pymdkit 1.4.5__tar.gz → 1.4.7__tar.gz

{pymdkit-1.4.5 → pymdkit-1.4.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.4.5
+Version: 1.4.7
 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
@@ -70,7 +70,7 @@ directory for job sub-folders automatically.
 | `vasp-fe` | List VASP job final energies from lowest to highest |
 | `gather-contcar` | Collect CONTCARs from VASP job folders into one folder, renamed `<folder>.vasp` |
 | `gpumd-thermo` | Export and plot GPUMD thermo data and detect sustained equilibrium changes |
-| `gpumd-trjcat` | Merge stable GPUMD trajectories and extract abnormal time regions |
+| `gpumd-trjcat` | Merge normal or all GPUMD trajectories and extract the first abnormal region |
 | `pca` | Reduce descriptor data to two dimensions; optional FPS sampling |
 | `trj-extract` | Extract a GPUMD XYZ trajectory by time range |
 | `trj-sparse` | Deterministically retain a requested fraction of XYZ trajectory frames |
@@ -137,6 +137,7 @@ pmk gpumd-thermo                              # current job, or recursively scan
 pmk gpumd-thermo -t thermo.out -in run.in
 pmk gpumd-trjcat                            # stable frames -> train.xyz; abnormal regions -> abnormal.xyz
 pmk gpumd-trjcat -i traj.xyz -o train.xyz -ao abnormal.xyz
+pmk gpumd-trjcat -all                       # merge every readable trajectory into train.xyz
 pmk trj-extract -it traj.xyz -in run.in -b 100 -e 200 -o traj-100ps-200ps.xyz
 pmk trj-sparse -it example.xyz -r 0.5 -o sparse-example.xyz
 
@@ -177,11 +178,11 @@ 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 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.
+`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. For an abnormal run it also writes `abnormal-time.txt`, with one `BEGIN ps to END ps` interval per line; a normal rerun removes a stale file. 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. An abnormal classification always requires a mapped potential-energy change. When at least two lattice-parameter or volume signals show the same mapped transition, they may enable a more sensitive noise-relative energy test; this avoids a fixed eV or percentage-of-total-energy threshold that would depend on system size. Cell signals can corroborate and refine the energy interval, but can never classify a run by themselves. Temperature and all six pressure components remain diagnostics only and cannot classify an otherwise stationary run as abnormal by themselves. A lone cell-axis drift, an isolated spike, or an empty anomaly mask never triggers a whole-run fallback. Thermo plots use Arial when available and Matplotlib's built-in qualitative `Dark2` color cycle. They plot all six pressure components, use frameless upper-right legends with added vertical headroom, preserve correct Å units, and show abnormal regions as shaded legend entries 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.
 
-`gpumd-trjcat` recursively scans job subfolders for `traj.xyz`, `thermo.out`, and `run.in`. Stable trajectories are merged in deterministic folder order into `train.xyz` (or `-o`). For an abnormal job, frames from the structurally corroborated potential-energy region are written to `abnormal.xyz` (or `-ao`); if no energy region can be resolved, the dominant structural transition is used as a fallback so an abnormal job cannot produce an empty abnormal output. Frame times are obtained from `time_step` and `dump_xyz` in that job's `run.in`. Missing, unreadable, or unmappable jobs are skipped. When `<job>/model.xyz` contains `Config_type`, that value is applied to every exported frame while all other extended-XYZ bytes remain unchanged.
+`gpumd-trjcat` recursively scans job subfolders for `traj.xyz`, `thermo.out`, and `run.in`. By default, normal trajectories are merged in deterministic folder order into `train.xyz` (or `-o`), while only frames from the earliest mapped abnormal interval of each abnormal job are written to `abnormal.xyz` (or `-ao`). With `-all`, every readable full trajectory is merged into `train.xyz` regardless of normal, abnormal, missing-thermo, or failed-thermo status; an analyzable abnormal job still contributes its earliest abnormal interval to `abnormal.xyz`. If no mapped abnormal frames are found, `abnormal.xyz` is not created and a stale file at the selected `-ao` path is removed. Frame times are obtained from `time_step` and `dump_xyz` in that job's `run.in`. In default mode, missing, unreadable, or unmappable jobs are skipped. When `<job>/model.xyz` contains `Config_type`, that value is applied to every exported frame while all other extended-XYZ bytes remain unchanged.
 
 `trj-sparse` keeps `max(1, floor(frame_count × ratio))` frames without rewriting their extended-XYZ content. Selection is deterministic and starts with frame zero; for 100 frames and `-r 0.5`, it writes source indices `0, 2, ..., 98`.
 

{pymdkit-1.4.5 → pymdkit-1.4.7}/README.md

@@ -44,7 +44,7 @@ directory for job sub-folders automatically.
 | `vasp-fe` | List VASP job final energies from lowest to highest |
 | `gather-contcar` | Collect CONTCARs from VASP job folders into one folder, renamed `<folder>.vasp` |
 | `gpumd-thermo` | Export and plot GPUMD thermo data and detect sustained equilibrium changes |
-| `gpumd-trjcat` | Merge stable GPUMD trajectories and extract abnormal time regions |
+| `gpumd-trjcat` | Merge normal or all GPUMD trajectories and extract the first abnormal region |
 | `pca` | Reduce descriptor data to two dimensions; optional FPS sampling |
 | `trj-extract` | Extract a GPUMD XYZ trajectory by time range |
 | `trj-sparse` | Deterministically retain a requested fraction of XYZ trajectory frames |
@@ -110,7 +110,8 @@ pmk umap -i descriptor.out -o umap-descriptor.txt -fps 0.01 -it train.xyz
 pmk gpumd-thermo                              # current job, or recursively scan job folders
 pmk gpumd-thermo -t thermo.out -in run.in
 pmk gpumd-trjcat                            # stable frames -> train.xyz; abnormal regions -> abnormal.xyz
-pmk gpumd-trjcat -i traj.xyz -o train.xyz -ao abnormal.xyz
+pmk gpumd-trjcat -i traj.xyz -o train.xyz -ao abnormal.xyz
+pmk gpumd-trjcat -all                       # merge every readable trajectory into train.xyz
 pmk trj-extract -it traj.xyz -in run.in -b 100 -e 200 -o traj-100ps-200ps.xyz
 pmk trj-sparse -it example.xyz -r 0.5 -o sparse-example.xyz
 
@@ -151,11 +152,11 @@ 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 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.
+`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. For an abnormal run it also writes `abnormal-time.txt`, with one `BEGIN ps to END ps` interval per line; a normal rerun removes a stale file. 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. An abnormal classification always requires a mapped potential-energy change. When at least two lattice-parameter or volume signals show the same mapped transition, they may enable a more sensitive noise-relative energy test; this avoids a fixed eV or percentage-of-total-energy threshold that would depend on system size. Cell signals can corroborate and refine the energy interval, but can never classify a run by themselves. Temperature and all six pressure components remain diagnostics only and cannot classify an otherwise stationary run as abnormal by themselves. A lone cell-axis drift, an isolated spike, or an empty anomaly mask never triggers a whole-run fallback. Thermo plots use Arial when available and Matplotlib's built-in qualitative `Dark2` color cycle. They plot all six pressure components, use frameless upper-right legends with added vertical headroom, preserve correct Å units, and show abnormal regions as shaded legend entries 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.
 
-`gpumd-trjcat` recursively scans job subfolders for `traj.xyz`, `thermo.out`, and `run.in`. Stable trajectories are merged in deterministic folder order into `train.xyz` (or `-o`). For an abnormal job, frames from the structurally corroborated potential-energy region are written to `abnormal.xyz` (or `-ao`); if no energy region can be resolved, the dominant structural transition is used as a fallback so an abnormal job cannot produce an empty abnormal output. Frame times are obtained from `time_step` and `dump_xyz` in that job's `run.in`. Missing, unreadable, or unmappable jobs are skipped. When `<job>/model.xyz` contains `Config_type`, that value is applied to every exported frame while all other extended-XYZ bytes remain unchanged.
+`gpumd-trjcat` recursively scans job subfolders for `traj.xyz`, `thermo.out`, and `run.in`. By default, normal trajectories are merged in deterministic folder order into `train.xyz` (or `-o`), while only frames from the earliest mapped abnormal interval of each abnormal job are written to `abnormal.xyz` (or `-ao`). With `-all`, every readable full trajectory is merged into `train.xyz` regardless of normal, abnormal, missing-thermo, or failed-thermo status; an analyzable abnormal job still contributes its earliest abnormal interval to `abnormal.xyz`. If no mapped abnormal frames are found, `abnormal.xyz` is not created and a stale file at the selected `-ao` path is removed. Frame times are obtained from `time_step` and `dump_xyz` in that job's `run.in`. In default mode, missing, unreadable, or unmappable jobs are skipped. When `<job>/model.xyz` contains `Config_type`, that value is applied to every exported frame while all other extended-XYZ bytes remain unchanged.
 
 `trj-sparse` keeps `max(1, floor(frame_count × ratio))` frames without rewriting their extended-XYZ content. Selection is deterministic and starts with frame zero; for 100 frames and `-r 0.5`, it writes source indices `0, 2, ..., 98`.
 

{pymdkit-1.4.5 → pymdkit-1.4.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.4.5"
+version = "1.4.7"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"

{pymdkit-1.4.5 → pymdkit-1.4.7}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.4.5"
+__version__ = "1.4.7"

{pymdkit-1.4.5 → pymdkit-1.4.7}/src/pymdkit/commands/_gpumd.py

@@ -310,8 +310,6 @@ def structural_abnormal_mask(lengths, volume):
     ]
     votes = np.sum(masks, axis=0)
     candidate = votes >= 2
-    if not candidate.any():
-        candidate = votes >= 1
     candidate = _bridge_mask(candidate, max(1, len(candidate) // 50))
     return _keep_major_regions(_clean_mask(candidate))
 
@@ -363,7 +361,9 @@ def load_thermo(thermo_path, run_path):
     thermo_path = Path(thermo_path)
     data = np.loadtxt(thermo_path, ndmin=2)
     if data.shape[1] != 18:
-        raise ValueError(f"{thermo_path} must use the official 18-column GPUMD format")
+        raise ValueError(
+            f"{thermo_path} must use the official 18-column GPUMD format"
+        )
 
     time_step, dump_interval, runs = parse_run_input(run_path)
     time = time_axis(len(data), time_step, dump_interval, runs)
@@ -373,59 +373,53 @@ def load_thermo(thermo_path, run_path):
     lengths, angles, volume = cell_quantities(data)
     start = equilibrium_start(len(data), runs)
 
-    structural_warnings = find_abnormal({
+    cell_warnings = find_abnormal({
         "lattice-parameter": lengths,
         "volume": volume,
+    }, start)
+    angle_warnings = find_abnormal({
         "lattice-angle": angles,
     }, start)
-    other_warnings = find_abnormal({
+    diagnostic_warnings = find_abnormal({
         "temperature": temperature,
         "pressure": pressure,
     }, start)
 
-    abnormal_mask = np.zeros(len(data), dtype=bool)
+    segment_length = len(data) - start
     segment_mask = potential_abnormal_mask(potential[start:])
-    abnormal_mask[start:] = segment_mask
-    warnings = []
+    warning_prefix = "potential-energy: localized"
 
-    if not segment_mask.any() and structural_warnings:
+    # Potential energy is mandatory evidence. Coherent cell changes may lower
+    # its threshold and refine the interval, but cannot classify a run alone.
+    if not segment_mask.any() and len(cell_warnings) >= 2:
         structural_mask = structural_abnormal_mask(
             lengths[start:], volume[start:]
         )
-        relaxed_energy = potential_abnormal_mask(
-            potential[start:], corroborated=True
-        )
-        overlap = relaxed_energy & structural_mask
-        if overlap.any():
-            segment_mask = _keep_major_regions(
-                _bridge_mask(overlap, max(1, len(overlap) // 20))
+        if structural_mask.any():
+            relaxed_energy = potential_abnormal_mask(
+                potential[start:], corroborated=True
             )
-            warning_prefix = "potential-energy: structurally corroborated"
-        elif structural_mask.any():
-            segment_mask = structural_mask
-            warning_prefix = "structure: mapped fallback"
-        else:
-            segment_mask = np.ones(len(potential) - start, dtype=bool)
-            warning_prefix = "structure: full equilibrium fallback"
-        abnormal_mask[start:] = segment_mask
-    else:
-        warning_prefix = "potential-energy: localized"
+            overlap = relaxed_energy & structural_mask
+            if overlap.any():
+                corroborated = _keep_major_regions(
+                    _bridge_mask(overlap, max(1, segment_length // 20))
+                )
+                if corroborated.any():
+                    segment_mask = corroborated
+                    warning_prefix = "potential-energy: structurally corroborated"
 
+    abnormal_mask = np.zeros(len(data), dtype=bool)
+    abnormal_mask[start:] = segment_mask
     intervals = mask_intervals(time, abnormal_mask)
+    warnings = []
     if intervals:
         warnings.append(
             f"{warning_prefix} abnormal region(s) at "
             + _format_intervals(intervals)
         )
-    else:
-        potential_reason = abnormal_reason(potential[start:])
-        if potential_reason:
-            warnings.append(f"potential-energy: {potential_reason}")
-            abnormal_mask[start:] = True
-
-    warnings.extend(structural_warnings)
-    if abnormal_mask.any():
-        warnings.extend(other_warnings)
+        warnings.extend(cell_warnings)
+        warnings.extend(angle_warnings)
+        warnings.extend(diagnostic_warnings)
 
     return ThermoData(
         time=time,

{pymdkit-1.4.5 → pymdkit-1.4.7}/src/pymdkit/commands/gpumd_thermo.py

@@ -15,33 +15,19 @@ except ImportError:
 COMMAND = "gpumd-thermo"
 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",
-]
-
+DARK2_NAME = "Dark2"
 
 def save_table(path, time, values, header):
     values = np.asarray(values)
     if values.ndim == 1:
         values = values[:, None]
-    np.savetxt(path, np.column_stack([time, values]), fmt="%.10g", header=header)
+    np.savetxt(
+        path,
+        np.column_stack([time, values]),
+        fmt="%.10g",
+        header=header,
+        encoding="utf-8",
+    )
 
 
 def scaled_plot_values(values, quantity, unit):
@@ -53,31 +39,18 @@ def scaled_plot_values(values, quantity, unit):
     return values, f"{quantity} ({unit})"
 
 
-def mark_abnormal_regions(axis, intervals):
-    for begin, end in intervals:
+def mark_abnormal_regions(axis, intervals, color):
+    for index, (begin, end) in enumerate(intervals):
         axis.axvspan(
-            begin, end, color=MORANDI_COLORS[12], alpha=0.35, linewidth=0, zorder=0
-        )
-        axis.text(
-            (begin + end) / 2.0,
-            0.97,
-            "abnormal region",
-            transform=axis.get_xaxis_transform(),
-            ha="center",
-            va="top",
-            fontsize=7,
-            color=MORANDI_COLORS[0],
-            bbox={
-                "facecolor": MORANDI_COLORS[2],
-                "edgecolor": "none",
-                "alpha": 0.8,
-                "pad": 1.0,
-            },
-            clip_on=True,
-            zorder=4,
+            begin,
+            end,
+            color=color,
+            alpha=0.25,
+            linewidth=0,
+            label="abnormal region" if index == 0 else "_nolegend_",
+            zorder=0,
         )
 
-
 def set_upper_headroom(axis, values):
     values = np.asarray(values, dtype=float)
     finite = values[np.isfinite(values)]
@@ -94,14 +67,18 @@ def plot_thermo(path, thermo):
     import matplotlib
     matplotlib.use("Agg")
     from cycler import cycler
+    colors = [
+        matplotlib.colors.to_hex(color)
+        for color in matplotlib.colormaps[DARK2_NAME].colors
+    ]
     matplotlib.rcParams.update({
         "font.family": "sans-serif",
         "font.sans-serif": ["Arial", "Liberation Sans", "DejaVu Sans"],
-        "axes.prop_cycle": cycler(color=MORANDI_COLORS),
+        "axes.prop_cycle": cycler(color=colors),
+        "image.cmap": DARK2_NAME,
     })
     import matplotlib.pyplot as plt
 
-    colors = MORANDI_COLORS
     legend_style = {
         "loc": "upper right",
         "frameon": False,
@@ -125,7 +102,9 @@ def plot_thermo(path, thermo):
         thermo.time, potential, color=colors[0], zorder=2
     )
     axes[0, 1].set_ylabel(potential_label)
-    mark_abnormal_regions(axes[0, 1], intervals)
+    mark_abnormal_regions(axes[0, 1], intervals, colors[7])
+    if intervals:
+        axes[0, 1].legend(**legend_style).set_zorder(4)
 
     for index, label in enumerate(("Pxx", "Pyy", "Pzz", "Pyz", "Pxz", "Pxy")):
         axes[0, 2].plot(
@@ -148,7 +127,7 @@ def plot_thermo(path, thermo):
             zorder=2,
         )
     axes[1, 0].set_ylabel("Lattice parameters (Å)")
-    mark_abnormal_regions(axes[1, 0], intervals)
+    mark_abnormal_regions(axes[1, 0], intervals, colors[7])
     set_upper_headroom(axes[1, 0], thermo.lengths)
     axes[1, 0].legend(**legend_style).set_zorder(4)
 
@@ -156,7 +135,9 @@ def plot_thermo(path, thermo):
         thermo.time, volume, color=colors[1], zorder=2
     )
     axes[1, 1].set_ylabel(volume_label)
-    mark_abnormal_regions(axes[1, 1], intervals)
+    mark_abnormal_regions(axes[1, 1], intervals, colors[7])
+    if intervals:
+        axes[1, 1].legend(**legend_style).set_zorder(4)
 
     for index, label in enumerate(("alpha", "beta", "gamma")):
         axes[1, 2].plot(
@@ -185,6 +166,25 @@ def plot_thermo(path, thermo):
     plt.close(fig)
 
 
+def write_abnormal_time(path, intervals):
+    path = Path(path)
+    if not intervals:
+        path.unlink(missing_ok=True)
+        return False
+
+    text = "".join(
+        f"{begin:.2f} ps to {end:.2f} ps\n"
+        for begin, end in intervals
+    )
+    temporary = path.with_name(f".{path.name}.pmk-tmp")
+    try:
+        temporary.write_text(text, encoding="utf-8")
+        temporary.replace(path)
+    except Exception:
+        temporary.unlink(missing_ok=True)
+        raise
+    return True
+
 def process_job(folder, thermo_name, run_name):
     thermo = load_thermo(folder / thermo_name, folder / run_name)
     save_table(
@@ -224,6 +224,10 @@ def process_job(folder, thermo_name, run_name):
         "time(ps) alpha(deg) beta(deg) gamma(deg)",
     )
     plot_thermo(folder / "thermo.png", thermo)
+    intervals = mask_intervals(thermo.time, thermo.abnormal_mask)
+    wrote_abnormal_time = write_abnormal_time(
+        folder / "abnormal-time.txt", intervals
+    )
 
     print(
         f"{folder}: {len(thermo.time)} thermo record(s), "
@@ -236,6 +240,8 @@ def process_job(folder, thermo_name, run_name):
     else:
         print("No sustained equilibrium drift or level shift detected.")
     print("Wrote thermo text tables and thermo.png")
+    if wrote_abnormal_time:
+        print("Wrote abnormal-time.txt")
 
 
 def discover_jobs(thermo_arg, run_arg):
@@ -291,4 +297,4 @@ def run(args) -> int:
 if __name__ == "__main__":
     _parser = argparse.ArgumentParser(description=__doc__)
     add_arguments(_parser)
-    raise SystemExit(run(_parser.parse_args()))
+    raise SystemExit(run(_parser.parse_args()))

{pymdkit-1.4.5 → pymdkit-1.4.7}/src/pymdkit/commands/gpumd_trjcat.py

@@ -1,4 +1,4 @@
-"""Merge stable GPUMD trajectories and extract abnormal trajectory regions."""
+"""Merge GPUMD trajectories and extract each job's first abnormal region."""
 
 from __future__ import annotations
 
@@ -16,7 +16,7 @@ except ImportError:
     from _gpumd import load_thermo, mask_intervals, trajectory_interval
 
 COMMAND = "gpumd-trjcat"
-HELP = "Merge stable GPUMD trajectories and extract abnormal regions."
+HELP = "Merge normal or all GPUMD trajectories; extract first abnormal regions."
 
 
 @dataclass(frozen=True)
@@ -44,6 +44,11 @@ def add_arguments(parser: argparse.ArgumentParser) -> None:
                         help="Structure filename supplying Config_type.")
 
 
+    parser.add_argument(
+        "-all", dest="all", action="store_true",
+        help="Merge every readable trajectory, regardless of thermo status.",
+    )
+
 def find_trajectories(root, input_name, outputs):
     root = Path(root).resolve()
     excluded = {Path(path).resolve() for path in outputs}
@@ -60,18 +65,6 @@ def find_trajectories(root, input_name, outputs):
 
 def inspect_job(trajectory, args):
     folder = trajectory.parent
-    thermo_path = folder / Path(args.thermo).name
-    run_path = folder / Path(args.run_input).name
-    missing = [path.name for path in (thermo_path, run_path) if not path.is_file()]
-    if missing:
-        return None, None, f"missing {', '.join(missing)}"
-
-    try:
-        thermo = load_thermo(thermo_path, run_path)
-        _, _, interval_ps = trajectory_interval(run_path, trajectory)
-    except Exception as exc:
-        return None, None, f"thermo check failed ({exc})"
-
     try:
         blocks, _ = read_blocks(trajectory)
     except Exception as exc:
@@ -88,21 +81,31 @@ def inspect_job(trajectory, args):
             print(f"{folder}: warning: could not read Config_type ({exc})")
 
     job = TrajectoryJob(trajectory, len(blocks), config_type)
-    return job, (thermo, interval_ps), None
+    thermo_path = folder / Path(args.thermo).name
+    run_path = folder / Path(args.run_input).name
+    missing = [path.name for path in (thermo_path, run_path) if not path.is_file()]
+    if missing:
+        return job, None, f"missing {', '.join(missing)}"
 
+    try:
+        thermo = load_thermo(thermo_path, run_path)
+        _, _, interval_ps = trajectory_interval(run_path, trajectory)
+    except Exception as exc:
+        return job, None, f"thermo check failed ({exc})"
+    return job, (thermo, interval_ps), None
 
 def abnormal_frame_indices(thermo, frame_count, interval_ps):
     intervals = mask_intervals(thermo.time, thermo.abnormal_mask)
+    if not intervals:
+        return ()
+
+    begin, end = intervals[0]
     tolerance = max(1e-12, interval_ps * 1e-9)
     return tuple(
         index for index in range(frame_count)
-        if any(
-            begin - tolerance <= index * interval_ps <= end + tolerance
-            for begin, end in intervals
-        )
+        if begin - tolerance <= index * interval_ps <= end + tolerance
     )
 
-
 def write_merged(output, jobs):
     output = Path(output)
     output.parent.mkdir(parents=True, exist_ok=True)
@@ -138,60 +141,103 @@ def run(args) -> int:
             f"Error: no {Path(args.input).name} files found in subfolders of {root}."
         )
 
-    stable_jobs = []
+    merged_jobs = []
     abnormal_jobs = []
     skipped = 0
     print(f"Found {len(trajectories)} trajectory file(s).")
     for trajectory in trajectories:
         job, analysis, reason = inspect_job(trajectory, args)
         relative_folder = trajectory.parent.relative_to(root)
-        if reason:
+        if job is None:
             skipped += 1
             print(f"{relative_folder}: skipped - {reason}")
             continue
 
-        thermo, interval_ps = analysis
         config = (
             f", Config_type={job.config_type}" if job.config_type is not None else ""
         )
+        if analysis is None:
+            if args.all:
+                merged_jobs.append(job)
+                print(
+                    f"{relative_folder}: included by -all - {job.frame_count} "
+                    f"frame(s){config}; thermo not checked ({reason})"
+                )
+            else:
+                skipped += 1
+                print(f"{relative_folder}: skipped - {reason}")
+            continue
+
+        thermo, interval_ps = analysis
         if not thermo.warnings:
-            stable_jobs.append(job)
-            print(f"{relative_folder}: stable - {job.frame_count} frame(s){config}")
+            merged_jobs.append(job)
+            status = "included by -all (normal)" if args.all else "stable"
+            print(
+                f"{relative_folder}: {status} - {job.frame_count} frame(s){config}"
+            )
             continue
 
+        if args.all:
+            merged_jobs.append(job)
         indices = abnormal_frame_indices(thermo, job.frame_count, interval_ps)
         details = "; ".join(thermo.warnings)
         if not indices:
-            skipped += 1
-            print(
-                f"{relative_folder}: abnormal but no potential-energy region "
-                f"mapped to trajectory frames - {details}"
-            )
+            if args.all:
+                print(
+                    f"{relative_folder}: included by -all - {job.frame_count} "
+                    f"frame(s){config}; abnormal interval could not be mapped - {details}"
+                )
+            else:
+                skipped += 1
+                print(
+                    f"{relative_folder}: abnormal but no potential-energy region "
+                    f"mapped to trajectory frames - {details}"
+                )
             continue
+
         abnormal_jobs.append(TrajectoryJob(
             job.trajectory, job.frame_count, job.config_type, indices
         ))
-        print(
-            f"{relative_folder}: abnormal - extracted {len(indices)} of "
-            f"{job.frame_count} frame(s){config} - {details}"
-        )
+        if args.all:
+            print(
+                f"{relative_folder}: included by -all (abnormal) - all "
+                f"{job.frame_count} frame(s){config}; extracted {len(indices)} "
+                f"frame(s) from the first abnormal region - {details}"
+            )
+        else:
+            print(
+                f"{relative_folder}: abnormal - extracted {len(indices)} of "
+                f"{job.frame_count} frame(s) from the first abnormal region"
+                f"{config} - {details}"
+            )
 
-    write_merged(output, stable_jobs)
-    write_merged(abnormal_output, abnormal_jobs)
-    stable_frames = sum(job.frame_count for job in stable_jobs)
+    write_merged(output, merged_jobs)
+    if abnormal_jobs:
+        write_merged(abnormal_output, abnormal_jobs)
+    else:
+        abnormal_output.unlink(missing_ok=True)
+    merged_frames = sum(job.frame_count for job in merged_jobs)
     abnormal_frames = sum(len(job.indices) for job in abnormal_jobs)
-    print(
-        f"Wrote {stable_frames} frame(s) from {len(stable_jobs)} stable job(s) "
-        f"to {args.output}"
-    )
-    print(
-        f"Wrote {abnormal_frames} frame(s) from {len(abnormal_jobs)} abnormal "
-        f"job(s) to {args.abnormal_output}"
-    )
+    if args.all:
+        print(
+            f"Wrote {merged_frames} frame(s) from {len(merged_jobs)} readable "
+            f"job(s) to {args.output}"
+        )
+    else:
+        print(
+            f"Wrote {merged_frames} frame(s) from {len(merged_jobs)} stable "
+            f"job(s) to {args.output}"
+        )
+    if abnormal_jobs:
+        print(
+            f"Wrote {abnormal_frames} frame(s) from {len(abnormal_jobs)} "
+            f"abnormal job(s) to {args.abnormal_output}"
+        )
+    else:
+        print(f"No abnormal frames found; did not write {args.abnormal_output}")
     print(f"Skipped {skipped} unreadable or unmappable job(s).")
     return 0
 
-
 if __name__ == "__main__":
     _parser = argparse.ArgumentParser(description=__doc__)
     add_arguments(_parser)

{pymdkit-1.4.5 → pymdkit-1.4.7}/src/pymdkit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.4.5
+Version: 1.4.7
 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
@@ -70,7 +70,7 @@ directory for job sub-folders automatically.
 | `vasp-fe` | List VASP job final energies from lowest to highest |
 | `gather-contcar` | Collect CONTCARs from VASP job folders into one folder, renamed `<folder>.vasp` |
 | `gpumd-thermo` | Export and plot GPUMD thermo data and detect sustained equilibrium changes |
-| `gpumd-trjcat` | Merge stable GPUMD trajectories and extract abnormal time regions |
+| `gpumd-trjcat` | Merge normal or all GPUMD trajectories and extract the first abnormal region |
 | `pca` | Reduce descriptor data to two dimensions; optional FPS sampling |
 | `trj-extract` | Extract a GPUMD XYZ trajectory by time range |
 | `trj-sparse` | Deterministically retain a requested fraction of XYZ trajectory frames |
@@ -137,6 +137,7 @@ pmk gpumd-thermo                              # current job, or recursively scan
 pmk gpumd-thermo -t thermo.out -in run.in
 pmk gpumd-trjcat                            # stable frames -> train.xyz; abnormal regions -> abnormal.xyz
 pmk gpumd-trjcat -i traj.xyz -o train.xyz -ao abnormal.xyz
+pmk gpumd-trjcat -all                       # merge every readable trajectory into train.xyz
 pmk trj-extract -it traj.xyz -in run.in -b 100 -e 200 -o traj-100ps-200ps.xyz
 pmk trj-sparse -it example.xyz -r 0.5 -o sparse-example.xyz
 
@@ -177,11 +178,11 @@ 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 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.
+`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. For an abnormal run it also writes `abnormal-time.txt`, with one `BEGIN ps to END ps` interval per line; a normal rerun removes a stale file. 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. An abnormal classification always requires a mapped potential-energy change. When at least two lattice-parameter or volume signals show the same mapped transition, they may enable a more sensitive noise-relative energy test; this avoids a fixed eV or percentage-of-total-energy threshold that would depend on system size. Cell signals can corroborate and refine the energy interval, but can never classify a run by themselves. Temperature and all six pressure components remain diagnostics only and cannot classify an otherwise stationary run as abnormal by themselves. A lone cell-axis drift, an isolated spike, or an empty anomaly mask never triggers a whole-run fallback. Thermo plots use Arial when available and Matplotlib's built-in qualitative `Dark2` color cycle. They plot all six pressure components, use frameless upper-right legends with added vertical headroom, preserve correct Å units, and show abnormal regions as shaded legend entries 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.
 
-`gpumd-trjcat` recursively scans job subfolders for `traj.xyz`, `thermo.out`, and `run.in`. Stable trajectories are merged in deterministic folder order into `train.xyz` (or `-o`). For an abnormal job, frames from the structurally corroborated potential-energy region are written to `abnormal.xyz` (or `-ao`); if no energy region can be resolved, the dominant structural transition is used as a fallback so an abnormal job cannot produce an empty abnormal output. Frame times are obtained from `time_step` and `dump_xyz` in that job's `run.in`. Missing, unreadable, or unmappable jobs are skipped. When `<job>/model.xyz` contains `Config_type`, that value is applied to every exported frame while all other extended-XYZ bytes remain unchanged.
+`gpumd-trjcat` recursively scans job subfolders for `traj.xyz`, `thermo.out`, and `run.in`. By default, normal trajectories are merged in deterministic folder order into `train.xyz` (or `-o`), while only frames from the earliest mapped abnormal interval of each abnormal job are written to `abnormal.xyz` (or `-ao`). With `-all`, every readable full trajectory is merged into `train.xyz` regardless of normal, abnormal, missing-thermo, or failed-thermo status; an analyzable abnormal job still contributes its earliest abnormal interval to `abnormal.xyz`. If no mapped abnormal frames are found, `abnormal.xyz` is not created and a stale file at the selected `-ao` path is removed. Frame times are obtained from `time_step` and `dump_xyz` in that job's `run.in`. In default mode, missing, unreadable, or unmappable jobs are skipped. When `<job>/model.xyz` contains `Config_type`, that value is applied to every exported frame while all other extended-XYZ bytes remain unchanged.
 
 `trj-sparse` keeps `max(1, floor(frame_count × ratio))` frames without rewriting their extended-XYZ content. Selection is deterministic and starts with frame zero; for 100 frames and `-r 0.5`, it writes source indices `0, 2, ..., 98`.