University of Oviedo
Quantum Chemistry Group
Universidad de Oviedo
Departamento de Química Física y Analítica
c/ Julián Clavería 8, 33006-Oviedo, Spain
Fax: (34) 985-103491
SS Quantum Chemistry group

Software

Programs

Active development

  1. Critic2: Generalized analysis of periodic electron densities.
  2. Tessel: a program for crystallographic modelling and computing.
  3. Gibbs2: thermodynamics, equations of state and phase diagrams of solids under hydrostatic (p,T) conditions.
  4. Asturfit: Robust fitting of discrete energy vs. volume data.

Maintained

  1. Runwien: A text-based interface for the WIEN2k suite.
  2. Optim: a program to drive n-dimensional minimizations on surfaces calculated by an external program.
  3. Derive: A program to determine numerical first and second derivatives of an arbitrary function that is calculated by an external program.
  4. Navigator: A program to drive searches for any Morse i-saddle critical point in surfaces calculated by an external program.

Legacy

  1. Gibbs: Calculation of p,T-dependent thermodynamic properties in solids under the Debye-Slater quasiharmonic model (see gibbs2).
  2. Critic: analysis of the electron density in crystals, with interfaces to WIEN2k and PI.

Libraries

  1. The Caleao crystallographic server (caleaocs): given the space group label, obtains the symmetry operations of the crystal in one of the ITA settings. Based on the work of U. Shmueli.
  2. Guess: given the cell lengths and angles, and the atomic positions in the unit cell of a crystal, determines the symmetry operations.

Scripts

  1. qewald: an octave script to calculate the electrostatic energy of a periodic crystal composed of point-like charges, optionally with a compensating uniform background charge, using Ewald method.
  2. vdw : Dispersion sum (r^-6) by Ewald-like method: an octave script to calculate lattice sums of the form c_6/r^-6, as in van der Waals interactions.
  3. cleanbib : a small AWK script to check the consistency of one or several BibTeX .bib files.

Critic2

Generalized analysis of periodic electron densities. Critic2 reads a variety of crystal structure formats (CIF, QE outputs, vasp, elk, wien2k, abinit,...) and scalar fields (wien2k, elk, pi, abinit, vasp, QE, gaussian,...) and does: i) topological analysis in the QTAIM framework (critical point localization), ii) basin integration, iii) plotting of relevant quantities, iv) NCIplot, v) arithmetic computations and calculation of cell integrals using different fields, and vi) interconversion between crystal geometry and scalar field formats.

Please visit the critic2 page or go directly to github.


Tessel

Tessel2 is a 3D "compiler" to produce crystal and molecular models, parametric surfaces and several forms of sphere tesselations.

Molecular models combine balls-and-sticks, arrows and coordination polyhedra representations of pure and defective crystals, finite molecules or clusters. The Madelung potential of an ionic system can be computed and depicted on an arbitrary plane or surface. The common crystallographic cell (parallepipedic), as well as the Wigner-Seitz cell or the irreducible components of the WS cell can be easily added to the plot.

Parametric surfaces are defined by means of analytical expressions and several space mappings can be used (i.e. cartesian, spherical coordinates, etc).

Several methods for tesselating the sphere are currently implemented, including: recursively subdividing a inscribed cube, tetrahedron or octahedron; geodesic division based on a number of meridians and parallels; and minimization of the electrostatic repulsion of a set of points lying on the sphere surface.

The program produces output to be rendered with POV-Ray 2 or 3, Geomview (OFF format), or any Virtual Reality renderer (VRML V1.0 format). In addition, a very simple output (POINTS) is provided for those applications in which a list of points is best suited.

Source. (Jul. 4th, 2011) [tar.bz2] [tar.gz]

Developers. Víctor Luaña, Alberto Otero de la Roza

Documentation. [TXT] [PDF] [HTML]

Examples.

License. GNU GPL v3

Contact. victor@carbono.quimica.uniovi.es


Gibbs2

Thermodynamics, equations of state and phase diagrams of solids under hydrostatic (p,T) conditions.

Source.

Download the development version of the code from: [github]

Static copy of gibbs2 (Jul. 4th, 2011): [tar.bz2] [tar.gz]

CPC library source. [CPC library], but the use of the links above is recommended.

Publications & citation of this software
The gibbs2 code: Comput. Phys. Commun. 182 (2011) 2232-2248

The EOS fitting techniques: Comput. Theor. Chem. 975 (2011) 111 and Comput. Phys. Commun. 182 (2011) 1708-1720

The empirical energy corrections: Phys. Rev. B 84 (2011) 024109 and Phys. Rev. B 84 (2011) 184103

Developers. Alberto Otero de la Roza, David Abbasi, Víctor Luaña.

Documentation. [TXT] [PDF]

Frequently asked questions. [TXT]

License. GNU GPL v3

Contact. alberto@carbono.quimica.uniovi.es


Asturfit

Robust fitting of static energy versus volume data.

Source.

Download the development version of the code from: [github]

A static copy of the code (October 30, 2014): [tar.bz2] [tar.gz]

CPC library source. [CPC library], but the use of the links above is recommended.

Publications & citation of this software
The asturfit code and algorithms: Comput. Theor. Chem. xx (2011) xxxx and Comput. Phys. Commun. 182 (2011) 1708-1720

Developers. Víctor Luaña, Alberto Otero de la Roza

Documentation. [TXT] [PDF]

License. GNU GPL v3

Contact. alberto@fluor.quimica.uniovi.es


Runwien

A text-based interface for the WIEN2k suite.

Source. Download the development version of the code from [github]

Static copy of runwien (Jul 6th, 2011): [tar.bz2] [tar.gz]

CPC library source. [CPC library], but the use of the links above is recommended.

Publications & citation of this software
The runwien code: Comput. Phys. Commun. 180 (2009) 800

Developers. Alberto Otero de la Roza, Víctor Luaña.

Documentation. [TXT] [PDF]

License. GNU GPL v3

Contact. alberto@carbono.quimica.uniovi.es


Optim

General optimization tool adapted to a UNIX environment. Minimizes a general function of several variables using one of several optimization methods. Optim uses system calls to run an external procedure at every trial point. The variables that define this point are passed to the procedure as shell parameters. The procedure returns the function value printing its value in an arbitrary file. This mechanism, some involved from a programmers point of view, is very flexible and well adapted to have a numerical experiment running fast. The system calls add some time to the optimization, but this is irrelevant when the time to compute a single point of the function is significant.

Source. (Sep. 25th, 2001) [tar.bz2] [tar.gz]

Developers. Víctor Luaña.

Documentation. [TXT]

Contact. victor@carbono.quimica.uniovi.es


Derive

Numerical computation of second derivatives of an arbitrary analytical function computed by means of an external procedure. Derive has been designed as a driver program working in unix environments. The programs performs system calls to run the external procedure, mechanism that adds some time to the computation, but represents a very flexible method easily adapted to many different tasks.

Source. (Apr. 5th, 1993) [tar.bz2] [tar.gz]

Developers. Víctor Luaña.

Documentation. [TXT]

Contact. victor@carbono.quimica.uniovi.es


Navigator

Navigator searches for specific critical points of a scalar function of several variables.

The function must be provided, at any point requested by the algorithm, by means of an external procedure. The gradient and hessian at any point may either be returned by the external procedure or be numerically determined by special navigator routines. Of course, an analytical gradient and hessian provided by the external procedure can be far more efficient and numerically more stable.

Navigator has been designed as a driver program working in unix environments. The programs performs system calls to run the external procedure, mechanism that adds some time to the computation, but represents a very flexible method easily adapted to many different tasks.

The navigation technique is based on the SJTO algorithm described in: J. Simmons, P. Jorgensen, H. Taylor, and J. Ozment, J. Phys. Chem. 87 (1983) 2745-53.

Numerical derivatives, when external gradient and hessian are not available, are obtained by means of O(h^2) central difference formulas iterated to O(h^2n) using a Richardson method.

Source. (Jun. 11th, 1993) [tar.bz2] [tar.gz]

Developers. Víctor Luaña and Miguel Álvarez Blanco.

Documentation. [TXT]

Contact. victor@carbono.quimica.uniovi.es


Gibbs

Calculation of p,T-dependent thermodynamic properties in solids under the Debye-Slater quasiharmonic model (see gibbs2).

Source. (May. 15th, 2010) [tar.bz2] [tar.gz]

CPC library source. [CPC library], but the use of the links above is recommended.

Publications & citation of this software
The gibbs code: Comput. Phys. Commun. 158 (2004) 57

Developers. Miguel Álvarez Blanco, Evelio Francisco and Víctor Luaña.

Documentation. [TXT]

Contact. victor@carbono.quimica.uniovi.es


Critic

Topological analysis (QTAIM) of solid-state electron densities. In this version, densities coming from WIEN2k and aiPI are read. The program can find the whole set of critical points in the cell, integrate basins and make beautiful plots. Active development has stopped and complex bugfixes are incorporated to the new version, critic2.

Source. (Jul. 6th, 2011) [tar.bz2] [tar.gz]

CPC library source. [CPC library], but the use of the links above is recommended.

Publications & citation of this software
The critic code: Comput. Phys. Commun. 180 (2009) 157-166

Developers. Alberto Otero de la Roza, Miguel Álvarez Blanco, Ángel Martín Pendás and Víctor Luaña.

Documentation. [TXT] [PDF]

License. GNU GPL v3

Contact. alberto@carbono.quimica.uniovi.es


The Caleao crystallographic server

The Caleao crystallographic server is a library (spgs) attached to a small test program. The objective is obtaining the space group operations in one of the ITA settings (conventional or not) given the space group label. Not very tested, use with care.

Source. (Jul. 6th, 2011) [tar.bz2] [tar.gz]

Developers. Alberto Otero de la Roza and Víctor Luaña.

Documentation. In the source code.

License. GNU GPL v3

Contact. alberto@carbono.quimica.uniovi.es


Guess

Given the cell lengths and angles, and the atomic positions in the unit cell of a crystal, determines the symmetry operations.

Source. (Jul. 6th, 2011) [f90]

Developers. Alberto Otero de la Roza and Víctor Luaña.

Documentation. In the source code.

License. GNU GPL v3

Contact. alberto@carbono.quimica.uniovi.es


Qewald

An octave script to calculate the electrostatic energy of a periodic crystal composed of point-like charges, optionally with a compensating uniform background charge, using Ewald method.

Source. (Jul. 6th, 2011) [m]

Developers. Alberto Otero de la Roza and Víctor Luaña.

Documentation. In the source code.

License. GNU GPL v3

Contact. alberto@carbono.quimica.uniovi.es


Vdw

Dispersion sum (r^-6) by Ewald-like method: an octave script to calculate lattice sums of the form c_6/r^-6, as in van der Waals interactions.

Source. (Jul. 6th, 2011) [m]

Developers. Alberto Otero de la Roza and Víctor Luaña.

Documentation. In the source code.

License. GNU GPL v3

Contact. alberto@carbono.quimica.uniovi.es


Cleanbib

The primary purpose of cleanbib is to detect duplicates in several bib (BibTeX) files and correct journal names. If a journal name is not registered in the code, modify the define_journals() function at the end of the script.

Source. (Jul. 6th, 2011) [awk]

Developers. Alberto Otero de la Roza and Víctor Luaña.

Documentation. In the source code.

License. GNU GPL v3

Contact. alberto@carbono.quimica.uniovi.es