Ángel Martín Pendás

Quantum Chemistry Group

Departamento de Química Física y Analítica
Universidad de Oviedo, 33006-Oviedo, Spain

This page can be found at: http://www.uniovi.es/~quimica.fisica/qcg/amp/amp.html
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Last modified: June 12, 1996

 * This page is under construction

Who, What, Where?

This page gathers a certain amount of information concerning my professional and not so professional interests. I'm a 31 Professor of Chemical Physics at the University of Oviedo, a ~200000 people city in the north of Spain. Unfortunately, most internet resources about this evergreen rainy region are written in spanish . Our University was founded in 1579 and holds a rich and tortuous history that you may be interested in.

My research activities are centered around the theoretical simulation of the electronic structure of crystalline materials using the methods provided by Quantum Mechanics. Along the years, our group has developed powerful computational methods based on the Theory of Electronic Separability that solve the Hartree-Fock (HF) equations of a solid in a localized Fock space. The resulting scheme, named the ab initio Perturbed Ion method (Comp. Phys. Comm. 77 107-134 (1993) ), is able to compete advantageously with standard techniques. It is currently several orders of magnitude faster than other HF programs, and may be obtained at no cost for non-profit purposes. Contact me if you are interested in it, or if you simply want some type of technical information. As a byside effect of my everyday work, I'm also really interested in computational problems. I usually develop my software applications on a i486-100 PC running Linux. If you haven't heard (really?) about the niceties of this transform-your-pc-into-a-powerful-workstation operating system, now it is a good moment to get more information in this same server.

The rest of the page is a collection of brief summaries of some of my works, together with some pointers to interesting web places. If you are looking for really technical information, you can pick up some of our papers


The Theory of Atoms in Molecules (AIM)

The main difficulty that Quantum Chemistry, as a discipline, has found in the main stream chemical community is rooted on the definition domain of the molecular wave function: the whole 3D space. This is the famous Hilbert space problem, and prevents that properties depending on a localized region of space be rigourously quantum mechanically defined. On the other hand, Chemistry is inseparable from local concepts, and much work has been done along the years to overcome this difficulty. None of the large number of approaches that have been proposed, except that of Prof. Bader (R. F. W. Bader, Atoms in Molecules: A Quantum Theory,(Oxford U. P., 1990)), is fully coherent from the theoretical point of view.

Bader's main concept is a theorem proving that non relativistic quantum mechanics is applicable to open regions of the 3D space if these regions are bounded by surfaces whose flux of the gradient of the electronic density vanishes. In this way, topological atoms may be defined. Any quantum-mechanical observable is then found to be the addition of the local expected values over the basins of the topological atoms.

The periodicity of a crystalline material changes a little bit the usual panorama of the theory. We have found new topological objects not previously defined and obtained very interesting connections between the topology of the electron density of a crystalline material and its energetic stability. More information can be found from Bader's own web Homepage, one of my colleagues page, one of our web papers, or a recent communication to the watoc conference

As an example of the kind of topological atoms that are obtained in a perovskite crystal, KCaF3, the figure on the left shows them superimposed on the crystal lattice. The gold objects are the calcium atoms. Notice how their wings envelope almost completeley the fluorines, in green. The potasium atoms are shown in red. The electronic densities were obtained with the aiPI program. The topological basins were then assembled with our AIM package (the CRITIC program). Finally, the surfaces were obtained with our TESSEL code, and rendered with POVRAY. Contact me about this codes for any question.

Pair Potentials from ab initio Calculations in Crystalline Materials

The simulation of the thermodynamical properties of solid bodies by means of both Molecular Dynamics or MonteCarlo techniques has always rested on the availability of suitable pair potentials feeding the calculations. It has only been very recently when Carr & Parrinello schemes have allowed true quantum mechanical simulations of materials, always from the density functional theory perspective. It is therefore very important that good, tested potentials be available to the scientific community.

We have devised a collection of methods to obtain reliable pair potentials from our quantum mechanical procedures. A general purpose code, named PAIRPOT, has been constructed to study the energetic and thermodynamic features of isolated clusters and pure or impurified crystals. The code accepts both numerical and/or analytic potentials, and has a built-in calculator that allows the user to define the geometry of the system examined in terms of freely configurable variables. Space group symmetry is explicitly taken into account, in such a way that crystal structures may be introduced directly from databases. The program optimizes or differentiates several aim functions, like the total, Helmholtz or Gibbs energies, simplifying considerably the analysis of results. It has also several built-in graphical capabilities. The code, freely available for non-profit purposes, is still in a beta stage.

Here there are some optimized geometries of small clusters of NaCl molecules, NanCln, where n ranges from 3 to 9. The calculations were made in my desktop PC with aiPI derived pair potentials. The pictures were rendered directly from PAIRPOT with the aid of a modified version of Roger Sayle's RASMOL Below this lines you will find the simple input file that optimizes and generates the picture corresponding to the Na3Cl3 cluster

Title Na3Cl3 Molecule
pairpot 1 r      #Na-Cl
" 412.387072*exp(-1.96648884*r) 
- 427.902284*exp(-1.7446128*r)/r"
pairpot 2 r      #Cl-Cl
 +4261.20479*exp(-1.69980330*r)/r +
x2=5 x3=5 y3=5 x4=0 y4=5 z4=0 x5=10
y5=0 z5=0 x6=10 y6=5 z6=0

   neqclus 1 +1.0 Na
      0 &  0 &  0
   neqclus 1 -1.0 Cl
      x2 & 0 & 0
   neqclus 1 +1.0 Na
     x3 & y3 &  0
   neqclus 1 -1.0 Cl
     x4 &  y4 & z4
   neqclus 1 +1.0 Na
     x5 & y5 &  z5
   neqclus 1 -1.0 Cl
     x6 &  y6 & z6
   describe Na Cl 1  Cl Cl 2
    optimize y3 x4 y4 z4 x5 y5 z5 x6 y6 z6 x2 x3
        CAMERA COP  1.0  & 10.0 & 1.0 &
        camera angles   20 &  40 & 30 
        light 2.0   40.0  2.0
        ball na 0.5  0.0 0.0 1.0
        ball cl  1.0  0.2 1.0 0.1
        stick na cl 7.1 0.2
        rasmol na3cl3

It is equally easy to obtain simple pictures of crystalline structures, like this one of the rock-salt phase of NaCl, that may be manipulated interactively, and transformed automatically to high quality ray-tracing images.

Automatic Quasi-Harmonic Thermodynamics of Crystals

The PAIRPOT code is also able to compute thermodynamic properties at non zero temperature at both the rigid- and quasi- harmonic approximations. The vibrational Helmoltz energy is obtained from the phonon frecuencies calculated automatically for any kind of pair potentials, analytic or numeric in nature. The dynamical matrix is not added up to first, second, or nth neighbours. On the contrary, every atom in the lattice makes its contribution until complete convergence is achieved. In this way, every module in the program is consistent with the general aim of the code. The following figure shows the total and projected density of vibrational states obtained for the NaCl crystal at the theoretical equilibrium distance using the same potentials as those of the molecular clusters examined above. The code that generates this figure is also shown.

title NaCl crystal DOS
# Initial variables:
a = 10.5
pairpot 1 r      #Na-Cl
Pairpot 2 r      #Cl-Cl
+4261.20479*exp(-1.69980330*r)/r +

 spg f m -3 m
 cell a & a & a & 90 & 90 & 90
 neq 0 & 0 & 0 & 1 Na
 neq 0.5 & 0.5 & 0.5 & -1 Cl
describe Cl Cl 2 describe  Na Cl 1 
optimize a
dos 5 dos.dat

As a final example of the actual capabilities of our code, you can enjoy the following display of the isofrequency surfaces of each phonon branch in the above NaCl crystal. Frequencies are given in cm-1. Branches are labelled in rows. Aren't they worth the work?

Frequency123 456

A flavour of Interesting Web Places

This zone is being actualized


UCLA Chempointers. A very complete, but not exhaustive list of chemistry homepages.
Ohio SuperComputer Comp. Chem.(CCL) Chem Page
OSC Chemistry Archive
Chemistry tutorials
Cambridge Crystallographic Data Center
The Geometry Center
NIH Molecular Modeling site
Chemical Examples of VRML. An interesting place to start searching for Virtual Reality Modelling Language experiences in Chemistry.
NIU Chemistry. One good starting point with lots of links to Chemistry related sites.
Molecular Modelling Software. A Rather Complete list.
Periodic Table. An interesting source of data from the University of Sheffield.
University of Girona List of meetings and forums related to Molecular Modelling and Molecular Modelling and Chemical Physics.
Oxford Molecular Group


APS Editorial Offices. The American Physical Society Editorial Offices.
OUP Oxford University Press


El PAIS. Perhaps the best Spanish daily newspaper.
El MUNDO. Another spanish paper. Good web resources.
PIC. Spanish Ministery of Culture information service. Good Gastronomy!
BOE. Spanish daily Official Bulletin.
Several Spanish Government services
National Spanish Library


AstroWeb Astronomy/Astrophysics on the Internet.
Planet Finder Use it.
NASA HomePage. Don't forget it. It's a good starting point.

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Copyright (c) 1996 Ángel Martín Pendás, Universidad de Oviedo.
Page dates: June 12, 1996 (creation), June 12, 1996 (last update).
Admin.: angel@carbono.quimica.uniovi.es