# 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

*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 "*

**active**`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:g(r)/G(r): requires a model box to be described.

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

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

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

Bonds and angles: no conditions.

Ring statistics: no conditions.

Chain statistics: no conditions.

Spherical harmonics: requires [5] to be completed.

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

- Visualisation of the results of the calculations
- Data and plot edition
- Mouse interaction with the data plot
- Saving the data
- Keyboard shortcuts

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