Python string_utils.latexify函数代码示例

 def print_name(self, entry):
     """
     Print entry name if single, else print multientry
     """
     str_name = ""
     if isinstance(entry, MultiEntry):
         if len(entry.entrylist) > 2:
             return str(self._pd.qhull_entries.index(entry))
         for e in entry.entrylist:
             str_name += latexify_ion(latexify(e.name)) + " + "
         str_name = str_name[:-3]
         return str_name
     else:
         return latexify_ion(latexify(entry.name))

    def _get_3d_plot(self, label_stable=True):
        """
        Shows the plot using pylab.  Usually I won"t do imports in methods,
        but since plotting is a fairly expensive library to load and not all
        machines have matplotlib installed, I have done it this way.
        """
        import matplotlib.pyplot as plt
        import mpl_toolkits.mplot3d.axes3d as p3
        from matplotlib.font_manager import FontProperties

        fig = plt.figure()
        ax = p3.Axes3D(fig)
        font = FontProperties()
        font.set_weight("bold")
        font.set_size(20)
        (lines, labels, unstable) = self.pd_plot_data
        count = 1
        newlabels = list()
        for x, y, z in lines:
            ax.plot(x, y, z, "bo-", linewidth=3, markeredgecolor="b", markerfacecolor="r", markersize=10)
        for coords in sorted(labels.keys()):
            entry = labels[coords]
            label = entry.name
            if label_stable:
                if len(entry.composition.elements) == 1:
                    ax.text(coords[0], coords[1], coords[2], label)
                else:
                    ax.text(coords[0], coords[1], coords[2], str(count))
                    newlabels.append("{} : {}".format(count, latexify(label)))
                    count += 1
        plt.figtext(0.01, 0.01, "\n".join(newlabels))
        ax.axis("off")
        return plt

 def plot_planes(self):
     """
     Plot the free energy planes as a function of pH and V
     """
     if self.show_unstable:
         entries = self._pd._all_entries
     else:
         entries = self._pd.stable_entries
     num_plots = len(entries)
     import matplotlib.pyplot as plt
     colormap = plt.cm.gist_ncar
     fig = plt.figure().gca(projection='3d')
     color_array = [colormap(i) for i in np.linspace(0, 0.9, num_plots)]
     labels = []
     color_index = -1
     for entry in entries:
         normal = np.array([-PREFAC * entry.npH, -entry.nPhi, +1])
         d = entry.g0
         color_index += 1
         pH, V = np.meshgrid(np.linspace(-10, 28, 100),
                             np.linspace(-3, 3, 100))
         g = (-normal[0] * pH - normal[1] * V + d) / normal[2]
         lbl = latexify_ion(
             latexify(entry._entry.composition.reduced_formula))
         labels.append(lbl)
         fig.plot_surface(pH, V, g, color=color_array[color_index],
                          label=lbl)
     plt.legend(labels)
     plt.xlabel("pH")
     plt.ylabel("E (V)")
     plt.show()

    def _get_plot(self, label_stable=True, label_unstable=False):
        """
        Plot convex hull of Pourbaix Diagram entries
        """
        import matplotlib.pyplot as plt
        import mpl_toolkits.mplot3d.axes3d as p3
        from matplotlib.font_manager import FontProperties
        fig = plt.figure()
        ax = p3.Axes3D(fig)
        font = FontProperties()
        font.set_weight("bold")
        font.set_size(14)
        (lines, labels, unstable) = self.pourbaix_hull_plot_data
        count = 1
        newlabels = list()
        for x, y, z in lines:
            ax.plot(x, y, z, "bo-", linewidth=3, markeredgecolor="b",
                    markerfacecolor="r", markersize=10)
        for coords in sorted(labels.keys()):
            entry = labels[coords]
            label = self.print_name(entry)
            if label_stable:
                ax.text(coords[0], coords[1], coords[2], str(count))
                newlabels.append("{} : {}".format(
                    count, latexify_ion(latexify(label))))
                count += 1

        if self.show_unstable:
            for entry in unstable.keys():
                label = self.print_name(entry)
                coords = unstable[entry]
                ax.plot([coords[0], coords[0]], [coords[1], coords[1]],
                        [coords[2], coords[2]], "bo", markerfacecolor="g",
                        markersize=10)
                ax.text(coords[0], coords[1], coords[2], str(count))
                newlabels.append("{} : {}".format(
                    count, latexify_ion(latexify(label))))
                count += 1

        plt.figtext(0.01, 0.01, "\n".join(newlabels))
        plt.xlabel("pH")
        plt.ylabel("V")
#        plt.tight_layout()
        return plt

 def test_latexify(self):
     self.assertEqual(latexify("Li3Fe2(PO4)3"),
                      "Li$_{3}$Fe$_{2}$(PO$_{4}$)$_{3}$")

    def get_chempot_range_map_plot(self, elements):
        """
        Returns a plot of the chemical potential range map. Currently works
        only for 3-component PDs.

        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
                [Element("Li"), Element("O")]
        Returns:
            A matplotlib plot object.
        """

        plt = get_publication_quality_plot(12, 8)
        analyzer = PDAnalyzer(self._pd)
        chempot_ranges = analyzer.get_chempot_range_map(elements)
        missing_lines = {}
        excluded_region = []
        for entry, lines in chempot_ranges.items():
            comp = entry.composition
            center_x = 0
            center_y = 0
            coords = []
            contain_zero = any([comp.get_atomic_fraction(el) == 0 for el in elements])
            is_boundary = (not contain_zero) and sum([comp.get_atomic_fraction(el) for el in elements]) == 1
            for line in lines:
                (x, y) = line.coords.transpose()
                plt.plot(x, y, "k-")

                for coord in line.coords:
                    if not in_coord_list(coords, coord):
                        coords.append(coord.tolist())
                        center_x += coord[0]
                        center_y += coord[1]
                if is_boundary:
                    excluded_region.extend(line.coords)

            if coords and contain_zero:
                missing_lines[entry] = coords
            else:
                xy = (center_x / len(coords), center_y / len(coords))
                plt.annotate(latexify(entry.name), xy, fontsize=22)

        ax = plt.gca()
        xlim = ax.get_xlim()
        ylim = ax.get_ylim()

        # Shade the forbidden chemical potential regions.
        excluded_region.append([xlim[1], ylim[1]])
        excluded_region = sorted(excluded_region, key=lambda c: c[0])
        (x, y) = np.transpose(excluded_region)
        plt.fill(x, y, "0.80")

        # The hull does not generate the missing horizontal and vertical lines.
        # The following code fixes this.
        el0 = elements[0]
        el1 = elements[1]
        for entry, coords in missing_lines.items():
            center_x = sum([c[0] for c in coords])
            center_y = sum([c[1] for c in coords])
            comp = entry.composition
            is_x = comp.get_atomic_fraction(el0) < 0.01
            is_y = comp.get_atomic_fraction(el1) < 0.01
            n = len(coords)
            if not (is_x and is_y):
                if is_x:
                    coords = sorted(coords, key=lambda c: c[1])
                    for i in [0, -1]:
                        x = [min(xlim), coords[i][0]]
                        y = [coords[i][1], coords[i][1]]
                        plt.plot(x, y, "k")
                        center_x += min(xlim)
                        center_y += coords[i][1]
                elif is_y:
                    coords = sorted(coords, key=lambda c: c[0])
                    for i in [0, -1]:
                        x = [coords[i][0], coords[i][0]]
                        y = [coords[i][1], min(ylim)]
                        plt.plot(x, y, "k")
                        center_x += coords[i][0]
                        center_y += min(ylim)
                xy = (center_x / (n + 2), center_y / (n + 2))
            else:
                center_x = sum(coord[0] for coord in coords) + xlim[0]
                center_y = sum(coord[1] for coord in coords) + ylim[0]
                xy = (center_x / (n + 1), center_y / (n + 1))

            plt.annotate(
                latexify(entry.name), xy, horizontalalignment="center", verticalalignment="center", fontsize=22
            )

        plt.xlabel("$\mu_{{{0}}} - \mu_{{{0}}}^0$ (eV)".format(el0.symbol))
        plt.ylabel("$\mu_{{{0}}} - \mu_{{{0}}}^0$ (eV)".format(el1.symbol))
        plt.tight_layout()
        return plt

    def _get_2d_plot(self, label_stable=True, label_unstable=True):
        """
        Shows the plot using pylab.  Usually I won"t do imports in methods,
        but since plotting is a fairly expensive library to load and not all
        machines have matplotlib installed, I have done it this way.
        """

        plt = get_publication_quality_plot(8, 6)
        from matplotlib.font_manager import FontProperties

        (lines, labels, unstable) = self.pd_plot_data
        for x, y in lines:
            plt.plot(x, y, "ko-", linewidth=3, markeredgecolor="k", markerfacecolor="b", markersize=15)
        font = FontProperties()
        font.set_weight("bold")
        font.set_size(24)

        # Sets a nice layout depending on the type of PD. Also defines a
        # "center" for the PD, which then allows the annotations to be spread
        # out in a nice manner.
        if len(self._pd.elements) == 3:
            plt.axis("equal")
            plt.xlim((-0.1, 1.2))
            plt.ylim((-0.1, 1.0))
            plt.axis("off")
            center = (0.5, math.sqrt(3) / 6)
        else:
            all_coords = labels.keys()
            miny = min([c[1] for c in all_coords])
            ybuffer = max(abs(miny) * 0.1, 0.1)
            plt.xlim((-0.1, 1.1))
            plt.ylim((miny - ybuffer, ybuffer))
            center = (0.5, miny / 2)
            plt.xlabel("Fraction", fontsize=28, fontweight="bold")
            plt.ylabel("Formation energy (eV/fu)", fontsize=28, fontweight="bold")

        for coords in sorted(labels.keys(), key=lambda x: -x[1]):
            entry = labels[coords]
            label = entry.name

            # The follow defines an offset for the annotation text emanating
            # from the center of the PD. Results in fairly nice layouts for the
            # most part.
            vec = np.array(coords) - center
            vec = vec / np.linalg.norm(vec) * 10 if np.linalg.norm(vec) != 0 else vec
            valign = "bottom" if vec[1] > 0 else "top"
            if vec[0] < -0.01:
                halign = "right"
            elif vec[0] > 0.01:
                halign = "left"
            else:
                halign = "center"
            if label_stable:
                plt.annotate(
                    latexify(label),
                    coords,
                    xytext=vec,
                    textcoords="offset points",
                    horizontalalignment=halign,
                    verticalalignment=valign,
                    fontproperties=font,
                )

        if self.show_unstable:
            font = FontProperties()
            font.set_size(16)
            for entry, coords in unstable.items():
                vec = np.array(coords) - center
                vec = vec / np.linalg.norm(vec) * 10
                label = entry.name
                plt.plot(
                    coords[0], coords[1], "ks", linewidth=3, markeredgecolor="k", markerfacecolor="r", markersize=8
                )
                if label_unstable:
                    plt.annotate(
                        latexify(label),
                        coords,
                        xytext=vec,
                        textcoords="offset points",
                        horizontalalignment=halign,
                        color="b",
                        verticalalignment=valign,
                        fontproperties=font,
                    )
        F = plt.gcf()
        F.set_size_inches((8, 6))
        plt.subplots_adjust(left=0.09, right=0.98, top=0.98, bottom=0.07)
        return plt

#.........这里部分代码省略.........
        font.set_weight("bold")
        font.set_size(24)

        # Sets a nice layout depending on the type of PD. Also defines a
        # "center" for the PD, which then allows the annotations to be spread
        # out in a nice manner.
        if len(self._pd.elements) == 3:
            plt.axis("equal")
            plt.xlim((-0.1, 1.2))
            plt.ylim((-0.1, 1.0))
            plt.axis("off")
            center = (0.5, math.sqrt(3) / 6)
        else:
            all_coords = labels.keys()
            miny = min([c[1] for c in all_coords])
            ybuffer = max(abs(miny) * 0.1, 0.1)
            plt.xlim((-0.1, 1.1))
            plt.ylim((miny - ybuffer, ybuffer))
            center = (0.5, miny / 2)
            plt.xlabel("Fraction", fontsize=28, fontweight='bold')
            plt.ylabel("Formation energy (eV/fu)", fontsize=28,
                       fontweight='bold')

        for coords in sorted(labels.keys(), key=lambda x: -x[1]):
            entry = labels[coords]
            label = entry.name

            # The follow defines an offset for the annotation text emanating
            # from the center of the PD. Results in fairly nice layouts for the
            # most part.
            vec = (np.array(coords) - center)
            vec = vec / np.linalg.norm(vec) * 10 if np.linalg.norm(vec) != 0 \
                else vec
            valign = "bottom" if vec[1] > 0 else "top"
            if vec[0] < -0.01:
                halign = "right"
            elif vec[0] > 0.01:
                halign = "left"
            else:
                halign = "center"
            if label_stable:
                if process_attributes and entry.attribute == 'new':
                    plt.annotate(latexify(label), coords, xytext=vec,
                                 textcoords="offset points",
                                 horizontalalignment=halign,
                                 verticalalignment=valign,
                                 fontproperties=font,
                                 color='g')
                else:
                    plt.annotate(latexify(label), coords, xytext=vec,
                                 textcoords="offset points",
                                 horizontalalignment=halign,
                                 verticalalignment=valign,
                                 fontproperties=font)

        if self.show_unstable:
            font = FontProperties()
            font.set_size(16)
            pda = PDAnalyzer(self._pd)
            energies_unstable = [pda.get_e_above_hull(entry)
                                 for entry, coord in unstable.items()]
            if energy_colormap is not None:
                energies.extend(energies_unstable)
                vals_unstable = _map.to_rgba(energies_unstable)
            ii = 0
            for entry, coords in unstable.items():
                vec = (np.array(coords) - center)
                vec = vec / np.linalg.norm(vec) * 10 \
                    if np.linalg.norm(vec) != 0 else vec
                label = entry.name
                if energy_colormap is None:
                    plt.plot(coords[0], coords[1], "ks", linewidth=3,
                             markeredgecolor="k", markerfacecolor="r",
                             markersize=8)
                else:
                    plt.plot(coords[0], coords[1], "s", linewidth=3,
                             markeredgecolor="k",
                             markerfacecolor=vals_unstable[ii],
                             markersize=8)
                if label_unstable:
                    plt.annotate(latexify(label), coords, xytext=vec,
                                 textcoords="offset points",
                                 horizontalalignment=halign, color="b",
                                 verticalalignment=valign,
                                 fontproperties=font)
                ii += 1
        if energy_colormap is not None and show_colorbar:
            _map.set_array(energies)
            cbar = plt.colorbar(_map)
            cbar.set_label(
                'Energy [meV/at] above hull (in red)\nInverse energy ['
                'meV/at] above hull (in green)',
                rotation=-90, ha='left', va='center')
            ticks = cbar.ax.get_yticklabels()
            cbar.ax.set_yticklabels(['${v}$'.format(
                v=float(t.get_text().strip('$'))*1000.0) for t in ticks])
        f = plt.gcf()
        f.set_size_inches((8, 6))
        plt.subplots_adjust(left=0.09, right=0.98, top=0.98, bottom=0.07)
        return plt

#.........这里部分代码省略.........
            V0_line = np.transpose([[xlim[0], 0], [xlim[1], 0]])
            return h_line, o_line, neutral_line, V0_line

        from matplotlib.patches import Polygon
        from pymatgen import Composition, Element
        from pymatgen.core.ion import Ion

        default_domain_font_size = 12
        default_solid_phase_color = '#b8f9e7'    # this slighly darker than the MP scheme, to
        default_cluster_phase_color = '#d0fbef'  # avoid making the cluster phase too light

        plt = get_publication_quality_plot(8, dpi=300)

        (stable, unstable) = self.pourbaix_plot_data(limits)
        num_of_overlaps = {key: 0 for key in stable.keys()}
        entry_dict_of_multientries = collections.defaultdict(list)
        for entry in stable:
            if isinstance(entry, MultiEntry):
                for e in entry.entrylist:
                    entry_dict_of_multientries[e.name].append(entry)
                    num_of_overlaps[entry] += 1
            else:
                entry_dict_of_multientries[entry.name].append(entry)

        xlim, ylim = limits[:2] if limits else self._analyzer.chempot_limits[:2]
        h_line, o_line, neutral_line, V0_line = special_lines(xlim, ylim)
        ax = plt.gca()
        ax.set_xlim(xlim)
        ax.set_ylim(ylim)
        ax.xaxis.set_major_formatter(FormatStrFormatter('%.1f'))
        ax.yaxis.set_major_formatter(FormatStrFormatter('%.1f'))
        ax.tick_params(direction='out')
        ax.xaxis.set_ticks_position('bottom')
        ax.yaxis.set_ticks_position('left')

        sorted_entry = list(entry_dict_of_multientries.keys())
        sorted_entry.sort(key=len_elts)

        if domain_fontsize is None:
            domain_fontsize = {en: default_domain_font_size for en in sorted_entry}
        if domain_color is None:
            domain_color = {en: default_solid_phase_color if '(s)' in en else
                            (default_cluster_phase_color if en in cluster_domains else 'w')
                            for i, en in enumerate(sorted_entry)}
        if bold_domains is None:
            bold_domains = [en for en in sorted_entry if '(s)' not in en]

        for entry in sorted_entry:
            x_coord, y_coord, npts = 0.0, 0.0, 0
            for e in entry_dict_of_multientries[entry]:
                xy = self.domain_vertices(e)
                if add_h2o_stablity_line:
                    c = self.get_distribution_corrected_center(stable[e], h_line, o_line, 0.3)
                else:
                    c = self.get_distribution_corrected_center(stable[e])
                x_coord += c[0]
                y_coord += c[1]
                npts += 1
                patch = Polygon(xy, facecolor=domain_color[entry],
                                closed=True, lw=domain_edge_lw, fill=True, antialiased=True)
                ax.add_patch(patch)
            xy_center = (x_coord / npts, y_coord / npts)
            if label_domains:
                if platform.system() == 'Darwin':
                    # Have to hack to the hard coded font path to get current font On Mac OS X
                    if entry in bold_domains:
                        font = FontProperties(fname='/Library/Fonts/Times New Roman Bold.ttf',
                                              size=domain_fontsize[entry])
                    else:
                        font = FontProperties(fname='/Library/Fonts/Times New Roman.ttf',
                                              size=domain_fontsize[entry])
                else:
                    if entry in bold_domains:
                        font = FontProperties(family='Times New Roman',
                                              weight='bold',
                                              size=domain_fontsize[entry])
                    else:
                        font = FontProperties(family='Times New Roman',
                                              weight='regular',
                                              size=domain_fontsize[entry])
                plt.text(*xy_center, s=latexify_ion(latexify(entry)), fontproperties=font,
                         horizontalalignment="center", verticalalignment="center",
                         multialignment="center", color=label_color)

        if add_h2o_stablity_line:
            dashes = (3, 1.5)
            line, = plt.plot(h_line[0], h_line[1], "k--", linewidth=h2o_lw, antialiased=True)
            line.set_dashes(dashes)
            line, = plt.plot(o_line[0], o_line[1], "k--", linewidth=h2o_lw, antialiased=True)
            line.set_dashes(dashes)
        if add_center_line:
            plt.plot(neutral_line[0], neutral_line[1], "k-.", linewidth=h2o_lw, antialiased=False)
            plt.plot(V0_line[0], V0_line[1], "k-.", linewidth=h2o_lw, antialiased=False)

        plt.xlabel("pH", fontname="Times New Roman", fontsize=18)
        plt.ylabel("E (V)", fontname="Times New Roman", fontsize=18)
        plt.xticks(fontname="Times New Roman", fontsize=16)
        plt.yticks(fontname="Times New Roman", fontsize=16)
        plt.title(title, fontsize=20, fontweight='bold', fontname="Times New Roman")
        return plt

#.........这里部分代码省略.........
                        num_of_overlaps[entry] += 1
            else:
                entry_dict_of_multientries[entry.name].append(entry)
        if limits:
            xlim = limits[0]
            ylim = limits[1]
        else:
            xlim = self._analyzer.chempot_limits[0]
            ylim = self._analyzer.chempot_limits[1]

        h_line = np.transpose([[xlim[0], -xlim[0] * PREFAC],
                               [xlim[1], -xlim[1] * PREFAC]])
        o_line = np.transpose([[xlim[0], -xlim[0] * PREFAC + 1.23],
                               [xlim[1], -xlim[1] * PREFAC + 1.23]])
        neutral_line = np.transpose([[7, ylim[0]], [7, ylim[1]]])
        V0_line = np.transpose([[xlim[0], 0], [xlim[1], 0]])

        ax = plt.gca()
        ax.set_xlim(xlim)
        ax.set_ylim(ylim)
        from pymatgen import Composition, Element
        from pymatgen.core.ion import Ion

        def len_elts(entry):
            if "(s)" in entry:
                comp = Composition(entry[:-3])
            else:
                comp = Ion.from_formula(entry)
            return len([el for el in comp.elements if el not in
                        [Element("H"), Element("O")]])

        sorted_entry = entry_dict_of_multientries.keys()
        sorted_entry.sort(key=len_elts)
        i = -1
        label_chr = map(chr, list(range(65, 91)))
        for entry in sorted_entry:
            color_indx = 0
            x_coord = 0.0
            y_coord = 0.0
            npts = 0
            i += 1
            for e in entry_dict_of_multientries[entry]:
                hc = 0
                fc = 0
                bc = 0
                xy = self.domain_vertices(e)
                c = self.get_center(stable[e])
                x_coord += c[0]
                y_coord += c[1]
                npts += 1
                color_indx = i
                if "(s)" in entry:
                    comp = Composition(entry[:-3])
                else:
                    comp = Ion.from_formula(entry)
                if len([el for el in comp.elements if el not in
                         [Element("H"), Element("O")]]) == 1:
                    if color_indx >= len(optim_colors):
                        color_indx = color_indx -\
                         int(color_indx / len(optim_colors)) * len(optim_colors)
                    patch = Polygon(xy, facecolor=optim_colors[color_indx],
                                     closed=True, lw=3.0, fill=True)
                    bc = optim_colors[color_indx]
                else:
                    if color_indx >= len(hatch):
                        color_indx = color_indx - int(color_indx / len(hatch)) * len(hatch)
                    patch = Polygon(xy, hatch=hatch[color_indx], closed=True, lw=3.0, fill=False)
                    hc = hatch[color_indx]
                ax.add_patch(patch)

            xy_center = (x_coord / npts, y_coord / npts)
            if label_domains:
                if color_indx >= len(optim_colors):
                    color_indx = color_indx -\
                        int(color_indx / len(optim_colors)) * len(optim_colors)
                fc = optim_font_color[color_indx]
                if bc and not hc:
                    bbox = dict(boxstyle="round", fc=fc)
                if hc and not bc:
                    bc = 'k'
                    fc = 'w'
                    bbox = dict(boxstyle="round", hatch=hc, fill=False)
                if bc and hc:
                    bbox = dict(boxstyle="round", hatch=hc, fc=fc)
#                 bbox.set_path_effects([PathEffects.withSimplePatchShadow()])
                plt.annotate(latexify_ion(latexify(entry)), xy_center,
                            color=bc, fontsize=30, bbox=bbox)
#                 plt.annotate(label_chr[i], xy_center,
#                               color=bc, fontsize=30, bbox=bbox)

        lw = 3
        plt.plot(h_line[0], h_line[1], "r--", linewidth=lw)
        plt.plot(o_line[0], o_line[1], "r--", linewidth=lw)
        plt.plot(neutral_line[0], neutral_line[1], "k-.", linewidth=lw)
        plt.plot(V0_line[0], V0_line[1], "k-.", linewidth=lw)

        plt.xlabel("pH")
        plt.ylabel("E (V)")
        plt.title(title, fontsize=20, fontweight='bold')
        return plt

 def test_latexify(self):
     self.assertEqual(latexify("Li3Fe2(PO4)3"), "Li$_{3}$Fe$_{2}$(PO$_{4}$)$_{3}$")
     self.assertEqual(latexify("Li0.2Na0.8Cl"), "Li$_{0.2}$Na$_{0.8}$Cl")