beach-bem 0.6.2__tar.gz

beach_bem-0.6.2/AGENTS.md

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+# AGENTS.md
+
+Always review in Japanese.
+
+## Project overview
+This repository provides **BEACH (BEM + Accumulated CHarge)**.
+
+- Main simulation engine: **Fortran** (`src/`, `app/`, managed by fpm)
+- Python layer: post-processing / visualization / workload utilities (`beach/`, `examples/`)
+
+Core batch loop (current Fortran implementation):
+1) compute E (and optional uniform B) from boundary-element charges
+2) advance particles with Boris pusher
+3) detect first collision against triangle elements
+4) deposit charge to hit element (insulator accumulation)
+5) commit charge deltas per batch and update stats/history
+
+v0.x focuses on insulator accumulation. Keep extension points for conductor/resistive models.
+
+## Repo layout
+- `src/`, `app/`: Fortran runtime and physics core
+- `tests/fortran`: Fortran unit/integration tests (fpm targets)
+- `beach/`: Python package for reading/plotting Fortran outputs
+- `tests/python`: Python tests for CLI/result utilities
+- `examples/`: runnable configs and helper scripts
+- `docs/`, `SPEC.md`: behavior/spec documentation
+
+## Setup
+Python utilities:
+- `python -m pip install "git+https://github.com/Nkzono99/BEACH.git"` (builds Python + Fortran `beach` binary via `make`)
+- `python -m pip install -U pip setuptools wheel`
+- `python -m pip install -e . --no-build-isolation`
+
+Fortran execution/testing requires a Fortran compiler (`gfortran` etc.) and `fpm`.
+
+## How to run
+Fortran main (recommended):
+- `python -m pip install "git+https://github.com/Nkzono99/BEACH.git"`
+- `beach examples/beach.toml`
+
+Fortran main (developer direct run):
+- `make`
+- `fpm run --profile release --flag "-fopenmp" -- examples/beach.toml`
+
+Python CLI examples:
+- `beach-inspect outputs/latest`
+- `beach-animate-history outputs/latest --quantity charge --save-gif outputs/latest/charge_history.gif`
+- `beach-estimate-workload examples/beach.toml --threads 8`
+
+## Tests / quality
+- Python tests: `pytest -q`
+- Python lint: `ruff check .`
+- Fortran tests: `fpm test` (or per-target via `fpm test --target <name>`)
+
+## Coding rules
+- Do not change public APIs without updating docs + examples.
+- For core simulation behavior, treat Fortran implementation and docs (`SPEC.md`) as source of truth.
+- Keep algorithms correctness-first; gate performance features behind flags.
+- Add/extend tests when modifying field, collision, boundary, injection, or resume logic.
+- Keep Python side lightweight; avoid heavy dependencies unless justified.
+
+## Simulator invariants (v0.x)
+- Interaction: absorption only (default).
+- Surface model: insulator accumulation only.
+- Batch execution: run for configured `sim.batch_count` batches.
+- Per-particle advance limit: `sim.max_step`.
+- `tol_rel` is currently a monitoring/output metric and **not** an early-stop condition.

beach_bem-0.6.2/LICENSE

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beach_bem-0.6.2/MANIFEST.in

@@ -0,0 +1,18 @@
+include LICENSE
+include README.md
+include AGENTS.md
+include SPEC.md
+include pyproject.toml
+include setup.py
+include Makefile
+include install.sh
+include fpm.toml
+
+recursive-include app *.f90
+recursive-include src *.f90 *.F90
+recursive-include beach *.py
+recursive-include docs *.md
+recursive-include env *.env *.md
+recursive-include examples *.toml *.py *.sh
+recursive-include tests/fortran *.f90
+recursive-include tests/python *.py

beach_bem-0.6.2/Makefile

@@ -0,0 +1,61 @@
+.PHONY: \
+	install install-local install-auto install-generic install-camphor install-camphor-local \
+	install-intel install-intel-local \
+	build run test \
+	build-mpi run-mpi test-mpi
+
+FPM ?= fpm
+PROFILE ?= release
+CONFIG ?= beach.toml
+OPENMP_FLAG ?= -fopenmp
+INSTALL_PROFILE ?= auto
+
+MPI_FC ?= mpiifort
+MPI_OPENMP_FLAG ?= -qopenmp
+MPI_CPP_FLAG ?= -fpp -DUSE_MPI
+MPI_NP ?= 2
+MPI_RUNNER ?= mpirun -n $(MPI_NP)
+
+install:
+	BUILD_PROFILE=$(INSTALL_PROFILE) ./install.sh
+
+install-local:
+	BUILD_PROFILE=$(INSTALL_PROFILE) PREFIX=$(PWD)/.local ./install.sh
+
+install-auto:
+	BUILD_PROFILE=auto ./install.sh
+
+install-generic:
+	BUILD_PROFILE=generic ./install.sh
+
+install-camphor:
+	BUILD_PROFILE=camphor ./install.sh
+
+install-camphor-local:
+	BUILD_PROFILE=camphor PREFIX=$(PWD)/.local-intel ./install.sh
+
+install-intel:
+	$(MAKE) install-camphor
+
+install-intel-local:
+	$(MAKE) install-camphor-local
+
+build:
+	$(FPM) build --profile $(PROFILE) --flag "$(OPENMP_FLAG)"
+
+run:
+	$(FPM) run --profile $(PROFILE) --flag "$(OPENMP_FLAG)" -- $(CONFIG)
+
+test:
+	$(FPM) test --profile debug --flag "$(OPENMP_FLAG)"
+
+build-mpi:
+	FPM_FC=$(MPI_FC) $(FPM) build --profile $(PROFILE) --flag "$(MPI_CPP_FLAG) $(MPI_OPENMP_FLAG)"
+
+run-mpi:
+	FPM_FC=$(MPI_FC) $(FPM) run --profile $(PROFILE) --flag "$(MPI_CPP_FLAG) $(MPI_OPENMP_FLAG)" \
+		--runner "$(MPI_RUNNER)" -- $(CONFIG)
+
+test-mpi:
+	FPM_FC=$(MPI_FC) $(FPM) test --target test_mpi_hybrid --profile debug \
+		--flag "$(MPI_CPP_FLAG) $(MPI_OPENMP_FLAG)" --runner "$(MPI_RUNNER)"

beach_bem-0.6.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: beach-bem
+Version: 0.6.2
+Summary: BEACH (BEM + Accumulated CHarge): BEM surface-charging + test-particle prototype (insulator mode) with hybrid E-field and Boris pusher.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: numpy>=1.24
+Requires-Dist: tomli>=2.0.1; python_version < "3.11"
+Dynamic: license-file
+
+# BEACH（BEM + Accumulated CHarge）
+
+BEACH は、**BEM（境界要素法）ベースの表面帯電 + テスト粒子追跡シミュレータ**です。  
+計算本体は Fortran（`fpm` 管理）、Python は後処理・可視化を担当します。
+
+v0.x の主対象は **insulator accumulation（絶縁体への電荷蓄積）** です。
+
+## 推奨ワークフロー
+
+通常利用では、**`pip install git+...` で導入して `beach` を実行する運用**を推奨します。  
+`pip install -e` や `make` は、開発に参加する場合の手順として扱います。
+
+## 1. 利用者向けセットアップ
+
+### 1.1 前提ツール
+
+```bash
+make --version
+gfortran --version
+fpm --version
+python --version
+```
+
+### 1.2 Git URL から一括インストール（推奨）
+
+```bash
+python -m pip install -U pip setuptools wheel
+python -m pip install "git+https://github.com/Nkzono99/BEACH.git"
+```
+
+このインストールでは、ビルド時に `make install` が実行され、Python 側と Fortran 実行バイナリ（`beach`）が同時に導入されます。
+ユーザーインストール時は `~/.local/bin` に入るため、必要なら PATH を追加してください。
+pip 経由のビルドでは既定で `INSTALL_PROFILE=auto` を使います。必要なら `INSTALL_PROFILE=camphor` などを環境変数で上書きできます。
+`auto` 失敗時は既定で `generic` へフォールバックします。無効化したい場合は `BEACH_PIP_FALLBACK_GENERIC=0` を指定してください。
+
+```bash
+export PATH="$HOME/.local/bin:$PATH"
+```
+
+## 2. 実行
+
+### 2.1 推奨: `beach` コマンド
+
+```bash
+beach examples/beach.toml
+```
+
+引数なしの場合は、カレントディレクトリの `beach.toml` を自動読込します。
+
+### 2.2 出力確認
+
+```bash
+ls outputs/latest
+beach-inspect outputs/latest
+```
+
+主な出力:
+
+- `summary.txt`
+- `charges.csv`
+- `mesh_triangles.csv`
+- `charge_history.csv`（`history_stride > 0` のとき）
+
+### 2.3 可視化
+
+```bash
+beach-inspect outputs/latest \
+  --save-bar outputs/latest/charges_bar.png \
+  --save-mesh outputs/latest/charges_mesh.png
+
+beach-animate-history outputs/latest \
+  --quantity charge \
+  --save-gif outputs/latest/charge_history.gif \
+  --total-frames 200
+
+beach-plot-potential-slices outputs/latest \
+  --grid-n 200 \
+  --vmin -20 --vmax 20 \
+  --save outputs/latest/potential_slices.png
+```
+
+## 3. 運用でよく使うコマンド
+
+### 3.1 負荷見積もり
+
+```bash
+beach-estimate-workload examples/beach.toml --threads 8
+```
+
+### 3.2 再開実行
+
+```toml
+[output]
+dir = "outputs/latest"
+resume = true
+```
+
+同じ `output.dir` で `beach` を再実行すると続きから計算します。
+
+## 4. 開発に携わる場合
+
+ローカル開発では、Python と Fortran を分けて運用するのが便利です。
+
+### 4.1 Python 側（編集可能インストール）
+
+```bash
+python -m pip install -U pip setuptools wheel
+python -m pip install -e . --no-build-isolation
+```
+
+### 4.2 Fortran 実行系（`make`）
+
+```bash
+make
+```
+
+`make` のデフォルトターゲットは `install` で、`BUILD_PROFILE=auto`（ホスト自動判定）を使います。
+必要に応じて明示指定できます。
+
+```bash
+make install-generic
+make install-camphor
+```
+
+### 4.3 `fpm` 直接実行（開発向け）
+
+```bash
+fpm run --profile release --flag "-fopenmp" -- examples/beach.toml
+```
+
+MPI + OpenMP（`USE_MPI` 有効化）:
+
+```bash
+FPM_FC=mpiifort \
+fpm run --profile release --flag "-fpp -DUSE_MPI -qopenmp" \
+  --runner "mpirun -n 4" -- examples/beach.toml
+```
+
+### 4.4 テスト
+
+```bash
+pytest -q
+fpm test
+```
+
+## 5. プロジェクト構成
+
+- [`src/`](src/), [`app/`](app/): Fortran 本体
+- [`tests/fortran/`](tests/fortran/): Fortran テスト
+- [`beach/`](beach/): Python 後処理ライブラリ
+- [`tests/python/`](tests/python/): Python テスト
+- [`examples/`](examples/): 設定例・補助スクリプト
+- [`docs/`](docs/): 運用ドキュメント
+- [`SPEC.md`](SPEC.md): 現行 Fortran 実装仕様
+
+## 6. ドキュメント案内
+
+- Fortran 実行フロー: [`docs/fortran_workflow.md`](docs/fortran_workflow.md)
+- `beach.toml` 仕様: [`docs/fortran_parameter_file.md`](docs/fortran_parameter_file.md)
+- 実装仕様（source of truth）: [`SPEC.md`](SPEC.md)
+- 設定サンプル: [`examples/beach.toml`](examples/beach.toml)

beach_bem-0.6.2/README.md

@@ -0,0 +1,161 @@
+# BEACH（BEM + Accumulated CHarge）
+
+BEACH は、**BEM（境界要素法）ベースの表面帯電 + テスト粒子追跡シミュレータ**です。  
+計算本体は Fortran（`fpm` 管理）、Python は後処理・可視化を担当します。
+
+v0.x の主対象は **insulator accumulation（絶縁体への電荷蓄積）** です。
+
+## 推奨ワークフロー
+
+通常利用では、**`pip install git+...` で導入して `beach` を実行する運用**を推奨します。  
+`pip install -e` や `make` は、開発に参加する場合の手順として扱います。
+
+## 1. 利用者向けセットアップ
+
+### 1.1 前提ツール
+
+```bash
+make --version
+gfortran --version
+fpm --version
+python --version
+```
+
+### 1.2 Git URL から一括インストール（推奨）
+
+```bash
+python -m pip install -U pip setuptools wheel
+python -m pip install "git+https://github.com/Nkzono99/BEACH.git"
+```
+
+このインストールでは、ビルド時に `make install` が実行され、Python 側と Fortran 実行バイナリ（`beach`）が同時に導入されます。
+ユーザーインストール時は `~/.local/bin` に入るため、必要なら PATH を追加してください。
+pip 経由のビルドでは既定で `INSTALL_PROFILE=auto` を使います。必要なら `INSTALL_PROFILE=camphor` などを環境変数で上書きできます。
+`auto` 失敗時は既定で `generic` へフォールバックします。無効化したい場合は `BEACH_PIP_FALLBACK_GENERIC=0` を指定してください。
+
+```bash
+export PATH="$HOME/.local/bin:$PATH"
+```
+
+## 2. 実行
+
+### 2.1 推奨: `beach` コマンド
+
+```bash
+beach examples/beach.toml
+```
+
+引数なしの場合は、カレントディレクトリの `beach.toml` を自動読込します。
+
+### 2.2 出力確認
+
+```bash
+ls outputs/latest
+beach-inspect outputs/latest
+```
+
+主な出力:
+
+- `summary.txt`
+- `charges.csv`
+- `mesh_triangles.csv`
+- `charge_history.csv`（`history_stride > 0` のとき）
+
+### 2.3 可視化
+
+```bash
+beach-inspect outputs/latest \
+  --save-bar outputs/latest/charges_bar.png \
+  --save-mesh outputs/latest/charges_mesh.png
+
+beach-animate-history outputs/latest \
+  --quantity charge \
+  --save-gif outputs/latest/charge_history.gif \
+  --total-frames 200
+
+beach-plot-potential-slices outputs/latest \
+  --grid-n 200 \
+  --vmin -20 --vmax 20 \
+  --save outputs/latest/potential_slices.png
+```
+
+## 3. 運用でよく使うコマンド
+
+### 3.1 負荷見積もり
+
+```bash
+beach-estimate-workload examples/beach.toml --threads 8
+```
+
+### 3.2 再開実行
+
+```toml
+[output]
+dir = "outputs/latest"
+resume = true
+```
+
+同じ `output.dir` で `beach` を再実行すると続きから計算します。
+
+## 4. 開発に携わる場合
+
+ローカル開発では、Python と Fortran を分けて運用するのが便利です。
+
+### 4.1 Python 側（編集可能インストール）
+
+```bash
+python -m pip install -U pip setuptools wheel
+python -m pip install -e . --no-build-isolation
+```
+
+### 4.2 Fortran 実行系（`make`）
+
+```bash
+make
+```
+
+`make` のデフォルトターゲットは `install` で、`BUILD_PROFILE=auto`（ホスト自動判定）を使います。
+必要に応じて明示指定できます。
+
+```bash
+make install-generic
+make install-camphor
+```
+
+### 4.3 `fpm` 直接実行（開発向け）
+
+```bash
+fpm run --profile release --flag "-fopenmp" -- examples/beach.toml
+```
+
+MPI + OpenMP（`USE_MPI` 有効化）:
+
+```bash
+FPM_FC=mpiifort \
+fpm run --profile release --flag "-fpp -DUSE_MPI -qopenmp" \
+  --runner "mpirun -n 4" -- examples/beach.toml
+```
+
+### 4.4 テスト
+
+```bash
+pytest -q
+fpm test
+```
+
+## 5. プロジェクト構成
+
+- [`src/`](src/), [`app/`](app/): Fortran 本体
+- [`tests/fortran/`](tests/fortran/): Fortran テスト
+- [`beach/`](beach/): Python 後処理ライブラリ
+- [`tests/python/`](tests/python/): Python テスト
+- [`examples/`](examples/): 設定例・補助スクリプト
+- [`docs/`](docs/): 運用ドキュメント
+- [`SPEC.md`](SPEC.md): 現行 Fortran 実装仕様
+
+## 6. ドキュメント案内
+
+- Fortran 実行フロー: [`docs/fortran_workflow.md`](docs/fortran_workflow.md)
+- `beach.toml` 仕様: [`docs/fortran_parameter_file.md`](docs/fortran_parameter_file.md)
+- 実装仕様（source of truth）: [`SPEC.md`](SPEC.md)
+- 設定サンプル: [`examples/beach.toml`](examples/beach.toml)