Computer graphics and graphical user interfaces as tools in simulations of matter at the atomic scale

Leach, 1996

Kokalj, 1999, J. Mol. Graphics Modell., 17, 176, 10.1016/S1093-3263(99)00028-5

A. Kokalj, M. Causà, XCrySDen: (X-window) CRYstalline Structures and DENsities, 2003. Available from: <http://www.xcrysden.org/>

V.R. Saunders, R. Doves, C. Roetti, M. Causá, N.M. Harrison, R. Orlando, C.M. Zicovich Wilson, Crystal98 1.0––user’s manual, University of Torino, Torino, 1999

Blaha, 2001

S. Baroni, A. Dal Corso, S. de Gironcoli, P. Giannozzi, PWSCF and PHONON: plane-wave pseudo-potential codes, 2001. Available from: <http://www.pwscf.org/>

Bockstedte, 1997, Comput. Phys. Commun., 107, 187, 10.1016/S0010-4655(97)00117-3

A. Kokalj, GUIB: Graphical User Interface Builder. Available from: <http://www-k3.ijs.si/kokalj/guib/>

OpenGL––high performance 2d/3d graphics, The official WEB site of OpenGL is <http://www.opengl.org/>

B. Paul, The Mesa 3d graphics library, The official WEB site of Mesa is <http://www.mesa3d.org/>

B. Paul, B. Bederson, Togl––a Tk Open GL widget, The official WEB site of Togl is <http://togl.sourceforge.net/>

XYZ format was the native format of the XMOL program developed by the Network Computing Services, Inc. The XMOL program is not developed anymore

Brookhavens protein databank PDB format, The official WEB site of PDB is <http://www.rcsb.org/pdb/> 1999

M.J. Frisch, G.W. Trucks, H.B. Schlegel, P.M.W. Gill, B.G. Johnson, M.A. Robb, J.R. Cheeseman, T. Keith, G.A. Petersson, J.A. Montgomery, K. Raghavachari, M.A. Al-Laham, V.G. Zakrzewski, J.V. Ortiz, J.B. Foresman, C.Y. Peng, P.Y. Ayala, W. Chen, M.W. Wong, J.L. Andres, E.S. Replogle, R. Gomperts, R.L. Martin, D.J. Fox, J.S. Binkley, D.J. Defrees, J. Baker, J.P. Stewart, M. Head-Gordon, C. Gonzalez, J.A. Pople, Gaussian, Inc., Pittsburgh PA, 1995

Kokalj, 2002, J. Phys. Chem. B, 106, 9839, 10.1021/jp025823k

Kokalj, 2003, Surf. Sci., 532–535, 191, 10.1016/S0039-6028(03)00452-7

T. Williams, C. Kelley, Gnuplot––an interactive plotting program, The official WEB site of Gnuplot is <http://www.gnuplot.info/>

Lorensen, 1987, Comput. Graphics, 21, 163, 10.1145/37402.37422

P. Bourke, Modelling, Accessible on WEB site: <http://astronomy.swin.edu.au/~pbourke/modelling/>

Information about [Incr Tcl] can be found on the Web site: <http://incrtcl.sourceforge.net/itcl/> while information about [Incr Tk] can be found on Web site: <http://incrtcl.sourceforge.net/itk/>

A. Kokalj, TkPWscf––a GUI for the PWscf, Available from: <http://www-k3.ijs.si/kokalj/tkpwscf/>