lammps-analysis-tools 1.0.0__py3-none-any.whl

lammps_analysis_tools-1.0.0.dist-info/LICENSE

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+Copyright (c) 2026 tgraphite. All rights reserved.
+
+This software and its accompanying documentation (the "Software") are
+proprietary. No permission is granted to use, copy, modify, merge, publish,
+distribute, sublicense, or sell copies of the Software without the prior
+written permission of the copyright holder.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lammps_analysis_tools-1.0.0.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: lammps-analysis-tools
+Version: 1.0.0
+Summary: Trajectory analysis for LAMMPS data/dump files, with GROMACS-compatible commands
+Author: tgraphite
+License: Proprietary
+Project-URL: Homepage, https://github.com/tgraphite/LammpsAnalysisTools
+Project-URL: Documentation, https://github.com/tgraphite/LammpsAnalysisTools/tree/main/docs/manual
+Project-URL: Repository, https://github.com/tgraphite/LammpsAnalysisTools
+Project-URL: Issues, https://github.com/tgraphite/LammpsAnalysisTools/issues
+Keywords: molecular dynamics,LAMMPS,GROMACS,trajectory analysis,RDF,hydrogen bonds,free volume,SASA
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: Other/Proprietary License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy >=1.22
+Requires-Dist: scipy >=1.8
+Requires-Dist: pyyaml >=5.4
+Requires-Dist: matplotlib >=3.5
+Requires-Dist: MDAnalysis >=2.4
+Requires-Dist: ase >=3.22
+
+# lat — LAMMPS Analysis Tool
+
+[![PyPI](https://img.shields.io/pypi/v/lammps-analysis-tools.svg)](https://pypi.org/project/lammps-analysis-tools/)
+[![Python](https://img.shields.io/pypi/pyversions/lammps-analysis-tools.svg)](https://pypi.org/project/lammps-analysis-tools/)
+
+面向 LAMMPS `data` / `lammpstrj` 的轨迹分析工具。命令风格对齐 GROMACS（`-s` 拓扑、`-f` 轨迹、单横线参数），
+输出统一为带审计头的 CSV，适合脚本批处理、回归与作图。
+
+## 特性
+
+- **直接读 LAMMPS**：`*.data` / `*.lmp` + `*.lammpstrj`，自动识别 `atom_style`，按质量推断元素。
+- **GROMACS 兼容输入**：`.tpr/.gro/.pdb` + `.xtc/.trr/.gro` 可直接分析，便于交叉验证。
+- **周期几何一致性**：所有距离、质心、整分子复原、网格与曲面都走同一套最小镜像实现。
+- **可复现输出**：文件名即意图；CSV 头记录命令、选择、参数、警告与标量；同名输出自动备份。
+- **自解释**：`lat --help` 列出模块，`lat <module> -h` 给出参数与默认值，`lat describe -module <name>` 给出完整契约。
+
+## 安装
+
+需要 Python ≥ 3.9。
+
+    pip install lammps-analysis-tools
+
+安装后命令是 `lat`：
+
+    lat --version
+    lat --help
+
+升级：
+
+    pip install --upgrade lammps-analysis-tools
+
+从源码或离线安装：
+
+    git clone https://github.com/tgraphite/LammpsAnalysisTools.git
+    cd LammpsAnalysisTools
+    bash install.sh
+    export PATH="$HOME/.local/bin:$PATH"
+
+`install.sh` 会建独立虚拟环境、安装依赖，并把 `lat` 放到 `~/.local/bin`；系统 Python < 3.9 时会用
+`uv` 引导一个私有 Python 3.11。也可以直接 `pip install .`。
+
+依赖：numpy、scipy、pyyaml、matplotlib、MDAnalysis、ase。
+
+## 快速开始
+
+    # 径向分布函数 + 配位数
+    lat rdf -s system.data -f run.lammpstrj -sel1 "type 2" -sel2 "type 5" -cutoff 10 -o out
+
+    # 沿 z 的密度剖面
+    lat density -s system.data -f run.lammpstrj -axis z -nbins 200 -o out
+
+    # 均方位移与扩散系数
+    lat msd -s system.data -f run.lammpstrj -sel "type 2" -o out
+
+    # 画图（输入是上一步的 CSV）
+    lat plot1d -f out.rdf.out.csv -o rdf.png
+
+结果写入当前目录或 `-o` 指定的基名：
+
+    out.rdf.out.csv
+    out.rdf.cn.out.csv
+
+## 支持输入
+
+| | 拓扑 | 轨迹 |
+|---|---|---|
+| LAMMPS（首选） | `.data` / `.lmp`：Masses、Atoms；含 Bonds 才能做氢键/整分子分析 | `.lammpstrj`（dump） |
+| GROMACS | `.tpr` / `.gro` / `.pdb` | `.xtc` / `.trr` / `.gro` |
+
+- 自动识别 `atomic`、`charge`、`molecular`、`full`，支持 `full/kk` 等加速器后缀；六列歧义时用 `-style`。
+- 类型→元素默认按质量 ±0.2% 匹配；不确定时用 `-types` 显式指定，或让 dump 带 `element` 列。
+- 坐标支持 `x/y/z`、`xu/yu/zu`、`xs/ys/zs`、`xsu/ysu/zsu`；带 `ix/iy/iz` 可解包。
+- 反应轨迹原子数逐帧变化时会报错，并提示用 `-frame_range` / `-stride` 限定到一致窗口。
+
+## 模块总览
+
+| 模块 | 用途 | 手册 |
+|---|---|---|
+| `rdf` | 径向分布函数 g(r) 与配位数 | [rdf](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/rdf.md) |
+| `density` | 一维/二维密度剖面 | [density](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/density.md) |
+| `msd` | 均方位移与扩散系数 | [msd](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/msd.md) |
+| `gyrate` | 回转半径 Rg | [gyrate](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/gyrate.md) |
+| `rms` | RMSD / RMSF | [rms](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/rms.md) |
+| `contact` | 两组间接触数与距离 | [contact](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/contact.md) |
+| `hbond` | 氢键数量、寿命与空间分布 | [hbond](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/hbond.md) |
+| `agg` | SSIP / CIP / AGG 离子聚合形态 | [agg](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/agg.md) |
+| `cluster` | 配位数与团簇尺寸分布 | [cluster](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/cluster.md) |
+| `pistack` | π–π 堆积 | [pistack](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/pistack.md) |
+| `freevol` | 自由体积、孔径分布、连通性 | [freevol](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/freevol.md) |
+| `sasa` | 溶剂可及表面积 | [sasa](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/sasa.md) |
+| `residence` | 配体滞留时间 | [residence](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/residence.md) |
+| `transport` | 扩散、Nernst–Einstein、Green–Kubo | [transport](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/transport.md) |
+| `occupancy` | 区域占据、穿越、首次通过 | [occupancy](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/occupancy.md) |
+| `select` | 检查选择、导出 .ndx | [select](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/select.md) |
+| `describe` | 模块清单与契约 | [describe](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/describe.md) |
+| `plot1d` | 一维 CSV 绘图 | [plot1d](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/plot1d.md) |
+| `plot2d` | 二维 CSV 绘图 | [plot2d](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/plot2d.md) |
+
+完整手册（公共参数、输入、选择语法、输出契约）：[docs/manual](https://github.com/tgraphite/LammpsAnalysisTools/tree/main/docs/manual)。
+
+## 公共参数
+
+| 参数 | 说明 |
+|---|---|
+| `-s, -topo` | 拓扑文件（分析模块必填） |
+| `-f, -traj` | 轨迹文件 |
+| `-o` | 输出基名；缺省用拓扑文件名 |
+| `-unit` | 长度单位：`real`、`metal`、`lj`；缺省用配置 |
+| `-style` | 强制 LAMMPS `atom_style` |
+| `-types` | type→元素映射文件，每行 `type element` |
+| `-index, -n` | GROMACS `.ndx`，为选择提供命名组 |
+| `-frame_range` | 帧窗口 `start:stop[:stride]`，stop 不含 |
+| `-stride` | 每隔多少帧取一帧 |
+| `-v` | 显示 INFO 进度 |
+| `-debug` | 额外写 JSON 审计 |
+| `-h` | 模块帮助（含默认值） |
+| `-V, --version` | 版本号 |
+
+PBC 始终开启，所有距离使用最小镜像。时间轴是帧号，不解析文件中的物理时间。
+
+## 选择语法
+
+MDAnalysis 风格子集，支持 `and`、`or`、`not` 与括号；相邻关键字隐含 `and`。
+
+| 关键字 | 含义 | LAMMPS | GROMACS |
+|---|---|---|---|
+| `all` | 全部原子 | 是 | 是 |
+| `type` | 原子类型 | 是 | 是 |
+| `element` | 元素符号 | 是（需推断或 `-types`） | 是 |
+| `mol` | 分子 ID | 是（需分子信息） | 是 |
+| `id` | 原子 id | 是 | 是 |
+| `index` | 0-based 原子序号 | 是 | 是 |
+| `name` | 原子名 | 否 | 是 |
+| `resname` | 残基名 | 否 | 是 |
+| `resid` | 残基号 | 否 | 是 |
+
+    -sel "type 2"
+    -sel "type 2 or type 5"
+    -sel1 "resname LI" -sel2 "resname FSI"
+    -sel "all and not type 1"
+
+单选择模块用 `-sel`；双选择模块用 `-sel1`/`-sel2`。先运行 `lat select` 验证命中。
+
+## 输出
+
+- 结果全部写入 CSV；stdout 为空，进度/警告/错误走 stderr。
+- 文件名：`<basename>.<tag>[.<mode>].out.csv`。
+- 文件头以 `#` 开头，包含 program、module、command、selections、definitions、frame_range、
+  scalars、warning、title、xlabel、ylabel、columns，最后是 `# --- data ---`。
+- 标量（首壳配位数、D、R²、寿命、积分等）在 `# scalars:` 行，分号分隔。
+- 同名文件先备份为 `.bak.1`、`.bak.2`……，不会静默覆盖。
+- 退出码：0 成功，1 参数/输入/计算错误，130 中断；警告不改变退出码。
+
+## 绘图
+
+`plot1d` / `plot2d` 只读 CSV，计算与绘图解耦。
+
+    lat plot1d -f out.rdf.out.csv -o rdf.png
+    lat plot1d -f out.agg.labels.out.csv -columns A_SSIP,A_CIP,A_AGG -o spec.png
+    lat plot1d -f out.agg.labels.out.csv -stack -o spec_stack.png
+    lat plot2d -f out.density.2d.out.csv -o density2d.png
+
+`-smooth`（`none`/`gaussian`/`savgol`）只在绘图阶段生效，CSV 始终是原始值；
+`-bar` 与 `-stack` 互斥，且不做平滑。
+
+## 配置
+
+默认值来自 `lat.yaml`：源码树是 `config/lat.yaml`，安装后是包内 `data/lat.yaml`。
+命令行覆盖配置。
+
+| 环境变量 | 作用 |
+|---|---|
+| `LAT_CONFIG` | 使用自定义配置文件 |
+| `LAT_VENV` | `install.sh` 创建的虚拟环境路径 |
+| `LAT_BIN` | `install.sh` 放置 `lat` 的目录 |
+| `PYTHON` | `install.sh` 使用的解释器 |
+
+## 文档
+
+- 逐模块手册：[docs/manual](https://github.com/tgraphite/LammpsAnalysisTools/tree/main/docs/manual)
+- 公共参数与输出契约：[common.md](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/manual/common.md)
+- 版本变更：[CHANGELOG.md](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/docs/CHANGELOG.md)
+
+## 常见问题
+
+**选择命中 0 个原子？** 用 `lat select` 检查表达式；LAMMPS 拓扑通常没有 `resname`/`name`。
+
+**元素推断失败？** 补 `Masses`，或让 dump 带 `element` 列，或用 `-types`。
+
+**氢键报 “no donor”？** 给体只认 N/O/F/S/Cl/Br/I 上的 H；C–H 不是给体。
+
+**MSD 提示没有 image flags？** 轨迹只有 wrapped 坐标，MSD 可能饱和；改用带 `xu/yu/zu` 或 `ix/iy/iz` 的 dump。
+
+**freevol 报三斜盒？** 体素网格只支持正交且固定的盒子；改用分子/原子对分析或正交化盒子。
+
+## 许可
+
+Proprietary。详见 [LICENSE](https://github.com/tgraphite/LammpsAnalysisTools/blob/main/LICENSE)。

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+lat/modules/describe.py,sha256=KHIRqZjv18KB7sXdWFHrJA7sD8xFMyBrf0EIzn_YB3g,1384
+lat/modules/freevol.py,sha256=9faFrq_WaQew4BG7AzKJhmi8-KFD1iX_LywrhBGxqPM,15415
+lat/modules/gyrate.py,sha256=ySh_mQFvSNeNFs1M8w-Sb_AHBOo0jN0gimEZCNcpX74,3582
+lat/modules/hbond.py,sha256=OhV68WM_kRYHLsbHmYe3iuFfE3J017fJVh8g_X_K2h0,14911
+lat/modules/msd.py,sha256=MyBtnZenjo5-MN3vDdEYsEmfRHYqYM65yu6QgaWDTt8,5586
+lat/modules/occupancy.py,sha256=5-xJXMH7thhr7K6DixcKlbx3Q_RmtFOC-bCpLEd62kw,7347
+lat/modules/pistack.py,sha256=d8LCLuGSgIXL-biURkhOjmIEBg9W-1AkV_ZvoVlCnoY,5618
+lat/modules/rdf.py,sha256=eJV981C55lYHQqHmD6BfzpIWbyZHP0748ku_zk2Eqr0,6867
+lat/modules/residence.py,sha256=kiqoUcmoz2Hs1-HoIoc8giLUpFL7vTMaoZrX3dPJktA,7577
+lat/modules/rms.py,sha256=jp093XWbmSK0lO0y8uT2CNpr8RQ9wIRfCFVVnneay-M,6139
+lat/modules/sasa.py,sha256=QkuvkNvd7bBL-tZM1Cst6vF4GDV5eI9gIojzR3KueVY,3359
+lat/modules/select.py,sha256=thtgMK28gEwB75os4YDYeaokybxg41njlNA1etpvX1E,2738
+lat/modules/transport.py,sha256=mh45dp9svltlZHXf-0uos0FoI3-EgaJohijJzWz8Mh8,7806
+lat/plotting/__init__.py,sha256=0ZnzpHadshqLFHpnIjGLiPUrHIyghXBEaxDdKEZ3xN0,189
+lat/plotting/plot1d.py,sha256=DhkM2ZF-0IvTdNEwhFrzLiaGhsyq7lJ_n-DkVUH-DzI,5781
+lat/plotting/plot2d.py,sha256=Hjr9CRZbtHa4YHqjBbh1HQhnJxSqASflBFZcdi4Gy9E,2760
+lammps_analysis_tools-1.0.0.dist-info/LICENSE,sha256=VoRURheY1Xmtlomv4tvkvlSZbBjH0BXJ_ncieFHd1Ug,777
+lammps_analysis_tools-1.0.0.dist-info/METADATA,sha256=tHltDQ7MlzGbZfr3VmxCHZDb_YmLvSTInQ9YXd4uRrI,11354
+lammps_analysis_tools-1.0.0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+lammps_analysis_tools-1.0.0.dist-info/entry_points.txt,sha256=VtlsI-b3Z3N06E5rchT1YUBrVCD6tsK5L-5NGEgzOjg,37
+lammps_analysis_tools-1.0.0.dist-info/top_level.txt,sha256=G6os795izf-wFzozl8F4xCW-epxSDb0hIH32xx1AGQY,4
+lammps_analysis_tools-1.0.0.dist-info/RECORD,,

lammps_analysis_tools-1.0.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: bdist_wheel (0.41.2)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

lammps_analysis_tools-1.0.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+lat = lat.cli:main

lammps_analysis_tools-1.0.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+lat

lat/__init__.py

@@ -0,0 +1,3 @@
+"""lat — LAMMPS Analysis Tool."""
+
+__version__ = "1.0.0"

lat/__main__.py

@@ -0,0 +1,6 @@
+import sys
+
+from .cli import main
+
+if __name__ == "__main__":
+    sys.exit(main())

lat/cli.py

@@ -0,0 +1,270 @@
+"""lat command line: lat <module> -s <data> -f <traj> [...]."""
+
+from __future__ import annotations
+
+import argparse
+import json
+import sys
+from pathlib import Path
+
+from . import __version__
+from .config import load as load_config
+from .core.context import Context
+from .core.errors import LatError, Logger, get_logger, set_logger
+from .core.io import open_system
+from .core.output import write_all
+from .core.selection import read_ndx
+from .modules import all_modules, get
+
+_ALLOWED_UNITS = {"real", "metal", "lj"}
+
+
+def _type_of(type_name):
+    return {"str": str, "int": int, "float": float}.get(type_name)
+
+
+def build_parser(cls, cfg=None) -> argparse.ArgumentParser:
+    epilog = (f"manual: docs/{cls.help_doc or 'manual/index.md'}  |  "
+              f"`lat describe -module {cls.name}` for the full contract; "
+              "defaults come from the lat config")
+    parser = argparse.ArgumentParser(
+        prog=f"lat {cls.name}", description=cls.summary, epilog=epilog,
+        formatter_class=argparse.RawDescriptionHelpFormatter, add_help=True
+    )
+    if getattr(cls, "requires_topology", True):
+        parser.add_argument("-s", "-topo", dest="topo", required=True,
+                            help="topology: LAMMPS .data/.lmp (or GROMACS .tpr/.gro/.pdb)")
+        parser.add_argument("-f", "-traj", dest="traj",
+                            help="trajectory: LAMMPS .lammpstrj (or GROMACS .xtc/.trr/.gro)")
+        parser.add_argument("-o", dest="output",
+                            help="output basename (default: topology file stem)")
+        parser.add_argument("-unit", dest="unit",
+                            help="length unit: real|metal|lj (default: config io.default_unit)")
+        parser.add_argument("-style", dest="style",
+                            help="force the LAMMPS atom_style when the Atoms header is ambiguous")
+        parser.add_argument("-types", dest="types",
+                            help="explicit type->element file (one 'type element' pair per line)")
+        parser.add_argument("-index", "-n", dest="index",
+                            help="GROMACS .ndx file providing named groups for selections")
+        parser.add_argument("-debug", dest="debug", action="store_true",
+                            help="also write a JSON audit next to the CSV")
+        parser.add_argument("-v", dest="verbose", action="store_true",
+                            help="show INFO progress on stderr")
+    for p in cls.params:
+        help_text = p.help
+        if p.config and cfg is not None:
+            val = cfg.get(p.config)
+            if val is not None:
+                help_text = f"{help_text} [default: {val}]".strip()
+        kwargs = {"help": help_text}
+        if p.choices:
+            kwargs["choices"] = list(p.choices)
+        if p.type == "flag":
+            parser.add_argument(*p.flags, dest=p.name, action="store_true", default=None, **kwargs)
+        else:
+            parser.add_argument(*p.flags, dest=p.name, type=_type_of(p.type), default=None, **kwargs)
+    return parser
+
+
+def _parse_types_file(path) -> dict[int, str]:
+    mapping = {}
+    with open(path) as fh:
+        for line in fh:
+            line = line.split("#")[0].strip()
+            if not line:
+                continue
+            parts = line.replace(",", " ").split()
+            if len(parts) < 2:
+                continue
+            a, b = parts[0], parts[1]
+            if a.isdigit():
+                mapping[int(a)] = b.capitalize()
+            elif b.isdigit():
+                mapping[int(b)] = a.capitalize()
+    if not mapping:
+        raise LatError(f"{path}: no type->element pairs parsed")
+    return mapping
+
+
+def _run_plot(kind: str, argv) -> int:
+    parser = argparse.ArgumentParser(prog=f"lat {kind}")
+    parser.add_argument("-f", dest="csv", required=True,
+                        help="lat output CSV (header carries title/xlabel/ylabel/columns)")
+    parser.add_argument("-o", dest="out", help="output image path")
+    parser.add_argument("-title", dest="title", help="override the header title")
+    parser.add_argument("-smooth", dest="smooth", choices=("none", "gaussian", "savgol"),
+                        help="smooth the plotted curve(s); the CSV stays raw")
+    if kind == "plot1d":
+        parser.add_argument("-columns", dest="columns", nargs="+", metavar="NAME",
+                            help="only draw these y columns (comma- or space-separated); "
+                                 "the x axis is always the first column")
+        parser.add_argument("-bar", dest="bar", action="store_true",
+                            help="grouped bar chart, one bar per y column")
+        parser.add_argument("-stack", dest="stack", action="store_true",
+                            help="stacked bar chart; y columns are normalized to "
+                                 "occupancy fractions")
+    args = parser.parse_args(argv)
+    from .plotting import plot1d, plot2d
+
+    cfg = load_config()
+    smooth = args.smooth or str(cfg.get("plot.smooth", default="none") or "none")
+    sm = {
+        "window": int(cfg.get("plot.savgol_window", default=5) or 5),
+        "order": int(cfg.get("plot.savgol_order", default=2) or 2),
+        "sigma": float(cfg.get("plot.gaussian_sigma", default=1.0) or 1.0),
+    }
+    if kind == "plot1d":
+        if args.bar and args.stack:
+            raise LatError("-bar and -stack are mutually exclusive")
+        col_sel = None
+        if args.columns:
+            col_sel = [c for tok in args.columns
+                       for c in (t.strip() for t in tok.split(",")) if c]
+        mode = "bar" if args.bar else "stack" if args.stack else "line"
+        out = plot1d(args.csv, out=args.out, title=args.title, smooth=smooth,
+                     columns=col_sel, mode=mode, **sm)
+    else:
+        out = plot2d(args.csv, out=args.out, title=args.title, smooth=smooth, **sm)
+    print(f"wrote {out}", file=sys.stderr)
+    return 0
+
+
+def _apply_config_paths(cfg) -> None:
+    pass
+
+
+def main(argv=None) -> int:
+    argv = list(sys.argv[1:] if argv is None else argv)
+    if not argv or argv[0] in ("-h", "--help", "help"):
+        _top_help()
+        return 0
+    if argv[0] in ("-V", "--version"):
+        print(f"lat {__version__}")
+        return 0
+
+    module_name = argv[0]
+    if module_name in ("plot1d", "plot2d"):
+        try:
+            return _run_plot(module_name, argv[1:])
+        except LatError as exc:
+            print(f"[lat ERROR] {exc}", file=sys.stderr)
+            return 1
+
+    try:
+        cfg = load_config()
+        logger = Logger(level="warning")
+        set_logger(logger)
+        cls = get(module_name)
+        parser = build_parser(cls, cfg)
+        args = parser.parse_args(argv[1:])
+
+        if getattr(args, "verbose", None):
+            logger.level = "info"
+        elif cfg.get("logger.level"):
+            logger.level = str(cfg.get("logger.level"))
+
+        command = "lat " + " ".join(argv)
+        _execute(cls, args, cfg, command)
+        return 0
+    except LatError as exc:
+        print(f"[lat ERROR] {exc}", file=sys.stderr)
+        return 1
+    except KeyboardInterrupt:
+        print("[lat ERROR] interrupted", file=sys.stderr)
+        return 130
+
+
+def _execute(cls, args, cfg, command):
+    logger = get_logger()
+    provided = {}
+    for p in cls.params:
+        provided[p.name] = getattr(args, p.name, None)
+    params = cls.resolve_defaults(cfg, provided)
+
+    mod = cls()
+    if not getattr(cls, "requires_topology", True):
+        mod.run(None, **params)
+        return []
+
+    unit = args.unit or cfg.get("io.default_unit")
+    if args.unit is None:
+        logger.info(f"no -unit given; assuming {unit} (Angstrom)")
+    if unit not in _ALLOWED_UNITS:
+        raise LatError(f"unit {unit!r} not supported (allowed: {sorted(_ALLOWED_UNITS)})")
+
+    ndx = read_ndx(args.index) if args.index else None
+    import time as _time
+    _t0 = _time.time()
+    logger.notice(f"reading topology {args.topo}")
+    topo, source = open_system(args.topo, args.traj, style=args.style, cfg=cfg)
+    logger.notice(f"  parsed {topo.n_atoms} atoms in {_time.time() - _t0:.1f}s"
+                  + (f"; trajectory {args.traj}" if args.traj else ""))
+
+    if args.types:
+        topo.type_element.update(_parse_types_file(args.types))
+        topo.element_problems = {}
+
+    ctx = Context(topo, source, cfg=cfg, unit=unit, command=command,
+                  debug=bool(args.debug), ndx=ndx)
+
+    tables = mod.run(ctx, **params)
+    emitted = set()
+    for t in tables:
+        for w in t.warnings:
+            if w not in emitted:
+                logger.warning(w)
+                emitted.add(w)
+    if getattr(cls, "screen_only", False) or not tables:
+        return tables
+
+    basename = args.output or Path(args.topo).stem
+    outdir = Path(basename).parent if Path(basename).parent != Path("") else Path(".")
+    stem = Path(basename).name
+    out_cfg = cfg.get("output", default={}) or {}
+    paths = write_all(
+        tables,
+        basename=stem,
+        outdir=outdir,
+        ext=out_cfg.get("ext", "csv"),
+        suffix=out_cfg.get("suffix", "out"),
+        prefix=out_cfg.get("header_prefix", "#"),
+        float_format=out_cfg.get("float_format", "%.6g"),
+        atomic=bool(out_cfg.get("atomic_write", True)),
+        backup_on_conflict=bool(cfg.get("io.backup_on_conflict", default=True)),
+        include_audit=bool(out_cfg.get("include_audit", True)),
+        command=command,
+        version=__version__,
+    )
+    for path in paths:
+        logger.notice(f"wrote {path}")
+    if args.debug and out_cfg.get("debug_json", False):
+        audit = {
+            "command": command,
+            "version": __version__,
+            "config": str(cfg.path),
+            "tables": [{"tag": t.tag, "rows": t.n_rows, "scalars": t.scalars,
+                        "selection": t.selection, "warnings": t.warnings} for t in tables],
+            "warnings": logger.warnings,
+        }
+        apath = Path(outdir) / f"{stem}.debug.json"
+        with open(apath, "w") as fh:
+            json.dump(audit, fh, indent=2)
+        logger.info(f"wrote {apath}")
+    return tables
+
+
+def _top_help() -> None:
+    print("lat — LAMMPS Analysis Tool")
+    print(f"version {__version__}")
+    print("\nusage: lat <module> -s <data> [-f <traj>] [options]\n")
+    print("modules:")
+    for name in sorted(all_modules()):
+        print(f"  {name:<12} {get(name).summary}")
+    print("\nplotting:")
+    print("  plot1d       plot a 1D CSV")
+    print("  plot2d       plot a 2D CSV")
+    print("\n  describe -module <name>   show a module's parameters and contract")
+
+
+if __name__ == "__main__":
+    sys.exit(main())