packmol-util 0.2.7__tar.gz → 0.2.8__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (18) hide show
  1. {packmol_util-0.2.7/src/packmol_util.egg-info → packmol_util-0.2.8}/PKG-INFO +32 -1
  2. {packmol_util-0.2.7 → packmol_util-0.2.8}/README.md +31 -0
  3. {packmol_util-0.2.7 → packmol_util-0.2.8}/pyproject.toml +1 -1
  4. {packmol_util-0.2.7 → packmol_util-0.2.8/src/packmol_util.egg-info}/PKG-INFO +32 -1
  5. {packmol_util-0.2.7 → packmol_util-0.2.8}/LICENSE +0 -0
  6. {packmol_util-0.2.7 → packmol_util-0.2.8}/setup.cfg +0 -0
  7. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/__init__.py +0 -0
  8. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util/__init__.py +0 -0
  9. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util/builder.py +0 -0
  10. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util/config.py +0 -0
  11. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util/model.py +0 -0
  12. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util/packmol.py +0 -0
  13. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util/packmol_inp.py +0 -0
  14. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util/param.py +0 -0
  15. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util.egg-info/SOURCES.txt +0 -0
  16. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util.egg-info/dependency_links.txt +0 -0
  17. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util.egg-info/requires.txt +0 -0
  18. {packmol_util-0.2.7 → packmol_util-0.2.8}/src/packmol_util.egg-info/top_level.txt +0 -0
{packmol_util-0.2.7/src/packmol_util.egg-info → packmol_util-0.2.8}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: packmol-util
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- Version: 0.2.7
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+ Version: 0.2.8
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  Summary: using packmol
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  Author-email: Kengo NAKADA <kengo.nakada@email.com>
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  Requires-Python: >=3.10
@@ -24,9 +24,15 @@ Requires-Dist: linkify-it-py
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  Dynamic: license-file
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  # packmol_util
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+
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  [![en](https://img.shields.io/badge/lang-en-red.svg)](https://github.com/ohara-lab-su/packmol_util/blob/main/README.md)
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  [![ja](https://img.shields.io/badge/lang-ja-yellow.svg)](https://github.com/ohara-lab-su/packmol_util/blob/main/README.ja.md)
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+ [![GitHub](https://img.shields.io/badge/GitHub-ohara--lab--su%2Fpackmol_util-181717?logo=github)](https://github.com/ohara-lab-su/packmol_util/)
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+ [![GitHub Pages](https://img.shields.io/badge/GitHub%20Pages-Documentation-222222?logo=githubpages&logoColor=white)](https://ohara-lab-su.github.io/packmol_util/en/)
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+ [![Ohara Lab](https://img.shields.io/badge/Ohara%20Lab-Home-4B5563?logo=homeassistant&logoColor=white)](https://ohara-lab-su.github.io/index.en.html)
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  A **Python utility kit for automatically generating amorphous initial structures (POSCAR)** for first-principles calculations (VASP) and molecular dynamics (MD) simulations using Packmol.
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@@ -66,3 +72,28 @@ src/
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  └── FeSiB/
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  └── make_FeSiB.py
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  ```
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+
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+ ## Example
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+
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+ ```python
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+ from packmol_util.builder import AmorphousBuilder
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+ from packmol_util.model import write_single_atom_xyz
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+
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+ for symbol in ("Fe", "Si", "B"):
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+ write_single_atom_xyz(f"{symbol}.xyz", symbol)
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+
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+ builder = AmorphousBuilder(
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+ symbols=["Fe", "Si", "B"], ratios=[80, 9, 11],
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+ total_atom_count=500, minimum_separation=2.0,
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+ mass_density=7.35,
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+ )
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+ for symbol, ratio in zip(builder.symbols, builder.ratios):
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+ builder.add_template(f"{symbol}.xyz", ratio * builder.multiplier)
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+ builder.build("FeSiB")
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+ ```
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+
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+ The outputs are `FeSiB_packmol.inp`, `FeSiB_packmol.xyz`, `FeSiB_packmol.log`, `POSCAR`, and `POSCAR.vasp`. An `.fnc` file is written when FNC pairs are registered. The POSCAR filenames are fixed. `AmorphousBuilder` adjusts the requested atom count to a nearby integer multiple of the stoichiometric ratio sum when needed.
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+
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+ ## Packmol and documentation
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+
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+ The Packmol executable must be installed separately. See the [English tutorial](https://ohara-lab-su.github.io/packmol_util/en/tutorial.html) for installation and input format, the [reference](https://ohara-lab-su.github.io/packmol_util/en/reference.html) for API and FNC details, and the [design philosophy](https://ohara-lab-su.github.io/packmol_util/en/philosophy.html) for component responsibilities.
{packmol_util-0.2.7 → packmol_util-0.2.8}/README.md RENAMED
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  # packmol_util
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+
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  [![en](https://img.shields.io/badge/lang-en-red.svg)](https://github.com/ohara-lab-su/packmol_util/blob/main/README.md)
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  [![ja](https://img.shields.io/badge/lang-ja-yellow.svg)](https://github.com/ohara-lab-su/packmol_util/blob/main/README.ja.md)
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+ [![GitHub](https://img.shields.io/badge/GitHub-ohara--lab--su%2Fpackmol_util-181717?logo=github)](https://github.com/ohara-lab-su/packmol_util/)
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+ [![GitHub Pages](https://img.shields.io/badge/GitHub%20Pages-Documentation-222222?logo=githubpages&logoColor=white)](https://ohara-lab-su.github.io/packmol_util/en/)
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+ [![Ohara Lab](https://img.shields.io/badge/Ohara%20Lab-Home-4B5563?logo=homeassistant&logoColor=white)](https://ohara-lab-su.github.io/index.en.html)
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  A **Python utility kit for automatically generating amorphous initial structures (POSCAR)** for first-principles calculations (VASP) and molecular dynamics (MD) simulations using Packmol.
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@@ -41,3 +47,28 @@ src/
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  └── FeSiB/
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  └── make_FeSiB.py
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  ```
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+
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+ ## Example
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+
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+ ```python
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+ from packmol_util.builder import AmorphousBuilder
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+ from packmol_util.model import write_single_atom_xyz
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+
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+ for symbol in ("Fe", "Si", "B"):
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+ write_single_atom_xyz(f"{symbol}.xyz", symbol)
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+
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+ builder = AmorphousBuilder(
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+ symbols=["Fe", "Si", "B"], ratios=[80, 9, 11],
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+ total_atom_count=500, minimum_separation=2.0,
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+ mass_density=7.35,
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+ )
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+ for symbol, ratio in zip(builder.symbols, builder.ratios):
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+ builder.add_template(f"{symbol}.xyz", ratio * builder.multiplier)
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+ builder.build("FeSiB")
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+ ```
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+
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+ The outputs are `FeSiB_packmol.inp`, `FeSiB_packmol.xyz`, `FeSiB_packmol.log`, `POSCAR`, and `POSCAR.vasp`. An `.fnc` file is written when FNC pairs are registered. The POSCAR filenames are fixed. `AmorphousBuilder` adjusts the requested atom count to a nearby integer multiple of the stoichiometric ratio sum when needed.
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+
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+ ## Packmol and documentation
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+
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+ The Packmol executable must be installed separately. See the [English tutorial](https://ohara-lab-su.github.io/packmol_util/en/tutorial.html) for installation and input format, the [reference](https://ohara-lab-su.github.io/packmol_util/en/reference.html) for API and FNC details, and the [design philosophy](https://ohara-lab-su.github.io/packmol_util/en/philosophy.html) for component responsibilities.
{packmol_util-0.2.7 → packmol_util-0.2.8}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "packmol-util"
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- version = "0.2.7"
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+ version = "0.2.8"
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  description = "using packmol"
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  authors = [
{packmol_util-0.2.7 → packmol_util-0.2.8/src/packmol_util.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: packmol-util
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- Version: 0.2.7
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+ Version: 0.2.8
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  Summary: using packmol
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  Author-email: Kengo NAKADA <kengo.nakada@email.com>
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  Requires-Python: >=3.10
@@ -24,9 +24,15 @@ Requires-Dist: linkify-it-py
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  Dynamic: license-file
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  # packmol_util
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+
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  [![en](https://img.shields.io/badge/lang-en-red.svg)](https://github.com/ohara-lab-su/packmol_util/blob/main/README.md)
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  [![ja](https://img.shields.io/badge/lang-ja-yellow.svg)](https://github.com/ohara-lab-su/packmol_util/blob/main/README.ja.md)
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+ [![GitHub](https://img.shields.io/badge/GitHub-ohara--lab--su%2Fpackmol_util-181717?logo=github)](https://github.com/ohara-lab-su/packmol_util/)
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+ [![GitHub Pages](https://img.shields.io/badge/GitHub%20Pages-Documentation-222222?logo=githubpages&logoColor=white)](https://ohara-lab-su.github.io/packmol_util/en/)
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+ [![Ohara Lab](https://img.shields.io/badge/Ohara%20Lab-Home-4B5563?logo=homeassistant&logoColor=white)](https://ohara-lab-su.github.io/index.en.html)
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+
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+
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  A **Python utility kit for automatically generating amorphous initial structures (POSCAR)** for first-principles calculations (VASP) and molecular dynamics (MD) simulations using Packmol.
32
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@@ -66,3 +72,28 @@ src/
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  └── FeSiB/
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  └── make_FeSiB.py
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  ```
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+
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+ ## Example
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+
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+ ```python
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+ from packmol_util.builder import AmorphousBuilder
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+ from packmol_util.model import write_single_atom_xyz
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+
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+ for symbol in ("Fe", "Si", "B"):
83
+ write_single_atom_xyz(f"{symbol}.xyz", symbol)
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+
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+ builder = AmorphousBuilder(
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+ symbols=["Fe", "Si", "B"], ratios=[80, 9, 11],
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+ total_atom_count=500, minimum_separation=2.0,
88
+ mass_density=7.35,
89
+ )
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+ for symbol, ratio in zip(builder.symbols, builder.ratios):
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+ builder.add_template(f"{symbol}.xyz", ratio * builder.multiplier)
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+ builder.build("FeSiB")
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+ ```
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+
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+ The outputs are `FeSiB_packmol.inp`, `FeSiB_packmol.xyz`, `FeSiB_packmol.log`, `POSCAR`, and `POSCAR.vasp`. An `.fnc` file is written when FNC pairs are registered. The POSCAR filenames are fixed. `AmorphousBuilder` adjusts the requested atom count to a nearby integer multiple of the stoichiometric ratio sum when needed.
96
+
97
+ ## Packmol and documentation
98
+
99
+ The Packmol executable must be installed separately. See the [English tutorial](https://ohara-lab-su.github.io/packmol_util/en/tutorial.html) for installation and input format, the [reference](https://ohara-lab-su.github.io/packmol_util/en/reference.html) for API and FNC details, and the [design philosophy](https://ohara-lab-su.github.io/packmol_util/en/philosophy.html) for component responsibilities.
{packmol_util-0.2.7 → packmol_util-0.2.8}/LICENSE RENAMED
File without changes
{packmol_util-0.2.7 → packmol_util-0.2.8}/setup.cfg RENAMED
File without changes