DAMQT 3: Advanced suite for the analysis of molecular density and related properties in large systems
Entity
UAM. Departamento de Química Física AplicadaDate
2022-07-08Citation
10.1016/j.cpc.2022.108460
Computer Physics Communications 279 (2022): 108460
ISSN
0010-4655 (print)DOI
10.1016/j.cpc.2022.108460Editor's Version
https://doi.org/10.1016/j.cpc.2022.108460Subjects
Electron density; Electrostatic potential; Electrostatics for Intermolecular Complexation; Hellmann-Feynman forces; Molecular density topology; Sigma-hole; Física; QuímicaRights
© 2022 The Author(s)Esta obra está bajo una licencia de Creative Commons Reconocimiento-NoComercial-SinObraDerivada 4.0 Internacional.
Abstract
A new version of the DAMQT package specially developed for large systems is reported. The graphical part has been entirely redesigned, using new OpenGL libraries (versions 3.3 or higher) for 3D display. Several 2D plotters and 3D viewers can be launched now in the same session and more than one molecule can be loaded in the same 3D window. Algorithms have been rescaled and modified to work with densities coming from ZDO computations in very big molecular systems (up to thousands of atoms) at a very moderate cost. New functionalities have been added including computation of molecular electrostatic potential over a molecular surface determined as a user-defined density isosurface. The method of Electrostatics for Intermolecular Complexation has been added to the package to serve as an auxiliary tool for cluster geometry optimization. Examples are provided which prove the good performance of the algorithms. Program summary: Program Title: DAMQT_3 CPC Library link to program files: https://doi.org/10.17632/2rxvgbsnhx.2 Licensing provisions: GPLv3 Programming language: Fortran90, C++ and Python Supplementary material: Quick-start guide and User's manual in PDF format included in the package. User's manual is also accessible from the GUI. External routines/libraries: Qt (5.10 or higher), OpenGL (3.3 or higher), ffmpeg (3.4 or higher), OpenBabel (2.3 or higher, optional) Nature of problem: Analysis and visualization of the molecular electron density, electrostatic potential, critical points, gradient paths, atomic basins, electric field and Hellmann-Feynman forces on nuclei, clusters optimization with EPIC. Solution method: Molecular electron density is partitioned into (pseudo)atomic fragments by means of the method of Deformed Atoms in Molecules [1]. Electron densities of the fragments are expanded as a series of spherical harmonics times radial factors. The partition is used for defining molecular density deformations and for the fast calculation of several properties associated with density, including electrostatic potential, electric field and Hellmann-Feynman forces over nuclei. Exploration of density and potential topology is facilitated, and the computation of electrostatic potential over an isodensity surface is implemented. Cluster optimization facility with EPIC is also implemented. Additional comments including restrictions and unusual features: Density matrix must come from an LCAO calculation (any computational level) with spherical (not Cartesian) Slater or Gaussian functions. The program contains an OPEN statement to binary files (stream) in several files. This statement does not have 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). References: [1] J. Fernández Rico, R. López, I. Ema, G. Ramírez, J. Mol. Struct., Theochem 727 (2005) 115
Files in this item
Google Scholar:Kumar, Anmol
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López Fernández, Rafael
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Martínez, Frank
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Ramírez Moreno, Guillermo
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Ema López, Ignacio de
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Zorrilla, David
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Yeole, Sachin D.
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Gadre, Shridhar R.
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