DAMQT 2.0: A new version of the DAMQT package for the analysis of electron density in molecules

被引:16
|
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; PARTITION-EXPANSION; REPRESENTATION; POTENTIALS;
D O I
10.1016/j.cpc.2015.02.027
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
DAMQT 2.0 is a new version of the DAMQT package for the analysis of electron density in molecules and the fast computation of the density, density deformations, electrostatic potential and field, and Hellmann-Feynman forces. Algorithms for the partition of the electron density and the computation of related properties like density deformations, electrostatic potential and field and Hellmann-Feynman forces have been improved and their codes, fully rewritten. MPI versions of the most computational demanding modules are now included in the package for parallel computation. The Graphical User Interface has been also enhanced, with new features including a 2D plotter and significant improvements in the 3D viewer. Program summary Program title: DAMQT 2.0 Catalogue identifier: AEDL_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDL_v2_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.: 317,270 No. of bytes in distributed program, including test data, etc.: 40,193,220 Distribution format: tar.gz Programming language: Fortran90 and C++. Computer: Any. Operating system: Linux, Windows (7, 8). RAM: 200 Mbytes Classification: 16.1. Catalogue identifier of previous version: AEDL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180(2009)1654 External routines: Qt (4.8 or higher), OpenGL (3.x or higher), freeGLUT 2.8.x 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 [11, 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: Density must come from an LCAO calculation (any level) with spherical (not Cartesian) Slater or Gaussian functions. Unusual features: The program contains an OPEN statement to binary files (stream) in several files. This statement has not a standard syntax in Fortran 90. Two possibilities are considered in conditional compilation: Intel's ifort and Fortran2003 standard. The latter is applied to compilers other than ifort (gfortran uses this one, for instance). Additional comments: Quick-start guide and User's manual in PDF format included in the package. User's manual is also accessible from the Graphical User Interface. The distribution file for this program is over 40 Mbytes and therefore is not delivered directly when downloaded or Email is requested. Instead an 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 and G. Ramirez, J. Mol. Struct. Theochem 727 (2005) 115. (C) 2015 Elsevier B.V. All rights reserved.
引用
收藏
页码:289 / 294
页数:6
相关论文
共 50 条
  • [1] DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules
    Kumar, Anmol
    Yeole, Sachin D.
    Gadre, Shridhar R.
    Lopez, Rafael
    Rico, Jaime F.
    Ramirez, Guillermo
    Ema, Ignacio
    Zorrilla, David
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2015, 36 (31) : 2350 - 2359
  • [2] DAMQT: A package for the analysis of electron density in molecules
    Lopez, Rafael
    Fernandez Rico, Jaime
    Ramirez, Guillermo
    Ema, Ignacio
    Zorrilla, David
    COMPUTER PHYSICS COMMUNICATIONS, 2009, 180 (09) : 1654 - 1660
  • [3] Topology of molecular electron density and electrostatic potential with DAMQT
    Lopez, Rafael
    Fernandez Rico, Jaime
    Ramirez, Guillermo
    Ema, Ignacio
    Zorrilla, David
    Kumar, Anmol
    Yeole, Sachin D.
    Gadre, Shridhar R.
    COMPUTER PHYSICS COMMUNICATIONS, 2017, 214 : 207 - 215
  • [4] DAMQT 3: Advanced suite for the analysis of molecular density and related properties in large systems
    Kumar, Anmol
    Lopez, Rafael
    Martinez, Frank
    Ramirez, Guillermo
    Ema, Ignacio
    Zorrilla, David
    Yeole, Sachin D.
    Gadre, Shridhar R.
    COMPUTER PHYSICS COMMUNICATIONS, 2022, 279
  • [5] VOLSCAT2.0: The new version of the package for electron and positron scattering off molecular targets
    Sanna, N.
    Morelli, G.
    Orlandini, S.
    Baccarelli, I.
    COMPUTER PHYSICS COMMUNICATIONS, 2019, 235 : 366 - 377
  • [6] DnaSP version 2.0: A novel software package for extensive molecular population genetics analysis
    Rozas, J
    Rozas, R
    COMPUTER APPLICATIONS IN THE BIOSCIENCES, 1997, 13 (03): : 307 - 311
  • [7] A new version of the NeQuick ionosphere electron density model
    Nava, B.
    Coisson, P.
    Radicella, S. M.
    JOURNAL OF ATMOSPHERIC AND SOLAR-TERRESTRIAL PHYSICS, 2008, 70 (15) : 1856 - 1862
  • [8] DETERMINATION OF ELECTRON MOMENTUM DENSITY FROM ELECTRON NUMBER DENSITY - NEW VERSION OF SEMICLASSICAL TRANSFORMATION
    KOKKO, K
    PHYSICA STATUS SOLIDI B-BASIC RESEARCH, 1989, 151 (01): : 139 - 144
  • [9] SLIMP 2.0: A new version of strong laser interaction model package for atoms and molecules, now with molecular orbital tomography based on high-order harmonic spectra
    Ren, Zhongxue
    Zhang, Bin
    Yang, Yan
    Zhu, Yalei
    Bai, Guangru
    Liu, Jinlei
    Zhao, Jing
    Zhao, Zengxiu
    COMPUTER PHYSICS COMMUNICATIONS, 2024, 301
  • [10] MCE2005 -: a new version of a program for fast interactive visualization of electron and similar density maps optimized for small molecules
    Rohlicek, Jan
    Husak, Michal
    JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2007, 40 : 600 - 601