DAMQT: A package for the analysis of electron density in molecules

被引:23
|
作者
Lopez, Rafael [1 ]
Fernandez Rico, Jaime [1 ]
Ramirez, Guillermo [1 ]
Ema, Ignacio [1 ]
Zorrilla, David [2 ]
机构
[1] Univ Autonoma Madrid, Fac Ciencias, Dept Quim Fis Aplicada, E-28049 Madrid, Spain
[2] Univ Cadiz, Fac Ciencias, Dept Quim Fis, Cadiz, Spain
关键词
Electron density; Electrostatic potential; Electric field; Hellmann-Feynman forces; Density deformations; DEFORMED ATOMS; CHARGE; REPRESENTATION; POTENTIALS; TOPOLOGY;
D O I
10.1016/j.cpc.2009.03.004
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
DAMQT is a package for the analysis of the electron density in molecules and the fast computation of the density, density deformations, electrostatic potential and field, and Hellmann-Feynman forces. The method is based on the partition of the electron density into atomic fragments by means of a least deformation criterion. Each atomic fragment of the density is expanded in regular spherical harmonics times radial factors, which are piecewise represented in terms of analytical functions. This representation is used for the fast evaluation of the electrostatic potential and field generated by the electron density and nuclei, as well as for the computation of the Hellmann-Feynman forces on the nuclei. An analysis of the atomic and molecular deformations of the density can be also carried out. yielding a picture that connects with several concepts of the empirical structural chemistry. Program summary Program title: DAMQT1.0 Catalogue identifier: AEDL_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast. N. Ireland Licensing provisions: GPLv3 No. of lines in distributed program, including test data. etc.: 278 356 No. of bytes in distributed program, including test data, etc.: 31065 317 Distribution format: tar.gz Programming language: Fortran90 and C++ Computer. Any Operating system: Linux, Windows (Xp. Vista) RAM: 190 Mbytes Classification: 16.1 External routines: Trolltech's Qt (4.3 or higher) (http://www.qtsoftware.com/products), OpenGL (1.1 or higher) (http://www.opengl.org/), GLUT 3.7 (http://www.opengl.org/resources/libraries/glut/). Nature of problem: Analysis of the molecular electron density and density deformations, including fast evaluation of electrostatic potential, electric field and Hellmann-Feynman forces on nuclei. Solution method: The method of Deformed Atoms in Molecules, reported elsewhere [1], is used for partitioning the molecular electron density into atomic fragments, which are further expanded in spherical harmonics times radial factors. The partition is used for defining molecular density deformations and for the fast calculation of several properties associated to density. Restrictions: The current version is limited to 120 atoms. 2000 contracted functions, and I-max = 5 in basis functions. Density must come from a LCAO calculation (any level) with spherical (not Cartesian) Gaussian functions. Unusual features: The program contains an OPEN statement to binary files (stream) in file GOPENMOL.F90. This statement has not a standard syntax in Fortran 90. Two possibilities are considered in conditional compilation: Intel's ifort and Fortran2003 standard. This latter is applied to compilers other than ifort (gfortran uses this one, for instance). Additional comments: The distribution file for this program is over 30 Mbytes and therefore is not delivered directly when download or e-mail is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Largely dependent on the system size and the module run (from fractions of a second to hours). References: [1] J. Fernandez Rico, R. Lopez. I. Ema, G. Ramirez, J. Mal. Struct. (Theochem) 727 (2005) 115. (C) 2009 Elsevier B.V. All rights reserved.
引用
收藏
页码:1654 / 1660
页数:7
相关论文
共 50 条
  • [41] SIGN OF THE ELECTRON SPIN DENSITY ON METHYL PROTONS IN AROMATIC MOLECULES
    FORMAN, A
    MURRELL, JN
    ORGEL, LE
    JOURNAL OF CHEMICAL PHYSICS, 1959, 31 (04): : 1129 - 1129
  • [42] Superposition of molecules: Electron density fitting by application of Fourier transforms
    Nissink, JWM
    Verdonk, ML
    Kroon, J
    Mietzner, T
    Klebe, G
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 1997, 18 (05) : 638 - 645
  • [43] The Halogen Bond to Ethers - Prototypic Molecules and Experimental Electron Density
    Schmidt, Annika
    Krupp, Anna
    Kleinheider, Johannes
    Binnenbrinkmann, Tamara M. L.
    Wang, Ruimin
    Englert, Ulli
    Strohmann, Carsten
    ACS OMEGA, 2024, 9 (32): : 35037 - 35045
  • [44] DIFFERENTIAL-EQUATION FOR THE ELECTRON-DENSITY IN LARGE MOLECULES
    MARCH, NH
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1986, : 3 - 8
  • [45] ELECTRON-DENSITY IN THE GROUND-STATES OF ATOMS AND MOLECULES
    MARCH, NH
    JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 1992, 92 : 273 - 298
  • [46] ELECTRON MOMENTUM DENSITY DISTRIBUTION IN HOMONUCLEAR DIATOMIC-MOLECULES
    ROZENDAAL, A
    BAERENDS, EJ
    CHEMICAL PHYSICS, 1984, 87 (02) : 263 - 272
  • [47] Reconstruction of the electron density of molecules with single-axis alignment
    Starodub, Dmitri
    Spence, John C. H.
    Saldin, Dilano K.
    IMAGE RECONSTRUCTION FROM INCOMPLETE DATA VI, 2010, 7800
  • [48] Electron density, and its interplay with the energy and properties of molecules and solids
    Contreras-Garcia, J.
    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2021, 77 : C27 - C27
  • [49] ELECTRON-DENSITY DISTRIBUTIONS IN HYDRIDE MOLECULES - AMMONIA MOLECULE
    BADER, RFW
    JONES, GA
    JOURNAL OF CHEMICAL PHYSICS, 1963, 38 (12): : 2791 - &
  • [50] Electron transfer from molecules to nanoparticles: Dependence on the density of states
    Lian, Tianquan
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2007, 233