Tutorial.2nd.mineral.physics
Tutorial: Molecular dynamics
Tutorial Presentation slides
Visualization tools:
1. JMOL: an open-source Java viewer for chemical structures in 3D
jmol address:
jmol download:
http://sourceforge.net/projects/jmol/files/latest/download?source=files
2. Example 1: Snapshot of Fe3C run
file @ http://perso.ens-lyon.fr/razvan.caracas/tutorial-cider/mdfe3c.xyz
3. VMD: visual molecular dynamics
address:
http://www.ks.uiuc.edu/Research/vmd/
Download:
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
4. Example 2: C in forsterite melt at mid-mantle conditions. files @
http://perso.ens-lyon.fr/razvan.caracas/tutorial-cider/a21-C.xyz.gz
http://perso.ens-lyon.fr/razvan.caracas/tutorial-cider/a21-CO2.xyz.gz
to visualize the structure with sticks and balls:
- go to Representations
- Create a first Representations "CPK". set the bond width to zero.
- Create a second representation "DynamicBonds". The bond length should reflect the coordination polyhedron around the central atom. FYI, Si-O bonds in an ambient pressure solid silicate is around 1.7-1.8. In these melts you could safely assume the Si-O bonds around 1.9-2.0 angstroms. Of course, play with the values to see what you get.
The g(r) utility is in extensions. If you used an "xyz" file as input you will need to define the unit cell parameters (a,b,c,alpha,beta,gamma) from the upper-left button. Then you define the selected pair of atoms, like "name atom C" "name atom O" to determine the coordination of C by oxygen. You can obviously choose also "name atom Si" and "name atom O" to obtain the silicate structure. The Si-Si setting will give you an insight on the polymerization of the melt.
You can compare the two, C and CO2, simulations see if there is any difference in the coordination of C. Please not that the first one correspond to forsterite + atomic C (very reducing conditions) and the second one to forsterite + CO2 molecule (more oxidizing conditions).
