Material Properties Calculation

This repository contains code for calculating various material properties using data obtained from molecular dynamics simulations (LAMMPS). Currently, the following calculations are supported:

1. Plot Strings in OVITO (property_type = 6)

This option allows you to visualize the string configuration using OVITO software. Strings are accessed by connecting mobile atoms i and j if: $$|\vec{r}_i(t)-\vec{r}_j(0)|<\delta$$ or $$|\vec{r}_j(t)-\vec{r}_i(0)|<\delta$$

Input Data Required (input.json):

• num_atoms: Total number of atoms in the system
• num_frame: Total number of steps
• num_types: Number of types of atoms in the system
• dim: The dimension you computed
• dt: The time step
• gap: gap * dt is the t in the equation above
• steps_read: The folder that you save for the STRINGS at time interval t
• initial_read: The folder that you save for the STRINGS at a specific initial time
• time_index: The time steps you would like to plot the strings

Required Files:

• STRINGS: Includes information about the strings
• conf.dump_all: Includes atom positions and velocities

2. Van Hove Self Correlation (property_type = 1)

The Van Hove self-correlation function quantifies the probability of finding an ion within a volume element dr, centered at r and time t, given that the ion was at the origin at time t=0. The formula is given by: $$G_s(\vec{r},t)=\left<\frac{1}{N} \sum_{i=1}^{N} \delta(\vec{r}-|\vec{r}_i(t)-\vec{r}_i(0)|)\right>$$

Input Data Required (input.json):

• num_atoms: Total number of atoms in the system
• num_frame: Total number of steps
• num_types: Number of types of atoms in the system
• dim: The dimension you computed
• dt: The time step
• rDel: The value of dr
• rCutoff: The cut-off distance
• time_series: The array that includes the different time intervals you would like to compute ( G_s )
• gap: For one run, the start of computing ( G_s ) is delayed by gap steps (different initial time)
• ave_num: The number of ( G_s ) calculations you are averaging

Required Files:

• conf.dump_all: Includes atom positions and velocities

3. VACF and PDOS (property_type = 0)

This option calculates the Velocity AutoCorrelation Function (VACF) and the Phonon Density of States (PDOS) for the material.

• VACF (Velocity AutoCorrelation Function): VACF provides information about particle motion and diffusion. It is defined as: $$C(t) = \frac{1}{N} \sum_{i=1}^{N} \vec{v}_i(t) \cdot \vec{v}_i(0)$$ Where $\vec{v}_i(t)$ is the velocity of particle i at time t, and N is the total number of particles.

• PDOS (Phonon Density of States): PDOS gives insights into the material's vibrational modes. It is calculated using Fourier transform techniques and provides the distribution of vibrational frequencies in the material.

Input Data Required (input.json):

• num_atoms: Total number of atoms in the system
• num_frame: Total number of steps
• num_types: Number of types of atoms in the system
• dim: The dimension you computed
• dt: The time step
• max_omega: The largest frequency to compute PDOS
• d_omega: The frequency step
• Nc: The correlation time for VACF
• compute_type: The array that specifies which atom type you are going to compute the VACF and PDOS for. If compute_type equals num_types + 1, then compute VACF for all the atoms.

Required Files:

• conf.dump_all: Includes atom positions and velocities

4. Imtermeidate Scattering Function (property_type=2)

This option calculates the imtermediate scattering function and dynamics structure factors for materials

5. Other Properties (Work in Progress)

Additional material properties are currently under development and will be added to the repository soon.

Stay tuned for updates and improvements!