Jaime Fernández Rico

DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules

DAMQT‐2.1.0 is a new version of DAMQT package which includes topographical analysis of molecular electron density (MED) and molecular electrostatic potential (MESP), such as mapping of critical points (CPs), creating molecular graphs, and atomic basins. Mapping of CPs is assisted with algorithmic determination of Euler characteristic in order to provide a necessary condition for locating all possible CPs. Apart from the mapping of CPs and determination of molecular graphs, the construction of MESP‐based atomic basin is a new and exclusive feature introduced in DAMQT‐2.1.0. The GUI in DAMQT provides a user‐friendly interface to run the code and visualize the final outputs. MPI libraries have been implemented for all the tasks to develop the parallel version of the software. Almost linear scaling of computational time is achieved with the increasing number of processors while performing various aspects of topography. A brief discussion of molecular graph and atomic basin is provided in the current article highlighting their chemical importance. Appropriate example sets have been presented for demonstrating the functions and efficiency of the code.

Chemical Notions from the Electron Density.

The study of density and the role played by its atomic representation is proposed as a way for the rationalization of chemical behavior. As this behavior has been long rationalized in terms of the basic concepts of empirical structural chemistry, a direct link between both approaches is searched for by using the exact representation of the density provided by the deformed atoms in molecules method (Rico, J. F.; López, R.; Ema, I.; Ramírez, G.; Ludeña, E. J. Comput. Chem. 2004, 25, 1355-1363). Noting that the spherical terms of the pseudoatoms cannot be mainly responsible for the chemical behavior, we study the small nonspherical deformations and find that they reflect and support all basic concepts of empirical structural chemistry. Lone pairs; single, double, and triple bonds; different classes of atoms; functional groups; and so forth are paralleled by the density deformations in a neat manner. These facts are illustrated with several examples.

Rotation of real spherical harmonics

Abstract In many physical problems, such as the calculation of interactions between multipoles, the rotation of spherical harmonics is necessary. In this paper, a computer program for the rotation of real spherical harmonics is reported. The program is designed for calculating sets of rotation matrices, for given Eulerian angles, and exploits some recurrence relations which make possible an important reduction of computational cost.

Calculation of two-center one-electron molecular integrals with STOs

Abstract A program for the calculation of two-center one-electron integrals (overlap, nuclear attraction and kinetic energy) between real Slater-type orbitals (STOs) is reported. The integrals are obtained by recursion over simple auxiliar matices, whose elements are calculated in terms of further auxiliary functions evaluated in a quick and accurate way.

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

Abstract 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, Queens 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.: 31 065 317 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: Trolltechs 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 l 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: Intels 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. Mol. Struct. (Theochem) 727 (2005) 115.

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

Abstract 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 [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: 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.

Searching critical points of fitted potential energy surfaces

Abstract The search for critical points of fitted potential energy surfaces is facilitated by the analytical character of the function and their derivatives, but can become complicated owing to the possible presence of spurious structures generated by the fitting procedure. In this paper, we examine the capability of the gradient extremal path for following techniques in this context. In all the test cases, with this method it was possible to localize all the extrema, allowing a subsequent study of the small minima and saddle points oriented towards elucidating their spurious or true character.

Repulsion integrals involving Slater-type functions and Yukawa potential

In range-separated functionals using basis sets of exponential functions, the Yukawa potential appears as the natural choice for the attenuated electron–electron repulsion. The development of these methods requires one- and two-center integrals involving two exponential functions and the Yukawa potential. In this work, general expressions are derived for these integrals, and stable algorithms for their efficient calculation, covering a wide range of screening parameters, are developed and tested.

Coulomb integrals for Gaussian, Slater, Bessel and polynomial-type functions

Abstract We present a unified study of two-center Coulomb integrals, involving Gaussian, Slater, Bessel and polynomial radial factors combined with Cartesian and spherical angular factors, performed with the shift operators technique. The master formula for these integrals appears as a linear combination of polynomials of the relative coordinates of the centers. These polynomials are independent of the type of radial factor, and only three families arise: two corresponding to angular factors of the same type and a mixed one. The coefficients depend on the types of both the angular and radial factors. We consider the 30 most important cases and give simple rules for obtaining them in terms of only six reference integrals.

Topology of molecular electron density and electrostatic potential with DAMQT

Abstract A new version of the DAMQT package incorporating topological analysis of the molecular electron density and electrostatic potential is reported. Evaluation of electron density, electrostatic potential and their first and second derivatives within DAM partition–expansion is discussed, and the pertaining equations are reported. An efficient algorithm for the search of critical points, gradient paths, atomic basins and Hessian analysis is implemented using these equations. 3D viewer built in DAMQT incorporates new facilities for visualization of these properties, as well as for distance and angle measurements. Full control of projection mode is also added to the viewer in DAMQT. Some examples are provided showing the excellent performance for large molecular systems. Program summary Program Title: DAMQT_2.1 Program Files doi: http://dx.doi.org/10.17632/2rxvgbsnhx.1 Licensing provisions: GPLv3 Programming language: Fortran90 and C++ 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. 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. 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 with density, including topological analysis of electron density and electrostatic potential. Restrictions: Density must come from a LCAO calculation (any computational 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 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). External routines/libraries: Qt (4.8 or higher), OpenGL (3.x or higher), freeGLUT 2.8.x References: [1] J. Fernandez Rico, R. Lopez, I. Ema and G. Ramirez, J. Mol. Struct. Theochem 727 (2005) 115. [2] [3]