Physico-chemical analysis in Atomes

In this chapter examples will be illustrated using an Atomes workspace presented in figure 4.1, this workspace contains 3 different projects, liquid GeSe systems with a similar chemistry yet obtained using a different set of DFT-GGA functionals. [1]

When a project is opened in the Atomes workspace, and if this project is the active project, then it it possible to compute the properties presented in section 3.4, and the parameter(s) of the calculation(s) can be adjusted via the associated dialog boxes accessible by using the "Analyze" menu [Fig. 3.1-d].
Some of the calculations of the "Analyze menu" are immediately available when a project is opened, other require some condition(s) to be full-filled before being accessible:

1. g(r)/G(r): requires a model box to be described.

2. S(q) from FFT[g(r)]: requires [1] to be completed.

3. S(q) from Debye equation: requires a model box to be described.

4. g(r)/G(r) from FFT[S(q)]: requires [3] to be completed.

5. Bonds and angles: no conditions.

6. Ring statistics: no conditions.

7. Chain statistics: no conditions.

8. Spherical harmonics: requires [5] to be completed.

9. Mean Squared Displacement: requires the project have more than 1 configuration (MD trajectory).

• Visualisation of the results of the calculations
• Data and plot edition
  • Data edition
  • Plot edition
• Mouse interaction with the data plot
  • Right button contextual menu
  • Left button zoom in and out
• Saving the data
• Keyboard shortcuts

1. S. Le Roux, A. Bouzid, M. Boero, and C. Massobrio, J. Chem. Phys., vol. 138, no. 17, p. 174505, 2013.