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Lecture notes  

• Lecture notes on thermostatistics (L3 Physics bachelor): pdf (to be completed)

• Lecture notes on statistical physics (Paris Physics Master): pdf

• Lecture notes on molecular dynamics and Monte Carlo simulations (SMNO Master): pdf

• Lecture notes on free-energy calculations (SMNO Master): pdf

• Some basic notes on kinetics, Langevin and Fokker-Planck equations: pdf

Software

• Input related to ice nucleation simulations in Physical Review Letters 119, 245701 (2017): https://github.com/physix-repo/plumed_input_nucleation

• Input related to supercooled water simulations in Journal of Chemical Physics 158, 014502 (2023): https://github.com/fabiopietrucci/plumed_input_supercooled_water

• Plumed 1.3 modified to include path collective variables based on coordination patterns (PNAS 112, 15030 (2015)), compatible with CPMD, QuantumEspresso, CP2K etc., with an example of usage: https://github.com/physix-repo/plumed_input_pathcoordtable

• Examples of input for Plumed 2.x for the study of chemical reactions with path collective variables based on coordination patterns (PNAS 112, 15030 (2015)): https://github.com/physix-repo/plumed_input_pathcoordtable

• METAGUI: a VMD interface to analyze MD and metadynamics simulations, aimed at constructing a cluster-based thermodynamic and kinetic model: www.plumed.org/contributions

• PIV clustering: a program to perform a structural cluster analysis of atomic trajectories obtained, e.g., from molecular dynamics simulations. The clustering is based on a general metric that includes on the same footing all degrees of freedom, thus allowing to analyse also disordered systems like solutions or amorphous solids: sourceforge.net/projects/pivclustering/