Welcome to the Molecular Geochemistry Laboratory

If chemistry is the central science, then geochemistry is the central science as applied to understanding the natural world around us.

Geochemists seek to answer questions relating to the evolution of life on Earth and how metalloenzymes may have evolved, the chemistry of the oceans and how they are affected by global warming, the interplay between flora, fauna and the environment in chemical terms, how pollutants interact with soils and minerals, and how radioactive waste can be securely stored for millennia. We do this by connecting the very big — mountains — with the very small — atoms and molecules, and the very fast — fundamental reactions — with the often very slow — weathering

If you share our passion for understanding and explaining how the world works — join us! To find out about opportunities in our laboratory, contact one of the group leaders: Jean-François BoilyMichael Holmboe, C. André Ohlin, Andrey Shchukarev, and Staffan Sjöberg.

Michael Holmboe lead-convener of a MD Workshop at Goldschmidt 2017 in Paris

Together with friends from Princeton (Ian C. Bourg) and UC Berkeley/LBNL (Laura Lammers, Karol Kulasinski), PI Michael Holmboe organized a 2-day course on Molecular Dynamics Simulations of (bio)inorganic systems at the Institut de Physique du Globe de Paris (www.ipgp.fr) prior last weeks Goldschmidt conference. Many thanks to the people at HPC2N for setting up guest accounts on  their computers (although unfortunately our wifi was not always that reliable…).

      

ECCE forked, hosted at https://github.com/FriendsofECCE/ECCE

The PNNL developed a Linux code called ECCE (Extensible Computational Chemistry Environment; http://ecce.emsl.pnl.gov/) in the 90s and 00s. Unfortunately, no more resources seem to be made available to maintain the code.

This is a shame since it has some interesting functionality:

  • can be used to prepare input files for gaussian and nwchem
  • can submit jobs either directly or to queue managers (SGE, Slurm)
  • can open and visualise the output

And on top of this it’s open source and runs on Linux.

I and Matt Asplund of BYU have thus decided to try to develop a community maintained version. We have put this at https://github.com/FriendsofECCE/ECCE

In addition to maintaining the code, we also have three standard build environment for which we release precompiled binaries.

You can thus download binaries for Centos 7, Ubuntu LTS 16.04.2 and Debian 8.8, in addition to the source code.

Currently there are three release versions:

7.0 — The unmodified PNNL code

7.0.1 — The PNNL code modified to allow it to compile without any further patching on CentOS, Ubuntu and Debian

7.1.0 — A heavily modified version of the PNNL code that introduces new functionality and fixes old bugs