CRYSTALpytools: A Python']Python infrastructure for the CRYSTAL code

被引:7
作者
Camino, Bruno [1 ]
Zhou, Huanyu [2 ,3 ]
Ascrizzi, Eleonora [4 ]
Boccuni, Alberto [4 ]
Bodo, Filippo [4 ,5 ]
Cossard, Alessandro [4 ]
Mitoli, Davide [4 ]
Ferrari, Anna Maria [4 ]
Erba, Alessandro [4 ]
Harrison, Nicholas M. [2 ,3 ]
机构
[1] UCL, Dept Chem, London WC1E 6BT, England
[2] Imperial Coll London, Dept Chem, White City Campus,80 Wood Lane, London W12 0BZ, England
[3] Imperial Coll London, Inst Mol Sci & Engn, White City Campus,80 Wood Lane, London W12 0BZ, England
[4] Univ Torino, Dipartimento Chim, I-10125 Turin, Italy
[5] Southern Methodist Univ, Dept Chem, Dallas, TX USA
关键词
Crystal; !text type='Python']Python[!/text; Jupyter Notebooks; Pymatgen; ASE; Computational materials science workflows; HARTREE-FOCK GRADIENTS; PERTURBATION-THEORY TREATMENT; AB-INITIO; MOLECULAR-CRYSTALS; ELECTRON-DENSITY; CELL PARAMETER; CHARGE-DENSITY; QUANTUM-THEORY; SYSTEMS; DISPERSION;
D O I
10.1016/j.cpc.2023.108853
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
CRYSTALpytools is an open source Python project available on GitHub that implements a user-friendly interface to the Crystal code for quantum-mechanical condensed matter simulations. CRYSTALpytools provides functionalities to: i) write and read Crystal input and output files for a range of calculations (single-point, electronic structure, geometry optimization, harmonic and quasi-harmonic lattice dynamics, elastic tensor evaluation, topological analysis of the electron density, electron transport, and others); ii) extract relevant information; iii) create workflows; iv) post-process computed quantities, and v) plot results in a variety of styles for rapid and precise visual analysis. Furthermore, CRYSTALpytools allows the user to translate Crystal objects (the central data structure of the project) to and from the Structure and Atoms objects of the pymatgen and ASE libraries, respectively. These tools can be used to create, manipulate and visualise complicated structures and write them efficiently to Crystal input files. Jupyter Notebooks have also been developed for the less Python savvy users to guide them in the use of CRYSTALpytools through a user-friendly graphical interface with predefined workflows to complete different specific tasks.
引用
收藏
页数:11
相关论文
共 82 条
  • [1] NWChem: Past, present, and future
    Apra, E.
    Bylaska, E. J.
    de Jong, W. A.
    Govind, N.
    Kowalski, K.
    Straatsma, T. P.
    Valiev, M.
    van Dam, H. J. J.
    Alexeev, Y.
    Anchell, J.
    Anisimov, V
    Aquino, F. W.
    Atta-Fynn, R.
    Autschbach, J.
    Bauman, N. P.
    Becca, J. C.
    Bernholdt, D. E.
    Bhaskaran-Nair, K.
    Bogatko, S.
    Borowski, P.
    Boschen, J.
    Brabec, J.
    Bruner, A.
    Cauet, E.
    Chen, Y.
    Chuev, G. N.
    Cramer, C. J.
    Daily, J.
    Deegan, M. J. O.
    Dunning, T. H., Jr.
    Dupuis, M.
    Dyall, K. G.
    Fann, G., I
    Fischer, S. A.
    Fonari, A.
    Fruechtl, H.
    Gagliardi, L.
    Garza, J.
    Gawande, N.
    Ghosh, S.
    Glaesemann, K.
    Goetz, A. W.
    Hammond, J.
    Helms, V
    Hermes, E. D.
    Hirao, K.
    Hirata, S.
    Jacquelin, M.
    Jensen, L.
    Johnson, B. G.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2020, 152 (18)
  • [2] QUANTUM-THEORY OF ATOMS IN MOLECULES - DALTON REVISITED
    BADER, RFW
    NGUYENDANG, TT
    [J]. ADVANCES IN QUANTUM CHEMISTRY, 1981, 14 : 63 - 124
  • [3] Thermodynamics and phonon dispersion of pyrope and grossular silicate garnets from ab initio simulations
    Baima, Jacopo
    Ferrabone, Matteo
    Orlando, Roberto
    Erba, Alessandro
    Dovesi, Roberto
    [J]. PHYSICS AND CHEMISTRY OF MINERALS, 2016, 43 (02) : 137 - 149
  • [4] Thermoelasticity in organic semiconductors determined with terahertz spectroscopy and quantum quasi-harmonic simulations
    Banks, Peter A.
    Maul, Jefferson
    Mancini, Mark T.
    Whalley, Adam C.
    Erba, Alessandro
    Ruggiero, Michael T.
    [J]. JOURNAL OF MATERIALS CHEMISTRY C, 2020, 8 (31) : 10917 - 10925
  • [5] FINITE ELASTIC STRAIN OF CUBIC CRYSTALS
    BIRCH, F
    [J]. PHYSICAL REVIEW, 1947, 71 (11): : 809 - 824
  • [6] WIEN2k: An APW+lo program for calculating the properties of solids
    Blaha, Peter
    Schwarz, Karlheinz
    Tran, Fabien
    Laskowski, Robert
    Madsen, Georg K. H.
    Marks, Laurence D.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2020, 152 (07)
  • [7] Spin current density functional theory of Weyl semimetals
    Bodo, Filippo
    Desmarais, Jacques K.
    Erba, Alessandro
    [J]. PHYSICAL REVIEW B, 2022, 105 (12)
  • [8] Electron density analysis of large (molecular and periodic) systems: A parallel implementation
    Casassa, Silvia
    Erba, Alessandro
    Baima, Jacopo
    Orlando, Roberto
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2015, 36 (26) : 1940 - 1946
  • [9] i-PI: A Python']Python interface for ab initio path integral molecular dynamics simulations
    Ceriotti, Michele
    More, Joshua
    Manolopoulos, David E.
    [J]. COMPUTER PHYSICS COMMUNICATIONS, 2014, 185 (03) : 1019 - 1026
  • [10] First principles methods using CASTEP
    Clark, SJ
    Segall, MD
    Pickard, CJ
    Hasnip, PJ
    Probert, MJ
    Refson, K
    Payne, MC
    [J]. ZEITSCHRIFT FUR KRISTALLOGRAPHIE, 2005, 220 (5-6): : 567 - 570