ChipSum's toolkits serve computational chemistry applications in CDCS, including molecular dynamics simulation and the calculation of the physical and chemical properities.
- Preproc: Some scripts to deal with the problems occur before calculation or simulation, such as the input parameters suggestion, format transformation and so on.
- Postproc: Some scripts to deal with the problems occur after calculation or simulation, such as the data analyse, plotting graph and so on.
MSDVASP.py is used to calculate MSD from VASP molecular dynamic simulation output file XDATCAR.
MSDQE.py is used to calculate MSD from QE molecular dynamic simulation output file .pos.
- Usage:
python3 MSDVASP.py/MSDQE.py - Note:
XDATCARfile shoule be in the directory. The detials are in the scripts.
bondVASP.py is used to calculate and analyze the bond length from VASP molecular dynamic simulation output file XDATCAR.
- Usage:
python3 bondVASP.py ele1 ele2 - Note:
ele1andele2are element symblo case-insensitive. The detials are in the scripts.
FFT.py is used to make FFT of atom position from MSDVASP.py and MSDQE.py output file .pos.
RDFVASP.py is used to calculate RDF of pair atoms from MSDVASP.py and MSDQE.py output file .pos.
- Usage:
python3 RDFVASP.py
plot_trajectory.py is used to plot motion trajectory graphs of atoms from MSDVASP.py and MSDQE.py output file .pos.
cal_SED.py is used to calculate the SED from MD trajectory and then Phonon dispersion and Phonon density of states (DOS).
- Note: Details are in the directory of
Postproc/SED/ - Example: SWNT
The VACF is an important tool to analyze the atom vibrations in the MD simulations. The script cal_VACF.py will output the VACF of different atoms seperated by atom ID and three axis. Furthermore, it will also calculated the FFT of VACF and give the Lorentz distribution fitting of it. Besides, the force constants of all the atoms in your system will be also calculated.
- Note: Details are in the directory of
Postproc/VACF/