dump2rotorang.py

• Overview
• Requirements
• Input files
• LAMMPS dump format
• Analysis details
• Output files
• Usage
• Example
• Notes
• Files managed in this repository

Overview

dump2rotorang.py analyzes LAMMPS trajectory files and calculates orientation and z-position distributions of benzene molecules.

The script reads LAMMPS dump trajectory files *.lammpstrj, extracts the coordinates of selected atoms in each molecule, and evaluates:

• the in-plane orientation angle of each benzene molecule
• the center z-position of each benzene molecule

The resulting histograms are saved as Python pickle files.

Requirements

This script requires Python 3 and the following Python packages:

• numpy
• pandas

Install them, for example, using pip:

pip install numpy pandas

Input files

The script searches for trajectory files with the following filename patterns:

D3d-o_*K.lammpstrj
D3d-p_*K.lammpstrj

For example:

D3d-o_300K.lammpstrj
D3d-o_400K.lammpstrj
D3d-p_300K.lammpstrj
D3d-p_400K.lammpstrj

The temperature is extracted from the filename using the pattern:

_(number)K.lammpstrj

For example, D3d-o_300K.lammpstrj is interpreted as 300 K.

LAMMPS dump format

The trajectory file is assumed to be a LAMMPS dump file containing unwrapped atomic coordinates:

xu yu zu

The script also assumes that the dump file contains a mol column, which is used to identify molecules.

A typical header should include columns such as:

ITEM: ATOMS id mol type xu yu zu

Analysis details

The benzene atoms are selected by the following atom indices within each molecule:

benzene_id = [24, 25, 26, 27, 28, 29]

These indices are hard-coded in the script.

The orientation of each benzene molecule is calculated from the vector between:

• the center of the selected benzene atoms
• the midpoint of atoms 25 and 26 in the selected benzene atom list

The orientation angle is calculated using:

np.arctan2(vec[:, 1], vec[:, 0])

The z-position is calculated as the mean z-coordinate of the selected benzene atoms.

Output files

The script creates the following pickle files:

D3d-o.pkl
D3d-p.pkl

Each pickle file contains a dictionary indexed by temperature.

For example:

dset[300]["orientation"]

contains a pandas DataFrame with the following columns:

Column	Description
angle	Bin center of orientation angle
angle_y	Histogram count of orientation angle
zpos	Bin center of z-position
zpos_y	Histogram count of z-position

Usage

Place dump2rotorang.py in the directory containing the LAMMPS trajectory files, then run:

python dump2rotorang.py hoge.lammpstrj

If trajectory files matching the expected patterns exist, the script will print the processed filenames and create pickle files.

Example:

D3d-o_300K.lammpstrj
D3d-o_400K.lammpstrj
D3d-o.pkl was created.
D3d-p_300K.lammpstrj
D3d-p_400K.lammpstrj
D3d-p.pkl was created.

Example

If example.lammpstrj is included as a sample trajectory file, rename or copy it to match the expected naming rule before running the script:

cp example.lammpstrj D3d-o_300K.lammpstrj
python dump2rotorang.py

This will create:

D3d-o.pkl

Notes

• The atom indices used for benzene are currently hard-coded.
• The script assumes that all molecules have the same number of atoms.
• The orientation histogram is calculated in the range from -pi to pi.
• The z-position histogram is calculated in the range from 24 to 25.
• If the target system or molecule definition is changed, the values of benzene_id and the histogram range for z-position may need to be modified.

Files managed in this repository

This repository is intended to manage only the following files:

dump2rotorang.py
example.lammpstrj
README.org
.gitignore