Goodies

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Molecular viewers and builders

There is a large zoo of viewers. Some are pretty good for very fast geometry checking, others can even do classical simulations and are highly scriptable. Our favorite one is VMD which is free to use for academic users. It is able to understand Python and TCL scripting languages and it can be personalized. The default settings are quite nice, and it is extremely fast so it can be considered the ultimate choice for most purposes. However, when it comes to editing an already built structure, VMD is not the best option.

As a molecular builder, I suggest using MacMolPlt. This is the code I use when I would like to build a molecule from scratch (Marton).

Other codes
  • Avogadro, molecular editor, works also as a builder
  • JMOL, mainly moleculer viewer, cross platform JAVA code
  • Molden, mainly for periodic system
  • Xcrysden, mainly for periodic systems, understands Quantum Espresso input files, good for checking input geometries

How to use VMD on Skynet:

 module load vmd/1.9

and VMD, Molden, Xcrysden on Mordor:

 module load qchem/molden
 module load qchem/vmd
 module load qchem/xcrysden

TODO: building 3D models, models with defects, molecular/nanocrystal builder, surface builders.

Rendering

Rendering is the process when a bitmap image is generated using a model. VMD has its own included rendering libraries (tachyon-internal), which produces nice pics using the default settings.

NVIDIA's gelato library makes very nice pics, however it is quite buggy and not anymore supported.

Animations

Gifsicle

Bitmap pictures

GIMP

Vector graphics

Free with Latex support: Inkscape

http://pav.iki.fi/software/textext/ http://www.kono.cis.iwate-u.ac.jp/~arakit/inkscape/inklatex.html http://www.julienvitard.eu/fr/eqtexsvg_fr.html

Script to convert text in EPS, PDF files to outline:

 gs -sDEVICE=pswrite -dNOCACHE -sOutputFile=- -q -dbatch -dNOPAUSE -dQUIET "$1" -c quit | ps2pdf - "`echo $1 | cut -f1 -d'.'`"-nofont.pdf

TODO: scalable formats: eps, ps, svg. Ghostscript.

Publishing

LaTeX systems: Miktex for Windows, TEXLive for Linux

Latex GUI:

TODO: Bibtex, Mendeley, Tamas' PhD template, nanogroup template?

SSH, SCP

Using ssh related tasks from Windows:

TODO: usual settings in putty without sshkey authentication, using putty with sshkey authentication.

Creating figures

Graph, diagram, plot makers:
  • Gnuplot: has its own scripting language, easy to learn for basic tasks, very good for fast checks, more cumbersome if you want to completely change the outlook. NO real GUI. Pretty good FAQ: http://t16web.lanl.gov/Kawano/gnuplot/index-e.html.
  • GLE: has its own scripting language, easy to learn and use for basic tasks, direct latex support (this is what I usually use for publications, Marton), basic GUI
  • Asymptote: C++-like plotting language, very STRONG capabilities, direct latex support, if something cannot be done in this that it is your fault! However, the learning curve is quite steep. No real GUI.
  • matplotlib: Python based