From bc5edc5960506f28530739f268fdf31752de2bea Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Wed, 15 Nov 2023 14:20:52 -0800 Subject: [PATCH] fix typos --- pymatgen/analysis/eos.py | 11 +++++------ pymatgen/analysis/phase_diagram.py | 4 ++-- pymatgen/analysis/quasiharmonic.py | 15 +++++++-------- pymatgen/analysis/surface_analysis.py | 18 +++++++++--------- pymatgen/command_line/gulp_caller.py | 2 +- pymatgen/core/surface.py | 22 +++++++++++----------- pymatgen/core/tensors.py | 8 ++++---- pymatgen/io/abinit/abiobjects.py | 2 +- 8 files changed, 40 insertions(+), 42 deletions(-) diff --git a/pymatgen/analysis/eos.py b/pymatgen/analysis/eos.py index 0323ade23f7..8621bd17e1e 100644 --- a/pymatgen/analysis/eos.py +++ b/pymatgen/analysis/eos.py @@ -42,7 +42,7 @@ def __init__(self, volumes, energies): self.volumes = np.array(volumes) self.energies = np.array(energies) # minimum energy(e0), buk modulus(b0), - # derivative of bulk modulus wrt pressure(b1), minimum volume(v0) + # derivative of bulk modulus w.r.t. pressure(b1), minimum volume(v0) self._params = None # the eos function parameters. It is the same as _params except for # equation of states that uses polynomial fits(delta_factor and @@ -147,7 +147,7 @@ def b0_GPa(self): @property def b1(self): - """Returns the derivative of bulk modulus wrt pressure(dimensionless).""" + """Returns the derivative of bulk modulus w.r.t. pressure(dimensionless).""" return self._params[2] @property @@ -191,7 +191,7 @@ def plot(self, width=8, height=None, ax: plt.Axes = None, dpi=None, **kwargs): f"Minimum energy = {self.e0:1.2f} eV", f"Minimum or reference volume = {self.v0:1.2f} Ang^3", f"Bulk modulus = {self.b0:1.2f} eV/Ang^3 = {self.b0_GPa:1.2f} GPa", - f"Derivative of bulk modulus wrt pressure = {self.b1:1.2f}", + f"Derivative of bulk modulus w.r.t. pressure = {self.b1:1.2f}", ] text = "\n".join(lines) text = kwargs.get("text", text) @@ -239,7 +239,7 @@ def plot_ax(self, ax: plt.Axes = None, fontsize=12, **kwargs): f"Minimum energy = {self.e0:1.2f} eV", f"Minimum or reference volume = {self.v0:1.2f} Ang^3", f"Bulk modulus = {self.b0:1.2f} eV/Ang^3 = {self.b0_GPa:1.2f} GPa", - f"Derivative of bulk modulus wrt pressure = {self.b1:1.2f}", + f"Derivative of bulk modulus w.r.t. pressure = {self.b1:1.2f}", ] text = "\n".join(lines) text = kwargs.get("text", text) @@ -357,8 +357,7 @@ def _set_params(self): and set to the _params attribute. """ fit_poly = np.poly1d(self.eos_params) - # the volume at min energy, used as the initial guess for the - # optimization wrt volume. + # the volume at min energy, used as the initial guess for the optimization w.r.t. volume. v_e_min = self.volumes[np.argmin(self.energies)] # evaluate e0, v0, b0 and b1 min_wrt_v = minimize(fit_poly, v_e_min) diff --git a/pymatgen/analysis/phase_diagram.py b/pymatgen/analysis/phase_diagram.py index 7c00efaf3fc..e0064004179 100644 --- a/pymatgen/analysis/phase_diagram.py +++ b/pymatgen/analysis/phase_diagram.py @@ -2374,7 +2374,7 @@ class (pymatgen.analysis.chempot_diagram). Args: elements: Sequence of elements to be considered as independent variables. E.g., if you want to show the stability ranges of - all Li-Co-O phases wrt to uLi and uO, you will supply + all Li-Co-O phases w.r.t. to uLi and uO, you will supply [Element("Li"), Element("O")] referenced: if True, gives the results with a reference being the energy of the elemental phase. If False, gives absolute values. @@ -2392,7 +2392,7 @@ class (pymatgen.analysis.chempot_diagram). Args: elements: Sequence of elements to be considered as independent variables. E.g., if you want to show the stability ranges of - all Li-Co-O phases wrt to uLi and uO, you will supply + all Li-Co-O phases w.r.t. to uLi and uO, you will supply [Element("Li"), Element("O")] referenced: if True, gives the results with a reference being the energy of the elemental phase. If False, gives absolute values. diff --git a/pymatgen/analysis/quasiharmonic.py b/pymatgen/analysis/quasiharmonic.py index c6300d51135..e74a13c7082 100644 --- a/pymatgen/analysis/quasiharmonic.py +++ b/pymatgen/analysis/quasiharmonic.py @@ -121,7 +121,7 @@ def __init__( def optimize_gibbs_free_energy(self): """ Evaluate the Gibbs free energy as a function of V, T and P i.e - G(V, T, P), minimize G(V, T, P) wrt V for each T and store the + G(V, T, P), minimize G(V, T, P) w.r.t. V for each T and store the optimum values. Note: The data points for which the equation of state fitting fails @@ -146,8 +146,7 @@ def optimize_gibbs_free_energy(self): def optimizer(self, temperature): """ - Evaluate G(V, T, P) at the given temperature(and pressure) and - minimize it wrt V. + Evaluate G(V, T, P) at the given temperature(and pressure) and minimize it w.r.t. V. 1. Compute the vibrational Helmholtz free energy, A_vib. 2. Compute the Gibbs free energy as a function of volume, temperature @@ -171,7 +170,7 @@ def optimizer(self, temperature): # fit equation of state, G(V, T, P) eos_fit = self.eos.fit(self.volumes, G_V) - # minimize the fit eos wrt volume + # minimize the fit EoS w.r.t. volume # Note: the ref energy and the ref volume(E0 and V0) not necessarily # the same as minimum energy and min volume. volume_guess = eos_fit.volumes[np.argmin(eos_fit.energies)] @@ -288,13 +287,13 @@ def gruneisen_parameter(self, temperature, volume): """ if isinstance(self.eos, PolynomialEOS): p = np.poly1d(self.eos.eos_params) - # first derivative of energy at 0K wrt volume evaluated at the + # first derivative of energy at 0K w.r.t. volume evaluated at the # given volume, in eV/Ang^3 dEdV = np.polyder(p, 1)(volume) - # second derivative of energy at 0K wrt volume evaluated at the + # second derivative of energy at 0K w.r.t. volume evaluated at the # given volume, in eV/Ang^6 d2EdV2 = np.polyder(p, 2)(volume) - # third derivative of energy at 0K wrt volume evaluated at the + # third derivative of energy at 0K w.r.t. volume evaluated at the # given volume, in eV/Ang^9 d3EdV3 = np.polyder(p, 3)(volume) else: @@ -314,7 +313,7 @@ def gruneisen_parameter(self, temperature, volume): ) # Slater-gamma formulation - # first derivative of bulk modulus wrt volume, eV/Ang^6 + # first derivative of bulk modulus w.r.t. volume, eV/Ang^6 dBdV = d2EdV2 + d3EdV3 * volume return -(1.0 / 6.0 + 0.5 * volume * dBdV / FloatWithUnit(self.ev_eos_fit.b0_GPa, "GPa").to("eV ang^-3")) diff --git a/pymatgen/analysis/surface_analysis.py b/pymatgen/analysis/surface_analysis.py index 2a7ed92ed76..a6e20b84ff3 100644 --- a/pymatgen/analysis/surface_analysis.py +++ b/pymatgen/analysis/surface_analysis.py @@ -858,7 +858,7 @@ def chempot_vs_gamma_plot_one( chempot_range = sorted(chempot_range) # use dashed lines for slabs that are not stoichiometric - # wrt bulk. Label with formula if non-stoichiometric + # w.r.t. bulk. Label with formula if non-stoichiometric ucell_comp = self.ucell_entry.composition.reduced_composition if entry.adsorbates: s = entry.cleaned_up_slab @@ -1134,7 +1134,7 @@ def surface_chempot_range_map( delu_dict=None, ax=None, annotate=True, - show_unphyiscal_only=False, + show_unphysical_only=False, fontsize=10, ) -> plt.Axes: """ @@ -1143,14 +1143,14 @@ def surface_chempot_range_map( energy stability. Currently works only for 2-component PDs. At the moment uses a brute force method by enumerating through the range of the first element chempot with a specified increment - and determines the chempot rangeo fht e second element for each + and determines the chempot range of the second element for each SlabEntry. Future implementation will determine the chempot range map first by solving systems of equations up to 3 instead of 2. Args: elements (list): Sequence of elements to be considered as independent variables. E.g., if you want to show the stability ranges of - all Li-Co-O phases wrt to duLi and duO, you will supply + all Li-Co-O phases w.r.t. to duLi and duO, you will supply [Element("Li"), Element("O")] miller_index ([h, k, l]): Miller index of the surface we are interested in ranges ([[range1], [range2]]): List of chempot ranges (max and min values) @@ -1164,7 +1164,7 @@ def surface_chempot_range_map( ax (plt.Axes): Axes object to plot on. If None, will create a new plot. annotate (bool): Whether to annotate each "phase" with the label of the entry. If no label, uses the reduced formula - show_unphyiscal_only (bool): Whether to only show the shaded region where + show_unphysical_only (bool): Whether to only show the shaded region where surface energy is negative. Useful for drawing other chempot range maps. fontsize (int): Font size of the annotation """ @@ -1219,7 +1219,7 @@ def surface_chempot_range_map( neg_dmu_range = [pt1[delu2][0][1], pt1[delu2][0][2]] # Shade the threshold and region at which se<=0 ax.plot([pt1[delu1], pt1[delu1]], neg_dmu_range, "k--") - elif pt1[delu2][1][0] < 0 and pt1[delu2][1][1] < 0 and not show_unphyiscal_only: + elif pt1[delu2][1][0] < 0 and pt1[delu2][1][1] < 0 and not show_unphysical_only: # Any chempot at this point will result # in se<0, shade the entire y range ax.plot([pt1[delu1], pt1[delu1]], range2, "k--") @@ -1227,7 +1227,7 @@ def surface_chempot_range_map( if ii == len(vertex) - 1: break pt2 = vertex[ii + 1] - if not show_unphyiscal_only: + if not show_unphysical_only: ax.plot( [pt1[delu1], pt2[delu1]], [pt1[delu2][0][0], pt2[delu2][0][0]], @@ -1243,7 +1243,7 @@ def surface_chempot_range_map( delu1, delu2 = pt xvals.extend([pt[delu1], pt[delu1]]) yvals.extend(pt[delu2][0]) - if not show_unphyiscal_only: + if not show_unphysical_only: ax.plot([pt[delu1], pt[delu1]], [pt[delu2][0][0], pt[delu2][0][-1]], "k") if annotate: @@ -1595,7 +1595,7 @@ class NanoscaleStability: polymorphs with respect to size. The Wulff shape will be the model for the nanoparticle. Stability will be determined by an energetic competition between the weighted surface energy (surface energy of the Wulff shape) and the bulk energy. A - future release will include a 2D phase diagram (e.g. wrt size vs chempot for adsorbed + future release will include a 2D phase diagram (e.g. w.r.t. size vs chempot for adsorbed or non-stoichiometric surfaces). Based on the following work: Kang, S., Mo, Y., Ong, S. P., & Ceder, G. (2014). Nanoscale diff --git a/pymatgen/command_line/gulp_caller.py b/pymatgen/command_line/gulp_caller.py index d0718b24c5e..17c183de913 100644 --- a/pymatgen/command_line/gulp_caller.py +++ b/pymatgen/command_line/gulp_caller.py @@ -176,7 +176,7 @@ "spatial", "storevectors", "nomolecularinternalke", - "voight", + "voigt", "zsisa", # Optimization method "conjugate", diff --git a/pymatgen/core/surface.py b/pymatgen/core/surface.py index ec63ec1bd6e..06eb59545ad 100644 --- a/pymatgen/core/surface.py +++ b/pymatgen/core/surface.py @@ -1125,23 +1125,23 @@ def repair_broken_bonds(self, slab, bonds): (Slab) A Slab object with a particular shifted oriented unit cell. """ for pair in bonds: - blength = bonds[pair] + bond_len = bonds[pair] # First lets determine which element should be the # reference (center element) to determine broken bonds. # e.g. P for a PO4 bond. Find integer coordination - # numbers of the pair of elements wrt to each other + # numbers of the pair of elements w.r.t. to each other cn_dict = {} for i, el in enumerate(pair): - cnlist = [] + cn_list = [] for site in self.oriented_unit_cell: poly_coord = 0 if site.species_string == el: - for nn in self.oriented_unit_cell.get_neighbors(site, blength): + for nn in self.oriented_unit_cell.get_neighbors(site, bond_len): if nn[0].species_string == pair[i - 1]: poly_coord += 1 - cnlist.append(poly_coord) - cn_dict[el] = cnlist + cn_list.append(poly_coord) + cn_dict[el] = cn_list # We make the element with the higher coordination our reference if max(cn_dict[pair[0]]) > max(cn_dict[pair[1]]): @@ -1153,7 +1153,7 @@ def repair_broken_bonds(self, slab, bonds): # Determine the coordination of our reference if site.species_string == element1: poly_coord = 0 - for neighbor in slab.get_neighbors(site, blength): + for neighbor in slab.get_neighbors(site, bond_len): poly_coord += 1 if neighbor.species_string == element2 else 0 # suppose we find an undercoordinated reference atom @@ -1164,7 +1164,7 @@ def repair_broken_bonds(self, slab, bonds): # find its NNs with the corresponding # species it should be coordinated with - neighbors = slab.get_neighbors(slab[i], blength, include_index=True) + neighbors = slab.get_neighbors(slab[i], bond_len, include_index=True) to_move = [nn[2] for nn in neighbors if nn[0].species_string == element2] to_move.append(i) # and then move those NNs along with the central @@ -1237,7 +1237,7 @@ def nonstoichiometric_symmetrized_slab(self, init_slab): if init_slab.is_symmetric(): return [init_slab] - nonstoich_slabs = [] + non_stoich_slabs = [] # Build an equivalent surface slab for each of the different surfaces for top in [True, False]: asym = True @@ -1261,12 +1261,12 @@ def nonstoichiometric_symmetrized_slab(self, init_slab): # Check if the altered surface is symmetric if slab.is_symmetric(): asym = False - nonstoich_slabs.append(slab) + non_stoich_slabs.append(slab) if len(slab) <= len(self.parent): warnings.warn("Too many sites removed, please use a larger slab size.") - return nonstoich_slabs + return non_stoich_slabs module_dir = os.path.dirname(os.path.abspath(__file__)) diff --git a/pymatgen/core/tensors.py b/pymatgen/core/tensors.py index 1ebd6265204..f54d5ac89c6 100644 --- a/pymatgen/core/tensors.py +++ b/pymatgen/core/tensors.py @@ -271,7 +271,7 @@ def symmetrized(self): @property def voigt_symmetrized(self): """Returns a "voigt"-symmetrized tensor, i. e. a voigt-notation - tensor such that it is invariant wrt permutation of indices. + tensor such that it is invariant w.r.t. permutation of indices. """ if not (self.rank % 2 == 0 and self.rank >= 2): raise ValueError("V-symmetrization requires rank even and >= 2") @@ -567,7 +567,7 @@ def populate( Args: structure (Structure): structure to base population on - prec (float): precision for determining a non-zero value + prec (float): precision for determining a non-zero value. Defaults to 1e-5. maxiter (int): maximum iterations for populating the tensor verbose (bool): whether to populate verbosely precond (bool): whether to precondition by cycling through @@ -747,7 +747,7 @@ def is_fit_to_structure(self, structure: Structure, tol: float = 1e-2): @property def voigt(self): - """TensorCollection where all tensors are in voight form.""" + """TensorCollection where all tensors are in Voigt form.""" return [t.voigt for t in self] @property @@ -804,7 +804,7 @@ def voigt_symmetrized(self): return self.__class__([t.voigt_symmetrized for t in self]) def as_dict(self, voigt=False): - """:param voigt: Whether to use voight form. + """:param voigt: Whether to use Voigt form. Returns: Dict representation of TensorCollection. diff --git a/pymatgen/io/abinit/abiobjects.py b/pymatgen/io/abinit/abiobjects.py index 23b2cc53b28..29c1e763271 100644 --- a/pymatgen/io/abinit/abiobjects.py +++ b/pymatgen/io/abinit/abiobjects.py @@ -65,7 +65,7 @@ def lattice_from_abivars(cls=None, *args, **kwargs): and abs(ang_deg[0] - 90.0) + abs(ang_deg[1] - 90.0) + abs(ang_deg[2] - 90) > tol12 ): # Treat the case of equal angles (except all right angles): - # generates trigonal symmetry wrt third axis + # generates trigonal symmetry w.r.t. third axis cos_ang = cos(pi * ang_deg[0] / 180.0) a2 = 2.0 / 3.0 * (1.0 - cos_ang) aa = sqrt(a2)