infretis 2023.3.dev1__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.
- infretis-2023.3.dev1/LICENSE +21 -0
- infretis-2023.3.dev1/PKG-INFO +35 -0
- infretis-2023.3.dev1/README.md +14 -0
- infretis-2023.3.dev1/infretis/bin.py +52 -0
- infretis-2023.3.dev1/infretis/classes/engines/cp2k.py +1296 -0
- infretis-2023.3.dev1/infretis/classes/engines/enginebase.py +805 -0
- infretis-2023.3.dev1/infretis/classes/engines/engineparts.py +476 -0
- infretis-2023.3.dev1/infretis/classes/engines/factory.py +82 -0
- infretis-2023.3.dev1/infretis/classes/engines/gromacs.py +1986 -0
- infretis-2023.3.dev1/infretis/classes/ensemble.py +54 -0
- infretis-2023.3.dev1/infretis/classes/formats/energy.py +168 -0
- infretis-2023.3.dev1/infretis/classes/formats/formatter.py +1234 -0
- infretis-2023.3.dev1/infretis/classes/formats/order.py +158 -0
- infretis-2023.3.dev1/infretis/classes/formats/path.py +102 -0
- infretis-2023.3.dev1/infretis/classes/orderparameter.py +541 -0
- infretis-2023.3.dev1/infretis/classes/path.py +699 -0
- infretis-2023.3.dev1/infretis/classes/repex.py +1020 -0
- infretis-2023.3.dev1/infretis/classes/rgen.py +819 -0
- infretis-2023.3.dev1/infretis/classes/system.py +56 -0
- infretis-2023.3.dev1/infretis/core/core.py +393 -0
- infretis-2023.3.dev1/infretis/core/tis.py +1648 -0
- infretis-2023.3.dev1/infretis/scheduler.py +36 -0
- infretis-2023.3.dev1/infretis/setup.py +174 -0
- infretis-2023.3.dev1/infretis/tools/conv_inf_py.py +66 -0
- infretis-2023.3.dev1/infretis/tools/hpc.py +10 -0
- infretis-2023.3.dev1/infretis/tools/minutes_since_start.py +52 -0
- infretis-2023.3.dev1/infretis/tools/pattern.py +146 -0
- infretis-2023.3.dev1/pyproject.toml +53 -0
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MIT License
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Copyright (c) 2022 infretis
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Metadata-Version: 2.1
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Name: infretis
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Version: 2023.3.dev1
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Summary: Infinite swapping parallel RETIS
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License: MIT
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Author: Daniel Zhang
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Author-email: daniel.t.zhang@ntnu.no
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Requires-Python: >=3.10,<4.0
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Requires-Dist: dask (==2023.3.0)
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Requires-Dist: distributed (==2023.3.0)
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Requires-Dist: matplotlib (>=3.7.2,<4.0.0)
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Requires-Dist: numpy (>=1.25.2,<2.0.0)
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Requires-Dist: tomli (>=2.0.1,<3.0.0)
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Requires-Dist: tomli-w (>=1.0.0,<2.0.0)
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Description-Content-Type: text/markdown
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# infretis
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[](https://coveralls.io/github/infretis/infretis?branch=main)
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[](https://github.com/psf/black)
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## Installation
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1. Clone the repository
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2. (Optional) Create a virtual environment
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3. Install with:
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```bash
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python -m pip install -e .
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```
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# infretis
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[](https://coveralls.io/github/infretis/infretis?branch=main)
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[](https://github.com/psf/black)
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## Installation
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1. Clone the repository
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2. (Optional) Create a virtual environment
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3. Install with:
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```bash
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python -m pip install -e .
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```
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"""The functions to be used to run infretis via the terminal."""
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import argparse
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from infretis.setup import setup_config
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from infretis.scheduler import scheduler
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from infretis.tools.conv_inf_py import print_pathens
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from infretis.tools.pattern import pattern
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def infretisrun():
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"""Read input and runs infretis."""
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parser = argparse.ArgumentParser()
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parser.add_argument(
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"-i", "--input", help="Location of infretis input file", required=True
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)
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args_dict = vars(parser.parse_args())
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input_file = args_dict["input"]
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config = setup_config(input_file)
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if config is None:
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return
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scheduler(config)
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def infretisanalyze():
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"""Convert infretis_data.txt to pyretis data."""
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parser = argparse.ArgumentParser()
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inp0 = "infretis_data.txt"
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inp1 = "pattern.txt"
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parser.add_argument(
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"-i",
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"--input",
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help="Location of infretis data file," + f" default is {inp0}",
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required=False,
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)
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parser.add_argument(
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"-p",
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"--pattern",
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help="Location of infretis pattern file," + f" default is {inp1}",
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required=False,
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)
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args_dict = vars(parser.parse_args())
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input_file = args_dict.get("input", inp0)
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pattern_file = args_dict.get("pattern", False)
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print_pathens(input_file)
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if pattern_file:
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pattern(pattern_file)
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def infretisinit():
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"""To generate initial *toml template and other features."""
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return
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