DJMol: An open-source modeling platform for computational chemistry and materials science with a Python']Python interpreter

被引:4
|
作者
Prasanna, Krishnamohan G. [1 ]
Sunil, Rahul [2 ]
Gupta, Kapil [3 ]
Lee, Seung-Cheol [3 ]
机构
[1] Mar Baselios Coll Engn & Technol, Dept Sci & Humanities, Trivandrum 695015, Kerala, India
[2] Mar Baselios Coll Engn & Technol, Dept Comp Sci, Trivandrum, Kerala, India
[3] Indo Korea Sci & Technol Ctr, Bengaluru, Karnataka, India
关键词
application programming interface; atomistic simulations; molecular modeling; !text type='Python']Python[!/text;
D O I
10.1002/jcc.26740
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
We present a modular and extendable software suite, DJMol, for performing molecular simulations and it is demonstrated with DFTB+, Siesta, Atomic Simulation Environment, and OpenMD codes. It supports many of the standard features of an integrated development environment and consists of a structure builder and viewer, which could be connected with these electronic structure codes along with a set of data analyzers. This program comprises Java and Python modules and its libraries to carry out a different set of modeling tasks in materials science and chemistry. By adopting a Python interpreter into the software, a range of scriptable Python codes, such as Pymatgen can be incorporated into this programmable modeling platform. DJMol, through its common application programming interface (API), supports multiple modeling codes in the backend and several post-processing tools. It benefits an experienced user by increasing efficiency, while a nonexpert user by easy to use API.
引用
收藏
页码:2116 / 2129
页数:14
相关论文
共 50 条
  • [1] Chemspyd: an open-source python']python interface for Chemspeed robotic chemistry and materials platforms
    Seifrid, Martin
    Strieth-Kalthoff, Felix
    Haddadnia, Mohammad
    Wu, Tony C.
    Alca, Emre
    Bodo, Leticia
    Arellano-Rubach, Sebastian
    Yoshikawa, Naruki
    Skreta, Marta
    Keunen, Rachel
    Aspuru-Guzik, Alan
    [J]. DIGITAL DISCOVERY, 2024, 3 (07): : 1319 - 1326
  • [2] Python']Python Materials Genomics (pymatgen): A robust, open-source python']python library for materials analysis
    Ong, Shyue Ping
    Richards, William Davidson
    Jain, Anubhav
    Hautier, Geoffroy
    Kocher, Michael
    Cholia, Shreyas
    Gunter, Dan
    Chevrier, Vincent L.
    Persson, Kristin A.
    Ceder, Gerbrand
    [J]. COMPUTATIONAL MATERIALS SCIENCE, 2013, 68 : 314 - 319
  • [3] Pypvcell: An Open-Source Solar Cell Modeling Library in Python']Python
    Lee, Kan-Hua
    Araki, Kenji
    Elleuch, Omar
    Kojima, Nobuaki
    Yamaguchi, Masafumi
    [J]. 2017 IEEE 44TH PHOTOVOLTAIC SPECIALIST CONFERENCE (PVSC), 2017, : 359 - 362
  • [4] NURBS-Python']Python: An open-source object-oriented NURBS modeling framework in Python']Python
    Bingol, Onur Rauf
    Krishnamurthy, Adarsh
    [J]. SOFTWAREX, 2019, 9 : 85 - 94
  • [5] EEGraph: An open-source Python']Python library for modeling electroencephalograms using graphs
    Maitin, Ana M.
    Nogales, Alberto
    Chazarra, Pedro
    Jose Garcia-Tejedor, Alvaro
    [J]. NEUROCOMPUTING, 2023, 519 : 127 - 134
  • [6] DRLinFluids: An open-source Python']Python platform of coupling deep reinforcement learning and OpenFOAM
    Wang, Qiulei
    Yan, Lei
    Hu, Gang
    Li, Chao
    Xiao, Yiqing
    Xiong, Hao
    Rabault, Jean
    Noack, Bernd R.
    [J]. PHYSICS OF FLUIDS, 2022, 34 (08)
  • [7] Python']Python-Microscope - a new open-source Python']Python library for the control of microscopes
    Pinto, David Miguel Susano
    Phillips, Mick A.
    Hall, Nicholas
    Mateos-Langerak, Julio
    Stoychev, Danail
    Pinto, Tiago Susano
    Booth, Martin J.
    Davis, Ilan
    Dobbie, Ian M.
    [J]. JOURNAL OF CELL SCIENCE, 2021, 134 (19)
  • [8] OSAFT Library: An Open-Source Python']Python Library for Acoustofluidics
    Fankhauser, Jonas
    Goering, Christoph
    Dual, Juerg
    [J]. FRONTIERS IN PHYSICS, 2022, 10
  • [9] Open-source coupled aerostructural optimization using Python']Python
    Jasa, John P.
    Hwang, John T.
    Martins, Joaquim R. R. A.
    [J]. STRUCTURAL AND MULTIDISCIPLINARY OPTIMIZATION, 2018, 57 (04) : 1815 - 1827
  • [10] Padasip: An open-source Python']Python toolbox for adaptive filtering
    Cejnek, Matous
    Vrba, Jan
    [J]. JOURNAL OF COMPUTATIONAL SCIENCE, 2022, 65