e63 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/tests/test_analyzer.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/tests/test_analyzer.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.tests.test_analyzer — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.tests.test_analyzer — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.tests.test_analyzer
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.tests.test_analyzer
-# coding: utf-8
-# Copyright (c) Pymatgen Development Team.
+# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
@@ -291,7 +290,7 @@ Source code for pymatgen.analysis.diffusion.tests.test_analyzer
# Diffusion vasprun.xmls are rather large. We are only going to use a
# very small preprocessed run for testing. Note that the results are
# unreliable for short runs.
- with open(os.path.join(module_dir, "DiffusionAnalyzer_NPT.json"), "r") as f:
+ with open(os.path.join(module_dir, "DiffusionAnalyzer_NPT.json")) as f:
dd = json.load(f)
d = DiffusionAnalyzer.from_dict(dd)
# large tolerance because scipy constants changed between 0.16.1 and 0.17
@@ -557,7 +556,7 @@ Source code for pymatgen.analysis.diffusion.tests.test_analyzer
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/utils/edge_data_from_sc.html b/docs/_modules/pymatgen/analysis/diffusion/utils/edge_data_from_sc.html
index 9ca84167..6798edf6 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/utils/edge_data_from_sc.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/utils/edge_data_from_sc.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.utils.edge_data_from_sc — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.utils.edge_data_from_sc — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.utils.edge_data_from_sc
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.utils.edge_data_from_sc
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
@@ -63,12 +62,13 @@ Source code for pymatgen.analysis.diffusion.utils.edge_data_from_sc
__date__ = "February 2, 2021"
import logging
-from typing import Tuple, Union
+from typing import Tuple
import numpy as np
from pymatgen.core.structure import Structure, PeriodicSite
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.analysis.diffusion.neb.full_path_mapper import MigrationGraph, MigrationHop
from pymatgen.analysis.diffusion.utils.parse_entries import get_matched_structure_mapping
+from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
logger = logging.getLogger(__name__)
@@ -79,7 +79,7 @@ Source code for pymatgen.analysis.diffusion.utils.edge_data_from_sc
e_sc: Structure,
data_array: list,
key: str = "custom_key",
- symprec: Union[None, float] = None,
+ use_host_sg: bool = True,
) -> None:
"""
Add a data entry and key to edges within FullPathMapper object with the same hop_label.
@@ -90,19 +90,18 @@ Source code for pymatgen.analysis.diffusion.utils.edge_data_from_sc
e_sc: Supercell structure containing working ion at ending position
data_array: The data to be added to the edges
key: Key of the edge attribute to be added
+ use_host_sg: Flag t whether or not to use the host structure's spacegroup to initiate MigrationHop
Returns:
None
"""
- if not symprec:
- symprec = mg.symprec
wi = list(mg.m_graph.graph.edges(data=True))[0][2]["hop"].isite.specie.name
i_wi = [x for x in i_sc.sites if x.species_string == wi]
e_wi = [x for x in e_sc.sites if x.species_string == wi]
if len(i_wi) != 1 or len(e_wi) != 1:
raise ValueError("The number of working ions in each supercell structure should be one")
isite, esite = i_wi[0], e_wi[0]
- uhop_index, mh_from_sc = get_unique_hop(mg, i_sc, isite, esite, symprec=symprec)
+ uhop_index, mh_from_sc = get_unique_hop(mg, i_sc, isite, esite, use_host_sg)
add_dict = {key: data_array}
mg.add_data_to_similar_edges(target_label=uhop_index, data=add_dict, m_hop=mh_from_sc)
@@ -130,7 +129,6 @@ Source code for pymatgen.analysis.diffusion.utils.edge_data_from_sc
if mapping is None:
raise ValueError("Cannot obtain inverse mapping, consider lowering tolerances " "in StructureMatcher")
sc_m, total_t = mapping
-
sc_ipos = isite.frac_coords
sc_ipos_t = sc_ipos - total_t
uc_ipos = sc_ipos_t.dot(sc_m)
@@ -190,7 +188,7 @@ Source code for pymatgen.analysis.diffusion.utils.edge_data_from_sc
sc: Structure,
isite: PeriodicSite,
esite: PeriodicSite,
- symprec: Union[None, float] = None,
+ use_host_sg: bool = True,
) -> Tuple[int, MigrationHop]:
"""Get the unique hop label that correspond to two end positions in the SC
@@ -199,15 +197,20 @@ Source code for pymatgen.analysis.diffusion.utils.edge_data_from_sc
sc: Structure of the supercell used for the NEB calculation
isite: Initial position in the supercell
esite: Final position in the supercell
+ use_host_sg: Flag t whether or not to use the host structure's spacegroup to initiate MigrationHop
Returns:
The index of the unique hop, the MigrationHop object trasformed from the SC
"""
- if not symprec:
- symprec = mg.symprec
sm = StructureMatcher(ignored_species=[list(mg.m_graph.graph.edges(data=True))[0][2]["hop"].isite.specie.name])
uc_isite, uc_msite, uc_esite = get_uc_pos(isite, esite, mg.symm_structure, sc, sm)
- mh_from_sc = MigrationHop(uc_isite, uc_esite, symm_structure=mg.symm_structure)
+ if use_host_sg:
+ base_ss = SpacegroupAnalyzer(mg.host_structure, symprec=mg.symprec).get_symmetrized_structure()
+ mh_from_sc = MigrationHop(
+ uc_isite, uc_esite, symm_structure=mg.symm_structure, host_symm_struct=base_ss, symprec=mg.symprec
+ )
+ else:
+ mh_from_sc = MigrationHop(uc_isite, uc_esite, symm_structure=mg.symm_structure, symprec=mg.symprec)
result = []
for k, v in mg.unique_hops.items():
# tolerance may be changed here
@@ -239,7 +242,7 @@ Source code for pymatgen.analysis.diffusion.utils.edge_data_from_sc
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/utils/parse_entries.html b/docs/_modules/pymatgen/analysis/diffusion/utils/parse_entries.html
index c55b7d16..87cad5ed 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/utils/parse_entries.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/utils/parse_entries.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.utils.parse_entries — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.utils.parse_entries — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.utils.parse_entries
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.utils.parse_entries
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
@@ -374,7 +373,7 @@ Source code for pymatgen.analysis.diffusion.utils.parse_entries
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/utils/supercells.html b/docs/_modules/pymatgen/analysis/diffusion/utils/supercells.html
index aa42e7df..fa5123c8 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/utils/supercells.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/utils/supercells.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.utils.supercells — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.utils.supercells — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.utils.supercells
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.utils.supercells
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
Functions for creating supercells for NEB calculations
@@ -260,7 +259,7 @@ Source code for pymatgen.analysis.diffusion.utils.supercells
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/utils/tests/test_edge_data_from_sc.html b/docs/_modules/pymatgen/analysis/diffusion/utils/tests/test_edge_data_from_sc.html
index ad396694..41d285c6 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/utils/tests/test_edge_data_from_sc.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/utils/tests/test_edge_data_from_sc.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc
@@ -48,16 +48,16 @@ Navigation
Source code for pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
import os
import numpy as np
+import pytest
from pymatgen.core.structure import Structure, PeriodicSite
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.analysis.diffusion.neb.full_path_mapper import MigrationGraph
-from pymatgen.analysis.diffusion.utils.edge_data_from_sc import add_edge_data_from_sc, get_uc_pos
+from pymatgen.analysis.diffusion.utils.edge_data_from_sc import add_edge_data_from_sc, get_uc_pos, get_unique_hop
test_dir = os.path.dirname(os.path.realpath(__file__))
@@ -69,15 +69,21 @@ Source code for pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_
input_struct_i = Structure.from_file(f"{test_dir}/test_files/Sr3Fe2O7_sc_i.vasp")
input_struct_e = Structure.from_file(f"{test_dir}/test_files/Sr3Fe2O7_sc_e.vasp")
+mg_uc_full_sites = Structure.from_file(f"{test_dir}/test_files/Mg3VOPO4_uc.vasp")
+mg_input_struct_i = Structure.from_file(f"{test_dir}/test_files/Mg3VOPO4_sc_i.vasp")
+mg_input_struct_e = Structure.from_file(f"{test_dir}/test_files/Mg3VOPO4_sc_e.vasp")
+
+mg_Li = MigrationGraph.with_distance(structure=uc_full_sites, migrating_specie="Li", max_distance=5)
+mg_Mg = MigrationGraph.with_distance(structure=mg_uc_full_sites, migrating_specie="Mg", max_distance=4)
+
[docs]def test_add_edge_data_from_sc():
errors = []
- mg = MigrationGraph.with_distance(structure=uc_full_sites, migrating_specie="Li", max_distance=5)
test_key = "test_key"
test_array = [0, 1, 2, 3, 4]
add_edge_data_from_sc(
- mg,
+ mg_Li,
i_sc=input_struct_i,
e_sc=input_struct_e,
data_array=test_array,
@@ -85,7 +91,7 @@ Source code for pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_
)
edge_data = []
- for u, v, d in mg.m_graph.graph.edges(data=True):
+ for u, v, d in mg_Li.m_graph.graph.edges(data=True):
edge_data.append(d)
hop_labels = []
for i in edge_data:
@@ -105,14 +111,13 @@ Source code for pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_
errors = []
# set up parameters to initiate get_uc_pos
- mg = MigrationGraph.with_distance(structure=uc_full_sites, migrating_specie="Li", max_distance=5)
- uc_lattice = mg.symm_structure.lattice
+ uc_lattice = mg_Li.symm_structure.lattice
isite = [x for x in input_struct_i.sites if x.species_string == "Li"][0]
esite = [x for x in input_struct_e.sites if x.species_string == "Li"][0]
- sm = StructureMatcher(ignored_species=[list(mg.m_graph.graph.edges(data=True))[0][2]["hop"].isite.specie.name])
- wi_specie = mg.symm_structure[-1].specie
+ sm = StructureMatcher(ignored_species=[list(mg_Li.m_graph.graph.edges(data=True))[0][2]["hop"].isite.specie.name])
+ wi_specie = mg_Li.symm_structure[-1].specie
- p0, p1, p2 = get_uc_pos(isite, esite, mg.symm_structure, input_struct_i, sm)
+ p0, p1, p2 = get_uc_pos(isite, esite, mg_Li.symm_structure, input_struct_i, sm)
# generate correct sites to compare
test_p0 = PeriodicSite(
@@ -133,6 +138,18 @@ Source code for pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_
errors.append("Ending site does not match")
assert not errors, "errors occured:\n" + "\n".join(errors)
+
+
+[docs]def test_get_unique_hop_host():
+ results = get_unique_hop(mg_Mg, mg_input_struct_i, mg_input_struct_i[0], mg_input_struct_e[0], use_host_sg=True)
+ assert results[0] == 2
+
+
+[docs]def test_get_unique_host_nonhost():
+ with pytest.raises(Exception) as exc_info:
+ get_unique_hop(mg_Mg, mg_input_struct_i, mg_input_struct_i[0], mg_input_struct_e[0], use_host_sg=False)
+ expected_exception = "No symmetrically equivalent site was found for [0.53593472 2.8352428 4.54752366] Mg"
+ assert exc_info.value.args[0] == expected_exception
@@ -151,7 +168,7 @@ Source code for pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_
Quick search
diff --git a/docs/_modules/pymatgen/analysis/diffusion/utils/tests/test_parse_entries.html b/docs/_modules/pymatgen/analysis/diffusion/utils/tests/test_parse_entries.html
index 26ba4854..42f3a06e 100644
--- a/docs/_modules/pymatgen/analysis/diffusion/utils/tests/test_parse_entries.html
+++ b/docs/_modules/pymatgen/analysis/diffusion/utils/tests/test_parse_entries.html
@@ -5,10 +5,10 @@
- pymatgen.analysis.diffusion.utils.tests.test_parse_entries — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ pymatgen.analysis.diffusion.utils.tests.test_parse_entries — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Module code »
pymatgen.analysis.diffusion.utils.tests.test_parse_entries
@@ -48,8 +48,7 @@ Navigation
Source code for pymatgen.analysis.diffusion.utils.tests.test_parse_entries
-# coding: utf-8
-# Copyright (c) Materials Virtual Lab.
+# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
from monty.serialization import loadfn
from pymatgen.entries.computed_entries import ComputedStructureEntry
@@ -159,11 +158,11 @@ Source code for pymatgen.analysis.diffusion.utils.tests.test_parse_entries[docs] def test_get_all_sym_sites(self):
struct11 = get_sym_migration_ion_sites(self.base.structure, self.inserted_1Li1.structure, migrating_ion="Li")
- self.assertEquals(struct11.composition["Li"], 4)
+ self.assertEqual(struct11.composition["Li"], 4)
struct12 = get_sym_migration_ion_sites(self.base.structure, self.inserted_1Li2.structure, migrating_ion="Li")
- self.assertEquals(struct12.composition["Li"], 4)
+ self.assertEqual(struct12.composition["Li"], 4)
struct22 = get_sym_migration_ion_sites(self.base.structure, self.inserted_2Li.structure, migrating_ion="Li")
- self.assertEquals(struct22.composition["Li"], 8)
+ self.assertEqual(struct22.composition["Li"], 8)
if __name__ == "__main__":
@@ -186,7 +185,7 @@ Source code for pymatgen.analysis.diffusion.utils.tests.test_parse_entriesQuick search
diff --git a/docs/_sources/pymatgen.analysis.rst.txt b/docs/_sources/pymatgen.analysis.rst.txt
index 25007431..4e1b7380 100644
--- a/docs/_sources/pymatgen.analysis.rst.txt
+++ b/docs/_sources/pymatgen.analysis.rst.txt
@@ -1,6 +1,8 @@
pymatgen.analysis namespace
===========================
+.. py:module:: pymatgen.analysis
+
Subpackages
-----------
diff --git a/docs/_sources/pymatgen.rst.txt b/docs/_sources/pymatgen.rst.txt
index 36816d3c..e823f4f2 100644
--- a/docs/_sources/pymatgen.rst.txt
+++ b/docs/_sources/pymatgen.rst.txt
@@ -1,2 +1,4 @@
pymatgen namespace
==================
+
+.. py:module:: pymatgen
diff --git a/docs/_static/basic.css b/docs/_static/basic.css
index b3bdc004..603f6a87 100644
--- a/docs/_static/basic.css
+++ b/docs/_static/basic.css
@@ -130,7 +130,7 @@ ul.search li a {
font-weight: bold;
}
-ul.search li div.context {
+ul.search li p.context {
color: #888;
margin: 2px 0 0 30px;
text-align: left;
@@ -508,6 +508,63 @@ table.hlist td {
vertical-align: top;
}
+/* -- object description styles --------------------------------------------- */
+
+.sig {
+ font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+}
+
+.sig-name, code.descname {
+ background-color: transparent;
+ font-weight: bold;
+}
+
+.sig-name {
+ font-size: 1.1em;
+}
+
+code.descname {
+ font-size: 1.2em;
+}
+
+.sig-prename, code.descclassname {
+ background-color: transparent;
+}
+
+.optional {
+ font-size: 1.3em;
+}
+
+.sig-paren {
+ font-size: larger;
+}
+
+.sig-param.n {
+ font-style: italic;
+}
+
+/* C++ specific styling */
+
+.sig-inline.c-texpr,
+.sig-inline.cpp-texpr {
+ font-family: unset;
+}
+
+.sig.c .k, .sig.c .kt,
+.sig.cpp .k, .sig.cpp .kt {
+ color: #0033B3;
+}
+
+.sig.c .m,
+.sig.cpp .m {
+ color: #1750EB;
+}
+
+.sig.c .s, .sig.c .sc,
+.sig.cpp .s, .sig.cpp .sc {
+ color: #067D17;
+}
+
/* -- other body styles ----------------------------------------------------- */
@@ -634,14 +691,6 @@ dl.glossary dt {
font-size: 1.1em;
}
-.optional {
- font-size: 1.3em;
-}
-
-.sig-paren {
- font-size: larger;
-}
-
.versionmodified {
font-style: italic;
}
@@ -682,8 +731,9 @@ dl.glossary dt {
.classifier:before {
font-style: normal;
- margin: 0.5em;
+ margin: 0 0.5em;
content: ":";
+ display: inline-block;
}
abbr, acronym {
@@ -770,8 +820,12 @@ div.code-block-caption code {
table.highlighttable td.linenos,
span.linenos,
-div.doctest > div.highlight span.gp { /* gp: Generic.Prompt */
- user-select: none;
+div.highlight span.gp { /* gp: Generic.Prompt */
+ user-select: none;
+ -webkit-user-select: text; /* Safari fallback only */
+ -webkit-user-select: none; /* Chrome/Safari */
+ -moz-user-select: none; /* Firefox */
+ -ms-user-select: none; /* IE10+ */
}
div.code-block-caption span.caption-number {
@@ -786,16 +840,6 @@ div.literal-block-wrapper {
margin: 1em 0;
}
-code.descname {
- background-color: transparent;
- font-weight: bold;
- font-size: 1.2em;
-}
-
-code.descclassname {
- background-color: transparent;
-}
-
code.xref, a code {
background-color: transparent;
font-weight: bold;
diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js
index 61ac9d26..8cbf1b16 100644
--- a/docs/_static/doctools.js
+++ b/docs/_static/doctools.js
@@ -301,12 +301,14 @@ var Documentation = {
window.location.href = prevHref;
return false;
}
+ break;
case 39: // right
var nextHref = $('link[rel="next"]').prop('href');
if (nextHref) {
window.location.href = nextHref;
return false;
}
+ break;
}
}
});
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 2a68eee7..d58e37f7 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: '2021.4.29',
+ VERSION: '2022.1.15',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
index 1a90152e..002e9c4a 100644
--- a/docs/_static/searchtools.js
+++ b/docs/_static/searchtools.js
@@ -282,7 +282,10 @@ var Search = {
complete: function(jqxhr, textstatus) {
var data = jqxhr.responseText;
if (data !== '' && data !== undefined) {
- listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
+ var summary = Search.makeSearchSummary(data, searchterms, hlterms);
+ if (summary) {
+ listItem.append(summary);
+ }
}
Search.output.append(listItem);
setTimeout(function() {
@@ -325,7 +328,9 @@ var Search = {
var results = [];
for (var prefix in objects) {
- for (var name in objects[prefix]) {
+ for (var iMatch = 0; iMatch != objects[prefix].length; ++iMatch) {
+ var match = objects[prefix][iMatch];
+ var name = match[4];
var fullname = (prefix ? prefix + '.' : '') + name;
var fullnameLower = fullname.toLowerCase()
if (fullnameLower.indexOf(object) > -1) {
@@ -339,7 +344,6 @@ var Search = {
} else if (parts[parts.length - 1].indexOf(object) > -1) {
score += Scorer.objPartialMatch;
}
- var match = objects[prefix][name];
var objname = objnames[match[1]][2];
var title = titles[match[0]];
// If more than one term searched for, we require other words to be
@@ -498,6 +502,9 @@ var Search = {
*/
makeSearchSummary : function(htmlText, keywords, hlwords) {
var text = Search.htmlToText(htmlText);
+ if (text == "") {
+ return null;
+ }
var textLower = text.toLowerCase();
var start = 0;
$.each(keywords, function() {
@@ -509,7 +516,7 @@ var Search = {
var excerpt = ((start > 0) ? '...' : '') +
$.trim(text.substr(start, 240)) +
((start + 240 - text.length) ? '...' : '');
- var rv = $('').text(excerpt);
+ var rv = $('
').text(excerpt);
$.each(hlwords, function() {
rv = rv.highlightText(this, 'highlighted');
});
diff --git a/docs/_static/underscore-1.13.1.js b/docs/_static/underscore-1.13.1.js
new file mode 100644
index 00000000..ffd77af9
--- /dev/null
+++ b/docs/_static/underscore-1.13.1.js
@@ -0,0 +1,2042 @@
+(function (global, factory) {
+ typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory() :
+ typeof define === 'function' && define.amd ? define('underscore', factory) :
+ (global = typeof globalThis !== 'undefined' ? globalThis : global || self, (function () {
+ var current = global._;
+ var exports = global._ = factory();
+ exports.noConflict = function () { global._ = current; return exports; };
+ }()));
+}(this, (function () {
+ // Underscore.js 1.13.1
+ // https://underscorejs.org
+ // (c) 2009-2021 Jeremy Ashkenas, Julian Gonggrijp, and DocumentCloud and Investigative Reporters & Editors
+ // Underscore may be freely distributed under the MIT license.
+
+ // Current version.
+ var VERSION = '1.13.1';
+
+ // Establish the root object, `window` (`self`) in the browser, `global`
+ // on the server, or `this` in some virtual machines. We use `self`
+ // instead of `window` for `WebWorker` support.
+ var root = typeof self == 'object' && self.self === self && self ||
+ typeof global == 'object' && global.global === global && global ||
+ Function('return this')() ||
+ {};
+
+ // Save bytes in the minified (but not gzipped) version:
+ var ArrayProto = Array.prototype, ObjProto = Object.prototype;
+ var SymbolProto = typeof Symbol !== 'undefined' ? Symbol.prototype : null;
+
+ // Create quick reference variables for speed access to core prototypes.
+ var push = ArrayProto.push,
+ slice = ArrayProto.slice,
+ toString = ObjProto.toString,
+ hasOwnProperty = ObjProto.hasOwnProperty;
+
+ // Modern feature detection.
+ var supportsArrayBuffer = typeof ArrayBuffer !== 'undefined',
+ supportsDataView = typeof DataView !== 'undefined';
+
+ // All **ECMAScript 5+** native function implementations that we hope to use
+ // are declared here.
+ var nativeIsArray = Array.isArray,
+ nativeKeys = Object.keys,
+ nativeCreate = Object.create,
+ nativeIsView = supportsArrayBuffer && ArrayBuffer.isView;
+
+ // Create references to these builtin functions because we override them.
+ var _isNaN = isNaN,
+ _isFinite = isFinite;
+
+ // Keys in IE < 9 that won't be iterated by `for key in ...` and thus missed.
+ var hasEnumBug = !{toString: null}.propertyIsEnumerable('toString');
+ var nonEnumerableProps = ['valueOf', 'isPrototypeOf', 'toString',
+ 'propertyIsEnumerable', 'hasOwnProperty', 'toLocaleString'];
+
+ // The largest integer that can be represented exactly.
+ var MAX_ARRAY_INDEX = Math.pow(2, 53) - 1;
+
+ // Some functions take a variable number of arguments, or a few expected
+ // arguments at the beginning and then a variable number of values to operate
+ // on. This helper accumulates all remaining arguments past the function’s
+ // argument length (or an explicit `startIndex`), into an array that becomes
+ // the last argument. Similar to ES6’s "rest parameter".
+ function restArguments(func, startIndex) {
+ startIndex = startIndex == null ? func.length - 1 : +startIndex;
+ return function() {
+ var length = Math.max(arguments.length - startIndex, 0),
+ rest = Array(length),
+ index = 0;
+ for (; index < length; index++) {
+ rest[index] = arguments[index + startIndex];
+ }
+ switch (startIndex) {
+ case 0: return func.call(this, rest);
+ case 1: return func.call(this, arguments[0], rest);
+ case 2: return func.call(this, arguments[0], arguments[1], rest);
+ }
+ var args = Array(startIndex + 1);
+ for (index = 0; index < startIndex; index++) {
+ args[index] = arguments[index];
+ }
+ args[startIndex] = rest;
+ return func.apply(this, args);
+ };
+ }
+
+ // Is a given variable an object?
+ function isObject(obj) {
+ var type = typeof obj;
+ return type === 'function' || type === 'object' && !!obj;
+ }
+
+ // Is a given value equal to null?
+ function isNull(obj) {
+ return obj === null;
+ }
+
+ // Is a given variable undefined?
+ function isUndefined(obj) {
+ return obj === void 0;
+ }
+
+ // Is a given value a boolean?
+ function isBoolean(obj) {
+ return obj === true || obj === false || toString.call(obj) === '[object Boolean]';
+ }
+
+ // Is a given value a DOM element?
+ function isElement(obj) {
+ return !!(obj && obj.nodeType === 1);
+ }
+
+ // Internal function for creating a `toString`-based type tester.
+ function tagTester(name) {
+ var tag = '[object ' + name + ']';
+ return function(obj) {
+ return toString.call(obj) === tag;
+ };
+ }
+
+ var isString = tagTester('String');
+
+ var isNumber = tagTester('Number');
+
+ var isDate = tagTester('Date');
+
+ var isRegExp = tagTester('RegExp');
+
+ var isError = tagTester('Error');
+
+ var isSymbol = tagTester('Symbol');
+
+ var isArrayBuffer = tagTester('ArrayBuffer');
+
+ var isFunction = tagTester('Function');
+
+ // Optimize `isFunction` if appropriate. Work around some `typeof` bugs in old
+ // v8, IE 11 (#1621), Safari 8 (#1929), and PhantomJS (#2236).
+ var nodelist = root.document && root.document.childNodes;
+ if (typeof /./ != 'function' && typeof Int8Array != 'object' && typeof nodelist != 'function') {
+ isFunction = function(obj) {
+ return typeof obj == 'function' || false;
+ };
+ }
+
+ var isFunction$1 = isFunction;
+
+ var hasObjectTag = tagTester('Object');
+
+ // In IE 10 - Edge 13, `DataView` has string tag `'[object Object]'`.
+ // In IE 11, the most common among them, this problem also applies to
+ // `Map`, `WeakMap` and `Set`.
+ var hasStringTagBug = (
+ supportsDataView && hasObjectTag(new DataView(new ArrayBuffer(8)))
+ ),
+ isIE11 = (typeof Map !== 'undefined' && hasObjectTag(new Map));
+
+ var isDataView = tagTester('DataView');
+
+ // In IE 10 - Edge 13, we need a different heuristic
+ // to determine whether an object is a `DataView`.
+ function ie10IsDataView(obj) {
+ return obj != null && isFunction$1(obj.getInt8) && isArrayBuffer(obj.buffer);
+ }
+
+ var isDataView$1 = (hasStringTagBug ? ie10IsDataView : isDataView);
+
+ // Is a given value an array?
+ // Delegates to ECMA5's native `Array.isArray`.
+ var isArray = nativeIsArray || tagTester('Array');
+
+ // Internal function to check whether `key` is an own property name of `obj`.
+ function has$1(obj, key) {
+ return obj != null && hasOwnProperty.call(obj, key);
+ }
+
+ var isArguments = tagTester('Arguments');
+
+ // Define a fallback version of the method in browsers (ahem, IE < 9), where
+ // there isn't any inspectable "Arguments" type.
+ (function() {
+ if (!isArguments(arguments)) {
+ isArguments = function(obj) {
+ return has$1(obj, 'callee');
+ };
+ }
+ }());
+
+ var isArguments$1 = isArguments;
+
+ // Is a given object a finite number?
+ function isFinite$1(obj) {
+ return !isSymbol(obj) && _isFinite(obj) && !isNaN(parseFloat(obj));
+ }
+
+ // Is the given value `NaN`?
+ function isNaN$1(obj) {
+ return isNumber(obj) && _isNaN(obj);
+ }
+
+ // Predicate-generating function. Often useful outside of Underscore.
+ function constant(value) {
+ return function() {
+ return value;
+ };
+ }
+
+ // Common internal logic for `isArrayLike` and `isBufferLike`.
+ function createSizePropertyCheck(getSizeProperty) {
+ return function(collection) {
+ var sizeProperty = getSizeProperty(collection);
+ return typeof sizeProperty == 'number' && sizeProperty >= 0 && sizeProperty <= MAX_ARRAY_INDEX;
+ }
+ }
+
+ // Internal helper to generate a function to obtain property `key` from `obj`.
+ function shallowProperty(key) {
+ return function(obj) {
+ return obj == null ? void 0 : obj[key];
+ };
+ }
+
+ // Internal helper to obtain the `byteLength` property of an object.
+ var getByteLength = shallowProperty('byteLength');
+
+ // Internal helper to determine whether we should spend extensive checks against
+ // `ArrayBuffer` et al.
+ var isBufferLike = createSizePropertyCheck(getByteLength);
+
+ // Is a given value a typed array?
+ var typedArrayPattern = /\[object ((I|Ui)nt(8|16|32)|Float(32|64)|Uint8Clamped|Big(I|Ui)nt64)Array\]/;
+ function isTypedArray(obj) {
+ // `ArrayBuffer.isView` is the most future-proof, so use it when available.
+ // Otherwise, fall back on the above regular expression.
+ return nativeIsView ? (nativeIsView(obj) && !isDataView$1(obj)) :
+ isBufferLike(obj) && typedArrayPattern.test(toString.call(obj));
+ }
+
+ var isTypedArray$1 = supportsArrayBuffer ? isTypedArray : constant(false);
+
+ // Internal helper to obtain the `length` property of an object.
+ var getLength = shallowProperty('length');
+
+ // Internal helper to create a simple lookup structure.
+ // `collectNonEnumProps` used to depend on `_.contains`, but this led to
+ // circular imports. `emulatedSet` is a one-off solution that only works for
+ // arrays of strings.
+ function emulatedSet(keys) {
+ var hash = {};
+ for (var l = keys.length, i = 0; i < l; ++i) hash[keys[i]] = true;
+ return {
+ contains: function(key) { return hash[key]; },
+ push: function(key) {
+ hash[key] = true;
+ return keys.push(key);
+ }
+ };
+ }
+
+ // Internal helper. Checks `keys` for the presence of keys in IE < 9 that won't
+ // be iterated by `for key in ...` and thus missed. Extends `keys` in place if
+ // needed.
+ function collectNonEnumProps(obj, keys) {
+ keys = emulatedSet(keys);
+ var nonEnumIdx = nonEnumerableProps.length;
+ var constructor = obj.constructor;
+ var proto = isFunction$1(constructor) && constructor.prototype || ObjProto;
+
+ // Constructor is a special case.
+ var prop = 'constructor';
+ if (has$1(obj, prop) && !keys.contains(prop)) keys.push(prop);
+
+ while (nonEnumIdx--) {
+ prop = nonEnumerableProps[nonEnumIdx];
+ if (prop in obj && obj[prop] !== proto[prop] && !keys.contains(prop)) {
+ keys.push(prop);
+ }
+ }
+ }
+
+ // Retrieve the names of an object's own properties.
+ // Delegates to **ECMAScript 5**'s native `Object.keys`.
+ function keys(obj) {
+ if (!isObject(obj)) return [];
+ if (nativeKeys) return nativeKeys(obj);
+ var keys = [];
+ for (var key in obj) if (has$1(obj, key)) keys.push(key);
+ // Ahem, IE < 9.
+ if (hasEnumBug) collectNonEnumProps(obj, keys);
+ return keys;
+ }
+
+ // Is a given array, string, or object empty?
+ // An "empty" object has no enumerable own-properties.
+ function isEmpty(obj) {
+ if (obj == null) return true;
+ // Skip the more expensive `toString`-based type checks if `obj` has no
+ // `.length`.
+ var length = getLength(obj);
+ if (typeof length == 'number' && (
+ isArray(obj) || isString(obj) || isArguments$1(obj)
+ )) return length === 0;
+ return getLength(keys(obj)) === 0;
+ }
+
+ // Returns whether an object has a given set of `key:value` pairs.
+ function isMatch(object, attrs) {
+ var _keys = keys(attrs), length = _keys.length;
+ if (object == null) return !length;
+ var obj = Object(object);
+ for (var i = 0; i < length; i++) {
+ var key = _keys[i];
+ if (attrs[key] !== obj[key] || !(key in obj)) return false;
+ }
+ return true;
+ }
+
+ // If Underscore is called as a function, it returns a wrapped object that can
+ // be used OO-style. This wrapper holds altered versions of all functions added
+ // through `_.mixin`. Wrapped objects may be chained.
+ function _$1(obj) {
+ if (obj instanceof _$1) return obj;
+ if (!(this instanceof _$1)) return new _$1(obj);
+ this._wrapped = obj;
+ }
+
+ _$1.VERSION = VERSION;
+
+ // Extracts the result from a wrapped and chained object.
+ _$1.prototype.value = function() {
+ return this._wrapped;
+ };
+
+ // Provide unwrapping proxies for some methods used in engine operations
+ // such as arithmetic and JSON stringification.
+ _$1.prototype.valueOf = _$1.prototype.toJSON = _$1.prototype.value;
+
+ _$1.prototype.toString = function() {
+ return String(this._wrapped);
+ };
+
+ // Internal function to wrap or shallow-copy an ArrayBuffer,
+ // typed array or DataView to a new view, reusing the buffer.
+ function toBufferView(bufferSource) {
+ return new Uint8Array(
+ bufferSource.buffer || bufferSource,
+ bufferSource.byteOffset || 0,
+ getByteLength(bufferSource)
+ );
+ }
+
+ // We use this string twice, so give it a name for minification.
+ var tagDataView = '[object DataView]';
+
+ // Internal recursive comparison function for `_.isEqual`.
+ function eq(a, b, aStack, bStack) {
+ // Identical objects are equal. `0 === -0`, but they aren't identical.
+ // See the [Harmony `egal` proposal](https://wiki.ecmascript.org/doku.php?id=harmony:egal).
+ if (a === b) return a !== 0 || 1 / a === 1 / b;
+ // `null` or `undefined` only equal to itself (strict comparison).
+ if (a == null || b == null) return false;
+ // `NaN`s are equivalent, but non-reflexive.
+ if (a !== a) return b !== b;
+ // Exhaust primitive checks
+ var type = typeof a;
+ if (type !== 'function' && type !== 'object' && typeof b != 'object') return false;
+ return deepEq(a, b, aStack, bStack);
+ }
+
+ // Internal recursive comparison function for `_.isEqual`.
+ function deepEq(a, b, aStack, bStack) {
+ // Unwrap any wrapped objects.
+ if (a instanceof _$1) a = a._wrapped;
+ if (b instanceof _$1) b = b._wrapped;
+ // Compare `[[Class]]` names.
+ var className = toString.call(a);
+ if (className !== toString.call(b)) return false;
+ // Work around a bug in IE 10 - Edge 13.
+ if (hasStringTagBug && className == '[object Object]' && isDataView$1(a)) {
+ if (!isDataView$1(b)) return false;
+ className = tagDataView;
+ }
+ switch (className) {
+ // These types are compared by value.
+ case '[object RegExp]':
+ // RegExps are coerced to strings for comparison (Note: '' + /a/i === '/a/i')
+ case '[object String]':
+ // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
+ // equivalent to `new String("5")`.
+ return '' + a === '' + b;
+ case '[object Number]':
+ // `NaN`s are equivalent, but non-reflexive.
+ // Object(NaN) is equivalent to NaN.
+ if (+a !== +a) return +b !== +b;
+ // An `egal` comparison is performed for other numeric values.
+ return +a === 0 ? 1 / +a === 1 / b : +a === +b;
+ case '[object Date]':
+ case '[object Boolean]':
+ // Coerce dates and booleans to numeric primitive values. Dates are compared by their
+ // millisecond representations. Note that invalid dates with millisecond representations
+ // of `NaN` are not equivalent.
+ return +a === +b;
+ case '[object Symbol]':
+ return SymbolProto.valueOf.call(a) === SymbolProto.valueOf.call(b);
+ case '[object ArrayBuffer]':
+ case tagDataView:
+ // Coerce to typed array so we can fall through.
+ return deepEq(toBufferView(a), toBufferView(b), aStack, bStack);
+ }
+
+ var areArrays = className === '[object Array]';
+ if (!areArrays && isTypedArray$1(a)) {
+ var byteLength = getByteLength(a);
+ if (byteLength !== getByteLength(b)) return false;
+ if (a.buffer === b.buffer && a.byteOffset === b.byteOffset) return true;
+ areArrays = true;
+ }
+ if (!areArrays) {
+ if (typeof a != 'object' || typeof b != 'object') return false;
+
+ // Objects with different constructors are not equivalent, but `Object`s or `Array`s
+ // from different frames are.
+ var aCtor = a.constructor, bCtor = b.constructor;
+ if (aCtor !== bCtor && !(isFunction$1(aCtor) && aCtor instanceof aCtor &&
+ isFunction$1(bCtor) && bCtor instanceof bCtor)
+ && ('constructor' in a && 'constructor' in b)) {
+ return false;
+ }
+ }
+ // Assume equality for cyclic structures. The algorithm for detecting cyclic
+ // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
+
+ // Initializing stack of traversed objects.
+ // It's done here since we only need them for objects and arrays comparison.
+ aStack = aStack || [];
+ bStack = bStack || [];
+ var length = aStack.length;
+ while (length--) {
+ // Linear search. Performance is inversely proportional to the number of
+ // unique nested structures.
+ if (aStack[length] === a) return bStack[length] === b;
+ }
+
+ // Add the first object to the stack of traversed objects.
+ aStack.push(a);
+ bStack.push(b);
+
+ // Recursively compare objects and arrays.
+ if (areArrays) {
+ // Compare array lengths to determine if a deep comparison is necessary.
+ length = a.length;
+ if (length !== b.length) return false;
+ // Deep compare the contents, ignoring non-numeric properties.
+ while (length--) {
+ if (!eq(a[length], b[length], aStack, bStack)) return false;
+ }
+ } else {
+ // Deep compare objects.
+ var _keys = keys(a), key;
+ length = _keys.length;
+ // Ensure that both objects contain the same number of properties before comparing deep equality.
+ if (keys(b).length !== length) return false;
+ while (length--) {
+ // Deep compare each member
+ key = _keys[length];
+ if (!(has$1(b, key) && eq(a[key], b[key], aStack, bStack))) return false;
+ }
+ }
+ // Remove the first object from the stack of traversed objects.
+ aStack.pop();
+ bStack.pop();
+ return true;
+ }
+
+ // Perform a deep comparison to check if two objects are equal.
+ function isEqual(a, b) {
+ return eq(a, b);
+ }
+
+ // Retrieve all the enumerable property names of an object.
+ function allKeys(obj) {
+ if (!isObject(obj)) return [];
+ var keys = [];
+ for (var key in obj) keys.push(key);
+ // Ahem, IE < 9.
+ if (hasEnumBug) collectNonEnumProps(obj, keys);
+ return keys;
+ }
+
+ // Since the regular `Object.prototype.toString` type tests don't work for
+ // some types in IE 11, we use a fingerprinting heuristic instead, based
+ // on the methods. It's not great, but it's the best we got.
+ // The fingerprint method lists are defined below.
+ function ie11fingerprint(methods) {
+ var length = getLength(methods);
+ return function(obj) {
+ if (obj == null) return false;
+ // `Map`, `WeakMap` and `Set` have no enumerable keys.
+ var keys = allKeys(obj);
+ if (getLength(keys)) return false;
+ for (var i = 0; i < length; i++) {
+ if (!isFunction$1(obj[methods[i]])) return false;
+ }
+ // If we are testing against `WeakMap`, we need to ensure that
+ // `obj` doesn't have a `forEach` method in order to distinguish
+ // it from a regular `Map`.
+ return methods !== weakMapMethods || !isFunction$1(obj[forEachName]);
+ };
+ }
+
+ // In the interest of compact minification, we write
+ // each string in the fingerprints only once.
+ var forEachName = 'forEach',
+ hasName = 'has',
+ commonInit = ['clear', 'delete'],
+ mapTail = ['get', hasName, 'set'];
+
+ // `Map`, `WeakMap` and `Set` each have slightly different
+ // combinations of the above sublists.
+ var mapMethods = commonInit.concat(forEachName, mapTail),
+ weakMapMethods = commonInit.concat(mapTail),
+ setMethods = ['add'].concat(commonInit, forEachName, hasName);
+
+ var isMap = isIE11 ? ie11fingerprint(mapMethods) : tagTester('Map');
+
+ var isWeakMap = isIE11 ? ie11fingerprint(weakMapMethods) : tagTester('WeakMap');
+
+ var isSet = isIE11 ? ie11fingerprint(setMethods) : tagTester('Set');
+
+ var isWeakSet = tagTester('WeakSet');
+
+ // Retrieve the values of an object's properties.
+ function values(obj) {
+ var _keys = keys(obj);
+ var length = _keys.length;
+ var values = Array(length);
+ for (var i = 0; i < length; i++) {
+ values[i] = obj[_keys[i]];
+ }
+ return values;
+ }
+
+ // Convert an object into a list of `[key, value]` pairs.
+ // The opposite of `_.object` with one argument.
+ function pairs(obj) {
+ var _keys = keys(obj);
+ var length = _keys.length;
+ var pairs = Array(length);
+ for (var i = 0; i < length; i++) {
+ pairs[i] = [_keys[i], obj[_keys[i]]];
+ }
+ return pairs;
+ }
+
+ // Invert the keys and values of an object. The values must be serializable.
+ function invert(obj) {
+ var result = {};
+ var _keys = keys(obj);
+ for (var i = 0, length = _keys.length; i < length; i++) {
+ result[obj[_keys[i]]] = _keys[i];
+ }
+ return result;
+ }
+
+ // Return a sorted list of the function names available on the object.
+ function functions(obj) {
+ var names = [];
+ for (var key in obj) {
+ if (isFunction$1(obj[key])) names.push(key);
+ }
+ return names.sort();
+ }
+
+ // An internal function for creating assigner functions.
+ function createAssigner(keysFunc, defaults) {
+ return function(obj) {
+ var length = arguments.length;
+ if (defaults) obj = Object(obj);
+ if (length < 2 || obj == null) return obj;
+ for (var index = 1; index < length; index++) {
+ var source = arguments[index],
+ keys = keysFunc(source),
+ l = keys.length;
+ for (var i = 0; i < l; i++) {
+ var key = keys[i];
+ if (!defaults || obj[key] === void 0) obj[key] = source[key];
+ }
+ }
+ return obj;
+ };
+ }
+
+ // Extend a given object with all the properties in passed-in object(s).
+ var extend = createAssigner(allKeys);
+
+ // Assigns a given object with all the own properties in the passed-in
+ // object(s).
+ // (https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object/assign)
+ var extendOwn = createAssigner(keys);
+
+ // Fill in a given object with default properties.
+ var defaults = createAssigner(allKeys, true);
+
+ // Create a naked function reference for surrogate-prototype-swapping.
+ function ctor() {
+ return function(){};
+ }
+
+ // An internal function for creating a new object that inherits from another.
+ function baseCreate(prototype) {
+ if (!isObject(prototype)) return {};
+ if (nativeCreate) return nativeCreate(prototype);
+ var Ctor = ctor();
+ Ctor.prototype = prototype;
+ var result = new Ctor;
+ Ctor.prototype = null;
+ return result;
+ }
+
+ // Creates an object that inherits from the given prototype object.
+ // If additional properties are provided then they will be added to the
+ // created object.
+ function create(prototype, props) {
+ var result = baseCreate(prototype);
+ if (props) extendOwn(result, props);
+ return result;
+ }
+
+ // Create a (shallow-cloned) duplicate of an object.
+ function clone(obj) {
+ if (!isObject(obj)) return obj;
+ return isArray(obj) ? obj.slice() : extend({}, obj);
+ }
+
+ // Invokes `interceptor` with the `obj` and then returns `obj`.
+ // The primary purpose of this method is to "tap into" a method chain, in
+ // order to perform operations on intermediate results within the chain.
+ function tap(obj, interceptor) {
+ interceptor(obj);
+ return obj;
+ }
+
+ // Normalize a (deep) property `path` to array.
+ // Like `_.iteratee`, this function can be customized.
+ function toPath$1(path) {
+ return isArray(path) ? path : [path];
+ }
+ _$1.toPath = toPath$1;
+
+ // Internal wrapper for `_.toPath` to enable minification.
+ // Similar to `cb` for `_.iteratee`.
+ function toPath(path) {
+ return _$1.toPath(path);
+ }
+
+ // Internal function to obtain a nested property in `obj` along `path`.
+ function deepGet(obj, path) {
+ var length = path.length;
+ for (var i = 0; i < length; i++) {
+ if (obj == null) return void 0;
+ obj = obj[path[i]];
+ }
+ return length ? obj : void 0;
+ }
+
+ // Get the value of the (deep) property on `path` from `object`.
+ // If any property in `path` does not exist or if the value is
+ // `undefined`, return `defaultValue` instead.
+ // The `path` is normalized through `_.toPath`.
+ function get(object, path, defaultValue) {
+ var value = deepGet(object, toPath(path));
+ return isUndefined(value) ? defaultValue : value;
+ }
+
+ // Shortcut function for checking if an object has a given property directly on
+ // itself (in other words, not on a prototype). Unlike the internal `has`
+ // function, this public version can also traverse nested properties.
+ function has(obj, path) {
+ path = toPath(path);
+ var length = path.length;
+ for (var i = 0; i < length; i++) {
+ var key = path[i];
+ if (!has$1(obj, key)) return false;
+ obj = obj[key];
+ }
+ return !!length;
+ }
+
+ // Keep the identity function around for default iteratees.
+ function identity(value) {
+ return value;
+ }
+
+ // Returns a predicate for checking whether an object has a given set of
+ // `key:value` pairs.
+ function matcher(attrs) {
+ attrs = extendOwn({}, attrs);
+ return function(obj) {
+ return isMatch(obj, attrs);
+ };
+ }
+
+ // Creates a function that, when passed an object, will traverse that object’s
+ // properties down the given `path`, specified as an array of keys or indices.
+ function property(path) {
+ path = toPath(path);
+ return function(obj) {
+ return deepGet(obj, path);
+ };
+ }
+
+ // Internal function that returns an efficient (for current engines) version
+ // of the passed-in callback, to be repeatedly applied in other Underscore
+ // functions.
+ function optimizeCb(func, context, argCount) {
+ if (context === void 0) return func;
+ switch (argCount == null ? 3 : argCount) {
+ case 1: return function(value) {
+ return func.call(context, value);
+ };
+ // The 2-argument case is omitted because we’re not using it.
+ case 3: return function(value, index, collection) {
+ return func.call(context, value, index, collection);
+ };
+ case 4: return function(accumulator, value, index, collection) {
+ return func.call(context, accumulator, value, index, collection);
+ };
+ }
+ return function() {
+ return func.apply(context, arguments);
+ };
+ }
+
+ // An internal function to generate callbacks that can be applied to each
+ // element in a collection, returning the desired result — either `_.identity`,
+ // an arbitrary callback, a property matcher, or a property accessor.
+ function baseIteratee(value, context, argCount) {
+ if (value == null) return identity;
+ if (isFunction$1(value)) return optimizeCb(value, context, argCount);
+ if (isObject(value) && !isArray(value)) return matcher(value);
+ return property(value);
+ }
+
+ // External wrapper for our callback generator. Users may customize
+ // `_.iteratee` if they want additional predicate/iteratee shorthand styles.
+ // This abstraction hides the internal-only `argCount` argument.
+ function iteratee(value, context) {
+ return baseIteratee(value, context, Infinity);
+ }
+ _$1.iteratee = iteratee;
+
+ // The function we call internally to generate a callback. It invokes
+ // `_.iteratee` if overridden, otherwise `baseIteratee`.
+ function cb(value, context, argCount) {
+ if (_$1.iteratee !== iteratee) return _$1.iteratee(value, context);
+ return baseIteratee(value, context, argCount);
+ }
+
+ // Returns the results of applying the `iteratee` to each element of `obj`.
+ // In contrast to `_.map` it returns an object.
+ function mapObject(obj, iteratee, context) {
+ iteratee = cb(iteratee, context);
+ var _keys = keys(obj),
+ length = _keys.length,
+ results = {};
+ for (var index = 0; index < length; index++) {
+ var currentKey = _keys[index];
+ results[currentKey] = iteratee(obj[currentKey], currentKey, obj);
+ }
+ return results;
+ }
+
+ // Predicate-generating function. Often useful outside of Underscore.
+ function noop(){}
+
+ // Generates a function for a given object that returns a given property.
+ function propertyOf(obj) {
+ if (obj == null) return noop;
+ return function(path) {
+ return get(obj, path);
+ };
+ }
+
+ // Run a function **n** times.
+ function times(n, iteratee, context) {
+ var accum = Array(Math.max(0, n));
+ iteratee = optimizeCb(iteratee, context, 1);
+ for (var i = 0; i < n; i++) accum[i] = iteratee(i);
+ return accum;
+ }
+
+ // Return a random integer between `min` and `max` (inclusive).
+ function random(min, max) {
+ if (max == null) {
+ max = min;
+ min = 0;
+ }
+ return min + Math.floor(Math.random() * (max - min + 1));
+ }
+
+ // A (possibly faster) way to get the current timestamp as an integer.
+ var now = Date.now || function() {
+ return new Date().getTime();
+ };
+
+ // Internal helper to generate functions for escaping and unescaping strings
+ // to/from HTML interpolation.
+ function createEscaper(map) {
+ var escaper = function(match) {
+ return map[match];
+ };
+ // Regexes for identifying a key that needs to be escaped.
+ var source = '(?:' + keys(map).join('|') + ')';
+ var testRegexp = RegExp(source);
+ var replaceRegexp = RegExp(source, 'g');
+ return function(string) {
+ string = string == null ? '' : '' + string;
+ return testRegexp.test(string) ? string.replace(replaceRegexp, escaper) : string;
+ };
+ }
+
+ // Internal list of HTML entities for escaping.
+ var escapeMap = {
+ '&': '&',
+ '<': '<',
+ '>': '>',
+ '"': '"',
+ "'": ''',
+ '`': '`'
+ };
+
+ // Function for escaping strings to HTML interpolation.
+ var _escape = createEscaper(escapeMap);
+
+ // Internal list of HTML entities for unescaping.
+ var unescapeMap = invert(escapeMap);
+
+ // Function for unescaping strings from HTML interpolation.
+ var _unescape = createEscaper(unescapeMap);
+
+ // By default, Underscore uses ERB-style template delimiters. Change the
+ // following template settings to use alternative delimiters.
+ var templateSettings = _$1.templateSettings = {
+ evaluate: /<%([\s\S]+?)%>/g,
+ interpolate: /<%=([\s\S]+?)%>/g,
+ escape: /<%-([\s\S]+?)%>/g
+ };
+
+ // When customizing `_.templateSettings`, if you don't want to define an
+ // interpolation, evaluation or escaping regex, we need one that is
+ // guaranteed not to match.
+ var noMatch = /(.)^/;
+
+ // Certain characters need to be escaped so that they can be put into a
+ // string literal.
+ var escapes = {
+ "'": "'",
+ '\\': '\\',
+ '\r': 'r',
+ '\n': 'n',
+ '\u2028': 'u2028',
+ '\u2029': 'u2029'
+ };
+
+ var escapeRegExp = /\\|'|\r|\n|\u2028|\u2029/g;
+
+ function escapeChar(match) {
+ return '\\' + escapes[match];
+ }
+
+ // In order to prevent third-party code injection through
+ // `_.templateSettings.variable`, we test it against the following regular
+ // expression. It is intentionally a bit more liberal than just matching valid
+ // identifiers, but still prevents possible loopholes through defaults or
+ // destructuring assignment.
+ var bareIdentifier = /^\s*(\w|\$)+\s*$/;
+
+ // JavaScript micro-templating, similar to John Resig's implementation.
+ // Underscore templating handles arbitrary delimiters, preserves whitespace,
+ // and correctly escapes quotes within interpolated code.
+ // NB: `oldSettings` only exists for backwards compatibility.
+ function template(text, settings, oldSettings) {
+ if (!settings && oldSettings) settings = oldSettings;
+ settings = defaults({}, settings, _$1.templateSettings);
+
+ // Combine delimiters into one regular expression via alternation.
+ var matcher = RegExp([
+ (settings.escape || noMatch).source,
+ (settings.interpolate || noMatch).source,
+ (settings.evaluate || noMatch).source
+ ].join('|') + '|$', 'g');
+
+ // Compile the template source, escaping string literals appropriately.
+ var index = 0;
+ var source = "__p+='";
+ text.replace(matcher, function(match, escape, interpolate, evaluate, offset) {
+ source += text.slice(index, offset).replace(escapeRegExp, escapeChar);
+ index = offset + match.length;
+
+ if (escape) {
+ source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'";
+ } else if (interpolate) {
+ source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'";
+ } else if (evaluate) {
+ source += "';\n" + evaluate + "\n__p+='";
+ }
+
+ // Adobe VMs need the match returned to produce the correct offset.
+ return match;
+ });
+ source += "';\n";
+
+ var argument = settings.variable;
+ if (argument) {
+ // Insure against third-party code injection. (CVE-2021-23358)
+ if (!bareIdentifier.test(argument)) throw new Error(
+ 'variable is not a bare identifier: ' + argument
+ );
+ } else {
+ // If a variable is not specified, place data values in local scope.
+ source = 'with(obj||{}){\n' + source + '}\n';
+ argument = 'obj';
+ }
+
+ source = "var __t,__p='',__j=Array.prototype.join," +
+ "print=function(){__p+=__j.call(arguments,'');};\n" +
+ source + 'return __p;\n';
+
+ var render;
+ try {
+ render = new Function(argument, '_', source);
+ } catch (e) {
+ e.source = source;
+ throw e;
+ }
+
+ var template = function(data) {
+ return render.call(this, data, _$1);
+ };
+
+ // Provide the compiled source as a convenience for precompilation.
+ template.source = 'function(' + argument + '){\n' + source + '}';
+
+ return template;
+ }
+
+ // Traverses the children of `obj` along `path`. If a child is a function, it
+ // is invoked with its parent as context. Returns the value of the final
+ // child, or `fallback` if any child is undefined.
+ function result(obj, path, fallback) {
+ path = toPath(path);
+ var length = path.length;
+ if (!length) {
+ return isFunction$1(fallback) ? fallback.call(obj) : fallback;
+ }
+ for (var i = 0; i < length; i++) {
+ var prop = obj == null ? void 0 : obj[path[i]];
+ if (prop === void 0) {
+ prop = fallback;
+ i = length; // Ensure we don't continue iterating.
+ }
+ obj = isFunction$1(prop) ? prop.call(obj) : prop;
+ }
+ return obj;
+ }
+
+ // Generate a unique integer id (unique within the entire client session).
+ // Useful for temporary DOM ids.
+ var idCounter = 0;
+ function uniqueId(prefix) {
+ var id = ++idCounter + '';
+ return prefix ? prefix + id : id;
+ }
+
+ // Start chaining a wrapped Underscore object.
+ function chain(obj) {
+ var instance = _$1(obj);
+ instance._chain = true;
+ return instance;
+ }
+
+ // Internal function to execute `sourceFunc` bound to `context` with optional
+ // `args`. Determines whether to execute a function as a constructor or as a
+ // normal function.
+ function executeBound(sourceFunc, boundFunc, context, callingContext, args) {
+ if (!(callingContext instanceof boundFunc)) return sourceFunc.apply(context, args);
+ var self = baseCreate(sourceFunc.prototype);
+ var result = sourceFunc.apply(self, args);
+ if (isObject(result)) return result;
+ return self;
+ }
+
+ // Partially apply a function by creating a version that has had some of its
+ // arguments pre-filled, without changing its dynamic `this` context. `_` acts
+ // as a placeholder by default, allowing any combination of arguments to be
+ // pre-filled. Set `_.partial.placeholder` for a custom placeholder argument.
+ var partial = restArguments(function(func, boundArgs) {
+ var placeholder = partial.placeholder;
+ var bound = function() {
+ var position = 0, length = boundArgs.length;
+ var args = Array(length);
+ for (var i = 0; i < length; i++) {
+ args[i] = boundArgs[i] === placeholder ? arguments[position++] : boundArgs[i];
+ }
+ while (position < arguments.length) args.push(arguments[position++]);
+ return executeBound(func, bound, this, this, args);
+ };
+ return bound;
+ });
+
+ partial.placeholder = _$1;
+
+ // Create a function bound to a given object (assigning `this`, and arguments,
+ // optionally).
+ var bind = restArguments(function(func, context, args) {
+ if (!isFunction$1(func)) throw new TypeError('Bind must be called on a function');
+ var bound = restArguments(function(callArgs) {
+ return executeBound(func, bound, context, this, args.concat(callArgs));
+ });
+ return bound;
+ });
+
+ // Internal helper for collection methods to determine whether a collection
+ // should be iterated as an array or as an object.
+ // Related: https://people.mozilla.org/~jorendorff/es6-draft.html#sec-tolength
+ // Avoids a very nasty iOS 8 JIT bug on ARM-64. #2094
+ var isArrayLike = createSizePropertyCheck(getLength);
+
+ // Internal implementation of a recursive `flatten` function.
+ function flatten$1(input, depth, strict, output) {
+ output = output || [];
+ if (!depth && depth !== 0) {
+ depth = Infinity;
+ } else if (depth <= 0) {
+ return output.concat(input);
+ }
+ var idx = output.length;
+ for (var i = 0, length = getLength(input); i < length; i++) {
+ var value = input[i];
+ if (isArrayLike(value) && (isArray(value) || isArguments$1(value))) {
+ // Flatten current level of array or arguments object.
+ if (depth > 1) {
+ flatten$1(value, depth - 1, strict, output);
+ idx = output.length;
+ } else {
+ var j = 0, len = value.length;
+ while (j < len) output[idx++] = value[j++];
+ }
+ } else if (!strict) {
+ output[idx++] = value;
+ }
+ }
+ return output;
+ }
+
+ // Bind a number of an object's methods to that object. Remaining arguments
+ // are the method names to be bound. Useful for ensuring that all callbacks
+ // defined on an object belong to it.
+ var bindAll = restArguments(function(obj, keys) {
+ keys = flatten$1(keys, false, false);
+ var index = keys.length;
+ if (index < 1) throw new Error('bindAll must be passed function names');
+ while (index--) {
+ var key = keys[index];
+ obj[key] = bind(obj[key], obj);
+ }
+ return obj;
+ });
+
+ // Memoize an expensive function by storing its results.
+ function memoize(func, hasher) {
+ var memoize = function(key) {
+ var cache = memoize.cache;
+ var address = '' + (hasher ? hasher.apply(this, arguments) : key);
+ if (!has$1(cache, address)) cache[address] = func.apply(this, arguments);
+ return cache[address];
+ };
+ memoize.cache = {};
+ return memoize;
+ }
+
+ // Delays a function for the given number of milliseconds, and then calls
+ // it with the arguments supplied.
+ var delay = restArguments(function(func, wait, args) {
+ return setTimeout(function() {
+ return func.apply(null, args);
+ }, wait);
+ });
+
+ // Defers a function, scheduling it to run after the current call stack has
+ // cleared.
+ var defer = partial(delay, _$1, 1);
+
+ // Returns a function, that, when invoked, will only be triggered at most once
+ // during a given window of time. Normally, the throttled function will run
+ // as much as it can, without ever going more than once per `wait` duration;
+ // but if you'd like to disable the execution on the leading edge, pass
+ // `{leading: false}`. To disable execution on the trailing edge, ditto.
+ function throttle(func, wait, options) {
+ var timeout, context, args, result;
+ var previous = 0;
+ if (!options) options = {};
+
+ var later = function() {
+ previous = options.leading === false ? 0 : now();
+ timeout = null;
+ result = func.apply(context, args);
+ if (!timeout) context = args = null;
+ };
+
+ var throttled = function() {
+ var _now = now();
+ if (!previous && options.leading === false) previous = _now;
+ var remaining = wait - (_now - previous);
+ context = this;
+ args = arguments;
+ if (remaining <= 0 || remaining > wait) {
+ if (timeout) {
+ clearTimeout(timeout);
+ timeout = null;
+ }
+ previous = _now;
+ result = func.apply(context, args);
+ if (!timeout) context = args = null;
+ } else if (!timeout && options.trailing !== false) {
+ timeout = setTimeout(later, remaining);
+ }
+ return result;
+ };
+
+ throttled.cancel = function() {
+ clearTimeout(timeout);
+ previous = 0;
+ timeout = context = args = null;
+ };
+
+ return throttled;
+ }
+
+ // When a sequence of calls of the returned function ends, the argument
+ // function is triggered. The end of a sequence is defined by the `wait`
+ // parameter. If `immediate` is passed, the argument function will be
+ // triggered at the beginning of the sequence instead of at the end.
+ function debounce(func, wait, immediate) {
+ var timeout, previous, args, result, context;
+
+ var later = function() {
+ var passed = now() - previous;
+ if (wait > passed) {
+ timeout = setTimeout(later, wait - passed);
+ } else {
+ timeout = null;
+ if (!immediate) result = func.apply(context, args);
+ // This check is needed because `func` can recursively invoke `debounced`.
+ if (!timeout) args = context = null;
+ }
+ };
+
+ var debounced = restArguments(function(_args) {
+ context = this;
+ args = _args;
+ previous = now();
+ if (!timeout) {
+ timeout = setTimeout(later, wait);
+ if (immediate) result = func.apply(context, args);
+ }
+ return result;
+ });
+
+ debounced.cancel = function() {
+ clearTimeout(timeout);
+ timeout = args = context = null;
+ };
+
+ return debounced;
+ }
+
+ // Returns the first function passed as an argument to the second,
+ // allowing you to adjust arguments, run code before and after, and
+ // conditionally execute the original function.
+ function wrap(func, wrapper) {
+ return partial(wrapper, func);
+ }
+
+ // Returns a negated version of the passed-in predicate.
+ function negate(predicate) {
+ return function() {
+ return !predicate.apply(this, arguments);
+ };
+ }
+
+ // Returns a function that is the composition of a list of functions, each
+ // consuming the return value of the function that follows.
+ function compose() {
+ var args = arguments;
+ var start = args.length - 1;
+ return function() {
+ var i = start;
+ var result = args[start].apply(this, arguments);
+ while (i--) result = args[i].call(this, result);
+ return result;
+ };
+ }
+
+ // Returns a function that will only be executed on and after the Nth call.
+ function after(times, func) {
+ return function() {
+ if (--times < 1) {
+ return func.apply(this, arguments);
+ }
+ };
+ }
+
+ // Returns a function that will only be executed up to (but not including) the
+ // Nth call.
+ function before(times, func) {
+ var memo;
+ return function() {
+ if (--times > 0) {
+ memo = func.apply(this, arguments);
+ }
+ if (times <= 1) func = null;
+ return memo;
+ };
+ }
+
+ // Returns a function that will be executed at most one time, no matter how
+ // often you call it. Useful for lazy initialization.
+ var once = partial(before, 2);
+
+ // Returns the first key on an object that passes a truth test.
+ function findKey(obj, predicate, context) {
+ predicate = cb(predicate, context);
+ var _keys = keys(obj), key;
+ for (var i = 0, length = _keys.length; i < length; i++) {
+ key = _keys[i];
+ if (predicate(obj[key], key, obj)) return key;
+ }
+ }
+
+ // Internal function to generate `_.findIndex` and `_.findLastIndex`.
+ function createPredicateIndexFinder(dir) {
+ return function(array, predicate, context) {
+ predicate = cb(predicate, context);
+ var length = getLength(array);
+ var index = dir > 0 ? 0 : length - 1;
+ for (; index >= 0 && index < length; index += dir) {
+ if (predicate(array[index], index, array)) return index;
+ }
+ return -1;
+ };
+ }
+
+ // Returns the first index on an array-like that passes a truth test.
+ var findIndex = createPredicateIndexFinder(1);
+
+ // Returns the last index on an array-like that passes a truth test.
+ var findLastIndex = createPredicateIndexFinder(-1);
+
+ // Use a comparator function to figure out the smallest index at which
+ // an object should be inserted so as to maintain order. Uses binary search.
+ function sortedIndex(array, obj, iteratee, context) {
+ iteratee = cb(iteratee, context, 1);
+ var value = iteratee(obj);
+ var low = 0, high = getLength(array);
+ while (low < high) {
+ var mid = Math.floor((low + high) / 2);
+ if (iteratee(array[mid]) < value) low = mid + 1; else high = mid;
+ }
+ return low;
+ }
+
+ // Internal function to generate the `_.indexOf` and `_.lastIndexOf` functions.
+ function createIndexFinder(dir, predicateFind, sortedIndex) {
+ return function(array, item, idx) {
+ var i = 0, length = getLength(array);
+ if (typeof idx == 'number') {
+ if (dir > 0) {
+ i = idx >= 0 ? idx : Math.max(idx + length, i);
+ } else {
+ length = idx >= 0 ? Math.min(idx + 1, length) : idx + length + 1;
+ }
+ } else if (sortedIndex && idx && length) {
+ idx = sortedIndex(array, item);
+ return array[idx] === item ? idx : -1;
+ }
+ if (item !== item) {
+ idx = predicateFind(slice.call(array, i, length), isNaN$1);
+ return idx >= 0 ? idx + i : -1;
+ }
+ for (idx = dir > 0 ? i : length - 1; idx >= 0 && idx < length; idx += dir) {
+ if (array[idx] === item) return idx;
+ }
+ return -1;
+ };
+ }
+
+ // Return the position of the first occurrence of an item in an array,
+ // or -1 if the item is not included in the array.
+ // If the array is large and already in sort order, pass `true`
+ // for **isSorted** to use binary search.
+ var indexOf = createIndexFinder(1, findIndex, sortedIndex);
+
+ // Return the position of the last occurrence of an item in an array,
+ // or -1 if the item is not included in the array.
+ var lastIndexOf = createIndexFinder(-1, findLastIndex);
+
+ // Return the first value which passes a truth test.
+ function find(obj, predicate, context) {
+ var keyFinder = isArrayLike(obj) ? findIndex : findKey;
+ var key = keyFinder(obj, predicate, context);
+ if (key !== void 0 && key !== -1) return obj[key];
+ }
+
+ // Convenience version of a common use case of `_.find`: getting the first
+ // object containing specific `key:value` pairs.
+ function findWhere(obj, attrs) {
+ return find(obj, matcher(attrs));
+ }
+
+ // The cornerstone for collection functions, an `each`
+ // implementation, aka `forEach`.
+ // Handles raw objects in addition to array-likes. Treats all
+ // sparse array-likes as if they were dense.
+ function each(obj, iteratee, context) {
+ iteratee = optimizeCb(iteratee, context);
+ var i, length;
+ if (isArrayLike(obj)) {
+ for (i = 0, length = obj.length; i < length; i++) {
+ iteratee(obj[i], i, obj);
+ }
+ } else {
+ var _keys = keys(obj);
+ for (i = 0, length = _keys.length; i < length; i++) {
+ iteratee(obj[_keys[i]], _keys[i], obj);
+ }
+ }
+ return obj;
+ }
+
+ // Return the results of applying the iteratee to each element.
+ function map(obj, iteratee, context) {
+ iteratee = cb(iteratee, context);
+ var _keys = !isArrayLike(obj) && keys(obj),
+ length = (_keys || obj).length,
+ results = Array(length);
+ for (var index = 0; index < length; index++) {
+ var currentKey = _keys ? _keys[index] : index;
+ results[index] = iteratee(obj[currentKey], currentKey, obj);
+ }
+ return results;
+ }
+
+ // Internal helper to create a reducing function, iterating left or right.
+ function createReduce(dir) {
+ // Wrap code that reassigns argument variables in a separate function than
+ // the one that accesses `arguments.length` to avoid a perf hit. (#1991)
+ var reducer = function(obj, iteratee, memo, initial) {
+ var _keys = !isArrayLike(obj) && keys(obj),
+ length = (_keys || obj).length,
+ index = dir > 0 ? 0 : length - 1;
+ if (!initial) {
+ memo = obj[_keys ? _keys[index] : index];
+ index += dir;
+ }
+ for (; index >= 0 && index < length; index += dir) {
+ var currentKey = _keys ? _keys[index] : index;
+ memo = iteratee(memo, obj[currentKey], currentKey, obj);
+ }
+ return memo;
+ };
+
+ return function(obj, iteratee, memo, context) {
+ var initial = arguments.length >= 3;
+ return reducer(obj, optimizeCb(iteratee, context, 4), memo, initial);
+ };
+ }
+
+ // **Reduce** builds up a single result from a list of values, aka `inject`,
+ // or `foldl`.
+ var reduce = createReduce(1);
+
+ // The right-associative version of reduce, also known as `foldr`.
+ var reduceRight = createReduce(-1);
+
+ // Return all the elements that pass a truth test.
+ function filter(obj, predicate, context) {
+ var results = [];
+ predicate = cb(predicate, context);
+ each(obj, function(value, index, list) {
+ if (predicate(value, index, list)) results.push(value);
+ });
+ return results;
+ }
+
+ // Return all the elements for which a truth test fails.
+ function reject(obj, predicate, context) {
+ return filter(obj, negate(cb(predicate)), context);
+ }
+
+ // Determine whether all of the elements pass a truth test.
+ function every(obj, predicate, context) {
+ predicate = cb(predicate, context);
+ var _keys = !isArrayLike(obj) && keys(obj),
+ length = (_keys || obj).length;
+ for (var index = 0; index < length; index++) {
+ var currentKey = _keys ? _keys[index] : index;
+ if (!predicate(obj[currentKey], currentKey, obj)) return false;
+ }
+ return true;
+ }
+
+ // Determine if at least one element in the object passes a truth test.
+ function some(obj, predicate, context) {
+ predicate = cb(predicate, context);
+ var _keys = !isArrayLike(obj) && keys(obj),
+ length = (_keys || obj).length;
+ for (var index = 0; index < length; index++) {
+ var currentKey = _keys ? _keys[index] : index;
+ if (predicate(obj[currentKey], currentKey, obj)) return true;
+ }
+ return false;
+ }
+
+ // Determine if the array or object contains a given item (using `===`).
+ function contains(obj, item, fromIndex, guard) {
+ if (!isArrayLike(obj)) obj = values(obj);
+ if (typeof fromIndex != 'number' || guard) fromIndex = 0;
+ return indexOf(obj, item, fromIndex) >= 0;
+ }
+
+ // Invoke a method (with arguments) on every item in a collection.
+ var invoke = restArguments(function(obj, path, args) {
+ var contextPath, func;
+ if (isFunction$1(path)) {
+ func = path;
+ } else {
+ path = toPath(path);
+ contextPath = path.slice(0, -1);
+ path = path[path.length - 1];
+ }
+ return map(obj, function(context) {
+ var method = func;
+ if (!method) {
+ if (contextPath && contextPath.length) {
+ context = deepGet(context, contextPath);
+ }
+ if (context == null) return void 0;
+ method = context[path];
+ }
+ return method == null ? method : method.apply(context, args);
+ });
+ });
+
+ // Convenience version of a common use case of `_.map`: fetching a property.
+ function pluck(obj, key) {
+ return map(obj, property(key));
+ }
+
+ // Convenience version of a common use case of `_.filter`: selecting only
+ // objects containing specific `key:value` pairs.
+ function where(obj, attrs) {
+ return filter(obj, matcher(attrs));
+ }
+
+ // Return the maximum element (or element-based computation).
+ function max(obj, iteratee, context) {
+ var result = -Infinity, lastComputed = -Infinity,
+ value, computed;
+ if (iteratee == null || typeof iteratee == 'number' && typeof obj[0] != 'object' && obj != null) {
+ obj = isArrayLike(obj) ? obj : values(obj);
+ for (var i = 0, length = obj.length; i < length; i++) {
+ value = obj[i];
+ if (value != null && value > result) {
+ result = value;
+ }
+ }
+ } else {
+ iteratee = cb(iteratee, context);
+ each(obj, function(v, index, list) {
+ computed = iteratee(v, index, list);
+ if (computed > lastComputed || computed === -Infinity && result === -Infinity) {
+ result = v;
+ lastComputed = computed;
+ }
+ });
+ }
+ return result;
+ }
+
+ // Return the minimum element (or element-based computation).
+ function min(obj, iteratee, context) {
+ var result = Infinity, lastComputed = Infinity,
+ value, computed;
+ if (iteratee == null || typeof iteratee == 'number' && typeof obj[0] != 'object' && obj != null) {
+ obj = isArrayLike(obj) ? obj : values(obj);
+ for (var i = 0, length = obj.length; i < length; i++) {
+ value = obj[i];
+ if (value != null && value < result) {
+ result = value;
+ }
+ }
+ } else {
+ iteratee = cb(iteratee, context);
+ each(obj, function(v, index, list) {
+ computed = iteratee(v, index, list);
+ if (computed < lastComputed || computed === Infinity && result === Infinity) {
+ result = v;
+ lastComputed = computed;
+ }
+ });
+ }
+ return result;
+ }
+
+ // Sample **n** random values from a collection using the modern version of the
+ // [Fisher-Yates shuffle](https://en.wikipedia.org/wiki/Fisher–Yates_shuffle).
+ // If **n** is not specified, returns a single random element.
+ // The internal `guard` argument allows it to work with `_.map`.
+ function sample(obj, n, guard) {
+ if (n == null || guard) {
+ if (!isArrayLike(obj)) obj = values(obj);
+ return obj[random(obj.length - 1)];
+ }
+ var sample = isArrayLike(obj) ? clone(obj) : values(obj);
+ var length = getLength(sample);
+ n = Math.max(Math.min(n, length), 0);
+ var last = length - 1;
+ for (var index = 0; index < n; index++) {
+ var rand = random(index, last);
+ var temp = sample[index];
+ sample[index] = sample[rand];
+ sample[rand] = temp;
+ }
+ return sample.slice(0, n);
+ }
+
+ // Shuffle a collection.
+ function shuffle(obj) {
+ return sample(obj, Infinity);
+ }
+
+ // Sort the object's values by a criterion produced by an iteratee.
+ function sortBy(obj, iteratee, context) {
+ var index = 0;
+ iteratee = cb(iteratee, context);
+ return pluck(map(obj, function(value, key, list) {
+ return {
+ value: value,
+ index: index++,
+ criteria: iteratee(value, key, list)
+ };
+ }).sort(function(left, right) {
+ var a = left.criteria;
+ var b = right.criteria;
+ if (a !== b) {
+ if (a > b || a === void 0) return 1;
+ if (a < b || b === void 0) return -1;
+ }
+ return left.index - right.index;
+ }), 'value');
+ }
+
+ // An internal function used for aggregate "group by" operations.
+ function group(behavior, partition) {
+ return function(obj, iteratee, context) {
+ var result = partition ? [[], []] : {};
+ iteratee = cb(iteratee, context);
+ each(obj, function(value, index) {
+ var key = iteratee(value, index, obj);
+ behavior(result, value, key);
+ });
+ return result;
+ };
+ }
+
+ // Groups the object's values by a criterion. Pass either a string attribute
+ // to group by, or a function that returns the criterion.
+ var groupBy = group(function(result, value, key) {
+ if (has$1(result, key)) result[key].push(value); else result[key] = [value];
+ });
+
+ // Indexes the object's values by a criterion, similar to `_.groupBy`, but for
+ // when you know that your index values will be unique.
+ var indexBy = group(function(result, value, key) {
+ result[key] = value;
+ });
+
+ // Counts instances of an object that group by a certain criterion. Pass
+ // either a string attribute to count by, or a function that returns the
+ // criterion.
+ var countBy = group(function(result, value, key) {
+ if (has$1(result, key)) result[key]++; else result[key] = 1;
+ });
+
+ // Split a collection into two arrays: one whose elements all pass the given
+ // truth test, and one whose elements all do not pass the truth test.
+ var partition = group(function(result, value, pass) {
+ result[pass ? 0 : 1].push(value);
+ }, true);
+
+ // Safely create a real, live array from anything iterable.
+ var reStrSymbol = /[^\ud800-\udfff]|[\ud800-\udbff][\udc00-\udfff]|[\ud800-\udfff]/g;
+ function toArray(obj) {
+ if (!obj) return [];
+ if (isArray(obj)) return slice.call(obj);
+ if (isString(obj)) {
+ // Keep surrogate pair characters together.
+ return obj.match(reStrSymbol);
+ }
+ if (isArrayLike(obj)) return map(obj, identity);
+ return values(obj);
+ }
+
+ // Return the number of elements in a collection.
+ function size(obj) {
+ if (obj == null) return 0;
+ return isArrayLike(obj) ? obj.length : keys(obj).length;
+ }
+
+ // Internal `_.pick` helper function to determine whether `key` is an enumerable
+ // property name of `obj`.
+ function keyInObj(value, key, obj) {
+ return key in obj;
+ }
+
+ // Return a copy of the object only containing the allowed properties.
+ var pick = restArguments(function(obj, keys) {
+ var result = {}, iteratee = keys[0];
+ if (obj == null) return result;
+ if (isFunction$1(iteratee)) {
+ if (keys.length > 1) iteratee = optimizeCb(iteratee, keys[1]);
+ keys = allKeys(obj);
+ } else {
+ iteratee = keyInObj;
+ keys = flatten$1(keys, false, false);
+ obj = Object(obj);
+ }
+ for (var i = 0, length = keys.length; i < length; i++) {
+ var key = keys[i];
+ var value = obj[key];
+ if (iteratee(value, key, obj)) result[key] = value;
+ }
+ return result;
+ });
+
+ // Return a copy of the object without the disallowed properties.
+ var omit = restArguments(function(obj, keys) {
+ var iteratee = keys[0], context;
+ if (isFunction$1(iteratee)) {
+ iteratee = negate(iteratee);
+ if (keys.length > 1) context = keys[1];
+ } else {
+ keys = map(flatten$1(keys, false, false), String);
+ iteratee = function(value, key) {
+ return !contains(keys, key);
+ };
+ }
+ return pick(obj, iteratee, context);
+ });
+
+ // Returns everything but the last entry of the array. Especially useful on
+ // the arguments object. Passing **n** will return all the values in
+ // the array, excluding the last N.
+ function initial(array, n, guard) {
+ return slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 : n)));
+ }
+
+ // Get the first element of an array. Passing **n** will return the first N
+ // values in the array. The **guard** check allows it to work with `_.map`.
+ function first(array, n, guard) {
+ if (array == null || array.length < 1) return n == null || guard ? void 0 : [];
+ if (n == null || guard) return array[0];
+ return initial(array, array.length - n);
+ }
+
+ // Returns everything but the first entry of the `array`. Especially useful on
+ // the `arguments` object. Passing an **n** will return the rest N values in the
+ // `array`.
+ function rest(array, n, guard) {
+ return slice.call(array, n == null || guard ? 1 : n);
+ }
+
+ // Get the last element of an array. Passing **n** will return the last N
+ // values in the array.
+ function last(array, n, guard) {
+ if (array == null || array.length < 1) return n == null || guard ? void 0 : [];
+ if (n == null || guard) return array[array.length - 1];
+ return rest(array, Math.max(0, array.length - n));
+ }
+
+ // Trim out all falsy values from an array.
+ function compact(array) {
+ return filter(array, Boolean);
+ }
+
+ // Flatten out an array, either recursively (by default), or up to `depth`.
+ // Passing `true` or `false` as `depth` means `1` or `Infinity`, respectively.
+ function flatten(array, depth) {
+ return flatten$1(array, depth, false);
+ }
+
+ // Take the difference between one array and a number of other arrays.
+ // Only the elements present in just the first array will remain.
+ var difference = restArguments(function(array, rest) {
+ rest = flatten$1(rest, true, true);
+ return filter(array, function(value){
+ return !contains(rest, value);
+ });
+ });
+
+ // Return a version of the array that does not contain the specified value(s).
+ var without = restArguments(function(array, otherArrays) {
+ return difference(array, otherArrays);
+ });
+
+ // Produce a duplicate-free version of the array. If the array has already
+ // been sorted, you have the option of using a faster algorithm.
+ // The faster algorithm will not work with an iteratee if the iteratee
+ // is not a one-to-one function, so providing an iteratee will disable
+ // the faster algorithm.
+ function uniq(array, isSorted, iteratee, context) {
+ if (!isBoolean(isSorted)) {
+ context = iteratee;
+ iteratee = isSorted;
+ isSorted = false;
+ }
+ if (iteratee != null) iteratee = cb(iteratee, context);
+ var result = [];
+ var seen = [];
+ for (var i = 0, length = getLength(array); i < length; i++) {
+ var value = array[i],
+ computed = iteratee ? iteratee(value, i, array) : value;
+ if (isSorted && !iteratee) {
+ if (!i || seen !== computed) result.push(value);
+ seen = computed;
+ } else if (iteratee) {
+ if (!contains(seen, computed)) {
+ seen.push(computed);
+ result.push(value);
+ }
+ } else if (!contains(result, value)) {
+ result.push(value);
+ }
+ }
+ return result;
+ }
+
+ // Produce an array that contains the union: each distinct element from all of
+ // the passed-in arrays.
+ var union = restArguments(function(arrays) {
+ return uniq(flatten$1(arrays, true, true));
+ });
+
+ // Produce an array that contains every item shared between all the
+ // passed-in arrays.
+ function intersection(array) {
+ var result = [];
+ var argsLength = arguments.length;
+ for (var i = 0, length = getLength(array); i < length; i++) {
+ var item = array[i];
+ if (contains(result, item)) continue;
+ var j;
+ for (j = 1; j < argsLength; j++) {
+ if (!contains(arguments[j], item)) break;
+ }
+ if (j === argsLength) result.push(item);
+ }
+ return result;
+ }
+
+ // Complement of zip. Unzip accepts an array of arrays and groups
+ // each array's elements on shared indices.
+ function unzip(array) {
+ var length = array && max(array, getLength).length || 0;
+ var result = Array(length);
+
+ for (var index = 0; index < length; index++) {
+ result[index] = pluck(array, index);
+ }
+ return result;
+ }
+
+ // Zip together multiple lists into a single array -- elements that share
+ // an index go together.
+ var zip = restArguments(unzip);
+
+ // Converts lists into objects. Pass either a single array of `[key, value]`
+ // pairs, or two parallel arrays of the same length -- one of keys, and one of
+ // the corresponding values. Passing by pairs is the reverse of `_.pairs`.
+ function object(list, values) {
+ var result = {};
+ for (var i = 0, length = getLength(list); i < length; i++) {
+ if (values) {
+ result[list[i]] = values[i];
+ } else {
+ result[list[i][0]] = list[i][1];
+ }
+ }
+ return result;
+ }
+
+ // Generate an integer Array containing an arithmetic progression. A port of
+ // the native Python `range()` function. See
+ // [the Python documentation](https://docs.python.org/library/functions.html#range).
+ function range(start, stop, step) {
+ if (stop == null) {
+ stop = start || 0;
+ start = 0;
+ }
+ if (!step) {
+ step = stop < start ? -1 : 1;
+ }
+
+ var length = Math.max(Math.ceil((stop - start) / step), 0);
+ var range = Array(length);
+
+ for (var idx = 0; idx < length; idx++, start += step) {
+ range[idx] = start;
+ }
+
+ return range;
+ }
+
+ // Chunk a single array into multiple arrays, each containing `count` or fewer
+ // items.
+ function chunk(array, count) {
+ if (count == null || count < 1) return [];
+ var result = [];
+ var i = 0, length = array.length;
+ while (i < length) {
+ result.push(slice.call(array, i, i += count));
+ }
+ return result;
+ }
+
+ // Helper function to continue chaining intermediate results.
+ function chainResult(instance, obj) {
+ return instance._chain ? _$1(obj).chain() : obj;
+ }
+
+ // Add your own custom functions to the Underscore object.
+ function mixin(obj) {
+ each(functions(obj), function(name) {
+ var func = _$1[name] = obj[name];
+ _$1.prototype[name] = function() {
+ var args = [this._wrapped];
+ push.apply(args, arguments);
+ return chainResult(this, func.apply(_$1, args));
+ };
+ });
+ return _$1;
+ }
+
+ // Add all mutator `Array` functions to the wrapper.
+ each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
+ var method = ArrayProto[name];
+ _$1.prototype[name] = function() {
+ var obj = this._wrapped;
+ if (obj != null) {
+ method.apply(obj, arguments);
+ if ((name === 'shift' || name === 'splice') && obj.length === 0) {
+ delete obj[0];
+ }
+ }
+ return chainResult(this, obj);
+ };
+ });
+
+ // Add all accessor `Array` functions to the wrapper.
+ each(['concat', 'join', 'slice'], function(name) {
+ var method = ArrayProto[name];
+ _$1.prototype[name] = function() {
+ var obj = this._wrapped;
+ if (obj != null) obj = method.apply(obj, arguments);
+ return chainResult(this, obj);
+ };
+ });
+
+ // Named Exports
+
+ var allExports = {
+ __proto__: null,
+ VERSION: VERSION,
+ restArguments: restArguments,
+ isObject: isObject,
+ isNull: isNull,
+ isUndefined: isUndefined,
+ isBoolean: isBoolean,
+ isElement: isElement,
+ isString: isString,
+ isNumber: isNumber,
+ isDate: isDate,
+ isRegExp: isRegExp,
+ isError: isError,
+ isSymbol: isSymbol,
+ isArrayBuffer: isArrayBuffer,
+ isDataView: isDataView$1,
+ isArray: isArray,
+ isFunction: isFunction$1,
+ isArguments: isArguments$1,
+ isFinite: isFinite$1,
+ isNaN: isNaN$1,
+ isTypedArray: isTypedArray$1,
+ isEmpty: isEmpty,
+ isMatch: isMatch,
+ isEqual: isEqual,
+ isMap: isMap,
+ isWeakMap: isWeakMap,
+ isSet: isSet,
+ isWeakSet: isWeakSet,
+ keys: keys,
+ allKeys: allKeys,
+ values: values,
+ pairs: pairs,
+ invert: invert,
+ functions: functions,
+ methods: functions,
+ extend: extend,
+ extendOwn: extendOwn,
+ assign: extendOwn,
+ defaults: defaults,
+ create: create,
+ clone: clone,
+ tap: tap,
+ get: get,
+ has: has,
+ mapObject: mapObject,
+ identity: identity,
+ constant: constant,
+ noop: noop,
+ toPath: toPath$1,
+ property: property,
+ propertyOf: propertyOf,
+ matcher: matcher,
+ matches: matcher,
+ times: times,
+ random: random,
+ now: now,
+ escape: _escape,
+ unescape: _unescape,
+ templateSettings: templateSettings,
+ template: template,
+ result: result,
+ uniqueId: uniqueId,
+ chain: chain,
+ iteratee: iteratee,
+ partial: partial,
+ bind: bind,
+ bindAll: bindAll,
+ memoize: memoize,
+ delay: delay,
+ defer: defer,
+ throttle: throttle,
+ debounce: debounce,
+ wrap: wrap,
+ negate: negate,
+ compose: compose,
+ after: after,
+ before: before,
+ once: once,
+ findKey: findKey,
+ findIndex: findIndex,
+ findLastIndex: findLastIndex,
+ sortedIndex: sortedIndex,
+ indexOf: indexOf,
+ lastIndexOf: lastIndexOf,
+ find: find,
+ detect: find,
+ findWhere: findWhere,
+ each: each,
+ forEach: each,
+ map: map,
+ collect: map,
+ reduce: reduce,
+ foldl: reduce,
+ inject: reduce,
+ reduceRight: reduceRight,
+ foldr: reduceRight,
+ filter: filter,
+ select: filter,
+ reject: reject,
+ every: every,
+ all: every,
+ some: some,
+ any: some,
+ contains: contains,
+ includes: contains,
+ include: contains,
+ invoke: invoke,
+ pluck: pluck,
+ where: where,
+ max: max,
+ min: min,
+ shuffle: shuffle,
+ sample: sample,
+ sortBy: sortBy,
+ groupBy: groupBy,
+ indexBy: indexBy,
+ countBy: countBy,
+ partition: partition,
+ toArray: toArray,
+ size: size,
+ pick: pick,
+ omit: omit,
+ first: first,
+ head: first,
+ take: first,
+ initial: initial,
+ last: last,
+ rest: rest,
+ tail: rest,
+ drop: rest,
+ compact: compact,
+ flatten: flatten,
+ without: without,
+ uniq: uniq,
+ unique: uniq,
+ union: union,
+ intersection: intersection,
+ difference: difference,
+ unzip: unzip,
+ transpose: unzip,
+ zip: zip,
+ object: object,
+ range: range,
+ chunk: chunk,
+ mixin: mixin,
+ 'default': _$1
+ };
+
+ // Default Export
+
+ // Add all of the Underscore functions to the wrapper object.
+ var _ = mixin(allExports);
+ // Legacy Node.js API.
+ _._ = _;
+
+ return _;
+
+})));
+//# sourceMappingURL=underscore-umd.js.map
diff --git a/docs/_static/underscore.js b/docs/_static/underscore.js
index 166240ef..cf177d42 100644
--- a/docs/_static/underscore.js
+++ b/docs/_static/underscore.js
@@ -1,6 +1,6 @@
-!function(n,r){"object"==typeof exports&&"undefined"!=typeof module?module.exports=r():"function"==typeof define&&define.amd?define("underscore",r):(n=n||self,function(){var t=n._,e=n._=r();e.noConflict=function(){return n._=t,e}}())}(this,(function(){
-// Underscore.js 1.12.0
+!function(n,r){"object"==typeof exports&&"undefined"!=typeof module?module.exports=r():"function"==typeof define&&define.amd?define("underscore",r):(n="undefined"!=typeof globalThis?globalThis:n||self,function(){var t=n._,e=n._=r();e.noConflict=function(){return n._=t,e}}())}(this,(function(){
+// Underscore.js 1.13.1
// https://underscorejs.org
-// (c) 2009-2020 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
+// (c) 2009-2021 Jeremy Ashkenas, Julian Gonggrijp, and DocumentCloud and Investigative Reporters & Editors
// Underscore may be freely distributed under the MIT license.
-var n="1.12.0",r="object"==typeof self&&self.self===self&&self||"object"==typeof global&&global.global===global&&global||Function("return this")()||{},t=Array.prototype,e=Object.prototype,u="undefined"!=typeof Symbol?Symbol.prototype:null,o=t.push,i=t.slice,a=e.toString,f=e.hasOwnProperty,c="undefined"!=typeof ArrayBuffer,l="undefined"!=typeof DataView,s=Array.isArray,p=Object.keys,v=Object.create,h=c&&ArrayBuffer.isView,y=isNaN,g=isFinite,d=!{toString:null}.propertyIsEnumerable("toString"),b=["valueOf","isPrototypeOf","toString","propertyIsEnumerable","hasOwnProperty","toLocaleString"],m=Math.pow(2,53)-1;function j(n,r){return r=null==r?n.length-1:+r,function(){for(var t=Math.max(arguments.length-r,0),e=Array(t),u=0;u=0&&t<=m}}function $(n){return function(r){return null==r?void 0:r[n]}}var G=$("byteLength"),H=J(G),Q=/\[object ((I|Ui)nt(8|16|32)|Float(32|64)|Uint8Clamped|Big(I|Ui)nt64)Array\]/;var X=c?function(n){return 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-
- krTheme Sphinx Style — pymatgen-diffusion 2021.4.29 documentation
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-
-
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+
+ krTheme Sphinx Style — pymatgen-diffusion 2022.1.15 documentation
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+
+
@@ -36,7 +37,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
krTheme Sphinx Style
@@ -46,7 +47,7 @@ Navigation
-
+
krTheme Sphinx Style¶
This repository contains sphinx styles Kenneth Reitz uses in most of
his projects. It is a drivative of Mitsuhiko’s themes for Flask and Flask related
@@ -70,7 +71,7 @@
krTheme Sphinx Stylekr_smallsmall one-page theme. Intended to be used by very small addon libraries.
+
@@ -94,7 +95,7 @@ This Page
Quick search
diff --git a/docs/change_log.html b/docs/change_log.html
index 4d5831f1..027b8448 100644
--- a/docs/change_log.html
+++ b/docs/change_log.html
@@ -4,11 +4,12 @@
-
- Change Log — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ Change Log — pymatgen-diffusion 2022.1.15 documentation
+
+
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@@ -36,7 +37,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Change Log
@@ -46,49 +47,49 @@ Navigation
-
+
Change Log¶
-
+
v2021.4.29¶
Fixed msite calc order (@hmlli)
Removed magmom (@jmmshn)
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v2021.3.6¶
Fix for bad release due to error in MANIFEST.in.
DiffusionAnalyzer has been migration from pymatgen to pymatgen.analysis.diffusion.analyzer for a more
self-contained suite of tools for diffusion analysis.
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-
+
+
v2021.3.5¶
pymatgen-diffusion is now released as a namespace package pymatgen-analysis-diffusion on PyPI. It should be
imported via pymatgen.analysis.diffusion instead pymatgen_diffusion.
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v2019.2.28¶
Py3k cleanup.
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v2018.1.4¶
Compatibility with pymatgen v2018+.
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v0.3.0¶
NEB tools, including an implementation of an IDPP solver.
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@@ -125,7 +126,7 @@ This Page
Quick search
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index 04f866bc..5e2f28c7 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -5,10 +5,10 @@
- Index — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ Index — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +36,7 @@ Navigation
modules |
- pymatgen-diffusion 2021.4.29 documentation »
+ pymatgen-diffusion 2022.1.15 documentation »
Index
@@ -105,7 +105,7 @@ C
- cluster() (Kmeans method)
- - coordination_number() (RadialDistributionFunction property)
+
- coordination_number (RadialDistributionFunction property)
- coords_ref (SiteOccupancyAnalyzer attribute)
@@ -299,7 +299,7 @@ G
H
@@ -337,7 +337,7 @@ K
L
@@ -365,6 +365,10 @@ M
module
+ - pymatgen
+
+ - pymatgen.analysis
+
- pymatgen.analysis.diffusion
- pymatgen.analysis.diffusion.aimd
@@ -442,7 +446,11 @@
N
O
@@ -473,6 +481,20 @@ P
- process_entries() (in module pymatgen.analysis.diffusion.utils.parse_entries)
-
+ pymatgen
+
+
+ - module
+
+
+ -
+ pymatgen.analysis
+
+
+ - module
+
+
+ -
pymatgen.analysis.diffusion
@@ -535,6 +557,8 @@ P
- module
+
-
pymatgen.analysis.diffusion.aimd.van_hove
@@ -542,8 +566,6 @@
P
- module
-
-
pymatgen.analysis.diffusion.analyzer
@@ -722,7 +744,7 @@
S
structures (MVLCINEBSetTest attribute)
- symm_structure() (MigrationGraph property)
+ symm_structure (MigrationGraph property)
T
test_get_inserted_on_base() (ParseEntriesTest method)
test_get_insertion_energy() (ParseEntriesTest method)
+
+ test_get_key_in_path() (MigrationGraphComplexTest method)
test_get_path() (MigrationGraphComplexTest method)
@@ -771,6 +795,8 @@ T
test_get_pos_and_migration_hop() (MigrationGraphSimpleTest method)
test_get_sc_structures() (MigrationHopTest method)
+
+ test_get_sc_structures_vacmode() (MigrationHopTest method)
test_get_start_end_structs_from_hop() (MigrationHopTest method)
@@ -783,15 +809,19 @@ T
test_get_uc_pos() (in module pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc)
+
+ test_get_unique_hop_host() (in module pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc)
+
+ test_get_unique_host_nonhost() (in module pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc)
test_group_and_label_hops() (MigrationGraphComplexTest method)
+
+
- test_incar() (MVLCINEBEndPointSetTest method)
@@ -817,6 +847,8 @@ T
- test_max_path_length() (DistinctPathFinderTest method)
- test_not_matching_first() (MigrationGraphComplexTest method)
+
+ - test_order_path() (MigrationGraphComplexTest method)
- test_periodic_dijkstra() (MigrationGraphComplexTest method)
@@ -858,7 +890,7 @@ T
U
@@ -913,7 +945,7 @@ W
Quick search
diff --git a/docs/index.html b/docs/index.html
index bf46bcae..14910c43 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -4,11 +4,12 @@
-
- Introduction — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ Introduction — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -40,7 +41,7 @@ Navigation
-
next |
-
+
@@ -50,7 +51,7 @@ Navigation
-
+
Introduction¶
This is an add-on to pymatgen for diffusion analysis that is developed
by the Materials Virtual Lab. Note that it relies on pymatgen for structural
@@ -60,12 +61,12 @@
Introduction
+
+
Change Log¶
-
-
+
+
Features (non-exhaustive!)¶
Van-Hove analysis
Features (non-exhaustive!)
+
API documentation¶
For detailed documentation of all modules and classes, please refer to the
API docs.
@@ -85,25 +86,25 @@ API documentation
+
+
+
Citing¶
If you use this package, please consider citing the relevant publications
documented in each analysis.
-
-
+
+
Contributing¶
We welcome contributions in all forms. If you’d like to contribute, please
fork this repository, make changes and send us a pull request!
-
-
+
+
Acknowledgements¶
This code is funded by the National Science Foundation’s Designing Materials
to Revolutionize and Engineer our Future (DMREF) program under Grant No.
1436976.
-
-
+
+
License¶
Pymatgen is released under the MIT License. The terms of the license are as
follows:
@@ -136,8 +137,8 @@ LicenseOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
+
+
Our Copyright Policy¶
-
-
+
+
Indices and tables¶
-
+
@@ -224,7 +225,7 @@ This Page
Quick search
diff --git a/docs/modules.html b/docs/modules.html
index d62ca1e0..6d0e2431 100644
--- a/docs/modules.html
+++ b/docs/modules.html
@@ -4,11 +4,12 @@
-
- pymatgen — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -44,7 +45,7 @@ Navigation
-
previous |
-
+
@@ -54,14 +55,14 @@ Navigation
-
+
pymatgen¶
-
+
@@ -87,7 +88,7 @@ This Page
Quick search
diff --git a/docs/objects.inv b/docs/objects.inv
index d6e9ea7f..b6b05aba 100644
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diff --git a/docs/py-modindex.html b/docs/py-modindex.html
index 622510e3..414d7ba6 100644
--- a/docs/py-modindex.html
+++ b/docs/py-modindex.html
@@ -5,10 +5,10 @@
- Python Module Index — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+ Python Module Index — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -39,7 +39,7 @@ Navigation
-
modules |
-
+
@@ -64,7 +64,12 @@ Python Module Index
- pymatgen
+ pymatgen
+
+
+
+ pymatgen.analysis
Python Module Index
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.aimd.clustering.html b/docs/pymatgen.analysis.diffusion.aimd.clustering.html
index be2d0b17..17f1deb1 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.clustering.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.clustering.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.aimd.clustering module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.aimd.clustering module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,14 +47,14 @@ Navigation
-
+
pymatgen.analysis.diffusion.aimd.clustering module¶
This module implements clustering algorithms to determine centroids, with
adaption for periodic boundary conditions. This can be used, for example, to
determine likely atomic positions from MD trajectories.
--
-class
Kmeans(max_iterations: int = 1000)[source]¶
+-
+class Kmeans(max_iterations: int = 1000)[source]¶
Bases: object
Simple kmeans clustering.
@@ -62,8 +63,8 @@ Navigation
--
-
cluster(points, k, initial_centroids=None)[source]¶
+-
+cluster(points, k, initial_centroids=None)[source]¶
- Parameters
@@ -86,8 +87,8 @@ Navigation
--
-static
get_centroids(points, labels, k, centroids)[source]¶
+-
+static get_centroids(points, labels, k, centroids)[source]¶
Each centroid is the geometric mean of the points that
have that centroid’s label. Important: If a centroid is empty (no
points have that centroid’s label) you should randomly re-initialize it.
@@ -104,8 +105,8 @@ Navigation
--
-static
get_labels(points, centroids)[source]¶
+-
+static get_labels(points, centroids)[source]¶
For each element in the dataset, chose the closest centroid.
Make that centroid the element’s label.
@@ -119,8 +120,8 @@ Navigation
--
-
should_stop(old_centroids, centroids, iterations)[source]¶
+-
+should_stop(old_centroids, centroids, iterations)[source]¶
Check for stopping conditions.
- Parameters
@@ -136,8 +137,8 @@ Navigation
--
-class
KmeansPBC(lattice, max_iterations=1000)[source]¶
+-
+class KmeansPBC(lattice, max_iterations=1000)[source]¶
Bases: pymatgen.analysis.diffusion.aimd.clustering.Kmeans
A version of KMeans that work with PBC. Distance metrics have to change,
as well as new centroid determination. The points supplied should be
@@ -151,8 +152,8 @@
Navigation
--
-
get_centroids(points, labels, k, centroids)[source]¶
+-
+get_centroids(points, labels, k, centroids)[source]¶
Each centroid is the geometric mean of the points that
have that centroid’s label. Important: If a centroid is empty (no
points have that centroid’s label) you should randomly re-initialize it.
@@ -169,8 +170,8 @@ Navigation
--
-
get_labels(points, centroids)[source]¶
+-
+get_labels(points, centroids)[source]¶
For each element in the dataset, chose the closest centroid.
Make that centroid the element’s label.
@@ -184,8 +185,8 @@ Navigation
--
-
should_stop(old_centroids, centroids, iterations)[source]¶
+-
+should_stop(old_centroids, centroids, iterations)[source]¶
Check for stopping conditions.
- Parameters
@@ -201,8 +202,8 @@ Navigation
-
+
@@ -249,7 +250,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.aimd.html b/docs/pymatgen.analysis.diffusion.aimd.html
index ca1c51c0..525299cd 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.aimd package — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.aimd package — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,14 +47,14 @@ Navigation
-
+
pymatgen.analysis.diffusion.aimd package¶
-
+
Subpackages¶
-
-
+
+
Submodules¶
@@ -63,12 +64,12 @@ Submodulespymatgen.analysis.diffusion.aimd.van_hove module
-
-
+
+
Module contents¶
Modules for AIMD simulation analysis.
-
-
+
+
@@ -102,7 +103,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.aimd.pathway.html b/docs/pymatgen.analysis.diffusion.aimd.pathway.html
index dc975d20..a93a0dd1 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.pathway.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.pathway.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.aimd.pathway module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.aimd.pathway module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,12 +47,12 @@ Navigation
-
+
pymatgen.analysis.diffusion.aimd.pathway module¶
Algorithms for diffusion pathway analysis
--
-class
ProbabilityDensityAnalysis(structure, trajectories, interval=0.5, species=('Li', 'Na'))[source]¶
+-
+class ProbabilityDensityAnalysis(structure, trajectories, interval=0.5, species=('Li', 'Na'))[source]¶
Bases: object
Compute the time-averaged probability density distribution of selected
species on a “uniform” (in terms of fractional coordinates) 3-D grid.
@@ -79,8 +80,8 @@
Navigation
--
-classmethod
from_diffusion_analyzer(diffusion_analyzer, interval=0.5, species=('Li', 'Na'))[source]¶
+-
+classmethod from_diffusion_analyzer(diffusion_analyzer, interval=0.5, species=('Li', 'Na'))[source]¶
Create a ProbabilityDensityAnalysis from a diffusion_analyzer object.
- Parameters
@@ -96,8 +97,8 @@ Navigation
--
-
generate_stable_sites(p_ratio=0.25, d_cutoff=1.0)[source]¶
+-
+generate_stable_sites(p_ratio=0.25, d_cutoff=1.0)[source]¶
Obtain a set of low-energy sites from probability density function with
given probability threshold ‘p_ratio’. The set of grid points with
probability density higher than the threshold will further be clustered
@@ -120,15 +121,15 @@
Navigation
--
-
get_full_structure()[source]¶
+-
+get_full_structure()[source]¶
Generate the structure with the low-energy sites included. In the end, a
pymatgen Structure object will be returned.
--
-
to_chgcar(filename='CHGCAR.vasp')[source]¶
+-
+to_chgcar(filename='CHGCAR.vasp')[source]¶
Save the probability density distribution in the format of CHGCAR,
which can be visualized by VESTA.
@@ -136,39 +137,39 @@ Navigation
--
-class
SiteOccupancyAnalyzer(structure, coords_ref, trajectories, species=('Li', 'Na'))[source]¶
+-
+class SiteOccupancyAnalyzer(structure, coords_ref, trajectories, species=('Li', 'Na'))[source]¶
Bases: object
A class that analyzes the site occupancy of given species using MD trajectories.
The occupancy of a site is determined based on the shortest distance scheme.
--
-
site_occ¶
--
-
N x 1 numpy array that stores the occupancy of all sites associated with
--
-
species. It has the same sequence as the given list of indices.
+-
+site_occ¶
+-
+N x 1 numpy array that stores the occupancy of all sites associated with
+-
+species. It has the same sequence as the given list of indices.
--
-
coords_ref¶
--
-
N x 3 numpy array of fractional coordinates of all reference sites.
+-
+coords_ref¶
+-
+N x 3 numpy array of fractional coordinates of all reference sites.
@@ -185,8 +186,8 @@ Navigation
--
-classmethod
from_diffusion_analyzer(coords_ref, diffusion_analyzer, species=('Li', 'Na'))[source]¶
+-
+classmethod from_diffusion_analyzer(coords_ref, diffusion_analyzer, species=('Li', 'Na'))[source]¶
Create a SiteOccupancyAnalyzer object using a diffusion_analyzer object.
- Parameters
@@ -202,14 +203,14 @@ Navigation
-
+
@@ -233,7 +234,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.aimd.rdf.html b/docs/pymatgen.analysis.diffusion.aimd.rdf.html
index d65880bf..4752de87 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.rdf.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.rdf.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.aimd.rdf module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.aimd.rdf module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,12 +47,12 @@ Navigation
-
+
pymatgen.analysis.diffusion.aimd.rdf module¶
RDF implementation.
--
-class
RadialDistributionFunction(structures: List, indices: List, reference_indices: List, ngrid: int = 101, rmax: float = 10.0, cell_range: int = 1, sigma: float = 0.1)[source]¶
+-
+class RadialDistributionFunction(structures: List, indices: List, reference_indices: List, ngrid: int = 101, rmax: float = 10.0, cell_range: int = 1, sigma: float = 0.1)[source]¶
Bases: object
Calculate the average radial distribution function for a given set of
structures.
@@ -73,9 +74,9 @@ Navigation
-
--
-property
coordination_number¶
+
+-
+property coordination_number¶
returns running coordination number
- Returns
@@ -85,8 +86,8 @@ Navigation
--
-
export_rdf(filename: str)[source]¶
+-
+export_rdf(filename: str)[source]¶
Output RDF data to a csv file.
- Parameters
@@ -98,8 +99,8 @@ Navigation
--
-classmethod
from_species(structures: List, ngrid: int = 101, rmax: float = 10.0, cell_range: int = 1, sigma: float = 0.1, species: Union[Tuple, List] = ('Li', 'Na'), reference_species: Optional[Union[Tuple, List]] = None)[source]¶
+-
+classmethod from_species(structures: List, ngrid: int = 101, rmax: float = 10.0, cell_range: int = 1, sigma: float = 0.1, species: Union[Tuple, List] = ('Li', 'Na'), reference_species: Optional[Union[Tuple, List]] = None)[source]¶
Initialize using species.
- Parameters
@@ -126,8 +127,8 @@ Navigation
--
-
get_rdf_plot(label: Optional[str] = None, xlim: tuple = (0.0, 8.0), ylim: tuple = (- 0.005, 3.0), loc_peak: bool = False)[source]¶
+-
+get_rdf_plot(label: Optional[str] = None, xlim: tuple = (0.0, 8.0), ylim: tuple = (- 0.005, 3.0), loc_peak: bool = False)[source]¶
Plot the average RDF function.
- Parameters
@@ -144,8 +145,8 @@ Navigation
--
-class
RadialDistributionFunctionFast(structures: Union[pymatgen.core.structure.Structure, List[pymatgen.core.structure.Structure]], rmin: float = 0.0, rmax: float = 10.0, ngrid: float = 101, sigma: float = 0.0, n_jobs=None)[source]¶
+-
+class RadialDistributionFunctionFast(structures: Union[pymatgen.core.structure.Structure, List[pymatgen.core.structure.Structure]], rmin: float = 0.0, rmax: float = 10.0, ngrid: float = 101, sigma: float = 0.0, n_jobs=None)[source]¶
Bases: object
Fast radial distribution analysis.
This method calculates rdf on np.linspace(rmin, rmax, ngrid) points.
@@ -162,8 +163,8 @@ Navigation
--
-
get_coordination_number(ref_species, species, is_average=True)[source]¶
+-
+get_coordination_number(ref_species, species, is_average=True)[source]¶
returns running coordination number
- Parameters
@@ -182,8 +183,8 @@ Navigation
--
-
get_one_rdf(ref_species: Union[str, List[str]], species: Union[str, List[str]], index=0)[source]¶
+-
+get_one_rdf(ref_species: Union[str, List[str]], species: Union[str, List[str]], index=0)[source]¶
Get the RDF for one structure, indicated by the index of the structure
in all structures
@@ -203,8 +204,8 @@ Navigation
+
@@ -248,7 +249,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.aimd.tests.test_clustering.html b/docs/pymatgen.analysis.diffusion.aimd.tests.test_clustering.html
index ba062667..d896962d 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.tests.test_clustering.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.tests.test_clustering.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.aimd.tests.test_clustering module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.aimd.tests.test_clustering module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,37 +47,37 @@ Navigation
-
+
pymatgen.analysis.diffusion.aimd.tests.test_clustering module¶
--
-class
KmeansPBCTest(methodName='runTest')[source]¶
+-
+class KmeansPBCTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
-
+
@@ -100,7 +101,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.aimd.tests.test_pathway.html b/docs/pymatgen.analysis.diffusion.aimd.tests.test_pathway.html
index 3dd5b9b8..07322113 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.tests.test_pathway.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.tests.test_pathway.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.aimd.tests.test_pathway module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.aimd.tests.test_pathway module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,52 +47,52 @@ Navigation
-
+
pymatgen.analysis.diffusion.aimd.tests.test_pathway module¶
--
-class
ProbabilityDensityTest(methodName='runTest')[source]¶
+-
+class ProbabilityDensityTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-class
SiteOccupancyTest(methodName='runTest')[source]¶
+-
+class SiteOccupancyTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
-
+
@@ -115,7 +116,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.aimd.tests.test_rdf.html b/docs/pymatgen.analysis.diffusion.aimd.tests.test_rdf.html
index 0856c24d..90416ab1 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.tests.test_rdf.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.tests.test_rdf.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.aimd.tests.test_rdf module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.aimd.tests.test_rdf module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,28 +47,28 @@ Navigation
-
+
pymatgen.analysis.diffusion.aimd.tests.test_rdf module¶
-
+
@@ -91,7 +92,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.aimd.tests.test_van_hove.html b/docs/pymatgen.analysis.diffusion.aimd.tests.test_van_hove.html
index fd6586ef..9fb9a315 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.tests.test_van_hove.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.tests.test_van_hove.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.aimd.tests.test_van_hove module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.aimd.tests.test_van_hove module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,87 +47,87 @@ Navigation
-
+
pymatgen.analysis.diffusion.aimd.tests.test_van_hove module¶
--
-class
EvolutionAnalyzerTest(methodName='runTest')[source]¶
+-
+class EvolutionAnalyzerTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-class
RDFTest(methodName='runTest')[source]¶
+-
+class RDFTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-
setUp()[source]¶
+-
+setUp()[source]¶
Hook method for setting up the test fixture before exercising it.
--
-
test_raises_ValueError_if_reference_species_not_in_structure()[source]¶
+-
+test_raises_ValueError_if_reference_species_not_in_structure()[source]¶
--
-
test_raises_ValueError_if_sigma_is_not_positive()[source]¶
+-
+test_raises_ValueError_if_sigma_is_not_positive()[source]¶
--
-
test_raises_ValueError_if_species_not_in_structure()[source]¶
+-
+test_raises_ValueError_if_species_not_in_structure()[source]¶
--
-class
VanHoveTest(methodName='runTest')[source]¶
+-
+class VanHoveTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
-
+
@@ -150,7 +151,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.aimd.van_hove.html b/docs/pymatgen.analysis.diffusion.aimd.van_hove.html
index dd78cc79..37cb1127 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.van_hove.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.van_hove.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.aimd.van_hove module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.aimd.van_hove module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,12 +47,12 @@ Navigation
-
+
pymatgen.analysis.diffusion.aimd.van_hove module¶
Van Hove analysis for correlations.
--
-class
EvolutionAnalyzer(structures: List, rmax: float = 10, step: int = 1, time_step: int = 2)[source]¶
+-
+class EvolutionAnalyzer(structures: List, rmax: float = 10, step: int = 1, time_step: int = 2)[source]¶
Bases: object
Analyze the evolution of structures during AIMD simulations.
Initialization the EvolutionAnalyzer from MD simulations. From the
@@ -76,8 +77,8 @@
Navigation
--
-static
atom_dist(structure: pymatgen.core.structure.Structure, specie: str, ngrid: int = 101, window: float = 1, direction: str = 'c')[source]¶
+-
+static atom_dist(structure: pymatgen.core.structure.Structure, specie: str, ngrid: int = 101, window: float = 1, direction: str = 'c')[source]¶
Get atomic distribution for a given specie.
- Parameters
@@ -100,8 +101,8 @@ Navigation
--
-
get_df(func: Callable, save_csv: Optional[str] = None, **kwargs)[source]¶
+-
+get_df(func: Callable, save_csv: Optional[str] = None, **kwargs)[source]¶
Get the data frame for a given pair. This step would be very slow if
there are hundreds or more structures to parse.
@@ -143,8 +144,8 @@ Navigation
--
-static
get_min_dist(df: pandas.core.frame.DataFrame, tol: float = 1e-10)[source]¶
+-
+static get_min_dist(df: pandas.core.frame.DataFrame, tol: float = 1e-10)[source]¶
Get the shortest pair distance from the given DataFrame.
- Parameters
@@ -161,8 +162,8 @@ Navigation
--
-static
get_pairs(structure: pymatgen.core.structure.Structure)[source]¶
+-
+static get_pairs(structure: pymatgen.core.structure.Structure)[source]¶
Get all element pairs in a structure.
- Parameters
@@ -175,8 +176,8 @@ Navigation
--
-
plot_atomic_evolution(specie: str, direction: str = 'c', cmap=<matplotlib.colors.LinearSegmentedColormap object>, df: Optional[pandas.core.frame.DataFrame] = None)[source]¶
+-
+plot_atomic_evolution(specie: str, direction: str = 'c', cmap=<matplotlib.colors.LinearSegmentedColormap object>, df: Optional[pandas.core.frame.DataFrame] = None)[source]¶
Plot the atomic distribution evolution with time for a given species.
- Parameters
@@ -195,8 +196,8 @@ Navigation
--
-static
plot_evolution_from_data(df: pandas.core.frame.DataFrame, x_label: Optional[str] = None, cb_label: Optional[str] = None, cmap=<matplotlib.colors.ListedColormap object>)[source]¶
+-
+static plot_evolution_from_data(df: pandas.core.frame.DataFrame, x_label: Optional[str] = None, cb_label: Optional[str] = None, cmap=<matplotlib.colors.ListedColormap object>)[source]¶
Plot the evolution with time for a given DataFrame. It can be RDF,
atomic distribution or other characterization data we might
implement in the future.
@@ -218,8 +219,8 @@ Navigation
--
-
plot_rdf_evolution(pair: Tuple, cmap=<matplotlib.colors.ListedColormap object>, df: Optional[pandas.core.frame.DataFrame] = None)[source]¶
+-
+plot_rdf_evolution(pair: Tuple, cmap=<matplotlib.colors.ListedColormap object>, df: Optional[pandas.core.frame.DataFrame] = None)[source]¶
Plot the RDF evolution with time for a given pair.
- Parameters
@@ -238,8 +239,8 @@ Navigation
--
-static
rdf(structure: pymatgen.core.structure.Structure, pair: Tuple, ngrid: int = 101, rmax: float = 10)[source]¶
+-
+static rdf(structure: pymatgen.core.structure.Structure, pair: Tuple, ngrid: int = 101, rmax: float = 10)[source]¶
Process rdf from a given structure and pair.
- Parameters
@@ -259,8 +260,8 @@ Navigation
--
-class
VanHoveAnalysis(diffusion_analyzer: pymatgen.analysis.diffusion.analyzer.DiffusionAnalyzer, avg_nsteps: int = 50, ngrid: int = 101, rmax: float = 10.0, step_skip: int = 50, sigma: float = 0.1, cell_range: int = 1, species: Union[Tuple, List] = ('Li', 'Na'), reference_species: Optional[Union[Tuple, List]] = None, indices: Optional[List] = None)[source]¶
+-
+class VanHoveAnalysis(diffusion_analyzer: pymatgen.analysis.diffusion.analyzer.DiffusionAnalyzer, avg_nsteps: int = 50, ngrid: int = 101, rmax: float = 10.0, step_skip: int = 50, sigma: float = 0.1, cell_range: int = 1, species: Union[Tuple, List] = ('Li', 'Na'), reference_species: Optional[Union[Tuple, List]] = None, indices: Optional[List] = None)[source]¶
Bases: object
Class for van Hove function analysis. In particular, self-part (Gs) and
distinct-part (Gd) of the van Hove correlation function G(r,t)
@@ -296,8 +297,8 @@
Navigation
-
+
@@ -345,7 +346,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.analyzer.html b/docs/pymatgen.analysis.diffusion.analyzer.html
index b02a44f0..a181e990 100644
--- a/docs/pymatgen.analysis.diffusion.analyzer.html
+++ b/docs/pymatgen.analysis.diffusion.analyzer.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.analyzer module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.analyzer module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,7 +47,7 @@ Navigation
-
+
pymatgen.analysis.diffusion.analyzer module¶
A module to perform diffusion analyses (e.g. calculating diffusivity from
mean square displacements etc.). If you use this module, please consider
@@ -63,8 +64,8 @@
Navigation
--
-class
DiffusionAnalyzer(structure, displacements, specie, temperature, time_step, step_skip, smoothed='max', min_obs=30, avg_nsteps=1000, lattices=None)[source]¶
+-
+class DiffusionAnalyzer(structure, displacements, specie, temperature, time_step, step_skip, smoothed='max', min_obs=30, avg_nsteps=1000, lattices=None)[source]¶
Bases: monty.json.MSONable
Class for performing diffusion analysis.
This constructor is meant to be used with pre-processed data.
@@ -125,14 +126,14 @@
Navigation
--
-
export_msdt(filename)[source]¶
+-
+export_msdt(filename)[source]¶
Writes MSD data to a csv file that can be easily plotted in other
software.
@@ -145,8 +146,8 @@ Navigation
--
-classmethod
from_dict(d)[source]¶
+-
+classmethod from_dict(d)[source]¶
- Parameters
d (dict) – Dict representation
@@ -156,8 +157,8 @@ Navigation
--
-classmethod
from_files(filepaths, specie, step_skip=10, ncores=None, initial_disp=None, initial_structure=None, **kwargs)[source]¶
+-
+classmethod from_files(filepaths, specie, step_skip=10, ncores=None, initial_disp=None, initial_structure=None, **kwargs)[source]¶
Convenient constructor that takes in a list of vasprun.xml paths to
perform diffusion analysis.
@@ -198,8 +199,8 @@ Navigation
--
-classmethod
from_structures(structures, specie, temperature, time_step, step_skip, initial_disp=None, initial_structure=None, **kwargs)[source]¶
+-
+classmethod from_structures(structures, specie, temperature, time_step, step_skip, initial_disp=None, initial_structure=None, **kwargs)[source]¶
Convenient constructor that takes in a list of Structure objects to
perform diffusion analysis.
@@ -233,8 +234,8 @@ Navigation
--
-classmethod
from_vaspruns(vaspruns, specie, initial_disp=None, initial_structure=None, **kwargs)[source]¶
+-
+classmethod from_vaspruns(vaspruns, specie, initial_disp=None, initial_structure=None, **kwargs)[source]¶
Convenient constructor that takes in a list of Vasprun objects to
perform diffusion analysis.
@@ -263,8 +264,8 @@ Navigation
--
-
get_drift_corrected_structures(start=None, stop=None, step=None)[source]¶
+-
+get_drift_corrected_structures(start=None, stop=None, step=None)[source]¶
Returns an iterator for the drift-corrected structures. Use of
iterator is to reduce memory usage as # of structures in MD can be
huge. You don’t often need all the structures all at once.
@@ -286,8 +287,8 @@ Navigation
--
-
get_framework_rms_plot(plt=None, granularity=200, matching_s=None)[source]¶
+-
+get_framework_rms_plot(plt=None, granularity=200, matching_s=None)[source]¶
Get the plot of rms framework displacement vs time. Useful for checking
for melting, especially if framework atoms can move via paddle-wheel
or similar mechanism (which would show up in max framework displacement
@@ -309,8 +310,8 @@
Navigation
--
-
get_msd_plot(plt=None, mode='specie')[source]¶
+-
+get_msd_plot(plt=None, mode='specie')[source]¶
Get the plot of the smoothed msd vs time graph. Useful for
checking convergence. This can be written to an image file.
@@ -327,8 +328,8 @@ Navigation
--
-
get_summary_dict(include_msd_t=False, include_mscd_t=False)[source]¶
+-
+get_summary_dict(include_msd_t=False, include_mscd_t=False)[source]¶
Provides a summary of diffusion information.
- Parameters
@@ -346,8 +347,8 @@ Navigation
--
-
plot_msd(mode='default')[source]¶
+-
+plot_msd(mode='default')[source]¶
Plot the smoothed msd vs time graph. Useful for checking convergence.
- Parameters
@@ -363,8 +364,8 @@ Navigation
--
-
fit_arrhenius(temps, diffusivities)[source]¶
+-
+fit_arrhenius(temps, diffusivities)[source]¶
- Returns Ea, c, standard error of Ea from the Arrhenius fit:
D = c * exp(-Ea/kT)
Navigation
--
-
get_arrhenius_plot(temps, diffusivities, diffusivity_errors=None, **kwargs)[source]¶
+-
+get_arrhenius_plot(temps, diffusivities, diffusivity_errors=None, **kwargs)[source]¶
Returns an Arrhenius plot.
- Parameters
@@ -402,8 +403,8 @@ Navigation
--
-
get_conversion_factor(structure, species, temperature)[source]¶
+-
+get_conversion_factor(structure, species, temperature)[source]¶
Conversion factor to convert between cm^2/s diffusivity measurements and
mS/cm conductivity measurements based on number of atoms of diffusing
species. Note that the charge is based on the oxidation state of the
@@ -425,8 +426,8 @@
Navigation
-
+
@@ -488,7 +489,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.html b/docs/pymatgen.analysis.diffusion.html
index 3283e012..656e2e05 100644
--- a/docs/pymatgen.analysis.diffusion.html
+++ b/docs/pymatgen.analysis.diffusion.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion package — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion package — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,9 +47,9 @@ Navigation
-
+
pymatgen.analysis.diffusion package¶
-
+
+
@@ -143,7 +144,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.neb.full_path_mapper.html b/docs/pymatgen.analysis.diffusion.neb.full_path_mapper.html
index 27883187..d350b5fb 100644
--- a/docs/pymatgen.analysis.diffusion.neb.full_path_mapper.html
+++ b/docs/pymatgen.analysis.diffusion.neb.full_path_mapper.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.neb.full_path_mapper module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.neb.full_path_mapper module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,12 +47,12 @@ Navigation
-
+
pymatgen.analysis.diffusion.neb.full_path_mapper module¶
Migraiton Graph Analysis
--
-class
ChargeBarrierGraph(structure: pymatgen.core.structure.Structure, m_graph: pymatgen.analysis.graphs.StructureGraph, potential_field: pymatgen.io.vasp.outputs.VolumetricData, potential_data_key: str, **kwargs)[source]¶
+-
+class ChargeBarrierGraph(structure: pymatgen.core.structure.Structure, m_graph: pymatgen.analysis.graphs.StructureGraph, potential_field: pymatgen.io.vasp.outputs.VolumetricData, potential_data_key: str, **kwargs)[source]¶
Bases: pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph
A Migration graph with additional charge density analysis on the charge density of the host material
Construct the MigrationGraph object using a VolumetricData object.
@@ -70,21 +71,21 @@
Navigation
--
-
get_least_chg_path()[source]¶
+-
+get_least_chg_path()[source]¶
obtain an intercolating pathway through the material that has the least amount of charge
:returns: list of hops
--
-
get_summary_dict(add_keys: Optional[List[str]] = None)[source]¶
+-
+get_summary_dict(add_keys: Optional[List[str]] = None)[source]¶
Dictionary format, for saving to database
--
-
populate_edges_with_chg_density_info(tube_radius=1)[source]¶
+-
+populate_edges_with_chg_density_info(tube_radius=1)[source]¶
- Parameters
tube_radius – Tube radius.
@@ -95,8 +96,8 @@ Navigation
--
-class
MigrationGraph(structure: pymatgen.core.structure.Structure, m_graph: pymatgen.analysis.graphs.StructureGraph, symprec=0.1, vac_mode=False)[source]¶
+-
+class MigrationGraph(structure: pymatgen.core.structure.Structure, m_graph: pymatgen.analysis.graphs.StructureGraph, symprec=0.1, vac_mode=False)[source]¶
Bases: monty.json.MSONable
A python object for handling the migratrion graph of a given base
structure and mobile specie sites within that base structure.
@@ -125,8 +126,8 @@ Navigation
--
-
add_data_to_similar_edges(target_label: Union[int, str], data: dict, m_hop: Optional[pymatgen.analysis.diffusion.neb.pathfinder.MigrationHop] = None)[source]¶
+-
+add_data_to_similar_edges(target_label: Union[int, str], data: dict, m_hop: Optional[pymatgen.analysis.diffusion.neb.pathfinder.MigrationHop] = None)[source]¶
Insert data to all edges with the same label
:param target_label: The edge uniqueness label are adding data
:param data: The data to passed to the different edges
@@ -135,8 +136,8 @@
Navigation
- Parameters
-max_val – Filter the graph by a cost
+
+max_val – Filter the graph by a cost
flip_hops – If true, hops in paths returned will be flipped so
+isites and esites match to form a coherent path.
+If false, hops will retain their original orientation
+from the migration graph.
- Returns
Each dict contains the information of a hop
@@ -168,8 +175,8 @@ Navigation
--
-static
get_structure_from_entries(entries: List[pymatgen.entries.computed_entries.ComputedStructureEntry], migrating_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, **kwargs) → List[pymatgen.core.structure.Structure][source]¶
+-
+static get_structure_from_entries(entries: List[pymatgen.entries.computed_entries.ComputedStructureEntry], migrating_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, **kwargs) List[pymatgen.core.structure.Structure][source]¶
Read in a list of base entries and inserted entries. Return a list of structures that contains metastable
sites for the migration species decorated with a “insertion_energy” property.
@@ -201,38 +208,38 @@ Navigation
--
-
get_summary_dict(added_keys: Optional[List[str]] = None) → dict[source]¶
+-
+get_summary_dict(added_keys: Optional[List[str]] = None) dict[source]¶
Dictionary format, for saving to database
-
--
-property
host_structure¶
+
+-
+property host_structure: pymatgen.core.structure.Structure¶
A structure that only contains the non-migrating species
-
--
-property
only_sites¶
+
+-
+property only_sites: pymatgen.core.structure.Structure¶
A structure that only contains the migrating species
-
--
-property
symm_structure¶
+
+-
+property symm_structure: pymatgen.symmetry.structure.SymmetrizedStructure¶
The symmetrized structure with the present item’s symprec value
-
--
-property
unique_hops¶
+
+-
+property unique_hops¶
The unique hops dictionary keyed by the hop label
--
-classmethod
with_base_structure(base_structure: pymatgen.core.structure.Structure, m_graph: pymatgen.analysis.graphs.StructureGraph, **kwargs) → pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph[source]¶
+-
+classmethod with_base_structure(base_structure: pymatgen.core.structure.Structure, m_graph: pymatgen.analysis.graphs.StructureGraph, **kwargs) pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph[source]¶
- Parameters
base_structure – base framework structure that does not contain any
@@ -245,8 +252,8 @@
Navigation
--
-classmethod
with_distance(structure: pymatgen.core.structure.Structure, migrating_specie: str, max_distance: float, **kwargs) → pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph[source]¶
+-
+classmethod with_distance(structure: pymatgen.core.structure.Structure, migrating_specie: str, max_distance: float, **kwargs) pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph[source]¶
Using a specific nn strategy to get the connectivity graph between all the migrating ion sites.
:param max_distance: Maximum length of NEB path in the unit
@@ -261,8 +268,8 @@ Navigation
--
-classmethod
with_local_env_strategy(structure: pymatgen.core.structure.Structure, migrating_specie: str, nn: pymatgen.analysis.local_env.NearNeighbors, **kwargs) → pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph[source]¶
+-
+classmethod with_local_env_strategy(structure: pymatgen.core.structure.Structure, migrating_specie: str, nn: pymatgen.analysis.local_env.NearNeighbors, **kwargs) pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph[source]¶
Using a specific nn strategy to get the connectivity graph between all the migrating ion sites.
:param structure: Input structure that contains all sites.
:param migrating_specie: The specie that migrates. E.g. “Li”.
@@ -277,14 +284,14 @@
Navigation
--
-
check_uc_hop(sc_hop, uc_hop)[source]¶
+-
+check_uc_hop(sc_hop, uc_hop)[source]¶
See if hop in the 2X2X2 supercell and a unit cell hop
are equilvalent under lattice translation
:param sc_hop: MigrationHop object form pymatgen-diffusion.
@@ -298,8 +305,8 @@
Navigation
--
-
generic_groupby(list_in: list, comp: Callable = <built-in function eq>)[source]¶
+-
+generic_groupby(list_in: list, comp: Callable = <built-in function eq>)[source]¶
Group a list of unsortable objects
:param list_in: A list of generic objects
:param comp: (Default value = operator.eq) The comparator
@@ -311,21 +318,23 @@ Navigation
--
-
get_hop_site_sequence(hop_list: List[Dict], start_u: Union[int, str]) → List[source]¶
-Read in a list of hop dictionaries and print the sequence of sites.
+
-
+get_hop_site_sequence(hop_list: List[Dict], start_u: Union[int, str], key: Optional[str] = None) List[source]¶
+Read in a list of hop dictionaries and print the sequence of sites (and relevant property values if any).
:param hop_list: a list of the data on a sequence of hops
-:param start_u: the site index of the starting sites
+:param start_u: the site index of the starting sites
+:param key: property to track in a hop (e.g.: “hop_distance”)
+:type key: optional
- Returns
-String representation of the hop sequence
+String representation of the hop sequence (and property values if any)
--
-
get_only_sites_from_structure(structure: pymatgen.core.structure.Structure, migrating_specie: str) → pymatgen.core.structure.Structure[source]¶
+-
+get_only_sites_from_structure(structure: pymatgen.core.structure.Structure, migrating_specie: str) pymatgen.core.structure.Structure[source]¶
Get a copy of the structure with only the migrating sites.
:param structure: The full_structure that contains all the sites
:param migrating_specie: The name of migrating species
@@ -340,8 +349,8 @@ Navigation
--
-
map_hop_sc2uc(sc_hop: pymatgen.analysis.diffusion.neb.pathfinder.MigrationHop, mg: pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph)[source]¶
+-
+map_hop_sc2uc(sc_hop: pymatgen.analysis.diffusion.neb.pathfinder.MigrationHop, mg: pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph)[source]¶
Map a given hop in the SC onto the UC.
:param sc_hop: MigrationHop object form pymatgen-diffusion.
:param mg: MigrationGraph object from pymatgen-diffusion.
@@ -355,7 +364,25 @@ Navigation
-
+
+-
+order_path(hop_list: List[Dict], start_u: Union[int, str]) List[Dict][source]¶
+Takes a list of hop dictionaries and flips hops (switches isite and esite)
+as needed to form a coherent path / sequence of sites according to
+get_hop_site_sequence().
+For example if hop_list = [{iindex:0, eindex:1, etc.}, {iindex:0, eindex:1, etc.}]
+then the output is [{iindex:0, eindex:1, etc.}, {iindex:1, eindex:0, etc.}] so that
+the following hop iindex matches the previous hop’s eindex.
+:param hop_list: a list of the data on a sequence of hops
+:param start_u: the site index of the starting sites
+
+- Returns
+a list of the data on a sequence of hops with hops in coherent orientation
+
+
+
+
@@ -379,7 +406,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.neb.html b/docs/pymatgen.analysis.diffusion.neb.html
index 84e96d7c..22b9ddc3 100644
--- a/docs/pymatgen.analysis.diffusion.neb.html
+++ b/docs/pymatgen.analysis.diffusion.neb.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.neb package — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.neb package — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,14 +47,14 @@ Navigation
-
+
pymatgen.analysis.diffusion.neb package¶
-
+
Subpackages¶
-
-
+
+
Submodules¶
@@ -63,12 +64,12 @@ Submodulespymatgen.analysis.diffusion.neb.periodic_dijkstra module
-
-
+
+
Module contents¶
Analysis tools for NEB calculations, inlcuding pathway analysis.
-
-
+
+
@@ -102,7 +103,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.neb.io.html b/docs/pymatgen.analysis.diffusion.neb.io.html
index b8bd6663..5c447561 100644
--- a/docs/pymatgen.analysis.diffusion.neb.io.html
+++ b/docs/pymatgen.analysis.diffusion.neb.io.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.neb.io module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.neb.io module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,12 +47,12 @@ Navigation
-
+
pymatgen.analysis.diffusion.neb.io module¶
Generate input fiels for NEB calculations.
--
-class
MVLCINEBEndPointSet(structure, **kwargs)[source]¶
+-
+class MVLCINEBEndPointSet(structure, **kwargs)[source]¶
Bases: pymatgen.io.vasp.sets.MITRelaxSet
Class for writing NEB end points relaxation inputs.
@@ -65,8 +66,8 @@ Navigation
--
-class
MVLCINEBSet(structures, **kwargs)[source]¶
+-
+class MVLCINEBSet(structures, **kwargs)[source]¶
Bases: pymatgen.io.vasp.sets.MITNEBSet
MAVRL-tested settings for CI-NEB calculations. Note that these parameters
requires the VTST modification of VASP from the Henkelman group. See
@@ -82,8 +83,8 @@
Navigation
-
+
@@ -149,7 +150,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.neb.pathfinder.html b/docs/pymatgen.analysis.diffusion.neb.pathfinder.html
index a53939cf..792d8e5a 100644
--- a/docs/pymatgen.analysis.diffusion.neb.pathfinder.html
+++ b/docs/pymatgen.analysis.diffusion.neb.pathfinder.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.neb.pathfinder module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.neb.pathfinder module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,12 +47,12 @@ Navigation
-
+
pymatgen.analysis.diffusion.neb.pathfinder module¶
Algorithms for NEB migration path analysis.
--
-class
DistinctPathFinder(structure, migrating_specie, max_path_length=None, symprec=0.1, perc_mode='>1d')[source]¶
+-
+class DistinctPathFinder(structure, migrating_specie, max_path_length=None, symprec=0.1, perc_mode='>1d')[source]¶
Bases: object
Determines symmetrically distinct paths between existing sites.
The path info can then be used to set up either vacancy or interstitial
@@ -74,8 +75,8 @@
Navigation
--
-
get_paths()[source]¶
+-
+get_paths()[source]¶
- Returns
[MigrationHop] All distinct migration paths.
@@ -84,8 +85,8 @@ Navigation
--
-
write_all_paths(fname, nimages=5, **kwargs)[source]¶
+-
+write_all_paths(fname, nimages=5, **kwargs)[source]¶
Write a file containing all paths, using hydrogen as a placeholder for
the images. H is chosen as it is the smallest atom. This is extremely
useful for path visualization in a standard software like VESTA.
@@ -103,8 +104,8 @@ Navigation
--
-class
IDPPSolver(structures)[source]¶
+-
+class IDPPSolver(structures)[source]¶
Bases: object
A solver using image dependent pair potential (IDPP) algo to get an improved
initial NEB path. For more details about this algo, please refer to
@@ -117,8 +118,8 @@
Navigation
--
-classmethod
from_endpoints(endpoints, nimages=5, sort_tol=1.0)[source]¶
+-
+classmethod from_endpoints(endpoints, nimages=5, sort_tol=1.0)[source]¶
A class method that starts with end-point structures instead. The
initial guess for the IDPP algo is then constructed using linear
interpolation.
@@ -136,15 +137,15 @@ Navigation
--
-static
get_unit_vector(vec)[source]¶
+-
+static get_unit_vector(vec)[source]¶
Calculate the unit vector of a vector.
:param vec: Vector.
--
-
run(maxiter=1000, tol=1e-05, gtol=0.001, step_size=0.05, max_disp=0.05, spring_const=5.0, species=None)[source]¶
+-
+run(maxiter=1000, tol=1e-05, gtol=0.001, step_size=0.05, max_disp=0.05, spring_const=5.0, species=None)[source]¶
Perform iterative minimization of the set of objective functions in an
NEB-like manner. In each iteration, the total force matrix for each
image is constructed, which comprises both the spring forces and true
@@ -178,8 +179,8 @@
Navigation
--
-class
MigrationHop(isite: pymatgen.core.sites.Site, esite: pymatgen.core.sites.Site, symm_structure: pymatgen.symmetry.structure.SymmetrizedStructure, symprec: float = 0.001)[source]¶
+-
+class MigrationHop(isite: pymatgen.core.sites.Site, esite: pymatgen.core.sites.Site, symm_structure: pymatgen.symmetry.structure.SymmetrizedStructure, host_symm_struct: Optional[pymatgen.symmetry.structure.SymmetrizedStructure] = None, symprec: float = 0.001)[source]¶
Bases: monty.json.MSONable
A convenience container representing a migration path.
@@ -188,13 +189,14 @@ Navigation
isite – Initial site
esite – End site
symm_structure – SymmetrizedStructure
host_symm_struct – SymmetrizedStructure of the host structure, used to for its spacegroup
symprec – used to determine equivalence
--
-
get_sc_structures(vac_mode: bool, min_atoms: int = 80, max_atoms: int = 240, min_length: float = 10.0) → Tuple[pymatgen.core.structure.Structure, pymatgen.core.structure.Structure, pymatgen.core.structure.Structure][source]¶
+-
+get_sc_structures(vac_mode: bool, min_atoms: int = 80, max_atoms: int = 240, min_length: float = 10.0) Tuple[pymatgen.core.structure.Structure, pymatgen.core.structure.Structure, pymatgen.core.structure.Structure][source]¶
Construct supercells that represents the start and end positions for migration analysis.
- Parameters
@@ -215,8 +217,8 @@ Navigation
-
+
@@ -295,7 +297,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.neb.periodic_dijkstra.html b/docs/pymatgen.analysis.diffusion.neb.periodic_dijkstra.html
index aadc9531..80b3692c 100644
--- a/docs/pymatgen.analysis.diffusion.neb.periodic_dijkstra.html
+++ b/docs/pymatgen.analysis.diffusion.neb.periodic_dijkstra.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.neb.periodic_dijkstra module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.neb.periodic_dijkstra module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,18 +47,18 @@ Navigation
-
+
pymatgen.analysis.diffusion.neb.periodic_dijkstra module¶
Dijkstra’s path search on a graph where the nodes are on a periodic graph
--
-
get_optimal_pathway_rev(path_parent: dict, leaf_node: tuple)[source]¶
+-
+get_optimal_pathway_rev(path_parent: dict, leaf_node: tuple)[source]¶
follow a leaf node all the way up to source.
--
-
periodic_dijkstra(G: networkx.classes.graph.Graph, sources: set, weight: str = 'weight', max_image: int = 2, target_reached: Callable = <function <lambda>>)[source]¶
+-
+periodic_dijkstra(G: networkx.classes.graph.Graph, sources: set, weight: str = 'weight', max_image: int = 2, target_reached: Callable = <function <lambda>>)[source]¶
Find the lowest cost pathway from a source point in the periodic graph.
Since the search can move many cells away without finding the target
we have to limit how many cells away from (0,0,0) to search.
@@ -85,8 +86,8 @@ Navigation
--
-
periodic_dijkstra_on_sgraph(sgraph: pymatgen.analysis.graphs.StructureGraph, sources: Set, weight: str = 'weight', max_image: int = 1, target_reached: Callable = <function <lambda>>)[source]¶
+-
+periodic_dijkstra_on_sgraph(sgraph: pymatgen.analysis.graphs.StructureGraph, sources: Set, weight: str = 'weight', max_image: int = 1, target_reached: Callable = <function <lambda>>)[source]¶
Find the lowest cost pathway from a source point in the periodic graph.
Since the search can move many cells away without finding the target
we have to limit how many cells away from (0,0,0) to search.
@@ -112,7 +113,7 @@ Navigation
-
+
@@ -136,7 +137,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.html b/docs/pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.html
index 2d75e68a..70658af1 100644
--- a/docs/pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.html
+++ b/docs/pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,35 +47,35 @@ Navigation
-
+
pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper module¶
--
-class
ChargeBarrierGraphTest(methodName='runTest')[source]¶
+-
+class ChargeBarrierGraphTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-
setUp()[source]¶
+-
+setUp()[source]¶
Hook method for setting up the test fixture before exercising it.
--
-
test_integration()[source]¶
+-
+test_integration()[source]¶
Sanity check: for a long enough diagonaly hop, if we turn the radius of the tube way up, it should cover the entire unit cell
--
-
test_populate_edges_with_chg_density_info()[source]¶
+-
+test_populate_edges_with_chg_density_info()[source]¶
Test that all of the sites with similar lengths have similar charge densities,
this will not always be true, but it valid in this Mn6O5F7
@@ -82,109 +83,119 @@ Navigation
--
-class
MigrationGraphComplexTest(methodName='runTest')[source]¶
+-
+class MigrationGraphComplexTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-
setUp()[source]¶
+-
+setUp()[source]¶
Hook method for setting up the test fixture before exercising it.
+
+
+
+
--
-class
MigrationGraphFromEntriesTest(methodName='runTest')[source]¶
+-
+class MigrationGraphFromEntriesTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-class
MigrationGraphSimpleTest(methodName='runTest')[source]¶
+-
+class MigrationGraphSimpleTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-
setUp()[source]¶
+-
+setUp()[source]¶
Hook method for setting up the test fixture before exercising it.
-
+
@@ -208,7 +219,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.neb.tests.test_io.html b/docs/pymatgen.analysis.diffusion.neb.tests.test_io.html
index 5d07bd3b..c3bd2d46 100644
--- a/docs/pymatgen.analysis.diffusion.neb.tests.test_io.html
+++ b/docs/pymatgen.analysis.diffusion.neb.tests.test_io.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.neb.tests.test_io module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.neb.tests.test_io module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,87 +47,87 @@ Navigation
-
+
pymatgen.analysis.diffusion.neb.tests.test_io module¶
--
-class
MVLCINEBEndPointSetTest(methodName='runTest')[source]¶
+-
+class MVLCINEBEndPointSetTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-
endpoint = Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]¶
+-
+endpoint = Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]¶
--
-class
MVLCINEBSetTest(methodName='runTest')[source]¶
+-
+class MVLCINEBSetTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-
structures = [Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628], Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, -5.0893, 1.8955) [0.2500, 0.2500, 0.2500] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628], Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, -10.1787, 3.7910) [0.5000, 0.5000, 0.5000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]]¶
+-
+structures = [Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628], Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, -5.0893, 1.8955) [0.2500, 0.2500, 0.2500] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628], Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, -10.1787, 3.7910) [0.5000, 0.5000, 0.5000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]]¶
--
-class
UtilityTest(methodName='runTest')[source]¶
+-
+class UtilityTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Unit test for outside methods in io.py
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-
structure = Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Na (0.0000, -10.1787, 3.7910) [0.5000, 0.5000, 0.5000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]¶
+-
+structure = Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Na (0.0000, -10.1787, 3.7910) [0.5000, 0.5000, 0.5000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]¶
-
+
@@ -150,7 +151,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.neb.tests.test_pathfinder.html b/docs/pymatgen.analysis.diffusion.neb.tests.test_pathfinder.html
index a4c44d4e..603437a7 100644
--- a/docs/pymatgen.analysis.diffusion.neb.tests.test_pathfinder.html
+++ b/docs/pymatgen.analysis.diffusion.neb.tests.test_pathfinder.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.neb.tests.test_pathfinder module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.neb.tests.test_pathfinder module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,92 +47,97 @@ Navigation
-
+
pymatgen.analysis.diffusion.neb.tests.test_pathfinder module¶
--
-class
DistinctPathFinderTest(methodName='runTest')[source]¶
+-
+class DistinctPathFinderTest(methodName='runTest')[source]¶
Bases: pymatgen.util.testing.PymatgenTest
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-class
IDPPSolverTest(methodName='runTest')[source]¶
+-
+class IDPPSolverTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-
final_struct = Structure Summary Lattice abc : 10.411723299877 12.0783517723596 9.47759961582329 angles : 90.0 90.0 90.0 volume : 1191.8693444977544 A : 10.411723299877 0.0 0.0 B : 0.0 12.0783517723596 0.0 C : 0.0 0.0 9.47759961582329 PeriodicSite: Li (5.1847, 6.1822, 2.4175) [0.4980, 0.5118, 0.2551] PeriodicSite: Li (5.2270, 11.9354, 2.3213) [0.5020, 0.9882, 0.2449] PeriodicSite: Li (5.1817, 12.0665, 7.0846) [0.4977, 0.9990, 0.7475] PeriodicSite: Li (5.2300, 6.0511, 7.1318) [0.5023, 0.5010, 0.7525] PeriodicSite: Li (0.0005, 3.0181, 0.0043) [0.0000, 0.2499, 0.0005] PeriodicSite: Li (10.4112, 3.0211, 4.7345) [1.0000, 0.2501, 0.4995] PeriodicSite: Li (10.4061, 9.0584, 0.0031) [0.9995, 0.7500, 0.0003] PeriodicSite: Li (0.0057, 9.0592, 4.7357) [0.0005, 0.7500, 0.4997] PeriodicSite: Li (5.2059, 3.0196, 2.3694) [0.5000, 0.2500, 0.2500] PeriodicSite: Li (5.2059, 3.0196, 7.1082) [0.5000, 0.2500, 0.7500] PeriodicSite: Li (5.2059, 9.0588, 7.1082) [0.5000, 0.7500, 0.7500] PeriodicSite: Li (10.4087, 12.0648, 0.0085) [0.9997, 0.9989, 0.0009] PeriodicSite: Li (0.0032, 12.0741, 4.7383) [0.0003, 0.9996, 0.5000] PeriodicSite: Li (10.4086, 6.0435, 0.0005) [0.9997, 0.5004, 0.0000] PeriodicSite: Li (0.0030, 6.0527, 4.7303) [0.0003, 0.5011, 0.4991] PeriodicSite: Fe (8.1412, 1.5110, 2.4871) [0.7819, 0.1251, 0.2624] PeriodicSite: Fe (8.1407, 1.5063, 7.2279) [0.7819, 0.1247, 0.7626] PeriodicSite: Fe (8.1001, 7.5688, 2.4722) [0.7780, 0.6266, 0.2608] PeriodicSite: Fe (8.1373, 7.5452, 7.2347) [0.7816, 0.6247, 0.7633] PeriodicSite: Fe (2.9469, 1.5019, 4.6127) [0.2830, 0.1243, 0.4867] PeriodicSite: Fe (2.9383, 1.5040, 9.3553) [0.2822, 0.1245, 0.9871] PeriodicSite: Fe (2.9571, 7.5783, 4.6085) [0.2840, 0.6274, 0.4863] PeriodicSite: Fe (2.9595, 7.5654, 9.3806) [0.2842, 0.6264, 0.9898] PeriodicSite: Fe (2.2705, 4.5282, 2.2517) [0.2181, 0.3749, 0.2376] PeriodicSite: Fe (2.2711, 4.5329, 6.9885) [0.2181, 0.3753, 0.7374] PeriodicSite: Fe (2.3116, 10.5488, 2.2666) [0.2220, 0.8734, 0.2392] PeriodicSite: Fe (2.2744, 10.5723, 6.9817) [0.2184, 0.8753, 0.7367] PeriodicSite: Fe (7.4648, 4.5373, 0.1261) [0.7170, 0.3757, 0.0133] PeriodicSite: Fe (7.4734, 4.5352, 4.8611) [0.7178, 0.3755, 0.5129] PeriodicSite: Fe (7.4547, 10.5392, 0.1303) [0.7160, 0.8726, 0.0137] PeriodicSite: Fe (7.4522, 10.5521, 4.8358) [0.7158, 0.8736, 0.5102] PeriodicSite: P (6.1978, 1.5072, 0.3753) [0.5953, 0.1248, 0.0396] PeriodicSite: P (6.2113, 1.5136, 5.1114) [0.5966, 0.1253, 0.5393] PeriodicSite: P (6.1961, 7.5476, 0.3633) [0.5951, 0.6249, 0.0383] PeriodicSite: P (6.2203, 7.5145, 5.1196) [0.5974, 0.6221, 0.5402] PeriodicSite: P (0.9887, 1.5041, 1.9896) [0.0950, 0.1245, 0.2099] PeriodicSite: P (0.9865, 1.5133, 6.7275) [0.0948, 0.1253, 0.7098] PeriodicSite: P (0.9818, 7.5439, 1.9926) [0.0943, 0.6246, 0.2102] PeriodicSite: P (0.9911, 7.5461, 6.7377) [0.0952, 0.6248, 0.7109] PeriodicSite: P (4.2139, 4.5319, 4.3635) [0.4047, 0.3752, 0.4604] PeriodicSite: P (4.2004, 4.5256, 9.1050) [0.4034, 0.3747, 0.9607] PeriodicSite: P (4.2156, 10.5699, 4.3756) [0.4049, 0.8751, 0.4617] PeriodicSite: P (4.1914, 10.6030, 9.0968) [0.4026, 0.8779, 0.9598] PeriodicSite: P (9.4230, 4.5351, 2.7492) [0.9050, 0.3755, 0.2901] PeriodicSite: P (9.4252, 4.5259, 7.4889) [0.9053, 0.3747, 0.7902] PeriodicSite: P (9.4299, 10.5737, 2.7462) [0.9057, 0.8754, 0.2898] PeriodicSite: P (9.4207, 10.5714, 7.4786) [0.9048, 0.8752, 0.7891] PeriodicSite: O (6.2228, 1.5268, 3.5773) [0.5977, 0.1264, 0.3775] PeriodicSite: O (6.2093, 1.5125, 8.3155) [0.5964, 0.1252, 0.8774] PeriodicSite: O (6.2747, 7.4398, 3.6014) [0.6027, 0.6160, 0.3800] PeriodicSite: O (6.2119, 7.5449, 8.2933) [0.5966, 0.6247, 0.8750] PeriodicSite: O (0.9902, 1.5124, 3.5258) [0.0951, 0.1252, 0.3720] PeriodicSite: O (0.9889, 1.5120, 8.2636) [0.0950, 0.1252, 0.8719] PeriodicSite: O (0.9898, 7.5475, 3.5295) [0.0951, 0.6249, 0.3724] PeriodicSite: O (0.9929, 7.5401, 8.2739) [0.0954, 0.6243, 0.8730] PeriodicSite: O (4.1889, 4.5124, 1.1615) [0.4023, 0.3736, 0.1225] PeriodicSite: O (4.2024, 4.5266, 5.9009) [0.4036, 0.3748, 0.6226] PeriodicSite: O (4.1370, 10.6778, 1.1374) [0.3973, 0.8840, 0.1200] PeriodicSite: O (4.1999, 10.5726, 5.9231) [0.4034, 0.8753, 0.6250] PeriodicSite: O (9.4215, 4.5268, 1.2130) [0.9049, 0.3748, 0.1280] PeriodicSite: O (9.4228, 4.5272, 5.9528) [0.9050, 0.3748, 0.6281] PeriodicSite: O (9.4220, 10.5700, 1.2093) [0.9049, 0.8751, 0.1276] PeriodicSite: O (9.4189, 10.5774, 5.9425) [0.9046, 0.8757, 0.6270] PeriodicSite: O (9.9678, 1.5135, 1.3791) [0.9574, 0.1253, 0.1455] PeriodicSite: O (9.9659, 1.5224, 6.1189) [0.9572, 0.1260, 0.6456] PeriodicSite: O (9.9630, 7.5428, 1.3832) [0.9569, 0.6245, 0.1459] PeriodicSite: O (9.9719, 7.5406, 6.1245) [0.9578, 0.6243, 0.6462] PeriodicSite: O (4.7657, 1.5202, 0.9751) [0.4577, 0.1259, 0.1029] PeriodicSite: O (4.7779, 1.5132, 5.7181) [0.4589, 0.1253, 0.6033] PeriodicSite: O (4.7627, 7.5033, 0.9219) [0.4574, 0.6212, 0.0973] PeriodicSite: O (4.7799, 7.5423, 5.7118) [0.4591, 0.6244, 0.6027] PeriodicSite: O (0.4439, 4.5256, 3.3597) [0.0426, 0.3747, 0.3545] PeriodicSite: O (0.4458, 4.5167, 8.0975) [0.0428, 0.3740, 0.8544] PeriodicSite: O (0.4487, 10.5747, 3.3556) [0.0431, 0.8755, 0.3541] PeriodicSite: O (0.4398, 10.5769, 8.0919) [0.0422, 0.8757, 0.8538] PeriodicSite: O (5.6461, 4.5190, 3.7637) [0.5423, 0.3741, 0.3971] PeriodicSite: O (5.6338, 4.5260, 8.4983) [0.5411, 0.3747, 0.8967] PeriodicSite: O (5.6490, 10.6142, 3.8169) [0.5426, 0.8788, 0.4027] PeriodicSite: O (5.6318, 10.5752, 8.5046) [0.5409, 0.8756, 0.8973] PeriodicSite: O (6.9383, 0.2665, 0.9991) [0.6664, 0.0221, 0.1054] PeriodicSite: O (6.9618, 0.2813, 5.7394) [0.6687, 0.0233, 0.6056] PeriodicSite: O (6.9424, 6.2988, 0.9884) [0.6668, 0.5215, 0.1043] PeriodicSite: O (6.9414, 6.2829, 5.8049) [0.6667, 0.5202, 0.6125] PeriodicSite: O (1.7379, 2.7394, 1.3635) [0.1669, 0.2268, 0.1439] PeriodicSite: O (1.7390, 2.7463, 6.1020) [0.1670, 0.2274, 0.6438] PeriodicSite: O (1.7293, 8.7758, 1.3621) [0.1661, 0.7266, 0.1437] PeriodicSite: O (1.7278, 8.7874, 6.1173) [0.1659, 0.7275, 0.6454] PeriodicSite: O (3.4593, 3.2999, 3.7365) [0.3322, 0.2732, 0.3942] PeriodicSite: O (3.4611, 3.2876, 8.4676) [0.3324, 0.2722, 0.8934] PeriodicSite: O (3.3893, 9.3739, 3.7965) [0.3255, 0.7761, 0.4006] PeriodicSite: O (3.4444, 9.3601, 8.4821) [0.3308, 0.7749, 0.8950] PeriodicSite: O (8.6876, 5.7754, 3.3730) [0.8344, 0.4782, 0.3559] PeriodicSite: O (8.6907, 5.7645, 8.1192) [0.8347, 0.4773, 0.8567] PeriodicSite: O (8.6853, 11.8141, 3.3664) [0.8342, 0.9781, 0.3552] PeriodicSite: O (8.6685, 11.8020, 8.1098) [0.8326, 0.9771, 0.8557] PeriodicSite: O (3.4734, 5.7727, 3.7397) [0.3336, 0.4779, 0.3946] PeriodicSite: O (3.4499, 5.7579, 8.4770) [0.3313, 0.4767, 0.8944] PeriodicSite: O (3.4693, 11.8187, 3.7504) [0.3332, 0.9785, 0.3957] PeriodicSite: O (3.4703, 11.8347, 8.4115) [0.3333, 0.9798, 0.8875] PeriodicSite: O (8.6738, 3.2998, 3.3753) [0.8331, 0.2732, 0.3561] PeriodicSite: O (8.6727, 3.2929, 8.1143) [0.8330, 0.2726, 0.8562] PeriodicSite: O (8.6824, 9.3417, 3.3767) [0.8339, 0.7734, 0.3563] PeriodicSite: O (8.6840, 9.3302, 8.0991) [0.8341, 0.7725, 0.8546] PeriodicSite: O (6.9525, 2.7393, 1.0023) [0.6678, 0.2268, 0.1058] PeriodicSite: O (6.9506, 2.7516, 5.7488) [0.6676, 0.2278, 0.6066] PeriodicSite: O (7.0224, 8.7437, 0.9423) [0.6745, 0.7239, 0.0994] PeriodicSite: O (6.9673, 8.7574, 5.7343) [0.6692, 0.7251, 0.6050] PeriodicSite: O (1.7242, 0.2638, 1.3658) [0.1656, 0.0218, 0.1441] PeriodicSite: O (1.7210, 0.2747, 6.0972) [0.1653, 0.0227, 0.6433] PeriodicSite: O (1.7264, 6.3034, 1.3724) [0.1658, 0.5219, 0.1448] PeriodicSite: O (1.7432, 6.3156, 6.1066) [0.1674, 0.5229, 0.6443]¶
+-
+final_struct = Structure Summary Lattice abc : 10.411723299877 12.0783517723596 9.47759961582329 angles : 90.0 90.0 90.0 volume : 1191.8693444977544 A : 10.411723299877 0.0 0.0 B : 0.0 12.0783517723596 0.0 C : 0.0 0.0 9.47759961582329 PeriodicSite: Li (5.1847, 6.1822, 2.4175) [0.4980, 0.5118, 0.2551] PeriodicSite: Li (5.2270, 11.9354, 2.3213) [0.5020, 0.9882, 0.2449] PeriodicSite: Li (5.1817, 12.0665, 7.0846) [0.4977, 0.9990, 0.7475] PeriodicSite: Li (5.2300, 6.0511, 7.1318) [0.5023, 0.5010, 0.7525] PeriodicSite: Li (0.0005, 3.0181, 0.0043) [0.0000, 0.2499, 0.0005] PeriodicSite: Li (10.4112, 3.0211, 4.7345) [1.0000, 0.2501, 0.4995] PeriodicSite: Li (10.4061, 9.0584, 0.0031) [0.9995, 0.7500, 0.0003] PeriodicSite: Li (0.0057, 9.0592, 4.7357) [0.0005, 0.7500, 0.4997] PeriodicSite: Li (5.2059, 3.0196, 2.3694) [0.5000, 0.2500, 0.2500] PeriodicSite: Li (5.2059, 3.0196, 7.1082) [0.5000, 0.2500, 0.7500] PeriodicSite: Li (5.2059, 9.0588, 7.1082) [0.5000, 0.7500, 0.7500] PeriodicSite: Li (10.4087, 12.0648, 0.0085) [0.9997, 0.9989, 0.0009] PeriodicSite: Li (0.0032, 12.0741, 4.7383) [0.0003, 0.9996, 0.5000] PeriodicSite: Li (10.4086, 6.0435, 0.0005) [0.9997, 0.5004, 0.0000] PeriodicSite: Li (0.0030, 6.0527, 4.7303) [0.0003, 0.5011, 0.4991] PeriodicSite: Fe (8.1412, 1.5110, 2.4871) [0.7819, 0.1251, 0.2624] PeriodicSite: Fe (8.1407, 1.5063, 7.2279) [0.7819, 0.1247, 0.7626] PeriodicSite: Fe (8.1001, 7.5688, 2.4722) [0.7780, 0.6266, 0.2608] PeriodicSite: Fe (8.1373, 7.5452, 7.2347) [0.7816, 0.6247, 0.7633] PeriodicSite: Fe (2.9469, 1.5019, 4.6127) [0.2830, 0.1243, 0.4867] PeriodicSite: Fe (2.9383, 1.5040, 9.3553) [0.2822, 0.1245, 0.9871] PeriodicSite: Fe (2.9571, 7.5783, 4.6085) [0.2840, 0.6274, 0.4863] PeriodicSite: Fe (2.9595, 7.5654, 9.3806) [0.2842, 0.6264, 0.9898] PeriodicSite: Fe (2.2705, 4.5282, 2.2517) [0.2181, 0.3749, 0.2376] PeriodicSite: Fe (2.2711, 4.5329, 6.9885) [0.2181, 0.3753, 0.7374] PeriodicSite: Fe (2.3116, 10.5488, 2.2666) [0.2220, 0.8734, 0.2392] PeriodicSite: Fe (2.2744, 10.5723, 6.9817) [0.2184, 0.8753, 0.7367] PeriodicSite: Fe (7.4648, 4.5373, 0.1261) [0.7170, 0.3757, 0.0133] PeriodicSite: Fe (7.4734, 4.5352, 4.8611) [0.7178, 0.3755, 0.5129] PeriodicSite: Fe (7.4547, 10.5392, 0.1303) [0.7160, 0.8726, 0.0137] PeriodicSite: Fe (7.4522, 10.5521, 4.8358) [0.7158, 0.8736, 0.5102] PeriodicSite: P (6.1978, 1.5072, 0.3753) [0.5953, 0.1248, 0.0396] PeriodicSite: P (6.2113, 1.5136, 5.1114) [0.5966, 0.1253, 0.5393] PeriodicSite: P (6.1961, 7.5476, 0.3633) [0.5951, 0.6249, 0.0383] PeriodicSite: P (6.2203, 7.5145, 5.1196) [0.5974, 0.6221, 0.5402] PeriodicSite: P (0.9887, 1.5041, 1.9896) [0.0950, 0.1245, 0.2099] PeriodicSite: P (0.9865, 1.5133, 6.7275) [0.0948, 0.1253, 0.7098] PeriodicSite: P (0.9818, 7.5439, 1.9926) [0.0943, 0.6246, 0.2102] PeriodicSite: P (0.9911, 7.5461, 6.7377) [0.0952, 0.6248, 0.7109] PeriodicSite: P (4.2139, 4.5319, 4.3635) [0.4047, 0.3752, 0.4604] PeriodicSite: P (4.2004, 4.5256, 9.1050) [0.4034, 0.3747, 0.9607] PeriodicSite: P (4.2156, 10.5699, 4.3756) [0.4049, 0.8751, 0.4617] PeriodicSite: P (4.1914, 10.6030, 9.0968) [0.4026, 0.8779, 0.9598] PeriodicSite: P (9.4230, 4.5351, 2.7492) [0.9050, 0.3755, 0.2901] PeriodicSite: P (9.4252, 4.5259, 7.4889) [0.9053, 0.3747, 0.7902] PeriodicSite: P (9.4299, 10.5737, 2.7462) [0.9057, 0.8754, 0.2898] PeriodicSite: P (9.4207, 10.5714, 7.4786) [0.9048, 0.8752, 0.7891] PeriodicSite: O (6.2228, 1.5268, 3.5773) [0.5977, 0.1264, 0.3775] PeriodicSite: O (6.2093, 1.5125, 8.3155) [0.5964, 0.1252, 0.8774] PeriodicSite: O (6.2747, 7.4398, 3.6014) [0.6027, 0.6160, 0.3800] PeriodicSite: O (6.2119, 7.5449, 8.2933) [0.5966, 0.6247, 0.8750] PeriodicSite: O (0.9902, 1.5124, 3.5258) [0.0951, 0.1252, 0.3720] PeriodicSite: O (0.9889, 1.5120, 8.2636) [0.0950, 0.1252, 0.8719] PeriodicSite: O (0.9898, 7.5475, 3.5295) [0.0951, 0.6249, 0.3724] PeriodicSite: O (0.9929, 7.5401, 8.2739) [0.0954, 0.6243, 0.8730] PeriodicSite: O (4.1889, 4.5124, 1.1615) [0.4023, 0.3736, 0.1225] PeriodicSite: O (4.2024, 4.5266, 5.9009) [0.4036, 0.3748, 0.6226] PeriodicSite: O (4.1370, 10.6778, 1.1374) [0.3973, 0.8840, 0.1200] PeriodicSite: O (4.1999, 10.5726, 5.9231) [0.4034, 0.8753, 0.6250] PeriodicSite: O (9.4215, 4.5268, 1.2130) [0.9049, 0.3748, 0.1280] PeriodicSite: O (9.4228, 4.5272, 5.9528) [0.9050, 0.3748, 0.6281] PeriodicSite: O (9.4220, 10.5700, 1.2093) [0.9049, 0.8751, 0.1276] PeriodicSite: O (9.4189, 10.5774, 5.9425) [0.9046, 0.8757, 0.6270] PeriodicSite: O (9.9678, 1.5135, 1.3791) [0.9574, 0.1253, 0.1455] PeriodicSite: O (9.9659, 1.5224, 6.1189) [0.9572, 0.1260, 0.6456] PeriodicSite: O (9.9630, 7.5428, 1.3832) [0.9569, 0.6245, 0.1459] PeriodicSite: O (9.9719, 7.5406, 6.1245) [0.9578, 0.6243, 0.6462] PeriodicSite: O (4.7657, 1.5202, 0.9751) [0.4577, 0.1259, 0.1029] PeriodicSite: O (4.7779, 1.5132, 5.7181) [0.4589, 0.1253, 0.6033] PeriodicSite: O (4.7627, 7.5033, 0.9219) [0.4574, 0.6212, 0.0973] PeriodicSite: O (4.7799, 7.5423, 5.7118) [0.4591, 0.6244, 0.6027] PeriodicSite: O (0.4439, 4.5256, 3.3597) [0.0426, 0.3747, 0.3545] PeriodicSite: O (0.4458, 4.5167, 8.0975) [0.0428, 0.3740, 0.8544] PeriodicSite: O (0.4487, 10.5747, 3.3556) [0.0431, 0.8755, 0.3541] PeriodicSite: O (0.4398, 10.5769, 8.0919) [0.0422, 0.8757, 0.8538] PeriodicSite: O (5.6461, 4.5190, 3.7637) [0.5423, 0.3741, 0.3971] PeriodicSite: O (5.6338, 4.5260, 8.4983) [0.5411, 0.3747, 0.8967] PeriodicSite: O (5.6490, 10.6142, 3.8169) [0.5426, 0.8788, 0.4027] PeriodicSite: O (5.6318, 10.5752, 8.5046) [0.5409, 0.8756, 0.8973] PeriodicSite: O (6.9383, 0.2665, 0.9991) [0.6664, 0.0221, 0.1054] PeriodicSite: O (6.9618, 0.2813, 5.7394) [0.6687, 0.0233, 0.6056] PeriodicSite: O (6.9424, 6.2988, 0.9884) [0.6668, 0.5215, 0.1043] PeriodicSite: O (6.9414, 6.2829, 5.8049) [0.6667, 0.5202, 0.6125] PeriodicSite: O (1.7379, 2.7394, 1.3635) [0.1669, 0.2268, 0.1439] PeriodicSite: O (1.7390, 2.7463, 6.1020) [0.1670, 0.2274, 0.6438] PeriodicSite: O (1.7293, 8.7758, 1.3621) [0.1661, 0.7266, 0.1437] PeriodicSite: O (1.7278, 8.7874, 6.1173) [0.1659, 0.7275, 0.6454] PeriodicSite: O (3.4593, 3.2999, 3.7365) [0.3322, 0.2732, 0.3942] PeriodicSite: O (3.4611, 3.2876, 8.4676) [0.3324, 0.2722, 0.8934] PeriodicSite: O (3.3893, 9.3739, 3.7965) [0.3255, 0.7761, 0.4006] PeriodicSite: O (3.4444, 9.3601, 8.4821) [0.3308, 0.7749, 0.8950] PeriodicSite: O (8.6876, 5.7754, 3.3730) [0.8344, 0.4782, 0.3559] PeriodicSite: O (8.6907, 5.7645, 8.1192) [0.8347, 0.4773, 0.8567] PeriodicSite: O (8.6853, 11.8141, 3.3664) [0.8342, 0.9781, 0.3552] PeriodicSite: O (8.6685, 11.8020, 8.1098) [0.8326, 0.9771, 0.8557] PeriodicSite: O (3.4734, 5.7727, 3.7397) [0.3336, 0.4779, 0.3946] PeriodicSite: O (3.4499, 5.7579, 8.4770) [0.3313, 0.4767, 0.8944] PeriodicSite: O (3.4693, 11.8187, 3.7504) [0.3332, 0.9785, 0.3957] PeriodicSite: O (3.4703, 11.8347, 8.4115) [0.3333, 0.9798, 0.8875] PeriodicSite: O (8.6738, 3.2998, 3.3753) [0.8331, 0.2732, 0.3561] PeriodicSite: O (8.6727, 3.2929, 8.1143) [0.8330, 0.2726, 0.8562] PeriodicSite: O (8.6824, 9.3417, 3.3767) [0.8339, 0.7734, 0.3563] PeriodicSite: O (8.6840, 9.3302, 8.0991) [0.8341, 0.7725, 0.8546] PeriodicSite: O (6.9525, 2.7393, 1.0023) [0.6678, 0.2268, 0.1058] PeriodicSite: O (6.9506, 2.7516, 5.7488) [0.6676, 0.2278, 0.6066] PeriodicSite: O (7.0224, 8.7437, 0.9423) [0.6745, 0.7239, 0.0994] PeriodicSite: O (6.9673, 8.7574, 5.7343) [0.6692, 0.7251, 0.6050] PeriodicSite: O (1.7242, 0.2638, 1.3658) [0.1656, 0.0218, 0.1441] PeriodicSite: O (1.7210, 0.2747, 6.0972) [0.1653, 0.0227, 0.6433] PeriodicSite: O (1.7264, 6.3034, 1.3724) [0.1658, 0.5219, 0.1448] PeriodicSite: O (1.7432, 6.3156, 6.1066) [0.1674, 0.5229, 0.6443]¶
--
-
init_struct = Structure Summary Lattice abc : 10.411723299877 12.0783517723596 9.47759961582329 angles : 90.0 90.0 90.0 volume : 1191.8693444977544 A : 10.411723299877 0.0 0.0 B : 0.0 12.0783517723596 0.0 C : 0.0 0.0 9.47759961582329 PeriodicSite: Li (5.1874, 8.9205, 2.4168) [0.4982, 0.7386, 0.2550] PeriodicSite: Li (5.2059, 12.0784, 2.3694) [0.5000, 1.0000, 0.2500] PeriodicSite: Li (5.2059, 12.0784, 7.1082) [0.5000, 1.0000, 0.7500] PeriodicSite: Li (5.2059, 6.0392, 7.1082) [0.5000, 0.5000, 0.7500] PeriodicSite: Li (10.4090, 3.0319, 0.0078) [0.9997, 0.2510, 0.0008] PeriodicSite: Li (0.0030, 3.0234, 4.7387) [0.0003, 0.2503, 0.5000] PeriodicSite: Li (10.4088, 9.0550, 0.0000) [0.9997, 0.7497, 0.0000] PeriodicSite: Li (0.0028, 9.0464, 4.7310) [0.0003, 0.7490, 0.4992] PeriodicSite: Li (5.2243, 3.1578, 2.3220) [0.5018, 0.2614, 0.2450] PeriodicSite: Li (5.1821, 3.0310, 7.0844) [0.4977, 0.2509, 0.7475] PeriodicSite: Li (5.2296, 9.0473, 7.1320) [0.5023, 0.7491, 0.7525] PeriodicSite: Li (0.0004, 0.0009, 0.0057) [0.0000, 0.0001, 0.0006] PeriodicSite: Li (10.4114, 12.0774, 4.7330) [1.0000, 0.9999, 0.4994] PeriodicSite: Li (10.4062, 6.0393, 0.0036) [0.9995, 0.5000, 0.0004] PeriodicSite: Li (0.0055, 6.0390, 4.7352) [0.0005, 0.5000, 0.4996] PeriodicSite: Fe (8.1421, 1.5086, 2.4873) [0.7820, 0.1249, 0.2624] PeriodicSite: Fe (8.1410, 1.5134, 7.2283) [0.7819, 0.1253, 0.7627] PeriodicSite: Fe (8.1009, 7.5290, 2.4716) [0.7781, 0.6233, 0.2608] PeriodicSite: Fe (8.1373, 7.5521, 7.2339) [0.7816, 0.6253, 0.7633] PeriodicSite: Fe (2.9469, 1.5185, 4.6137) [0.2830, 0.1257, 0.4868] PeriodicSite: Fe (2.9385, 1.5169, 9.3552) [0.2822, 0.1256, 0.9871] PeriodicSite: Fe (2.9564, 7.5201, 4.6074) [0.2839, 0.6226, 0.4861] PeriodicSite: Fe (2.9587, 7.5328, 9.3801) [0.2842, 0.6237, 0.9897] PeriodicSite: Fe (2.3108, 4.5494, 2.2672) [0.2219, 0.3767, 0.2392] PeriodicSite: Fe (2.2744, 4.5263, 6.9825) [0.2184, 0.3747, 0.7367] PeriodicSite: Fe (2.2697, 10.5698, 2.2515) [0.2180, 0.8751, 0.2376] PeriodicSite: Fe (2.2707, 10.5649, 6.9880) [0.2181, 0.8747, 0.7373] PeriodicSite: Fe (7.4553, 4.5583, 0.1314) [0.7161, 0.3774, 0.0139] PeriodicSite: Fe (7.4530, 4.5455, 4.8363) [0.7158, 0.3763, 0.5103] PeriodicSite: Fe (7.4648, 10.5599, 0.1251) [0.7170, 0.8743, 0.0132] PeriodicSite: Fe (7.4732, 10.5614, 4.8612) [0.7178, 0.8744, 0.5129] PeriodicSite: P (6.1981, 1.5112, 0.3753) [0.5953, 0.1251, 0.0396] PeriodicSite: P (6.2113, 1.5050, 5.1115) [0.5966, 0.1246, 0.5393] PeriodicSite: P (6.1957, 7.5503, 0.3633) [0.5951, 0.6251, 0.0383] PeriodicSite: P (6.2199, 7.5836, 5.1189) [0.5974, 0.6279, 0.5401] PeriodicSite: P (0.9888, 1.5155, 1.9897) [0.0950, 0.1255, 0.2099] PeriodicSite: P (0.9865, 1.5064, 6.7280) [0.0947, 0.1247, 0.7099] PeriodicSite: P (0.9815, 7.5544, 1.9920) [0.0943, 0.6254, 0.2102] PeriodicSite: P (0.9909, 7.5520, 6.7372) [0.0952, 0.6252, 0.7109] PeriodicSite: P (4.2160, 4.5281, 4.3755) [0.4049, 0.3749, 0.4617] PeriodicSite: P (4.1918, 4.4947, 9.0976) [0.4026, 0.3721, 0.9599] PeriodicSite: P (4.2137, 10.5672, 4.3635) [0.4047, 0.8749, 0.4604] PeriodicSite: P (4.2004, 10.5734, 9.1049) [0.4034, 0.8754, 0.9607] PeriodicSite: P (9.4302, 4.5240, 2.7468) [0.9057, 0.3746, 0.2898] PeriodicSite: P (9.4208, 4.5264, 7.4792) [0.9048, 0.3747, 0.7891] PeriodicSite: P (9.4229, 10.5629, 2.7491) [0.9050, 0.8745, 0.2901] PeriodicSite: P (9.4253, 10.5720, 7.4884) [0.9053, 0.8753, 0.7901] PeriodicSite: O (6.2224, 1.4923, 3.5773) [0.5976, 0.1236, 0.3775] PeriodicSite: O (6.2101, 1.5049, 8.3154) [0.5965, 0.1246, 0.8774] PeriodicSite: O (6.2743, 7.6582, 3.6007) [0.6026, 0.6340, 0.3799] PeriodicSite: O (6.2108, 7.5517, 8.2934) [0.5965, 0.6252, 0.8751] PeriodicSite: O (0.9903, 1.5073, 3.5259) [0.0951, 0.1248, 0.3720] PeriodicSite: O (0.9896, 1.5080, 8.2642) [0.0950, 0.1248, 0.8720] PeriodicSite: O (0.9900, 7.5502, 3.5288) [0.0951, 0.6251, 0.3723] PeriodicSite: O (0.9927, 7.5581, 8.2733) [0.0953, 0.6258, 0.8729] PeriodicSite: O (4.1374, 4.4202, 1.1381) [0.3974, 0.3660, 0.1201] PeriodicSite: O (4.2009, 4.5266, 5.9230) [0.4035, 0.3748, 0.6249] PeriodicSite: O (4.1893, 10.5860, 1.1615) [0.4024, 0.8764, 0.1225] PeriodicSite: O (4.2016, 10.5735, 5.9010) [0.4035, 0.8754, 0.6226] PeriodicSite: O (9.4217, 4.5281, 1.2100) [0.9049, 0.3749, 0.1277] PeriodicSite: O (9.4190, 4.5202, 5.9431) [0.9047, 0.3742, 0.6271] PeriodicSite: O (9.4215, 10.5710, 1.2129) [0.9049, 0.8752, 0.1280] PeriodicSite: O (9.4221, 10.5704, 5.9522) [0.9050, 0.8752, 0.6280] PeriodicSite: O (9.9681, 1.5052, 1.3785) [0.9574, 0.1246, 0.1454] PeriodicSite: O (9.9658, 1.4966, 6.1196) [0.9572, 0.1239, 0.6457] PeriodicSite: O (9.9624, 7.5551, 1.3829) [0.9568, 0.6255, 0.1459] PeriodicSite: O (9.9718, 7.5569, 6.1240) [0.9577, 0.6257, 0.6462] PeriodicSite: O (4.7659, 1.5002, 0.9756) [0.4577, 0.1242, 0.1029] PeriodicSite: O (4.7782, 1.5064, 5.7191) [0.4589, 0.1247, 0.6034] PeriodicSite: O (4.7625, 7.5958, 0.9216) [0.4574, 0.6289, 0.0972] PeriodicSite: O (4.7791, 7.5563, 5.7097) [0.4590, 0.6256, 0.6024] PeriodicSite: O (0.4493, 4.5232, 3.3559) [0.0432, 0.3745, 0.3541] PeriodicSite: O (0.4400, 4.5214, 8.0924) [0.0423, 0.3743, 0.8538] PeriodicSite: O (0.4436, 10.5732, 3.3603) [0.0426, 0.8754, 0.3546] PeriodicSite: O (0.4459, 10.5818, 8.0968) [0.0428, 0.8761, 0.8543] PeriodicSite: O (5.6492, 4.4825, 3.8172) [0.5426, 0.3711, 0.4028] PeriodicSite: O (5.6326, 4.5220, 8.5067) [0.5410, 0.3744, 0.8976] PeriodicSite: O (5.6458, 10.5782, 3.7632) [0.5423, 0.8758, 0.3971] PeriodicSite: O (5.6335, 10.5719, 8.4973) [0.5411, 0.8753, 0.8966] PeriodicSite: O (6.9512, 0.2785, 1.0032) [0.6676, 0.0231, 0.1058] PeriodicSite: O (6.9495, 0.2660, 5.7483) [0.6675, 0.0220, 0.6065] PeriodicSite: O (7.0219, 6.3538, 0.9424) [0.6744, 0.5261, 0.0994] PeriodicSite: O (6.9656, 6.3395, 5.7329) [0.6690, 0.5249, 0.6049] PeriodicSite: O (1.7248, 2.7555, 1.3661) [0.1657, 0.2281, 0.1441] PeriodicSite: O (1.7211, 2.7446, 6.0973) [0.1653, 0.2272, 0.6433] PeriodicSite: O (1.7255, 8.7949, 1.3716) [0.1657, 0.7282, 0.1447] PeriodicSite: O (1.7426, 8.7823, 6.1058) [0.1674, 0.7271, 0.6442] PeriodicSite: O (3.4692, 3.2784, 3.7520) [0.3332, 0.2714, 0.3959] PeriodicSite: O (3.4699, 3.2636, 8.4112) [0.3333, 0.2702, 0.8875] PeriodicSite: O (3.4720, 9.3269, 3.7396) [0.3335, 0.7722, 0.3946] PeriodicSite: O (3.4483, 9.3419, 8.4769) [0.3312, 0.7734, 0.8944] PeriodicSite: O (8.6826, 5.7559, 3.3769) [0.8339, 0.4765, 0.3563] PeriodicSite: O (8.6832, 5.7673, 8.0990) [0.8340, 0.4775, 0.8545] PeriodicSite: O (8.6740, 11.7982, 3.3753) [0.8331, 0.9768, 0.3561] PeriodicSite: O (8.6732, 11.8051, 8.1140) [0.8330, 0.9774, 0.8561] PeriodicSite: O (3.3898, 5.7246, 3.7964) [0.3256, 0.4740, 0.4006] PeriodicSite: O (3.4461, 5.7388, 8.4835) [0.3310, 0.4751, 0.8951] PeriodicSite: O (3.4605, 11.7998, 3.7356) [0.3324, 0.9769, 0.3942] PeriodicSite: O (3.4622, 11.8123, 8.4681) [0.3325, 0.9780, 0.8935] PeriodicSite: O (8.6862, 3.2835, 3.3672) [0.8343, 0.2718, 0.3553] PeriodicSite: O (8.6691, 3.2960, 8.1106) [0.8326, 0.2729, 0.8558] PeriodicSite: O (8.6869, 9.3228, 3.3727) [0.8343, 0.7719, 0.3559] PeriodicSite: O (8.6906, 9.3337, 8.1191) [0.8347, 0.7728, 0.8567] PeriodicSite: O (6.9397, 2.7514, 0.9992) [0.6665, 0.2278, 0.1054] PeriodicSite: O (6.9635, 2.7364, 5.7395) [0.6688, 0.2266, 0.6056] PeriodicSite: O (6.9425, 8.8000, 0.9868) [0.6668, 0.7286, 0.1041] PeriodicSite: O (6.9418, 8.8148, 5.8052) [0.6667, 0.7298, 0.6125] PeriodicSite: O (1.7378, 0.2801, 1.3635) [0.1669, 0.0232, 0.1439] PeriodicSite: O (1.7385, 0.2732, 6.1024) [0.1670, 0.0226, 0.6439] PeriodicSite: O (1.7291, 6.3224, 1.3619) [0.1661, 0.5235, 0.1437] PeriodicSite: O (1.7285, 6.3110, 6.1174) [0.1660, 0.5225, 0.6455]¶
+-
+init_struct = Structure Summary Lattice abc : 10.411723299877 12.0783517723596 9.47759961582329 angles : 90.0 90.0 90.0 volume : 1191.8693444977544 A : 10.411723299877 0.0 0.0 B : 0.0 12.0783517723596 0.0 C : 0.0 0.0 9.47759961582329 PeriodicSite: Li (5.1874, 8.9205, 2.4168) [0.4982, 0.7386, 0.2550] PeriodicSite: Li (5.2059, 12.0784, 2.3694) [0.5000, 1.0000, 0.2500] PeriodicSite: Li (5.2059, 12.0784, 7.1082) [0.5000, 1.0000, 0.7500] PeriodicSite: Li (5.2059, 6.0392, 7.1082) [0.5000, 0.5000, 0.7500] PeriodicSite: Li (10.4090, 3.0319, 0.0078) [0.9997, 0.2510, 0.0008] PeriodicSite: Li (0.0030, 3.0234, 4.7387) [0.0003, 0.2503, 0.5000] PeriodicSite: Li (10.4088, 9.0550, 0.0000) [0.9997, 0.7497, 0.0000] PeriodicSite: Li (0.0028, 9.0464, 4.7310) [0.0003, 0.7490, 0.4992] PeriodicSite: Li (5.2243, 3.1578, 2.3220) [0.5018, 0.2614, 0.2450] PeriodicSite: Li (5.1821, 3.0310, 7.0844) [0.4977, 0.2509, 0.7475] PeriodicSite: Li (5.2296, 9.0473, 7.1320) [0.5023, 0.7491, 0.7525] PeriodicSite: Li (0.0004, 0.0009, 0.0057) [0.0000, 0.0001, 0.0006] PeriodicSite: Li (10.4114, 12.0774, 4.7330) [1.0000, 0.9999, 0.4994] PeriodicSite: Li (10.4062, 6.0393, 0.0036) [0.9995, 0.5000, 0.0004] PeriodicSite: Li (0.0055, 6.0390, 4.7352) [0.0005, 0.5000, 0.4996] PeriodicSite: Fe (8.1421, 1.5086, 2.4873) [0.7820, 0.1249, 0.2624] PeriodicSite: Fe (8.1410, 1.5134, 7.2283) [0.7819, 0.1253, 0.7627] PeriodicSite: Fe (8.1009, 7.5290, 2.4716) [0.7781, 0.6233, 0.2608] PeriodicSite: Fe (8.1373, 7.5521, 7.2339) [0.7816, 0.6253, 0.7633] PeriodicSite: Fe (2.9469, 1.5185, 4.6137) [0.2830, 0.1257, 0.4868] PeriodicSite: Fe (2.9385, 1.5169, 9.3552) [0.2822, 0.1256, 0.9871] PeriodicSite: Fe (2.9564, 7.5201, 4.6074) [0.2839, 0.6226, 0.4861] PeriodicSite: Fe (2.9587, 7.5328, 9.3801) [0.2842, 0.6237, 0.9897] PeriodicSite: Fe (2.3108, 4.5494, 2.2672) [0.2219, 0.3767, 0.2392] PeriodicSite: Fe (2.2744, 4.5263, 6.9825) [0.2184, 0.3747, 0.7367] PeriodicSite: Fe (2.2697, 10.5698, 2.2515) [0.2180, 0.8751, 0.2376] PeriodicSite: Fe (2.2707, 10.5649, 6.9880) [0.2181, 0.8747, 0.7373] PeriodicSite: Fe (7.4553, 4.5583, 0.1314) [0.7161, 0.3774, 0.0139] PeriodicSite: Fe (7.4530, 4.5455, 4.8363) [0.7158, 0.3763, 0.5103] PeriodicSite: Fe (7.4648, 10.5599, 0.1251) [0.7170, 0.8743, 0.0132] PeriodicSite: Fe (7.4732, 10.5614, 4.8612) [0.7178, 0.8744, 0.5129] PeriodicSite: P (6.1981, 1.5112, 0.3753) [0.5953, 0.1251, 0.0396] PeriodicSite: P (6.2113, 1.5050, 5.1115) [0.5966, 0.1246, 0.5393] PeriodicSite: P (6.1957, 7.5503, 0.3633) [0.5951, 0.6251, 0.0383] PeriodicSite: P (6.2199, 7.5836, 5.1189) [0.5974, 0.6279, 0.5401] PeriodicSite: P (0.9888, 1.5155, 1.9897) [0.0950, 0.1255, 0.2099] PeriodicSite: P (0.9865, 1.5064, 6.7280) [0.0947, 0.1247, 0.7099] PeriodicSite: P (0.9815, 7.5544, 1.9920) [0.0943, 0.6254, 0.2102] PeriodicSite: P (0.9909, 7.5520, 6.7372) [0.0952, 0.6252, 0.7109] PeriodicSite: P (4.2160, 4.5281, 4.3755) [0.4049, 0.3749, 0.4617] PeriodicSite: P (4.1918, 4.4947, 9.0976) [0.4026, 0.3721, 0.9599] PeriodicSite: P (4.2137, 10.5672, 4.3635) [0.4047, 0.8749, 0.4604] PeriodicSite: P (4.2004, 10.5734, 9.1049) [0.4034, 0.8754, 0.9607] PeriodicSite: P (9.4302, 4.5240, 2.7468) [0.9057, 0.3746, 0.2898] PeriodicSite: P (9.4208, 4.5264, 7.4792) [0.9048, 0.3747, 0.7891] PeriodicSite: P (9.4229, 10.5629, 2.7491) [0.9050, 0.8745, 0.2901] PeriodicSite: P (9.4253, 10.5720, 7.4884) [0.9053, 0.8753, 0.7901] PeriodicSite: O (6.2224, 1.4923, 3.5773) [0.5976, 0.1236, 0.3775] PeriodicSite: O (6.2101, 1.5049, 8.3154) [0.5965, 0.1246, 0.8774] PeriodicSite: O (6.2743, 7.6582, 3.6007) [0.6026, 0.6340, 0.3799] PeriodicSite: O (6.2108, 7.5517, 8.2934) [0.5965, 0.6252, 0.8751] PeriodicSite: O (0.9903, 1.5073, 3.5259) [0.0951, 0.1248, 0.3720] PeriodicSite: O (0.9896, 1.5080, 8.2642) [0.0950, 0.1248, 0.8720] PeriodicSite: O (0.9900, 7.5502, 3.5288) [0.0951, 0.6251, 0.3723] PeriodicSite: O (0.9927, 7.5581, 8.2733) [0.0953, 0.6258, 0.8729] PeriodicSite: O (4.1374, 4.4202, 1.1381) [0.3974, 0.3660, 0.1201] PeriodicSite: O (4.2009, 4.5266, 5.9230) [0.4035, 0.3748, 0.6249] PeriodicSite: O (4.1893, 10.5860, 1.1615) [0.4024, 0.8764, 0.1225] PeriodicSite: O (4.2016, 10.5735, 5.9010) [0.4035, 0.8754, 0.6226] PeriodicSite: O (9.4217, 4.5281, 1.2100) [0.9049, 0.3749, 0.1277] PeriodicSite: O (9.4190, 4.5202, 5.9431) [0.9047, 0.3742, 0.6271] PeriodicSite: O (9.4215, 10.5710, 1.2129) [0.9049, 0.8752, 0.1280] PeriodicSite: O (9.4221, 10.5704, 5.9522) [0.9050, 0.8752, 0.6280] PeriodicSite: O (9.9681, 1.5052, 1.3785) [0.9574, 0.1246, 0.1454] PeriodicSite: O (9.9658, 1.4966, 6.1196) [0.9572, 0.1239, 0.6457] PeriodicSite: O (9.9624, 7.5551, 1.3829) [0.9568, 0.6255, 0.1459] PeriodicSite: O (9.9718, 7.5569, 6.1240) [0.9577, 0.6257, 0.6462] PeriodicSite: O (4.7659, 1.5002, 0.9756) [0.4577, 0.1242, 0.1029] PeriodicSite: O (4.7782, 1.5064, 5.7191) [0.4589, 0.1247, 0.6034] PeriodicSite: O (4.7625, 7.5958, 0.9216) [0.4574, 0.6289, 0.0972] PeriodicSite: O (4.7791, 7.5563, 5.7097) [0.4590, 0.6256, 0.6024] PeriodicSite: O (0.4493, 4.5232, 3.3559) [0.0432, 0.3745, 0.3541] PeriodicSite: O (0.4400, 4.5214, 8.0924) [0.0423, 0.3743, 0.8538] PeriodicSite: O (0.4436, 10.5732, 3.3603) [0.0426, 0.8754, 0.3546] PeriodicSite: O (0.4459, 10.5818, 8.0968) [0.0428, 0.8761, 0.8543] PeriodicSite: O (5.6492, 4.4825, 3.8172) [0.5426, 0.3711, 0.4028] PeriodicSite: O (5.6326, 4.5220, 8.5067) [0.5410, 0.3744, 0.8976] PeriodicSite: O (5.6458, 10.5782, 3.7632) [0.5423, 0.8758, 0.3971] PeriodicSite: O (5.6335, 10.5719, 8.4973) [0.5411, 0.8753, 0.8966] PeriodicSite: O (6.9512, 0.2785, 1.0032) [0.6676, 0.0231, 0.1058] PeriodicSite: O (6.9495, 0.2660, 5.7483) [0.6675, 0.0220, 0.6065] PeriodicSite: O (7.0219, 6.3538, 0.9424) [0.6744, 0.5261, 0.0994] PeriodicSite: O (6.9656, 6.3395, 5.7329) [0.6690, 0.5249, 0.6049] PeriodicSite: O (1.7248, 2.7555, 1.3661) [0.1657, 0.2281, 0.1441] PeriodicSite: O (1.7211, 2.7446, 6.0973) [0.1653, 0.2272, 0.6433] PeriodicSite: O (1.7255, 8.7949, 1.3716) [0.1657, 0.7282, 0.1447] PeriodicSite: O (1.7426, 8.7823, 6.1058) [0.1674, 0.7271, 0.6442] PeriodicSite: O (3.4692, 3.2784, 3.7520) [0.3332, 0.2714, 0.3959] PeriodicSite: O (3.4699, 3.2636, 8.4112) [0.3333, 0.2702, 0.8875] PeriodicSite: O (3.4720, 9.3269, 3.7396) [0.3335, 0.7722, 0.3946] PeriodicSite: O (3.4483, 9.3419, 8.4769) [0.3312, 0.7734, 0.8944] PeriodicSite: O (8.6826, 5.7559, 3.3769) [0.8339, 0.4765, 0.3563] PeriodicSite: O (8.6832, 5.7673, 8.0990) [0.8340, 0.4775, 0.8545] PeriodicSite: O (8.6740, 11.7982, 3.3753) [0.8331, 0.9768, 0.3561] PeriodicSite: O (8.6732, 11.8051, 8.1140) [0.8330, 0.9774, 0.8561] PeriodicSite: O (3.3898, 5.7246, 3.7964) [0.3256, 0.4740, 0.4006] PeriodicSite: O (3.4461, 5.7388, 8.4835) [0.3310, 0.4751, 0.8951] PeriodicSite: O (3.4605, 11.7998, 3.7356) [0.3324, 0.9769, 0.3942] PeriodicSite: O (3.4622, 11.8123, 8.4681) [0.3325, 0.9780, 0.8935] PeriodicSite: O (8.6862, 3.2835, 3.3672) [0.8343, 0.2718, 0.3553] PeriodicSite: O (8.6691, 3.2960, 8.1106) [0.8326, 0.2729, 0.8558] PeriodicSite: O (8.6869, 9.3228, 3.3727) [0.8343, 0.7719, 0.3559] PeriodicSite: O (8.6906, 9.3337, 8.1191) [0.8347, 0.7728, 0.8567] PeriodicSite: O (6.9397, 2.7514, 0.9992) [0.6665, 0.2278, 0.1054] PeriodicSite: O (6.9635, 2.7364, 5.7395) [0.6688, 0.2266, 0.6056] PeriodicSite: O (6.9425, 8.8000, 0.9868) [0.6668, 0.7286, 0.1041] PeriodicSite: O (6.9418, 8.8148, 5.8052) [0.6667, 0.7298, 0.6125] PeriodicSite: O (1.7378, 0.2801, 1.3635) [0.1669, 0.0232, 0.1439] PeriodicSite: O (1.7385, 0.2732, 6.1024) [0.1670, 0.0226, 0.6439] PeriodicSite: O (1.7291, 6.3224, 1.3619) [0.1661, 0.5235, 0.1437] PeriodicSite: O (1.7285, 6.3110, 6.1174) [0.1660, 0.5225, 0.6455]¶
--
-class
MigrationHopTest(methodName='runTest')[source]¶
+-
+class MigrationHopTest(methodName='runTest')[source]¶
Bases: pymatgen.util.testing.PymatgenTest
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-
setUp()[source]¶
+-
+setUp()[source]¶
Hook method for setting up the test fixture before exercising it.
+
+
-
+
@@ -155,7 +161,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.tests.test_analyzer.html b/docs/pymatgen.analysis.diffusion.tests.test_analyzer.html
index 9cc3f03a..68c03686 100644
--- a/docs/pymatgen.analysis.diffusion.tests.test_analyzer.html
+++ b/docs/pymatgen.analysis.diffusion.tests.test_analyzer.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.tests.test_analyzer module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.tests.test_analyzer module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,52 +47,52 @@ Navigation
-
+
pymatgen.analysis.diffusion.tests.test_analyzer module¶
--
-class
DiffusionAnalyzerTest(methodName='runTest')[source]¶
+-
+class DiffusionAnalyzerTest(methodName='runTest')[source]¶
Bases: pymatgen.util.testing.PymatgenTest
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
--
-class
FuncTest(methodName='runTest')[source]¶
+-
+class FuncTest(methodName='runTest')[source]¶
Bases: pymatgen.util.testing.PymatgenTest
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
-
+
@@ -115,7 +116,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.utils.edge_data_from_sc.html b/docs/pymatgen.analysis.diffusion.utils.edge_data_from_sc.html
index 036c7678..bb7e08fe 100644
--- a/docs/pymatgen.analysis.diffusion.utils.edge_data_from_sc.html
+++ b/docs/pymatgen.analysis.diffusion.utils.edge_data_from_sc.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.utils.edge_data_from_sc module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.utils.edge_data_from_sc module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,12 +47,12 @@ Navigation
-
+
pymatgen.analysis.diffusion.utils.edge_data_from_sc module¶
Function to add edge data to MigrationGraph through 2 SC structures
--
-
add_edge_data_from_sc(mg: pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph, i_sc: pymatgen.core.structure.Structure, e_sc: pymatgen.core.structure.Structure, data_array: list, key: str = 'custom_key', symprec: Union[None, float] = None) → None[source]¶
+-
+add_edge_data_from_sc(mg: pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph, i_sc: pymatgen.core.structure.Structure, e_sc: pymatgen.core.structure.Structure, data_array: list, key: str = 'custom_key', use_host_sg: bool = True) None[source]¶
Add a data entry and key to edges within FullPathMapper object with the same hop_label.
These hops are equivalent by symmetry to the 2 positions given in the supercell structures.
@@ -61,6 +62,7 @@ Navigation
e_sc – Supercell structure containing working ion at ending position
data_array – The data to be added to the edges
key – Key of the edge attribute to be added
use_host_sg – Flag t whether or not to use the host structure’s spacegroup to initiate MigrationHop
- Returns
@@ -70,8 +72,8 @@ Navigation
--
-
get_uc_pos(isite: pymatgen.core.sites.PeriodicSite, esite: pymatgen.core.sites.PeriodicSite, uc: pymatgen.core.structure.Structure, sc: pymatgen.core.structure.Structure, sm: pymatgen.analysis.structure_matcher.StructureMatcher) → Tuple[pymatgen.core.sites.PeriodicSite, pymatgen.core.sites.PeriodicSite, pymatgen.core.sites.PeriodicSite][source]¶
+-
+get_uc_pos(isite: pymatgen.core.sites.PeriodicSite, esite: pymatgen.core.sites.PeriodicSite, uc: pymatgen.core.structure.Structure, sc: pymatgen.core.structure.Structure, sm: pymatgen.analysis.structure_matcher.StructureMatcher) Tuple[pymatgen.core.sites.PeriodicSite, pymatgen.core.sites.PeriodicSite, pymatgen.core.sites.PeriodicSite][source]¶
Take positions in the supercel and transform into the unitcell positions
- Parameters
@@ -90,8 +92,8 @@ Navigation
--
-
get_unique_hop(mg: pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph, sc: pymatgen.core.structure.Structure, isite: pymatgen.core.sites.PeriodicSite, esite: pymatgen.core.sites.PeriodicSite, symprec: Union[None, float] = None) → Tuple[int, pymatgen.analysis.diffusion.neb.pathfinder.MigrationHop][source]¶
+-
+get_unique_hop(mg: pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph, sc: pymatgen.core.structure.Structure, isite: pymatgen.core.sites.PeriodicSite, esite: pymatgen.core.sites.PeriodicSite, use_host_sg: bool = True) Tuple[int, pymatgen.analysis.diffusion.neb.pathfinder.MigrationHop][source]¶
Get the unique hop label that correspond to two end positions in the SC
- Parameters
@@ -100,6 +102,7 @@ Navigation
sc – Structure of the supercell used for the NEB calculation
isite – Initial position in the supercell
esite – Final position in the supercell
use_host_sg – Flag t whether or not to use the host structure’s spacegroup to initiate MigrationHop
- Returns
@@ -109,8 +112,8 @@ Navigation
-
+
@@ -149,7 +152,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.utils.html b/docs/pymatgen.analysis.diffusion.utils.html
index 08f98029..d8bd0cf0 100644
--- a/docs/pymatgen.analysis.diffusion.utils.html
+++ b/docs/pymatgen.analysis.diffusion.utils.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.utils package — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.utils package — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,14 +47,14 @@ Navigation
-
+
pymatgen.analysis.diffusion.utils package¶
-
+
Subpackages¶
-
-
+
+
Submodules¶
@@ -63,12 +64,12 @@ Submodulespymatgen.analysis.diffusion.utils.supercells module
-
-
+
+
Module contents¶
Utils Modules
-
-
+
+
@@ -102,7 +103,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.utils.maggma.html b/docs/pymatgen.analysis.diffusion.utils.maggma.html
index d82bf904..0876e7fb 100644
--- a/docs/pymatgen.analysis.diffusion.utils.maggma.html
+++ b/docs/pymatgen.analysis.diffusion.utils.maggma.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.utils.maggma module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.utils.maggma module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,9 +47,9 @@ Navigation
-
+
pymatgen.analysis.diffusion.utils.maggma module¶
-
+
@@ -72,7 +73,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.utils.parse_entries.html b/docs/pymatgen.analysis.diffusion.utils.parse_entries.html
index 55bb620e..d7793e2b 100644
--- a/docs/pymatgen.analysis.diffusion.utils.parse_entries.html
+++ b/docs/pymatgen.analysis.diffusion.utils.parse_entries.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.utils.parse_entries module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.utils.parse_entries module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,12 +47,12 @@ Navigation
-
+
pymatgen.analysis.diffusion.utils.parse_entries module¶
Functions for combining many ComputedEntry objects into MigrationGraph objects.
--
-
get_inserted_on_base(base_ent: pymatgen.entries.computed_entries.ComputedStructureEntry, inserted_ent: pymatgen.entries.computed_entries.ComputedStructureEntry, migrating_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, sm: pymatgen.analysis.structure_matcher.StructureMatcher) → Optional[pymatgen.core.structure.Structure][source]¶
+-
+get_inserted_on_base(base_ent: pymatgen.entries.computed_entries.ComputedStructureEntry, inserted_ent: pymatgen.entries.computed_entries.ComputedStructureEntry, migrating_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, sm: pymatgen.analysis.structure_matcher.StructureMatcher) Optional[pymatgen.core.structure.Structure][source]¶
For a structured-matched pair of base and inserted entries, map all of the Li positions in the inserted entry to
positions in the base entry and return a new structure where all the sites are decorated with the insertion
energy. Since the calculation of the insertion energy needs the energy of the metallic working ion,
@@ -72,8 +73,8 @@
Navigation
--
-
get_insertion_energy(base_entry: pymatgen.entries.computed_entries.ComputedStructureEntry, inserted_entry: pymatgen.entries.computed_entries.ComputedStructureEntry, migrating_ion_entry: pymatgen.entries.computed_entries.ComputedEntry) → float[source]¶
+-
+get_insertion_energy(base_entry: pymatgen.entries.computed_entries.ComputedStructureEntry, inserted_entry: pymatgen.entries.computed_entries.ComputedStructureEntry, migrating_ion_entry: pymatgen.entries.computed_entries.ComputedEntry) float[source]¶
Calculate the insertion energy for a given inserted entry
:param base_entry: The entry for the host structure
:param inserted_entry: The entry for the inserted structure
@@ -88,8 +89,8 @@
Navigation
--
-
get_matched_structure_mapping(base: pymatgen.core.structure.Structure, inserted: pymatgen.core.structure.Structure, sm: pymatgen.analysis.structure_matcher.StructureMatcher)[source]¶
+-
+get_matched_structure_mapping(base: pymatgen.core.structure.Structure, inserted: pymatgen.core.structure.Structure, sm: pymatgen.analysis.structure_matcher.StructureMatcher)[source]¶
Get the mapping from the inserted structure onto the base structure,
assuming that the inserted structure sans the working ion is some kind
of SC of the base.
@@ -112,8 +113,8 @@ Navigation
--
-
get_sym_migration_ion_sites(base_struct: pymatgen.core.structure.Structure, inserted_struct: pymatgen.core.structure.Structure, migrating_ion: str, symprec: float = 0.01, angle_tol: float = 5.0) → pymatgen.core.structure.Structure[source]¶
+-
+get_sym_migration_ion_sites(base_struct: pymatgen.core.structure.Structure, inserted_struct: pymatgen.core.structure.Structure, migrating_ion: str, symprec: float = 0.01, angle_tol: float = 5.0) pymatgen.core.structure.Structure[source]¶
Take one inserted entry then map out all symmetry equivalent copies of the cation sites in base entry.
Each site is decorated with the insertion energy calculated from the base and inserted entries.
@@ -133,8 +134,8 @@ Navigation
--
-
process_entries(base_entries: List[pymatgen.entries.computed_entries.ComputedStructureEntry], inserted_entries: List[pymatgen.entries.computed_entries.ComputedStructureEntry], migrating_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, symprec: float = 0.01, ltol: float = 0.2, stol: float = 0.3, angle_tol: float = 5.0) → List[Dict][source]¶
+-
+process_entries(base_entries: List[pymatgen.entries.computed_entries.ComputedStructureEntry], inserted_entries: List[pymatgen.entries.computed_entries.ComputedStructureEntry], migrating_ion_entry: pymatgen.entries.computed_entries.ComputedEntry, symprec: float = 0.01, ltol: float = 0.2, stol: float = 0.3, angle_tol: float = 5.0) List[Dict][source]¶
Process a list of base entries and inserted entries to create input for migration path analysis Each inserted
entries can be mapped to more than one base entry. Return groups of structures decorated with the working ions
to indicate the metastable sites, ranked by the number of working ion sites (highest number is the first).
@@ -163,7 +164,7 @@ Navigation
-
+
@@ -187,7 +188,7 @@ This Page
Quick search
diff --git a/docs/pymatgen.analysis.diffusion.utils.supercells.html b/docs/pymatgen.analysis.diffusion.utils.supercells.html
index 20eef806..7a9068f9 100644
--- a/docs/pymatgen.analysis.diffusion.utils.supercells.html
+++ b/docs/pymatgen.analysis.diffusion.utils.supercells.html
@@ -4,11 +4,12 @@
-
- pymatgen.analysis.diffusion.utils.supercells module — pymatgen-diffusion 2021.4.29 documentation
-
-
-
+
+
+ pymatgen.analysis.diffusion.utils.supercells module — pymatgen-diffusion 2022.1.15 documentation
+
+
+
@@ -36,7 +37,7 @@ Navigation
-
modules |
-
+
@@ -46,12 +47,12 @@ Navigation
-
+
pymatgen.analysis.diffusion.utils.supercells module¶
Functions for creating supercells for NEB calculations
--
-
get_sc_fromstruct(base_struct: pymatgen.core.structure.Structure, min_atoms: int = 80, max_atoms: int = 240, min_length: float = 10.0) → List[List[int]][source]¶
+-
+get_sc_fromstruct(base_struct: pymatgen.core.structure.Structure, min_atoms: int = 80, max_atoms: int = 240, min_length: float = 10.0) List[List[int]][source]¶
Generate the best supercell from a unitcell.
The CubicSupercellTransformation from PMG is much faster but don’t iterate over as many
supercell configurations so it’s less able to find the best configuration in a give cell size.
@@ -76,8 +77,8 @@
Navigation
--
-
get_start_end_structures(isite: pymatgen.core.sites.PeriodicSite, esite: pymatgen.core.sites.PeriodicSite, base_struct: pymatgen.core.structure.Structure, sc_mat: List[List[Union[int, float]]], vac_mode: bool, debug: bool = False) → Tuple[pymatgen.core.structure.Structure, pymatgen.core.structure.Structure, pymatgen.core.structure.Structure][source]¶
+-
+get_start_end_structures(isite: pymatgen.core.sites.PeriodicSite, esite: pymatgen.core.sites.PeriodicSite, base_struct: pymatgen.core.structure.Structure, sc_mat: List[List[Union[int, float]]], vac_mode: bool, debug: bool = False) Tuple[pymatgen.core.structure.Structure, pymatgen.core.structure.Structure, pymatgen.core.structure.Structure][source]¶
Obtain the starting and terminating structures in a supercell for NEB calculations.
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pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc module¶
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pymatgen.analysis.diffusion.utils.tests.test_parse_entries module¶
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ParseEntriesTest(methodName='runTest')[source]¶
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+class ParseEntriesTest(methodName='runTest')[source]¶
Bases: unittest.case.TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
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Sphinx Style","Change Log","Introduction","pymatgen","pymatgen namespace","pymatgen.analysis namespace","pymatgen.analysis.diffusion package","pymatgen.analysis.diffusion.aimd package","pymatgen.analysis.diffusion.aimd.clustering module","pymatgen.analysis.diffusion.aimd.pathway module","pymatgen.analysis.diffusion.aimd.rdf module","pymatgen.analysis.diffusion.aimd.tests.test_clustering module","pymatgen.analysis.diffusion.aimd.tests.test_pathway module","pymatgen.analysis.diffusion.aimd.tests.test_rdf module","pymatgen.analysis.diffusion.aimd.tests.test_van_hove module","pymatgen.analysis.diffusion.aimd.van_hove module","pymatgen.analysis.diffusion.analyzer module","pymatgen.analysis.diffusion.neb package","pymatgen.analysis.diffusion.neb.full_path_mapper module","pymatgen.analysis.diffusion.neb.io module","pymatgen.analysis.diffusion.neb.pathfinder module","pymatgen.analysis.diffusion.neb.periodic_dijkstra module","pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper module","pymatgen.analysis.diffusion.neb.tests.test_io module","pymatgen.analysis.diffusion.neb.tests.test_pathfinder module","pymatgen.analysis.diffusion.tests.test_analyzer module","pymatgen.analysis.diffusion.utils package","pymatgen.analysis.diffusion.utils.edge_data_from_sc module","pymatgen.analysis.diffusion.utils.maggma module","pymatgen.analysis.diffusion.utils.parse_entries module","pymatgen.analysis.diffusion.utils.supercells module","pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc module","pymatgen.analysis.diffusion.utils.tests.test_maggma module","pymatgen.analysis.diffusion.utils.tests.test_parse_entries module","pymatgen_diffusion package","pymatgen_diffusion.aimd package","pymatgen_diffusion.neb package"],titleterms:{"0":1,"1":1,"2":1,"28":1,"29":1,"3":1,"4":1,"5":1,"6":1,acknowledg:2,aimd:[7,8,9,10,11,12,13,14,15,35],analysi:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33],analyz:16,api:2,chang:[1,2],cite:2,cluster:[8,35],content:[6,7,17,26,34,35,36],contribut:2,copyright:2,diffus:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33],document:2,edge_data_from_sc:27,exhaust:2,featur:2,full_path_mapp:[18,36],indic:2,introduct:2,io:[19,36],krtheme:0,licens:2,log:[1,2],maggma:28,modul:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36],namespac:[4,5],neb:[17,18,19,20,21,22,23,24,36],non:2,our:2,packag:[6,7,17,26,34,35,36],parse_entri:29,pathfind:[20,36],pathwai:[9,35],periodic_dijkstra:[21,36],polici:2,pymatgen:[3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33],pymatgen_diffus:[34,35,36],rdf:[10,35],sphinx:0,style:0,submodul:[6,7,17,26,35,36],subpackag:[5,6,7,17,26,34,35,36],supercel:30,tabl:2,test:[11,12,13,14,22,23,24,25,31,32,33],test_analyz:25,test_clust:11,test_edge_data_from_sc:31,test_full_path_mapp:22,test_io:23,test_maggma:32,test_parse_entri:33,test_pathfind:24,test_pathwai:12,test_rdf:13,test_van_hov:14,util:[26,27,28,29,30,31,32,33],v0:1,v2018:1,v2019:1,v2021:1,van_hov:[15,35]}})
\ No newline at end of file
diff --git a/docs_rst/pymatgen.analysis.rst b/docs_rst/pymatgen.analysis.rst
index 25007431..4e1b7380 100644
--- a/docs_rst/pymatgen.analysis.rst
+++ b/docs_rst/pymatgen.analysis.rst
@@ -1,6 +1,8 @@
pymatgen.analysis namespace
===========================
+.. py:module:: pymatgen.analysis
+
Subpackages
-----------
diff --git a/docs_rst/pymatgen.rst b/docs_rst/pymatgen.rst
index 36816d3c..e823f4f2 100644
--- a/docs_rst/pymatgen.rst
+++ b/docs_rst/pymatgen.rst
@@ -1,2 +1,4 @@
pymatgen namespace
==================
+
+.. py:module:: pymatgen
diff --git a/pymatgen/analysis/diffusion/__init__.py b/pymatgen/analysis/diffusion/__init__.py
index e627a779..04c0d65c 100644
--- a/pymatgen/analysis/diffusion/__init__.py
+++ b/pymatgen/analysis/diffusion/__init__.py
@@ -4,4 +4,4 @@
__author__ = "Materials Virtual Lab"
__email__ = "ongsp@eng.ucsd.edu"
-__version__ = "2021.4.29"
+__version__ = "2022.1.15"
\ No newline at end of file
diff --git a/setup.py b/setup.py
index df32cb13..3c0f87b7 100644
--- a/setup.py
+++ b/setup.py
@@ -14,7 +14,7 @@
setup(
name="pymatgen-analysis-diffusion",
packages=find_namespace_packages(include=["pymatgen.analysis.*"]),
- version="2021.4.29",
+ version="2022.1.15",
install_requires=["pymatgen>=2022.0.3", "joblib"],
extras_require={},
package_data={},
