Modified CP2K source code implementing the rotational constraint, developed by @jtyang-chem and reproduced here for convenience. For details, see https://doi.org/10.1063/5.0216913.
MD input file and initial/final configurations.
optimized_geometry in POSCAR format.
Code reads MD trajectories in DCD (CP2K) or XYZ format and then calculates the free energy curve/surface, reorientation frequency, and the time-correlation function of angular velocity, etc.
Compute rotor reorientation frequencies from MD trajectories, either by direct integration (fast rotors) or by an Ivanov model fit (slow rotors).
- Demo instructions
Instructions to run on data: Edit the user parameters in frequency.py, including TRAJ_LIST, DT_FS, INIT_FRAME_XYZ, DCD_TEMPLATE, DCD_STRIDE, and PS_CUTOFF, so that they point to the input XYZ frame and DCD trajectory files. Then run:
python frequency.py
By default, the script computes the first- and second-order orientational correlation functions for each trajectory. After the C1_traj*.npy and C2_traj*.npy files have been generated, edit the main block to call either fast_rotor() or slow_rotor() to extract the reorientation frequency.
Expected output: The correlation step generates C1_traj{n}.npy and C2_traj{n}.npy files for each trajectory index n in TRAJ_LIST. The frequency-analysis step prints the extracted relaxation time and reorientation frequency to the terminal. For slow rotors, the script reports tau0, jump angle Delta, and frequency nu, including SEM-based error estimates across trajectories.
Expected run time: The run time depends on the number and length of DCD trajectories. For a DCD trajectory of approximately 4 GB, the analysis is expected to finish within a few minutes.
The computed mean square (dipole) displacements of six solid electrolytes, along with the script used to compute them.
The VASP input files for point defect calculations for Na3OBH4, using a sodium vacancy with a charge of -2 as an example.
The CP2K input files for well-tempered metadynamics simulations of LiBH4, together with the post-processing scripts.
Repo tested with Python 3.10.