DL_POLYとは
DL_POLY公式サイト
公式サイトであることの裏付け：
DL_POLYのチュートリアル資料
DL_POLYの使い方
The input files for DL_POLY typically include:
https://dl-sdg.github.io/RESOURCES/TUTORIALS/dlp_3.html#:~:text=The%20input%20files,start%20of%20simulation
- CONTROL – simulation controls
- FIELD – contents of simulation (particles, molecules) and interactions
- CONFIG – initial configuration specifying positions etc. at start of simulation
DL_POLYを動かすサンプル動画
DL_POLYのインストール（ログ）| 240516
- インストール場所：WSL上のUbuntu
python3 -m pip install dlpoly-pyDefaulting to user installation because normal site-packages is not writeable
Collecting dlpoly-py
Downloading dlpoly_py-0.4.1-py3-none-any.whl.metadata (4.9 kB)
Requirement already satisfied: numpy>=1.5.0 in ./.local/lib/python3.10/site-packages (from dlpoly-py) (1.23.4)
Requirement already satisfied: matplotlib>=2.0.0 in ./.local/lib/python3.10/site-packages (from dlpoly-py) (3.7.0)
Requirement already satisfied: flake8 in ./.local/lib/python3.10/site-packages (from dlpoly-py) (6.1.0)
Requirement already satisfied: ruamel.yaml in ./.local/lib/python3.10/site-packages (from dlpoly-py) (0.17.26)
Collecting coverage (from dlpoly-py)
Downloading coverage-7.5.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.2 kB)
Collecting pytest (from dlpoly-py)
Downloading pytest-8.2.0-py3-none-any.whl.metadata (7.5 kB)
Collecting pytest-cov (from dlpoly-py)
Downloading pytest_cov-5.0.0-py3-none-any.whl.metadata (27 kB)
Collecting tox (from dlpoly-py)
Downloading tox-4.15.0-py3-none-any.whl.metadata (5.0 kB)
Requirement already satisfied: sphinx in /usr/lib/python3/dist-packages (from dlpoly-py) (4.3.2)
Requirement already satisfied: contourpy>=1.0.1 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py) (1.0.7)
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Requirement already satisfied: fonttools>=4.22.0 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py) (4.38.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py) (1.4.4)
Requirement already satisfied: packaging>=20.0 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py) (23.0)
Requirement already satisfied: pillow>=6.2.0 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py) (9.4.0)
Requirement already satisfied: pyparsing>=2.3.1 in /usr/lib/python3/dist-packages (from matplotlib>=2.0.0->dlpoly-py) (2.4.7)
Requirement already satisfied: python-dateutil>=2.7 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py) (2.8.2)
Requirement already satisfied: mccabe<0.8.0,>=0.7.0 in ./.local/lib/python3.10/site-packages (from flake8->dlpoly-py) (0.7.0)
Requirement already satisfied: pycodestyle<2.12.0,>=2.11.0 in ./.local/lib/python3.10/site-packages (from flake8->dlpoly-py) (2.11.1)
Requirement already satisfied: pyflakes<3.2.0,>=3.1.0 in ./.local/lib/python3.10/site-packages (from flake8->dlpoly-py) (3.1.0)
Collecting iniconfig (from pytest->dlpoly-py)
Downloading iniconfig-2.0.0-py3-none-any.whl.metadata (2.6 kB)
Collecting pluggy<2.0,>=1.5 (from pytest->dlpoly-py)
Downloading pluggy-1.5.0-py3-none-any.whl.metadata (4.8 kB)
Collecting exceptiongroup>=1.0.0rc8 (from pytest->dlpoly-py)
Downloading exceptiongroup-1.2.1-py3-none-any.whl.metadata (6.6 kB)
Requirement already satisfied: tomli>=1 in ./.local/lib/python3.10/site-packages (from pytest->dlpoly-py) (2.0.1)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in ./.local/lib/python3.10/site-packages (from ruamel.yaml->dlpoly-py) (0.2.7)
Collecting cachetools>=5.3.2 (from tox->dlpoly-py)
Downloading cachetools-5.3.3-py3-none-any.whl.metadata (5.3 kB)
Collecting chardet>=5.2 (from tox->dlpoly-py)
Downloading chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
Collecting colorama>=0.4.6 (from tox->dlpoly-py)
Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)
Collecting filelock>=3.13.1 (from tox->dlpoly-py)
Downloading filelock-3.14.0-py3-none-any.whl.metadata (2.8 kB)
Collecting packaging>=20.0 (from matplotlib>=2.0.0->dlpoly-py)
Downloading packaging-24.0-py3-none-any.whl.metadata (3.2 kB)
Collecting platformdirs>=4.1 (from tox->dlpoly-py)
Downloading platformdirs-4.2.2-py3-none-any.whl.metadata (11 kB)
Collecting pyproject-api>=1.6.1 (from tox->dlpoly-py)
Downloading pyproject_api-1.6.1-py3-none-any.whl.metadata (2.8 kB)
Collecting virtualenv>=20.25 (from tox->dlpoly-py)
Downloading virtualenv-20.26.2-py3-none-any.whl.metadata (4.4 kB)
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.7->matplotlib>=2.0.0->dlpoly-py) (1.16.0)
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox->dlpoly-py)
Downloading distlib-0.3.8-py2.py3-none-any.whl.metadata (5.1 kB)
Downloading dlpoly_py-0.4.1-py3-none-any.whl (37 kB)
Downloading coverage-7.5.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (231 kB)
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Downloading pytest-8.2.0-py3-none-any.whl (339 kB)
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Downloading pytest_cov-5.0.0-py3-none-any.whl (21 kB)
Downloading tox-4.15.0-py3-none-any.whl (155 kB)
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Downloading cachetools-5.3.3-py3-none-any.whl (9.3 kB)
Downloading chardet-5.2.0-py3-none-any.whl (199 kB)
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Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)
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Downloading filelock-3.14.0-py3-none-any.whl (12 kB)
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Downloading platformdirs-4.2.2-py3-none-any.whl (18 kB)
Downloading pluggy-1.5.0-py3-none-any.whl (20 kB)
Downloading pyproject_api-1.6.1-py3-none-any.whl (12 kB)
Downloading virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
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Downloading iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Downloading distlib-0.3.8-py2.py3-none-any.whl (468 kB)
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Installing collected packages: distlib, pluggy, platformdirs, packaging, iniconfig, filelock, exceptiongroup, coverage, colorama, chardet, cachetools, virtualenv, pytest, pyproject-api, tox, pytest-cov, dlpoly-py
Attempting uninstall: platformdirs
Found existing installation: platformdirs 3.2.0
Uninstalling platformdirs-3.2.0:
Successfully uninstalled platformdirs-3.2.0
Attempting uninstall: packaging
Found existing installation: packaging 23.0
Uninstalling packaging-23.0:
Successfully uninstalled packaging-23.0
Attempting uninstall: filelock
Found existing installation: filelock 3.12.0
Uninstalling filelock-3.12.0:
Successfully uninstalled filelock-3.12.0
ERROR: pip’s dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
optuna 3.0.5 requires scipy<1.9.0,>=1.7.0, but you have scipy 1.11.4 which is incompatible.
Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 coverage-7.5.1 distlib-0.3.8 dlpoly-py-0.4.1 exceptiongroup-1.2.1 filelock-3.14.0 iniconfig-2.0.0 packaging-24.0 platformdirs-4.2.2 pluggy-1.5.0 pyproject-api-1.6.1 pytest-8.2.0 pytest-cov-5.0.0 tox-4.15.0 virtualenv-20.26.2
[notice] A new release of pip is available: 23.3.1 -> 24.0
[notice] To update, run: python3 -m pip install –upgrade pip
- gitから
pip install git+https://gitlab.com/drFaustroll/dlpoly-py.gitDefaulting to user installation because normal site-packages is not writeable
Collecting git+https://gitlab.com/drFaustroll/dlpoly-py.git
Cloning https://gitlab.com/drFaustroll/dlpoly-py.git to /tmp/pip-req-build-ybqlh_rp
Running command git clone –filter=blob:none –quiet https://gitlab.com/drFaustroll/dlpoly-py.git /tmp/pip-req-build-ybqlh_rp
Resolved https://gitlab.com/drFaustroll/dlpoly-py.git to commit 07d5cd456f7fa4d080d78afcee36743eb112bd17
Installing build dependencies … done
Getting requirements to build wheel … done
Preparing metadata (pyproject.toml) … done
Requirement already satisfied: numpy>=1.5.0 in ./.local/lib/python3.10/site-packages (from dlpoly-py==0.4.1) (1.23.4)
Requirement already satisfied: matplotlib>=2.0.0 in ./.local/lib/python3.10/site-packages (from dlpoly-py==0.4.1) (3.7.0)
Requirement already satisfied: flake8 in ./.local/lib/python3.10/site-packages (from dlpoly-py==0.4.1) (6.1.0)
Requirement already satisfied: ruamel.yaml in ./.local/lib/python3.10/site-packages (from dlpoly-py==0.4.1) (0.17.26)
Requirement already satisfied: coverage in ./.local/lib/python3.10/site-packages (from dlpoly-py==0.4.1) (7.5.1)
Requirement already satisfied: pytest in ./.local/lib/python3.10/site-packages (from dlpoly-py==0.4.1) (8.2.0)
Requirement already satisfied: pytest-cov in ./.local/lib/python3.10/site-packages (from dlpoly-py==0.4.1) (5.0.0)
Requirement already satisfied: tox in ./.local/lib/python3.10/site-packages (from dlpoly-py==0.4.1) (4.15.0)
Requirement already satisfied: sphinx in /usr/lib/python3/dist-packages (from dlpoly-py==0.4.1) (4.3.2)
Requirement already satisfied: contourpy>=1.0.1 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py==0.4.1) (1.0.7)
Requirement already satisfied: cycler>=0.10 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py==0.4.1) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py==0.4.1) (4.38.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py==0.4.1) (1.4.4)
Requirement already satisfied: packaging>=20.0 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py==0.4.1) (24.0)
Requirement already satisfied: pillow>=6.2.0 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py==0.4.1) (9.4.0)
Requirement already satisfied: pyparsing>=2.3.1 in /usr/lib/python3/dist-packages (from matplotlib>=2.0.0->dlpoly-py==0.4.1) (2.4.7)
Requirement already satisfied: python-dateutil>=2.7 in ./.local/lib/python3.10/site-packages (from matplotlib>=2.0.0->dlpoly-py==0.4.1) (2.8.2)
Requirement already satisfied: mccabe<0.8.0,>=0.7.0 in ./.local/lib/python3.10/site-packages (from flake8->dlpoly-py==0.4.1) (0.7.0)
Requirement already satisfied: pycodestyle<2.12.0,>=2.11.0 in ./.local/lib/python3.10/site-packages (from flake8->dlpoly-py==0.4.1) (2.11.1)
Requirement already satisfied: pyflakes<3.2.0,>=3.1.0 in ./.local/lib/python3.10/site-packages (from flake8->dlpoly-py==0.4.1) (3.1.0)
Requirement already satisfied: iniconfig in ./.local/lib/python3.10/site-packages (from pytest->dlpoly-py==0.4.1) (2.0.0)
Requirement already satisfied: pluggy<2.0,>=1.5 in ./.local/lib/python3.10/site-packages (from pytest->dlpoly-py==0.4.1) (1.5.0)
Requirement already satisfied: exceptiongroup>=1.0.0rc8 in ./.local/lib/python3.10/site-packages (from pytest->dlpoly-py==0.4.1) (1.2.1)
Requirement already satisfied: tomli>=1 in ./.local/lib/python3.10/site-packages (from pytest->dlpoly-py==0.4.1) (2.0.1)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in ./.local/lib/python3.10/site-packages (from ruamel.yaml->dlpoly-py==0.4.1) (0.2.7)
Requirement already satisfied: cachetools>=5.3.2 in ./.local/lib/python3.10/site-packages (from tox->dlpoly-py==0.4.1) (5.3.3)
Requirement already satisfied: chardet>=5.2 in ./.local/lib/python3.10/site-packages (from tox->dlpoly-py==0.4.1) (5.2.0)
Requirement already satisfied: colorama>=0.4.6 in ./.local/lib/python3.10/site-packages (from tox->dlpoly-py==0.4.1) (0.4.6)
Requirement already satisfied: filelock>=3.13.1 in ./.local/lib/python3.10/site-packages (from tox->dlpoly-py==0.4.1) (3.14.0)
Requirement already satisfied: platformdirs>=4.1 in ./.local/lib/python3.10/site-packages (from tox->dlpoly-py==0.4.1) (4.2.2)
Requirement already satisfied: pyproject-api>=1.6.1 in ./.local/lib/python3.10/site-packages (from tox->dlpoly-py==0.4.1) (1.6.1)
Requirement already satisfied: virtualenv>=20.25 in ./.local/lib/python3.10/site-packages (from tox->dlpoly-py==0.4.1) (20.26.2)
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.7->matplotlib>=2.0.0->dlpoly-py==0.4.1) (1.16.0)
Requirement already satisfied: distlib<1,>=0.3.7 in ./.local/lib/python3.10/site-packages (from virtualenv>=20.25->tox->dlpoly-py==0.4.1) (0.3.8)
git clone https://gitlab.com/ccp5/dlpoly-py.gitCloning into ‘dlpoly-py’…
remote: Enumerating objects: 2078, done.
remote: Counting objects: 100% (1573/1573), done.
remote: Compressing objects: 100% (442/442), done.
remote: Total 2078 (delta 1242), reused 1334 (delta 1127), pack-reused 505 (from 1)
Receiving objects: 100% (2078/2078), 15.77 MiB | 6.35 MiB/s, done.
Resolving deltas: 100% (1242/1242), done.
cd dlpoly-py/
lsLICENSE MANIFEST.in README.rst dlpoly doc examples hooks pyproject.toml requirements.txt setup.py tests tools tox.ini
$ pwd
/home/morii-k/dlpoly-py
$ ls -CF
LICENSE MANIFEST.in README.rst dlpoly/ doc/ examples/ hooks* pyproject.toml requirements.txt setup.py* tests/ tools/ tox.ini
$ mkdir MD_Argon_240516
$ touch run_check.ipynb
$ cp -r examples/Ar MD_Argon_240516/
$ cd MD_Argon_240516/
$ ls -CF
Ar/ run_check.ipynb run_check_dl_poly.ipynb
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