This repository contains input and analysis scripts supporting the findings of *Heat conductivity from energy-density fluctuations*, by E. Drigo, M. G. Izzo and S. Baroni

Content:

- **README.md**: this file, information about the repository
- **spce**: folder containing scripts to run the LAMMPS input for 216 SPCE water molecules in the NVE ensemble as described in the paper. 
	- ** system* ** files generated from moltemplate for the simulation.
	- ** input.in ** input file for the LAMMPS run.
	- ** readtraj.job ** job file for the computation of the Fourier transform of the densities.
	- ** nlttcepstral* ** files of the computed thermal conductivity at finite wave-vector with the associated error bar.
- **argon**: folder containing scripts to run the LAMMPS input for the Argon system.
	- ** argon.in ** input file for the LAMMPS run.
	- ** enka.npy ** Fourier transform of the energy density computed from the ** readtraj.job ** file.
	- ** nk*a.npy ** Fourier transform of the number density computed from the ** readtraj.job ** file.
	- ** readtraj.job ** job file for the computation of the Fourier transform of the densities.
	- ** Ar.lammps.npy ** LAMMPS log file turned into a numpy dictionary.
	- ** nlttcepstral* ** files of the computed thermal conductivity at finite wave-vector with the associated error bar.
- **aSiO2**: folder containing scripts to compute the thermal conductivity
	- ** buck.lmp ** initial configuration of amorphous silica taken from Ref. [36].
	- ** in.aSiO2.IFC.lmp ** input file for the LAMMPS run.
	- ** readtraj.job ** job file for the computation of the Fourier transform of the densities.
	- ** nlttcepstral* ** files of the computed thermal conductivity at finite wave-vector with the associated error bar.
- **transportwithdensities**: modules needed for the computation of the thermal conductivity via the energy density. Requirements: numba, numpy, scipy, sportran, pickle and matplotlib
- **thermal_konductivity_COMPARE_argon_spce_aSiO2.ipynb**: Jupiter notebook from which one can reproduce Fig. 2 and Fig. 3. 
- **thermal_konductivity_argon.ipynb**: Jupiter notebook from which one can reproduce Fig. 1 and compute the thermal conductivity of Argon as described in the paper.
- **thermal_Konductivity_20ns_size.ipynb**: Jupiter notebook from which one can reproduce Fig. 4 and Fig. 5.