Metadata-Version: 2.1
Name: mddatasetbuilder
Version: 1.3.4
Summary: A script to make molecular dynamics (MD) datasets for neural networks from given LAMMPS trajectories automatically.
Home-page: https://github.com/njzjz/mddatasetbuilder
Author: Jinzhe Zeng
Author-email: jzzeng@stu.ecnu.edu.cn
License: UNKNOWN
Description: # MDDatasetBuilder
        
        [![DOI:10.1038/s41467-020-19497-z](https://img.shields.io/badge/DOI-10.1038%2Fs41467--020--19497--z-blue)](https://doi.org/10.1038/s41467-020-19497-z)
        [![Citations](https://citations.njzjz.win/10.1038/s41467-020-19497-z)](https://doi.org/10.1038/s41467-020-19497-z)
        [![python version](https://img.shields.io/pypi/pyversions/mddatasetbuilder.svg?logo=python&logoColor=white)](https://pypi.org/project/mddatasetbuilder)
        [![PyPI](https://img.shields.io/pypi/v/mddatasetbuilder.svg)](https://pypi.org/project/mddatasetbuilder)
        [![codecov](https://codecov.io/gh/njzjz/mddatasetbuilder/branch/master/graph/badge.svg)](https://codecov.io/gh/njzjz/mddatasetbuilder)
        [![Research Group](https://img.shields.io/website-up-down-green-red/https/computchem.cn.svg?label=Research%20Group)](https://computchem.cn)
        
        MDDatasetBuilder is a script to construct reference datasets for the training of neural network potentials from given LAMMPS trajectories.
        
        Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation, Nature Communications, **11**, 5713 (2020), DOI: [10.1038/s41467-020-19497-z](https://doi.org/10.1038/s41467-020-19497-z)
        
        **Author**: Jinzhe Zeng
        
        **Email**: jzzeng@stu.ecnu.edu.cn
        
        ## Installation
        
        MDDatasetBuilder can be installed with pip:
        
        ```
        pip install mddatasetbuilder
        ```
        
        The installation process should be very quick, taking only a few minutes on a “normal” desktop computer. 
        
        ## Usage
        ### Simple example
        
        A [LAMMPS dump file](https://lammps.sandia.gov/doc/dump.html) should be prepared. A [LAMMPS bond file](http://lammps.sandia.gov/doc/fix_reax_bonds.html) can be added for the addition information.
        
        ```bash
        datasetbuilder -d dump.ch4 -b bonds.reaxc.ch4_new -a C H O -n ch4 -i 25
        ```
        
        Here, `dump.ch4` is the name of the dump file. `bonds.reaxc.ch4_new` is the name of the bond file, which is optional. `C H O` is the element in the trajectory. `ch4` is the name of the dataset. `25` means the time step interval and the default value is 1.
        
        Then you can generate Gaussian input files for each structure in the dataset and calculate the potential energy & atomic forces (assume the Gaussian 16 has already been installed.):
        
        ```bash
        qmcalc -d dataset_ch4_GJf/000
        qmcalc -d dataset_ch4_GJf/001
        ```
        
        Next, prepare a DeePMD dataset and use [DeePMD-kit](https://github.com/deepmodeling/deepmd-kit) to train a NN model.
        
        ```bash
        preparedeepmd -p dataset_ch4_GJf
        cd train && dp train train.json
        ```
        
        The runtime of the software depends on the amount of data. It is more suited to running on a server rather than desktop computer.
        
        ### DP-GEN
        [![DOI:10.1021/acs.energyfuels.0c03211](https://img.shields.io/badge/DOI-10.1021%2Facs.energyfuels.0c03211-blue)](https://doi.org/10.1021/acs.energyfuels.0c03211)
        [![Citations](https://citations.njzjz.win/10.1021/acs.energyfuels.0c03211)](https://doi.org/10.1021/acs.energyfuels.0c03211)
        
        In a [follow-up work](10.1021/acs.energyfuels.0c03211), the MDDatasetBuilder package has been integrated with [DP-GEN](https://github.com/deepmodeling/dpgen) software as a part of the DP-GEN workflow:
        ```bash
        dpgen init_reaction reaction.json machine.json
        ```
        where an example of `reaction.json` can be found [here](https://github.com/deepmodeling/dpgen/blob/v0.9.1/examples/init/reaction.json). `machine.json` is described [here](https://docs.deepmodeling.com/projects/dpgen/en/devel/init/init-reaction-mdata.html), where
        `reaxff_command` is the LAMMPS command (`lmp`), `build_command` is the MDDatasetbuilder command (`datasetbuilder`), and `fp_command` is the Gaussian 16 command (`g16 < input`).
        
        The genereated data can be used to continue DP-GEN concurrent learning workflow. Read [Energy & Fuels, 2021, 35 (1), 762–769](https://doi.org/10.1021/acs.energyfuels.0c03211) for details.
        
Keywords: molecular dynamics dataset
Platform: UNKNOWN
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Software Development :: Version Control :: Git
Requires-Python: ~=3.6
Description-Content-Type: text/markdown
Provides-Extra: test
