chemparseplot 1.9.1__tar.gz → 1.9.3__tar.gz

{chemparseplot-1.9.1 → chemparseplot-1.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chemparseplot
-Version: 1.9.1
+Version: 1.9.3
 Summary: Parsers and plotting tools for computational chemistry
 Project-URL: Documentation, https://chemparseplot.rgoswami.me
 Project-URL: Issues, https://github.com/HaoZeke/chemparseplot/issues

{chemparseplot-1.9.1 → chemparseplot-1.9.3}/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '1.9.1'
-__version_tuple__ = version_tuple = (1, 9, 1)
+__version__ = version = '1.9.3'
+__version_tuple__ = version_tuple = (1, 9, 3)
 
 __commit_id__ = commit_id = None

{chemparseplot-1.9.1 → chemparseplot-1.9.3}/chemparseplot/plot/neb.py

@@ -1577,27 +1577,102 @@ def landscape_projection_basis(global_basis, final_r, final_p):
     return compute_projection_basis(final_r, final_p)
 
 
-def landscape_half_span(x_limits, final_r, final_p, additional_atoms_data, global_basis):
-    """Expand the symmetric landscape half-span to keep extra markers visible."""
+def landscape_half_span(
+    x_limits,
+    final_r,
+    final_p,
+    additional_atoms_data,
+    global_basis,
+    *,
+    path_pad: float = 1.15,
+    min_half: float = 0.02,
+):
+    """Symmetric |d| half-span from the path (and optional overlays), not s/2.
 
-    half_span = (x_limits[1] - x_limits[0]) / 2
-    if not additional_atoms_data:
-        return half_span
+    Using the reaction-progress half-width as the default forced a near-square
+    frame and large empty bands above/below paths that stay near ``d=0``.
+    """
 
     basis = landscape_projection_basis(global_basis, final_r, final_p)
-    for overlay in additional_atoms_data:
-        _, add_d = project_to_sd(np.array([overlay.r]), np.array([overlay.p]), basis)
-        half_span = max(half_span, abs(float(add_d[0])) * 1.15)
-    return half_span
+    _s, _d = project_to_sd(np.asarray(final_r), np.asarray(final_p), basis)
+    half_span = max(abs(float(_d.max())), abs(float(_d.min())), min_half) * path_pad
+    for overlay in additional_atoms_data or []:
+        _, add_d = project_to_sd(
+            np.array([overlay.r]), np.array([overlay.p]), basis
+        )
+        half_span = max(half_span, abs(float(add_d[0])) * path_pad)
+    # Tiny floor only (absolute), never a fraction of s — that reintroduced the
+    # empty top/bottom bands on near-linear paths.
+    del x_limits  # reserved for future asymmetric s handling
+    return max(half_span, min_half)
 
 
-def save_plot(output_file, dpi, *, has_strip):
-    """Save plots without tight-bbox strip overflow."""
+def mark_saddle_point(
+    ax,
+    x,
+    y,
+    *,
+    label: str = "SP",
+    font_size: float = 12.0,
+    vline: bool = False,
+    annotate: bool = True,
+):
+    """Draw a high-contrast saddle marker (gold star) on a profile or landscape."""
 
-    save_kwargs = {"transparent": False, "pad_inches": 0.1, "dpi": dpi}
-    if not has_strip:
-        save_kwargs["bbox_inches"] = "tight"
-    plt.savefig(output_file, **save_kwargs)
+    ax.scatter(
+        float(x),
+        float(y),
+        marker="*",
+        s=max(280, int(font_size**2 * 3.2)),
+        c="#FFD700",
+        edgecolors="black",
+        linewidths=1.8,
+        zorder=100,
+        label=label,
+    )
+    if vline:
+        ax.axvline(
+            float(x),
+            color="black",
+            linestyle="--",
+            linewidth=1.4,
+            alpha=0.75,
+            zorder=50,
+        )
+    if annotate:
+        ax.annotate(
+            label,
+            xy=(float(x), float(y)),
+            xytext=(10, 14),
+            textcoords="offset points",
+            fontsize=int(font_size * 1.05),
+            fontweight="bold",
+            color="black",
+            zorder=101,
+            bbox={
+                "boxstyle": "round,pad=0.2",
+                "facecolor": "white",
+                "edgecolor": "black",
+                "linewidth": 0.8,
+                "alpha": 0.92,
+            },
+        )
+
+
+def save_plot(output_file, dpi, *, has_strip):
+    """Save plots, cropping unused figure canvas (including strip layouts)."""
+
+    # Strips use imshow+Text (not unclipped AnnotationBbox growth), so tight
+    # bbox is safe and removes the large whitespace left by equal-aspect
+    # landscape axes inside a tall/wide figure.
+    del has_strip  # kept for API compatibility with callers
+    plt.savefig(
+        output_file,
+        transparent=False,
+        dpi=dpi,
+        bbox_inches="tight",
+        pad_inches=0.05,
+    )
 
 
 def profile_structure_indices(atoms_list, y_values, plot_structures, plot_mode):
@@ -1617,15 +1692,22 @@ def profile_strip_payload(atoms_list, x_values, y_values, plot_structures, plot_
     """Build an ordered strip payload for profile plots."""
 
     payload = []
+    saddle_idx = (
+        int(np.argmax(y_values[1:-1]) + 1)
+        if plot_mode == "energy" and len(y_values) > 2
+        else int(np.argmin(y_values))
+    )
     for index in profile_structure_indices(
         atoms_list, y_values, plot_structures, plot_mode
     ):
-        if plot_structures == "all":
-            label = str(index)
-        elif index == 0:
+        if index == 0:
             label = "R"
         elif index == len(atoms_list) - 1:
             label = "P"
+        elif index == saddle_idx:
+            label = "SP"
+        elif plot_structures == "all":
+            label = str(index)
         else:
             label = "SP"
         payload.append(