RT journal article
T1 DAMQT 3: Advanced suite for the analysis of molecular density and related properties in large systems
A1 Kumar, Anmol
A1 López, Rafael
A1 Martínez, Frank
A1 Ramírez, Guillermo
A1 Ema, Ignacio
A1 Zorrilla Cuenca, David
A1 Yeole, Sachin D.
A1 Gadre, Shridhar R.
A2 Química Física
K1 Electron density
K1 Electrostatic potential
K1 Molecular density topology
K1 Sigma-hole
K1 Electrostatics for Intermolecular
K1 Complexation
K1 Hellmann-Feynman forces
AB 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 summaryProgram Title: DAMQT_3CPC Library link to program files: https://doi .org /10 .17632 /2rxvgbsnhx .2Licensing provisions: GPLv3Programming language: Fortran90, C++ and PythonSupplementary 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. Fernandez Rico, R. Lopez, I. Ema, G. Ramirez, J. Mol. Struct., Theochem 727 (2005) 115.(c) 2022 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
PB ELSEVIER
SN 0010-4655
YR 2022
FD 2022-10
LK http://hdl.handle.net/10498/27936
UL http://hdl.handle.net/10498/27936
LA eng
DS Repositorio Institucional de la Universidad de Cádiz
RD 11-nov-2026