chemparseplot 1.5.4__tar.gz → 1.6.0__tar.gz

{chemparseplot-1.5.4 → chemparseplot-1.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chemparseplot
-Version: 1.5.4
+Version: 1.6.0
 Summary: Parsers and plotting tools for computational chemistry
 Project-URL: Documentation, https://chemparseplot.rgoswami.me
 Project-URL: Issues, https://github.com/HaoZeke/chemparseplot/issues
@@ -26,6 +26,7 @@ Requires-Dist: cmcrameri>=1.7; extra == 'all'
 Requires-Dist: h5py>=3.0; extra == 'all'
 Requires-Dist: matplotlib>=3.8.2; extra == 'all'
 Requires-Dist: polars>=0.20; extra == 'all'
+Requires-Dist: readcon>=0.7.0; extra == 'all'
 Requires-Dist: xyzrender>=0.1.2; extra == 'all'
 Provides-Extra: doc
 Requires-Dist: mdit-py-plugins>=0.3.4; extra == 'doc'
@@ -44,6 +45,7 @@ Provides-Extra: neb
 Requires-Dist: ase>=3.22; extra == 'neb'
 Requires-Dist: h5py>=3.0; extra == 'neb'
 Requires-Dist: polars>=0.20; extra == 'neb'
+Requires-Dist: readcon>=0.7.0; extra == 'neb'
 Provides-Extra: plot
 Requires-Dist: cmcrameri>=1.7; extra == 'plot'
 Requires-Dist: matplotlib>=3.8.2; extra == 'plot'

{chemparseplot-1.5.4 → chemparseplot-1.6.0}/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '1.5.4'
-__version_tuple__ = version_tuple = (1, 5, 4)
+__version__ = version = '1.6.0'
+__version_tuple__ = version_tuple = (1, 6, 0)
 
 __commit_id__ = commit_id = None

{chemparseplot-1.5.4 → chemparseplot-1.6.0}/chemparseplot/parse/eon/dimer_trajectory.py

@@ -15,8 +15,8 @@ from pathlib import Path
 
 import numpy as np
 import polars as pl
+import readcon
 from ase import Atoms
-from ase.io import read as ase_read
 
 log = logging.getLogger(__name__)
 
@@ -76,8 +76,7 @@ def parse_climb_con(path: Path) -> list[Atoms]:
         List of ASE Atoms objects, one per iteration.
     """
     # eOn .con files may not have a .con extension for movie files
-    atoms_list = ase_read(str(path), index=":", format="eon")
-    return list(atoms_list)
+    return readcon.read_con_as_ase(str(path))
 
 
 def _find_initial_structure(job_dir: Path) -> Atoms | None:
@@ -85,7 +84,7 @@ def _find_initial_structure(job_dir: Path) -> Atoms | None:
     for name in ("reactant.con", "pos.con"):
         p = job_dir / name
         if p.exists():
-            return ase_read(str(p), format="eon")
+            return readcon.read_con_as_ase(str(p))[0]
     return None
 
 
@@ -141,7 +140,7 @@ def load_dimer_trajectory(job_dir: Path) -> DimerTrajectoryData:
         initial = atoms_list[0]
 
     saddle_path = job_dir / "saddle.con"
-    saddle = ase_read(str(saddle_path), format="eon") if saddle_path.exists() else None
+    saddle = readcon.read_con_as_ase(str(saddle_path))[0] if saddle_path.exists() else None
 
     mode = _load_mode_dat(job_dir / "mode.dat")
 

{chemparseplot-1.5.4 → chemparseplot-1.6.0}/chemparseplot/parse/eon/min_trajectory.py

@@ -14,8 +14,8 @@ from dataclasses import dataclass
 from pathlib import Path
 
 import polars as pl
+import readcon
 from ase import Atoms
-from ase.io import read as ase_read
 
 log = logging.getLogger(__name__)
 
@@ -71,8 +71,7 @@ def parse_min_con(path: Path) -> list[Atoms]:
     list[Atoms]
         List of ASE Atoms objects, one per iteration.
     """
-    atoms_list = ase_read(str(path), index=":", format="eon")
-    return list(atoms_list)
+    return readcon.read_con_as_ase(str(path))
 
 
 def load_min_trajectory(
@@ -121,7 +120,7 @@ def load_min_trajectory(
     # Final structure: prefer explicit min.con, fall back to last movie frame
     min_con = job_dir / "min.con"
     if min_con.exists():
-        final = ase_read(str(min_con), format="eon")
+        final = readcon.read_con_as_ase(str(min_con))[0]
     else:
         final = atoms_list[-1]
 

{chemparseplot-1.5.4 → chemparseplot-1.6.0}/chemparseplot/plot/neb.py

@@ -837,12 +837,15 @@ def plot_landscape_surface(
                 s_min, s_max = min(s_min, extra_s.min()), max(s_max, extra_s.max())
                 d_min, d_max = min(d_min, extra_d.min()), max(d_max, extra_d.max())
 
-            xg_1d = np.linspace(
-                s_min - (s_max - s_min) * 0.1, s_max + (s_max - s_min) * 0.1, 150
-            )
+            s_pad = (s_max - s_min) * 0.1
+            xg_1d = np.linspace(s_min - s_pad, s_max + s_pad, 150)
             # Y-grid centered on 0, covering at least the data range
             x_span = xg_1d.max() - xg_1d.min()
             y_half = max(x_span / 2, abs(d_data.max()), abs(d_data.min())) * 1.1
+            # If extra points pushed Y much larger, expand X to match
+            if 2 * y_half > x_span:
+                x_center = (s_min + s_max) / 2
+                xg_1d = np.linspace(x_center - y_half, x_center + y_half, 150)
             yg_1d = np.linspace(-y_half, y_half, 150)
 
         xg, yg = np.meshgrid(xg_1d, yg_1d)

{chemparseplot-1.5.4 → chemparseplot-1.6.0}/pyproject.toml

@@ -43,7 +43,7 @@ doc = [
   "sphinxcontrib-apidoc>=0.4",
 ]
 plot = ["cmcrameri>=1.7", "matplotlib>=3.8.2"]
-neb = ["ase>=3.22", "h5py>=3.0", "polars>=0.20"]
+neb = ["ase>=3.22", "h5py>=3.0", "polars>=0.20", "readcon>=0.7.0"]
 xyzrender = ["xyzrender>=0.1.2"]
 all = ["chemparseplot[plot,neb,xyzrender]"]
 test = ["pytest>=7.4.3", "pytest-cov>=4.1.0"]