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+#+TITLE: dump2rotorang.py
+#+AUTHOR:
+#+DATE:
+
+* 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:
+
+#+begin_src sh
+pip install numpy pandas
+#+end_src
+
+* Input files
+
+The script searches for trajectory files with the following filename
+patterns:
+
+#+begin_src text
+D3d-o_*K.lammpstrj
+D3d-p_*K.lammpstrj
+#+end_src
+
+For example:
+
+#+begin_src text
+D3d-o_300K.lammpstrj
+D3d-o_400K.lammpstrj
+D3d-p_300K.lammpstrj
+D3d-p_400K.lammpstrj
+#+end_src
+
+The temperature is extracted from the filename using the pattern:
+
+#+begin_src text
+_(number)K.lammpstrj
+#+end_src
+
+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:
+
+#+begin_src text
+xu yu zu
+#+end_src
+
+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:
+
+#+begin_src text
+ITEM: ATOMS id mol type xu yu zu
+#+end_src
+
+* Analysis details
+
+The benzene atoms are selected by the following atom indices within each
+molecule:
+
+#+begin_src python
+benzene_id = [24, 25, 26, 27, 28, 29]
+#+end_src
+
+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:
+
+#+begin_src python
+np.arctan2(vec[:, 1], vec[:, 0])
+#+end_src
+
+The z-position is calculated as the mean z-coordinate of the selected
+benzene atoms.
+
+* Output files
+
+The script creates the following pickle files:
+
+#+begin_src text
+D3d-o.pkl
+D3d-p.pkl
+#+end_src
+
+Each pickle file contains a dictionary indexed by temperature.
+
+For example:
+
+#+begin_src python
+dset[300]["orientation"]
+#+end_src
+
+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:
+
+#+begin_src sh
+python dump2rotorang.py
+#+end_src
+
+If trajectory files matching the expected patterns exist, the script will
+print the processed filenames and create pickle files.
+
+Example:
+
+#+begin_src text
+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.
+#+end_src
+
+* 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:
+
+#+begin_src sh
+cp example.lammpstrj D3d-o_300K.lammpstrj
+python dump2rotorang.py
+#+end_src
+
+This will create:
+
+#+begin_src text
+D3d-o.pkl
+#+end_src
+
+* 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:
+
+#+begin_src text
+dump2rotorang.py
+example.lammpstrj
+README.org
+.gitignore
+#+end_src
+
+