runops 0.2.0__py3-none-any.whl

runops/templates/adapters/beach/summarize.py

@@ -0,0 +1,272 @@
+from __future__ import annotations
+
+import csv
+from pathlib import Path
+from typing import Any
+
+
+def _append_figure(summary: dict[str, Any], rel_path: str, caption: str) -> None:
+    figures = summary.setdefault("figures", [])
+    if not isinstance(figures, list):
+        return
+    figures.append({"path": rel_path, "caption": caption})
+
+
+def _find_output_dir(work_dir: Path) -> Path:
+    for candidate in (
+        work_dir / "latest",
+        work_dir / "outputs" / "latest",
+        work_dir / "outputs",
+        work_dir,
+    ):
+        if candidate.is_dir():
+            return candidate
+    return work_dir
+
+
+def _parse_summary_txt(path: Path) -> dict[str, Any]:
+    data: dict[str, Any] = {}
+    if not path.is_file():
+        return data
+
+    for line in path.read_text(encoding="utf-8").splitlines():
+        stripped = line.strip()
+        if not stripped or "=" not in stripped:
+            continue
+        key, value = stripped.split("=", 1)
+        key = key.strip()
+        value = value.strip()
+        try:
+            data[key] = int(value)
+            continue
+        except ValueError:
+            pass
+        try:
+            data[key] = float(value)
+            continue
+        except ValueError:
+            pass
+        data[key] = value
+    return data
+
+
+def _read_numeric_column(path: Path, field_name: str) -> list[float]:
+    if not path.is_file():
+        return []
+
+    values: list[float] = []
+    with open(path, encoding="utf-8", newline="") as f:
+        reader = csv.DictReader(f)
+        for row in reader:
+            if row is None:
+                continue
+            raw = row.get(field_name, "").strip()
+            if not raw:
+                continue
+            try:
+                values.append(float(raw))
+            except ValueError:
+                continue
+    return values
+
+
+def _save_fig(fig, output_path: Path) -> bool:
+    try:
+        fig.savefig(output_path, dpi=150, bbox_inches="tight")
+        import matplotlib.pyplot as plt
+
+        plt.close(fig)
+    except Exception:
+        return False
+    return True
+
+
+def _save_line_plot(
+    x_values: list[float],
+    y_values: list[float],
+    *,
+    title: str,
+    xlabel: str,
+    ylabel: str,
+    output_path: Path,
+) -> bool:
+    try:
+        import matplotlib
+
+        matplotlib.use("Agg")
+        import matplotlib.pyplot as plt
+    except Exception:
+        return False
+
+    fig, ax = plt.subplots(figsize=(6.0, 4.0))
+    ax.plot(x_values, y_values, linewidth=1.6)
+    ax.set_title(title)
+    ax.set_xlabel(xlabel)
+    ax.set_ylabel(ylabel)
+    ax.grid(True, linestyle=":", alpha=0.35)
+    fig.tight_layout()
+    return _save_fig(fig, output_path)
+
+
+def _save_bar_plot(
+    x_values: list[float],
+    y_values: list[float],
+    *,
+    title: str,
+    xlabel: str,
+    ylabel: str,
+    output_path: Path,
+) -> bool:
+    try:
+        import matplotlib
+
+        matplotlib.use("Agg")
+        import matplotlib.pyplot as plt
+    except Exception:
+        return False
+
+    fig, ax = plt.subplots(figsize=(6.4, 4.0))
+    ax.bar(x_values, y_values, width=0.9)
+    ax.set_title(title)
+    ax.set_xlabel(xlabel)
+    ax.set_ylabel(ylabel)
+    ax.grid(True, axis="y", linestyle=":", alpha=0.35)
+    fig.tight_layout()
+    return _save_fig(fig, output_path)
+
+
+def _try_make_beach_plots(
+    output_dir: Path,
+    fig_dir: Path,
+    summary: dict[str, Any],
+) -> None:
+    try:
+        from beach import Beach
+    except Exception:
+        return
+
+    try:
+        run = Beach(output_dir)
+    except Exception:
+        return
+
+    try:
+        fig, _ = run.plot_bar()
+        if _save_fig(fig, fig_dir / "charges_bar.png"):
+            _append_figure(summary, "figures/charges_bar.png", "Charge bar chart")
+    except Exception:
+        pass
+
+    try:
+        result = run.result
+        if result.triangles is not None:
+            fig, _ = run.plot_mesh()
+            if _save_fig(fig, fig_dir / "charge_mesh.png"):
+                _append_figure(summary, "figures/charge_mesh.png", "Charge mesh")
+    except Exception:
+        pass
+
+    try:
+        result = run.result
+        if result.triangles is not None:
+            fig, _ = run.plot_potential()
+            if _save_fig(fig, fig_dir / "potential_mesh.png"):
+                _append_figure(
+                    summary,
+                    "figures/potential_mesh.png",
+                    "Reconstructed potential mesh",
+                )
+    except Exception:
+        pass
+
+
+def summarize(run_dir: Path, base_summary: dict[str, Any]) -> dict[str, Any]:
+    """BEACH post-process scaffold."""
+
+    summary = dict(base_summary)
+    analysis_dir = run_dir / "analysis"
+    fig_dir = analysis_dir / "figures"
+    fig_dir.mkdir(parents=True, exist_ok=True)
+
+    output_dir = _find_output_dir(run_dir / "work")
+
+    for key, value in _parse_summary_txt(output_dir / "summary.txt").items():
+        summary.setdefault(key, value)
+
+    charges = _read_numeric_column(output_dir / "charges.csv", "charge_C")
+    if charges:
+        summary["charge_elements"] = len(charges)
+        summary["charge_total_c"] = float(sum(charges))
+        summary["charge_abs_sum_c"] = float(sum(abs(value) for value in charges))
+        summary["charge_abs_max_c"] = float(max(abs(value) for value in charges))
+        if _save_bar_plot(
+            [float(idx) for idx in range(len(charges))],
+            charges,
+            title="Charge by Element",
+            xlabel="Element index",
+            ylabel="Charge [C]",
+            output_path=fig_dir / "charge_distribution.png",
+        ):
+            _append_figure(
+                summary,
+                "figures/charge_distribution.png",
+                "Element charge distribution",
+            )
+
+    charge_history = _read_numeric_column(output_dir / "charge_history.csv", "charge_C")
+    if charge_history:
+        summary["charge_history_samples"] = len(charge_history)
+        if _save_line_plot(
+            [float(idx) for idx in range(len(charge_history))],
+            charge_history,
+            title="Charge History",
+            xlabel="Sample",
+            ylabel="Charge [C]",
+            output_path=fig_dir / "charge_history.png",
+        ):
+            _append_figure(
+                summary,
+                "figures/charge_history.png",
+                "Charge history trace",
+            )
+
+    potential_history = _read_numeric_column(
+        output_dir / "potential_history.csv",
+        "potential_V",
+    )
+    if potential_history:
+        summary["potential_history_samples"] = len(potential_history)
+        summary["potential_final_v"] = float(potential_history[-1])
+        if _save_line_plot(
+            [float(idx) for idx in range(len(potential_history))],
+            potential_history,
+            title="Potential History",
+            xlabel="Sample",
+            ylabel="Potential [V]",
+            output_path=fig_dir / "potential_history.png",
+        ):
+            _append_figure(
+                summary,
+                "figures/potential_history.png",
+                "Potential history trace",
+            )
+
+    performance_path = output_dir / "performance_profile.csv"
+    if performance_path.is_file():
+        try:
+            from beach.cli.plot_performance_profile import load_performance_profile
+        except Exception:
+            pass
+        else:
+            try:
+                _metadata, rows = load_performance_profile(performance_path)
+                if rows:
+                    hottest = max(rows, key=lambda row: float(row["rank_max_s"]))
+                    summary["profile_region_hottest"] = str(hottest["region"])
+                    summary["profile_rank_max_s"] = float(hottest["rank_max_s"])
+            except Exception:
+                pass
+
+    _try_make_beach_plots(output_dir, fig_dir, summary)
+
+    return summary

runops/templates/adapters/emses/agent_guide.md

@@ -0,0 +1,39 @@
+### EMSES (Electromagnetic Particle-in-Cell Simulator)
+
+#### 概要
+EMSES は 3D 電磁粒子シミュレーション (PIC) コード。
+MPI 並列で実行し、電磁場と荷電粒子の自己無撞着な時間発展を計算する。
+
+#### 入力ファイル
+- **`input/plasma.toml`** — メイン設定ファイル (TOML 形式)
+  - `[jobcon]`: `nstep` (総ステップ数) が最重要パラメータ
+  - `[tmgrid]`: `nx`, `ny`, `nz` (グリッド数), `dt` (時間刻み)
+  - `[[species]]`: 粒子種の定義 (質量比, 温度, 密度 etc.)
+  - `[emfield]`: 外部磁場・電場の設定
+  - `[[ptcond.objects]]`: 境界条件・導体オブジェクト
+
+#### 出力ファイル (`work/latest/` 以下)
+- `*.h5` — HDF5 形式の電磁場データ (ex, ey, ez, bx, by, bz, etc.)
+- `energy` — エネルギー時系列 (ASCII)。最終行のステップ番号で完了判定
+- `SNAPSHOT1/esdat*.h5` — リスタート用スナップショット
+- 各種診断ファイル: `ewave`, `chgacm1`, `influx`, `icur` 等
+
+#### 完了判定
+- `work/latest/energy` の最終行のステップ番号 ≥ `nstep` → completed
+- stderr に "error", "segmentation fault", "killed" → failed
+
+#### パラメータサーベイでよく変えるパラメータ
+- `tmgrid.dt`, `tmgrid.nx/ny/nz`
+- `species[0].temperature`, `species[0].density`
+- `emfield.ex0`, `emfield.bx0` (外部場)
+- `jobcon.nstep`
+
+#### ドキュメント・参考
+- EMSES ソースリポジトリの README / docs/
+- `plasma.toml` のスキーマは `format_version = 2` (structured TOML)
+- パラメータの dot 記法例: `tmgrid.nx=128`, `species.0.temperature=1.0e6`
+
+#### 実行コマンド
+```
+srun mpiemses3D input/plasma.toml -o work/latest
+```

runops/templates/adapters/emses/case.toml

@@ -0,0 +1,18 @@
+[case]
+name = ""
+simulator = "emses"
+launcher = "default"
+description = ""
+
+[params]
+# "tmgrid.nx" = 64
+# "tmgrid.ny" = 64
+# "tmgrid.nz" = 64
+# "tmgrid.dt" = 1.0
+# "jobcon.nstep" = 10000
+
+[job]
+partition = ""
+nodes = 1
+ntasks = 1
+walltime = "01:00:00"

runops/templates/adapters/emses/plasma.toml

@@ -0,0 +1,118 @@
+#:schema https://raw.githubusercontent.com/CS12-Laboratory/mpiemses3d-schema/refs/heads/main/plasma.schema.json
+#
+# Minimal EMSES plasma.toml stub generated by `runops case new -s emses`.
+#
+# This template is a small working starting point — enough to launch a
+# 1D test plasma run without external boundaries.  Adjust species, grid,
+# boundary conditions, and ptcond to match your problem.  See
+# `refs/MPIEMSES3D/docs/Parameters.md` (or the project's CLAUDE.md) for
+# the full parameter reference, or run `runops case new ... ` without
+# `--minimal` to drop in the full reference template via refs/.
+
+[meta]
+format_version = 2
+
+[meta.unit_conversion]
+dx = 0.5
+to_c = 10000.0
+
+# ===========================================================================
+# Species — one electron + one ion (proton).  Add more [[species]] blocks as
+# needed.  Run `emu generate -u plasma.toml` to populate [meta.physical] with
+# SI values derived from the simulation units below.
+# ===========================================================================
+
+[[species]]
+wp = 2.10390362104881
+qm = -1.0
+path = 44.237443494336965
+peth = 44.237443494336965
+vdri = 0.0
+vdthz = 0.0
+vdthxy = 0.0
+npin = 5242880
+np = 10485760
+npbnd = [0, 0, 2]
+inpf = 1
+inpb = 1
+injct = 1
+npr = 524288
+nflag_emit = 0
+nepl = 0
+ipahdf = 0
+ipadig = 1024
+ipaxyz = [0, 0, 0, 0, 0, 0, 0]
+
+[[species]]
+wp = 0.04909886429062906
+qm = 0.000544617021778308
+path = 1.032370595764297
+peth = 1.032370595764297
+vdri = 0.0
+vdthz = 0.0
+vdthxy = 0.0
+npin = 5242880
+np = 10485760
+npbnd = [0, 0, 2]
+inpf = 1
+inpb = 1
+injct = 1
+npr = 524288
+nflag_emit = 0
+nepl = 0
+ipahdf = 0
+ipadig = 1024
+
+# ===========================================================================
+[esorem]
+emflag = 0   # 0 = electrostatic, 1 = electromagnetic
+
+[jobcon]
+jobnum = [0, 1]
+nstep = 10000
+
+[digcon]
+hdfdigstart = 0
+intfoc = 100
+ifdiag = 1000
+ijdiag = 1000
+daverg = 1
+ifxyz = [1, 1, 1, 1, 1, 1, 1]
+ijxyz = [1, 1, 1]
+
+[plasma]
+wc = 0.0
+cv = 10000.0
+phiz = 0.0
+phixy = 0.0
+
+[tmgrid]
+dt = 0.002
+nx = 32
+ny = 32
+nz = 256
+
+[system]
+ionchg = 0
+nfbnd = [0, 0, 1]
+mtd_vbnd = [0, 0, 1]
+nflag_ecrct = 1
+
+[ptcond]
+modeww = -2
+zssurf = 60.0
+npc = 0
+npcg = 0
+pcgs = [0]
+ccgs = [0]
+mtd_vchg = [0]
+
+[[ptcond.boundaries]]
+type = "flat-surface"
+
+[mpi]
+nodes = [2, 4, 32]
+
+[gradema]
+grad_coef = 1.0
+smooth_coef = 1.0