infretis 2023.3.dev1__tar.gz

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Files changed (28) hide show
  1. infretis-2023.3.dev1/LICENSE +21 -0
  2. infretis-2023.3.dev1/PKG-INFO +35 -0
  3. infretis-2023.3.dev1/README.md +14 -0
  4. infretis-2023.3.dev1/infretis/bin.py +52 -0
  5. infretis-2023.3.dev1/infretis/classes/engines/cp2k.py +1296 -0
  6. infretis-2023.3.dev1/infretis/classes/engines/enginebase.py +805 -0
  7. infretis-2023.3.dev1/infretis/classes/engines/engineparts.py +476 -0
  8. infretis-2023.3.dev1/infretis/classes/engines/factory.py +82 -0
  9. infretis-2023.3.dev1/infretis/classes/engines/gromacs.py +1986 -0
  10. infretis-2023.3.dev1/infretis/classes/ensemble.py +54 -0
  11. infretis-2023.3.dev1/infretis/classes/formats/energy.py +168 -0
  12. infretis-2023.3.dev1/infretis/classes/formats/formatter.py +1234 -0
  13. infretis-2023.3.dev1/infretis/classes/formats/order.py +158 -0
  14. infretis-2023.3.dev1/infretis/classes/formats/path.py +102 -0
  15. infretis-2023.3.dev1/infretis/classes/orderparameter.py +541 -0
  16. infretis-2023.3.dev1/infretis/classes/path.py +699 -0
  17. infretis-2023.3.dev1/infretis/classes/repex.py +1020 -0
  18. infretis-2023.3.dev1/infretis/classes/rgen.py +819 -0
  19. infretis-2023.3.dev1/infretis/classes/system.py +56 -0
  20. infretis-2023.3.dev1/infretis/core/core.py +393 -0
  21. infretis-2023.3.dev1/infretis/core/tis.py +1648 -0
  22. infretis-2023.3.dev1/infretis/scheduler.py +36 -0
  23. infretis-2023.3.dev1/infretis/setup.py +174 -0
  24. infretis-2023.3.dev1/infretis/tools/conv_inf_py.py +66 -0
  25. infretis-2023.3.dev1/infretis/tools/hpc.py +10 -0
  26. infretis-2023.3.dev1/infretis/tools/minutes_since_start.py +52 -0
  27. infretis-2023.3.dev1/infretis/tools/pattern.py +146 -0
  28. infretis-2023.3.dev1/pyproject.toml +53 -0
@@ -0,0 +1,21 @@
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+ MIT License
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+
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+ Copyright (c) 2022 infretis
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+
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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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+
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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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+
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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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+
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+ # infretis
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+ ![Tests](https://github.com/infretis/infretis/actions/workflows/test.yaml/badge.svg)
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+ [![Coverage Status](https://coveralls.io/repos/github/infretis/infretis/badge.svg?branch=main)](https://coveralls.io/github/infretis/infretis?branch=main)
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+ [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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+
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+
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+ ## Installation
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+
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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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+
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+ # infretis
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+ ![Tests](https://github.com/infretis/infretis/actions/workflows/test.yaml/badge.svg)
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+ [![Coverage Status](https://coveralls.io/repos/github/infretis/infretis/badge.svg?branch=main)](https://coveralls.io/github/infretis/infretis?branch=main)
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+ [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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+
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+
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+ ## Installation
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+
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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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+
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+
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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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+
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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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+
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+
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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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+
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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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+
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+
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+ def infretisinit():
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+ """To generate initial *toml template and other features."""
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+ return