pymdkit 1.4.4__tar.gz → 1.4.5__tar.gz

{pymdkit-1.4.4/src/pymdkit.egg-info → pymdkit-1.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.4.4
+Version: 1.4.5
 Summary: A unified command-line toolkit for atomistic / MD structure workflows.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later
@@ -177,7 +177,7 @@ When `pca` or `umap` receives `-it train.xyz`, it reads `Config_type` from every
 
 For folder conversion, `convert -if INPUT -of OUTPUT` writes `.xyz` by default. Set another target extension with `-oe`, for example `-oe cif` or `-oe vasp`. Single-file and trajectory modes infer the target format from `-o` and `-ot`.
 
-`gpumd-thermo` writes `temperature.txt`, `potential-energy.txt`, `pressure.txt`, `lattice-parameters.txt`, `volume.txt`, `lattice-angles.txt`, and a headless `thermo.png` in every detected GPUMD job folder. Potential energy is the primary equilibrium signal. Detection requires a persistent change with a meaningful magnitude relative to the robust natural energy fluctuations, so ordinary correlated thermal noise and isolated spikes are not classified as abnormal. When multiple lattice or volume measures independently show a transition, a more sensitive noise-relative potential-energy test is enabled; this avoids a fixed eV or percentage-of-total-energy threshold that would depend on system size. Lattice parameters, volume, temperature, pressure, and angles remain supporting diagnostics. Thermo plots use Arial when available, opaque legends, correct Å units, and shaded abnormal regions on potential energy, lattice parameters, and volume. Potential energy and volume are divided by 1000 and labeled ×10³ only when their absolute plotted values reach 1000. The analysis uses the last `run` segment, or the last 80% when `run.in` has no `run` record; inspect the plot before making a final scientific judgment.
+`gpumd-thermo` writes `temperature.txt`, `potential-energy.txt`, `pressure.txt`, `lattice-parameters.txt`, `volume.txt`, `lattice-angles.txt`, and a headless `thermo.png` in every detected GPUMD job folder. Potential energy is the primary equilibrium signal. Detection requires a persistent change with a meaningful magnitude relative to the robust natural energy fluctuations, so ordinary correlated thermal noise and isolated spikes are not classified as abnormal. When multiple lattice or volume measures independently show a transition, a more sensitive noise-relative potential-energy test is enabled; this avoids a fixed eV or percentage-of-total-energy threshold that would depend on system size. Lattice parameters and volume can corroborate an energy transition. Temperature and all six pressure components remain diagnostics only and cannot classify an otherwise stationary run as abnormal by themselves. Thermo plots use Arial when available and the Morandi color cycle. They plot all six pressure components, use frameless upper-right legends with added vertical headroom, preserve correct Å units, and shade abnormal regions on potential energy, lattice parameters, and volume. Potential energy and volume are divided by 1000 and labeled ×10³ only when their absolute plotted values reach 1000. The analysis uses the last `run` segment, or the last 80% when `run.in` has no `run` record; inspect the plot before making a final scientific judgment.
 
 The thermo parser follows the [official GPUMD thermo.out format](https://gpumd.org/gpumd/output_files/thermo_out.html): 18 columns are required, `pressure.txt` exports `Pxx Pyy Pzz Pyz Pxz Pxy`, box vectors are interpreted as a full 3×3 matrix, `time_step` propagates between runs, and `dump_thermo` does not.
 

{pymdkit-1.4.4 → pymdkit-1.4.5}/README.md

@@ -151,7 +151,7 @@ When `pca` or `umap` receives `-it train.xyz`, it reads `Config_type` from every
 
 For folder conversion, `convert -if INPUT -of OUTPUT` writes `.xyz` by default. Set another target extension with `-oe`, for example `-oe cif` or `-oe vasp`. Single-file and trajectory modes infer the target format from `-o` and `-ot`.
 
-`gpumd-thermo` writes `temperature.txt`, `potential-energy.txt`, `pressure.txt`, `lattice-parameters.txt`, `volume.txt`, `lattice-angles.txt`, and a headless `thermo.png` in every detected GPUMD job folder. Potential energy is the primary equilibrium signal. Detection requires a persistent change with a meaningful magnitude relative to the robust natural energy fluctuations, so ordinary correlated thermal noise and isolated spikes are not classified as abnormal. When multiple lattice or volume measures independently show a transition, a more sensitive noise-relative potential-energy test is enabled; this avoids a fixed eV or percentage-of-total-energy threshold that would depend on system size. Lattice parameters, volume, temperature, pressure, and angles remain supporting diagnostics. Thermo plots use Arial when available, opaque legends, correct Å units, and shaded abnormal regions on potential energy, lattice parameters, and volume. Potential energy and volume are divided by 1000 and labeled ×10³ only when their absolute plotted values reach 1000. The analysis uses the last `run` segment, or the last 80% when `run.in` has no `run` record; inspect the plot before making a final scientific judgment.
+`gpumd-thermo` writes `temperature.txt`, `potential-energy.txt`, `pressure.txt`, `lattice-parameters.txt`, `volume.txt`, `lattice-angles.txt`, and a headless `thermo.png` in every detected GPUMD job folder. Potential energy is the primary equilibrium signal. Detection requires a persistent change with a meaningful magnitude relative to the robust natural energy fluctuations, so ordinary correlated thermal noise and isolated spikes are not classified as abnormal. When multiple lattice or volume measures independently show a transition, a more sensitive noise-relative potential-energy test is enabled; this avoids a fixed eV or percentage-of-total-energy threshold that would depend on system size. Lattice parameters and volume can corroborate an energy transition. Temperature and all six pressure components remain diagnostics only and cannot classify an otherwise stationary run as abnormal by themselves. Thermo plots use Arial when available and the Morandi color cycle. They plot all six pressure components, use frameless upper-right legends with added vertical headroom, preserve correct Å units, and shade abnormal regions on potential energy, lattice parameters, and volume. Potential energy and volume are divided by 1000 and labeled ×10³ only when their absolute plotted values reach 1000. The analysis uses the last `run` segment, or the last 80% when `run.in` has no `run` record; inspect the plot before making a final scientific judgment.
 
 The thermo parser follows the [official GPUMD thermo.out format](https://gpumd.org/gpumd/output_files/thermo_out.html): 18 columns are required, `pressure.txt` exports `Pxx Pyy Pzz Pyz Pxz Pxy`, box vectors are interpreted as a full 3×3 matrix, `time_step` propagates between runs, and `dump_thermo` does not.
 

{pymdkit-1.4.4 → pymdkit-1.4.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.4.4"
+version = "1.4.5"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"

{pymdkit-1.4.4 → pymdkit-1.4.5}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.4.4"
+__version__ = "1.4.5"

{pymdkit-1.4.4 → pymdkit-1.4.5}/src/pymdkit/commands/_gpumd.py

@@ -424,12 +424,8 @@ def load_thermo(thermo_path, run_path):
             abnormal_mask[start:] = True
 
     warnings.extend(structural_warnings)
-    warnings.extend(other_warnings)
-    if warnings and not abnormal_mask.any():
-        abnormal_mask[start:] = True
-        warnings.insert(
-            0, "region mapping: full equilibrium segment used as fallback"
-        )
+    if abnormal_mask.any():
+        warnings.extend(other_warnings)
 
     return ThermoData(
         time=time,

{pymdkit-1.4.4 → pymdkit-1.4.5}/src/pymdkit/commands/gpumd_thermo.py

@@ -13,7 +13,28 @@ except ImportError:
     from _gpumd import load_thermo, mask_intervals
 
 COMMAND = "gpumd-thermo"
-HELP = "Export and plot GPUMD thermo.out data and warn about instability."
+HELP = "Export and plot GPUMD thermo.out data and warn about instability."
+
+MORANDI_COLORS = [
+    "#686789",
+    "#B77F70",
+    "#E5E2B9",
+    "#BEB1A8",
+    "#A79A89",
+    "#8A95A9",
+    "#ECCED0",
+    "#7D7465",
+    "#E8D3C0",
+    "#7A8A71",
+    "#789798",
+    "#B57C82",
+    "#9FABB9",
+    "#B0B1B6",
+    "#99857E",
+    "#88878D",
+    "#91A0A5",
+    "#9AA690",
+]
 
 
 def save_table(path, time, values, header):
@@ -35,7 +56,7 @@ def scaled_plot_values(values, quantity, unit):
 def mark_abnormal_regions(axis, intervals):
     for begin, end in intervals:
         axis.axvspan(
-            begin, end, color="#d9e8f5", alpha=0.85, linewidth=0, zorder=0
+            begin, end, color=MORANDI_COLORS[12], alpha=0.35, linewidth=0, zorder=0
         )
         axis.text(
             (begin + end) / 2.0,
@@ -45,9 +66,9 @@ def mark_abnormal_regions(axis, intervals):
             ha="center",
             va="top",
             fontsize=7,
-            color="#315a7d",
+            color=MORANDI_COLORS[0],
             bbox={
-                "facecolor": "white",
+                "facecolor": MORANDI_COLORS[2],
                 "edgecolor": "none",
                 "alpha": 0.8,
                 "pad": 1.0,
@@ -57,22 +78,33 @@ def mark_abnormal_regions(axis, intervals):
         )
 
 
+def set_upper_headroom(axis, values):
+    values = np.asarray(values, dtype=float)
+    finite = values[np.isfinite(values)]
+    if not finite.size:
+        return
+    minimum = float(np.min(finite))
+    maximum = float(np.max(finite))
+    span = maximum - minimum
+    if span == 0:
+        span = max(abs(maximum) * 0.05, 1.0)
+    axis.set_ylim(minimum - 0.05 * span, maximum + 0.4 * span)
+
 def plot_thermo(path, thermo):
     import matplotlib
     matplotlib.use("Agg")
+    from cycler import cycler
     matplotlib.rcParams.update({
         "font.family": "sans-serif",
         "font.sans-serif": ["Arial", "Liberation Sans", "DejaVu Sans"],
+        "axes.prop_cycle": cycler(color=MORANDI_COLORS),
     })
     import matplotlib.pyplot as plt
 
-    colors = ("#d22027", "#015699", "#fac00f")
+    colors = MORANDI_COLORS
     legend_style = {
-        "loc": "best",
-        "frameon": True,
-        "facecolor": "white",
-        "edgecolor": "none",
-        "framealpha": 1.0,
+        "loc": "upper right",
+        "frameon": False,
     }
     intervals = mask_intervals(thermo.time, thermo.abnormal_mask)
     potential, potential_label = scaled_plot_values(
@@ -95,7 +127,7 @@ def plot_thermo(path, thermo):
     axes[0, 1].set_ylabel(potential_label)
     mark_abnormal_regions(axes[0, 1], intervals)
 
-    for index, label in enumerate(("Pxx", "Pyy", "Pzz")):
+    for index, label in enumerate(("Pxx", "Pyy", "Pzz", "Pyz", "Pxz", "Pxy")):
         axes[0, 2].plot(
             thermo.time,
             thermo.pressure[:, index],
@@ -104,7 +136,8 @@ def plot_thermo(path, thermo):
             zorder=2,
         )
     axes[0, 2].set_ylabel("Pressure (GPa)")
-    axes[0, 2].legend(**legend_style).set_zorder(4)
+    set_upper_headroom(axes[0, 2], thermo.pressure)
+    axes[0, 2].legend(**legend_style, ncol=2).set_zorder(4)
 
     for index, label in enumerate(("a", "b", "c")):
         axes[1, 0].plot(
@@ -116,6 +149,7 @@ def plot_thermo(path, thermo):
         )
     axes[1, 0].set_ylabel("Lattice parameters (Å)")
     mark_abnormal_regions(axes[1, 0], intervals)
+    set_upper_headroom(axes[1, 0], thermo.lengths)
     axes[1, 0].legend(**legend_style).set_zorder(4)
 
     axes[1, 1].plot(

{pymdkit-1.4.4 → pymdkit-1.4.5/src/pymdkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.4.4
+Version: 1.4.5
 Summary: A unified command-line toolkit for atomistic / MD structure workflows.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later
@@ -177,7 +177,7 @@ When `pca` or `umap` receives `-it train.xyz`, it reads `Config_type` from every
 
 For folder conversion, `convert -if INPUT -of OUTPUT` writes `.xyz` by default. Set another target extension with `-oe`, for example `-oe cif` or `-oe vasp`. Single-file and trajectory modes infer the target format from `-o` and `-ot`.
 
-`gpumd-thermo` writes `temperature.txt`, `potential-energy.txt`, `pressure.txt`, `lattice-parameters.txt`, `volume.txt`, `lattice-angles.txt`, and a headless `thermo.png` in every detected GPUMD job folder. Potential energy is the primary equilibrium signal. Detection requires a persistent change with a meaningful magnitude relative to the robust natural energy fluctuations, so ordinary correlated thermal noise and isolated spikes are not classified as abnormal. When multiple lattice or volume measures independently show a transition, a more sensitive noise-relative potential-energy test is enabled; this avoids a fixed eV or percentage-of-total-energy threshold that would depend on system size. Lattice parameters, volume, temperature, pressure, and angles remain supporting diagnostics. Thermo plots use Arial when available, opaque legends, correct Å units, and shaded abnormal regions on potential energy, lattice parameters, and volume. Potential energy and volume are divided by 1000 and labeled ×10³ only when their absolute plotted values reach 1000. The analysis uses the last `run` segment, or the last 80% when `run.in` has no `run` record; inspect the plot before making a final scientific judgment.
+`gpumd-thermo` writes `temperature.txt`, `potential-energy.txt`, `pressure.txt`, `lattice-parameters.txt`, `volume.txt`, `lattice-angles.txt`, and a headless `thermo.png` in every detected GPUMD job folder. Potential energy is the primary equilibrium signal. Detection requires a persistent change with a meaningful magnitude relative to the robust natural energy fluctuations, so ordinary correlated thermal noise and isolated spikes are not classified as abnormal. When multiple lattice or volume measures independently show a transition, a more sensitive noise-relative potential-energy test is enabled; this avoids a fixed eV or percentage-of-total-energy threshold that would depend on system size. Lattice parameters and volume can corroborate an energy transition. Temperature and all six pressure components remain diagnostics only and cannot classify an otherwise stationary run as abnormal by themselves. Thermo plots use Arial when available and the Morandi color cycle. They plot all six pressure components, use frameless upper-right legends with added vertical headroom, preserve correct Å units, and shade abnormal regions on potential energy, lattice parameters, and volume. Potential energy and volume are divided by 1000 and labeled ×10³ only when their absolute plotted values reach 1000. The analysis uses the last `run` segment, or the last 80% when `run.in` has no `run` record; inspect the plot before making a final scientific judgment.
 
 The thermo parser follows the [official GPUMD thermo.out format](https://gpumd.org/gpumd/output_files/thermo_out.html): 18 columns are required, `pressure.txt` exports `Pxx Pyy Pzz Pyz Pxz Pxy`, box vectors are interpreted as a full 3×3 matrix, `time_step` propagates between runs, and `dump_thermo` does not.