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
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 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.
Free with Latex support: Inkscape
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.
TODO: Bibtex, Mendeley, Tamas' PhD template, nanogroup template?
SSH, SCPUsing ssh related tasks from Windows:
TODO: usual settings in putty without sshkey authentication, using putty with sshkey authentication.
Creating figuresGraph, 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