Dear All,

I am working on a project in which we have formed a spherical polymer system of 100 chains with each chain having 140 atoms. I want to compute the density of the sphere bining with respect to radius of the sphere from the lammpstrj file obtained from the lammps trajectory. I tried with my own code but ended with error. Could anyone please help me out in this regard?

the code that I used

import numpy as np

def compute_density_from_lammps(trajectory_file, num_chains, chain_length, bin_size):

# Read LAMMPS trajectory file

with open(trajectory_file, ‘r’) as file:

lines = file.readlines()

```
# Extract atom coordinates at each time step
coordinates = []
atom_start = False
for line in lines:
if 'ITEM: TIMESTEP' in line:
atom_start = False
if len(coordinates) > 0:
break
if atom_start:
coords = line.split()[2:5]
coordinates.append([float(coord) for coord in coords])
if 'ITEM: ATOMS' in line:
atom_start = True
coordinates = np.array(coordinates)
# Calculate the center coordinates of the system
center = np.mean(coordinates, axis=0)
# Calculate the distances of particles from the center
distances = np.linalg.norm(coordinates - center, axis=1)
# Define radial bins
max_distance = np.max(distances)
num_bins = int(max_distance / bin_size) + 1
bins = np.linspace(0, max_distance, num=num_bins)
# Count particles in each bin
atom_counts = np.histogram(distances, bins=bins)[0]
# Calculate bin volumes
bin_volumes = (4/3) * np.pi * (bins[1:]**3 - bins[:-1]**3)
# Compute densities
densities = atom_counts / bin_volumes
# Average densities over chains
average_density = np.mean(densities) * chain_length / num_chains
return average_density
```

# Example usage

trajectory_file = ‘lammps_trajectory.txt’

num_chains = 100

chain_length = 140

bin_size = 1.0

density = compute_density_from_lammps(trajectory_file, num_chains, chain_length, bin_size)

print(“Average density:”, density)

Thank you all

With regards,

Kesavan