Archive for the ‘Chemistry’ Category

July 7th, 2010

I was recently asked to install 32bit Gaussian 03 binaries on an Ubuntu 9.10 machine and when I tried to run a test job I got the following error message

Erroneous write during file extend. write -1 instead of 4096
Probably out of disk space.
Erroneous write during file extend. write -1 instead of 4096
Probably out of disk space.
Write error in NtrExt1
Write error in NtrExt1: Bad address
Segmentation fault

A bit of googling suggested that the following might work

sudo echo 0 > /proc/sys/kernel/randomize_va_space

but this will result in permission denied (explanation here). The command you really want to use is

sudo bash -c "echo 0 > /proc/sys/kernel/randomize_va_space"

Once this was done, Gaussian worked as advertised. Maybe this post will help a googler sometime in the future.

March 27th, 2008

If you work in the field of Chemistry then it’s highly likely that you will want to produce Lewis Dot diagrams at some point in your career. If you have never heard of them then essentially what they do is show the distribution of electrons in atoms and molecules in schematic form. For example, the diagram below is the Lewis dot diagram for ethane (original source here)

Over at the Teaching College Math Technology Blog, Maria has produced a tutorial video that shows how to produce these diagrams using Design Science’s MathType. In addition she has posted a second tutorial that has been produced by an employee of Design Science – well worth a look if this is something you need to do.

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