Dear Aouchenni, You can also try DENEB (for Windows or Linux), it allows you to create fdf files easily, but not only that, it can make your whole siesta calculation experience a bliss :). See for example the video: http://www.youtube.com/watch?v=xzmlwYQcWMA
Here is a partial list of features elaborating a bit on the differences between the trial (free) and full (80% off now, because of our anniversary) versions of DENEB. For visualization purposes you may use, free of charge and with no time restriction the trial version of DENEB currently available for downloading in our web site. See the item entitled: "DENEB 1.26 trial with Siesta plugin _ Windows installer" in the "Downloads" section of https://www.atelgraphics.com. Or the item entitled "DENEB 1.26 trial with Siesta plugin _ Linux installer", depending on your preferred system. "DENEB 1.26 trial with Siesta plugin" would allow you to (among others): Visualize: -- Load and visualize any sample file that is in DENEB (.dns) or non-DENEB format (xyz, fdf,...) -- Visualize simultaneously from 3 view points (Main view, side view, detached view). -- Visualize at will the unit-cell box, and the 3D-cartesian axes. -- Place in the same 3D space any number of samples at any point relative to each other. -- Change your point of view by: - Sliders and buttons (accurate reproducible view angles), - Mouse drag (click and drag to spin), or - Key Navigation (limitless "dive through" using keys) -- Quick visualization within DENEB's "NanoExplorer" data base of samples. and customizable visualization (and edition) using DENEB's "Sample Manipulator". Edition-Modificaton: -- Modify at will the radius, color, glowing state of atoms and bonds representation. -- Modify them in any imaginable way. (Add-remove atoms, molecules or arbitrary sets, shift, rotate, etc) -- Group them at will into new samples or molecules. Redefine these groups as you will. -- Filter using logic mathematical expressions (for example to sculpt-out a sphere out of a block of atoms) -- The "Midas" process: change atomic numbers at will. Trajectory visualization-edition: -- Visualize molecular dynamics "videos" stored in files of format XYZ (or .ANI). Play, pause, advance, rewind, automaticaly or step-by-step, at your chosen speed. -- Place sample's with a trajectory (from a video file) in the same 3D-space together with any other sample. -- Edit any frame of a video; any atom's position at that frame. Build: -- Build from scratch, atom by atom or aggregating molecules/samples/groups. -- Use Builders: Nanotubes (hexagonal, triangular, One or two chemical species ...) I/O: -- Import any sample of any number of atoms from files in DENEB's sample format (.dns), and non-DENEB's formats (xyz, fdf, ...) -- Export any sample of any number of atoms to files in DENEB's sample format (.dns). -- Export any sample of 20 atoms or less to file in non-DENEB formats. [*] -- Your "NanoExplorer" samples database has persistence "built in": it automatically saves its state at every change. Computational parameters: -- Load any fdf (Siesta input file) into DENEB's Parameter Editor -- Modify any of those parameters at will (add, remove, change values) -- Couple the parameters with any sample, to create simulations. -- Classify simulations into projects using DENEB's Project Browser. -- Save-Retrieve the whole Project Browser tree structure of simulations with a single action. Remote execution of simulations: -- Launch simulations to remote (or local) hosts with a single click. -- Monitors in real time all launched jobs state. -- Retrieve the output-log and any output file at will with a single click. This trial version (DENEB 1.26 trial) requires no license file and has no time limit. Its limitation therefore is that it will export no more than 20 atoms to non-DENEB formats. You can import and visualize with no restriction. The full version requires a license file (follow instructions upon installation) and will allow you to export to non DENEB formats samples of any number of atoms. It will therefore allow you to launch simulations for remote execution with any number of atoms. Prices of the full license depend on the time requested (yearly, permanent, etc), on your institution: academic, industry, etc, and the number of requested licenses. If you can give us roughly some of these data we will happily specify prices for you. Yours Sincerelly Jose A. -- Jose A. Torres, PhD Founder, CTO AtelGraphics SL Faraday 7, Edif. CLAID, Scientific Park of Madrid, 28049 Madrid, Spain https://www.atelgraphics.com ________________________________ De: aouchenni boudjemaa <[email protected]> Para: [email protected] Enviado: Viernes 24 de Mayo de 2013 15:45 Asunto: [SIESTA-L] fdf Hi siesta users, I am a new siesta user, I would like ask you how we can create an fdf file input. thanks for all Aouchenni
