Fuster Franck

General Presentation

The TopMod package enables the calculation of the ELF function on a 3-dimensional grid, the assignment of the basins and the calculation of the basin populations and of their variance. It uses wave functions written in a wfn file which is available as output file generated by Gaussian92/94/98/03 and GAMESS ab initio softwares. The modules are written in FORTRAN 90 in order to enable dynamic memory allocation.

In order to carry out a standard ELF analysis three programs have to be run in the following order:

• grid09: calculates ELF on a 3-D grid parallel to the standard axis defined in the MO calculation (this allows to exploit the factorization of the gaussian functions),
• bas09: assigns the grid points to basins,
• pop09: calculates the basin populations and variances.

The other modules do the following tasks:

• top_sym: exploits abelian symmetry operations,
• search09: localizes the critical points of the ELF gradient field,
• mod_wfn: enables to remove atoms in the case of large systems in order to focuss the calculation on the region of interest,
• sym_wfn: symmetrizes the wfn file for 2Π states of linear molecules,
• bas_to_syn: assigns basin types from bas.sbf file,
• sbf_to_cube: converts sbf files to cube files for Molekel,
• sbf_to_am: converts sbf files to iam files for Amira,
• wfn_to_line: generates a wireframe, stick or ball and stick molecular skeletons for Amira.
• basin_prob: computes the probabilities of having ν electrons in given basins or group of basins.

Gaussian and GAMESS inputs

• Gamess
• Gaussian

Visualization

Useful reading and references

• A. Becke and K. E. Edgecombe,J. Chem. Phys., 92, 5397-5404 (1990)
• B. Silvi and A. Savin, Nature, 371, 683-686 (1994)
• A. Savin, B. Silvi and F. Colonna, Can. J. Chem., 74, 1088-1096 (1996)
• X. Krokidis, S. Noury and B. Silvi, J. Phys. Chem. A, 101, 7277-7282 (1997)
• B. Silvi, A. Savin, and F.R. Wagner, In Modeling of Minerals and Silicated Materials, B. Silvi and Ph. D'Arco Eds., Kluwer Academic Publisher, Dordrecht, 1997
• S. Noury, F. Colonna, A. Savin and B. Silvi, J. Mol. Struct., 450, 59-68 (1998)

please cite:

• S. Noury, X. Krokidis, F. Fuster and B. Silvi, TopMod package, 1997.
• S. Noury, X. Krokidis, F. Fuster and B. Silvi, Computers and Chemistry, 23, 597. (1999)
• M. Calatayud, J. Andrés, A. Beltrán and B. Silvi, Theoret. Chem. Acc., 105, 299 (2001)
• B. Silvi, J. Mol. Struct., 614, 3 (2002)
• B. Silvi, J. Phys. Chem. A, 107, 3081 (2003)
• B. Silvi, Phys. Chem. Chem. Phys., 6, 256 (2204)
• E. Cancès, R. Keriven, F. Lodier and A. Savin, Theoret. Chem. Acc., 111, 373 (2004)
• E. Matito, B. Silvi, M. Duran and M. Solà, J. Chem. Phys., 125, 024301 (2006)
• F. Feixas, E. Matito, M. Duran, M. Solà and B. Silvi, J. Chem. Theor. and Comp., 2010, 2736-2742 (2010)

please report bugs or problems via electronic mail at:

• silvi@lct.jussieu.fr