Scripts of KGZ

本教程基于 HPC of zhenggroup 集群环境
https://github.com/LU-SONG/Computational-Chemistry/blob/main/scripts/scripts.md

python脚本(2024)

-脚本名称- -功能- -使用方法-
add_H2O.py Add H2O to the slab. python3 add_H2O.py
add_site_ads.py 添加中间体的吸附位点，top/bridge/hollow python3 add_site_ads.py -h
bader2pqr.py 将bader转化为pqr格式，可视化 python3 bader2pqr.py
ck-multi.py 查看串行脚本的运行情况 python3 ck-multi.py multi_job.pbs
d-band.py d带中心分析（需要先做完pdos计算） python3 d-band.py
plot_pdos.py plot the projected density of states (PDOS) from data and save the figure. python3 plot_pdos.py
eps2jpg.py convert an EPS file to a high-resolution PNG image. python eps2png.py
fix_slab.py fix the slab in POSCAR. python3 fix_slab.py -The number of atoms you want to fix.
get_cp.py data to a quadratic polynomial and calculate related statistical quantities. python get_cp.py
get_db.py store the calculated crystal structure data into a SQLite database. python get_db.py
get_dimer.py Extract vibrational mode information from a OUTCAR file and add it to a new POSCAR_dimer file for dimer (two-molecule) calculations. python get_dimer.py
neighbor_multi_atoms.py Calculate and analyze the neighboring atoms of a specified atom in the crystal structure , generate a Markdown formatted table to display the neighboring atoms. python neighbor_multi_atoms.py -filename -central_atom_index -cutoff
out_view.py Read the crystal structure data from the CONTCAR file and use the matplotlib library to generate top views and two side views (XZ and YZ planes) of the atomic structure. python out_view.py
pos2arc.py transfer POSCAR to .arc or transfer .arc to POSCAR. python pos2arc.py -pos2arc/-arc2pos
RDF.py Read data from a Radial Distribution Function (RDF) data file, calculate the average RDF, and plot the RDF graph. python RDF.py
revise_boundary_length.py Revise boundry atoms view. Python revise_boundary_length.py filename
sort_poscar_atoms.py sort the same elements in POSCAR. python sort_poscar_atoms.py
vector2ort.py Converted cells into orthorhombic system python vector2ort.py

shell脚本（2024）

-脚本名称- -功能- -使用方法-
bader.sh Perform Bader charge analysis of the charge density around atoms to obtain the valence electron count of the atoms. bader.sh
checkinput.sh get energy and force from OUTCAR/OSZICAR checkinput.sh
checkpospot.sh Check for VASP input files POSCAR and POTCAR in the current directory and its subdirectories. checkpospot.sh
correct_H.sh Traverse the current directory and its subdirectories, looking for VASP calculation result files OUTCAR, and use the vaspkit tool to calculate the thermodynamic correction value (deltaG). correct_H.sh
correct-cp2k.sh Traverse the current directory and its subdirectories, looking for CP2K calculation result files cp2k.out, and use a tool called Shermo to calculate the thermodynamic correction value (deltaG). correct-cp2k.sh
CP2K_OUTPUT_save.sh Extract the execution time and computation duration from a CP2K calculation result file named cp2k.out, then create a new backup folder based on this information, and copy the relevant CP2K input and output files into this folder. CP2K_OUTPUT_save.sh
fix_all_slab.sh Batch execute the Python script fix_slab.py. fix_all_slab.sh
g16_out2gjf.sh Convert geometry (final, input orientation) in all Gaussian .out files in current folder to .gjf file by Multiwfn g16_out2gjf.sh
get_force.sh eliminate forces of fixed atoms get_force.sh -fix_value
get_hol_ele_cub.sh generate three different cube files (hole.cub, electron.cub, and CDD.cub), and rename them to include a serial number in the file name. get_hol_ele_cub.sh
incar_modi.sh Find all lines containing IDIPOL=3 in the INCAR file and comment out these lines. incar_modi.sh
kpoints.sh To generate KPOINTS file kpoints.sh 3 3 1
mk_pwdfreq.sh Prepare and modify input files for VASP calculations. mk_pwdfreq.sh
mkfreq.sh Prepare and modify input files for VASP calculations, and organize all related files into a temporary directory. mkfreq.sh
mk-pbs.sh Generate job submission scripts (sub.pbs) for different computational tasks, which are used to submit jobs on high-performance computing clusters. mk-pbs.sh
multi_qsub48.sh Batch modify the NCORE parameter in the INCAR files of all subdirectories under the current directory, setting it to 12, then copy a PBS job submission script named multisub48.pbs to the current directory, and submit the script using the qsub command. multi_qsub48.sh
multi_qsub56.sh Batch modify the NCORE parameter in the INCAR files of all subdirectories under the current directory, setting it to 14, then copy a PBS job submission script named multisub56.pbs to the current directory, and submit the script using the qsub command. multi_qsub56.sh
pos2potall.sh Batch generate POTCAR in all subdirectories pos2potall.sh
potall.sh Batch generate POTCAR in all subdirectories potall.sh
potcar.sh Rename the old POTCAR to old-POTCAR, and look for POTCAR files matching the command-line arguments from the specified pseudopotential repository path, then concatenate them into the POTCAR file in the current directory. potcar Cu C H O
q48.sh Check the NCORE parameter in INCAR and submit the 48kgz.pbs job script to the job scheduling system. q48.sh
q56.sh Check the NCORE parameter in INCAR and submit the 56kgz.pbs job script to the job scheduling system. q56.sh
qsuball.sh Iterate through all subdirectories in the current directory and execute the qsub command in each subdirectory to submit all .pbs files as jobs. qsuball.sh
save+zip_all_OUTPUT.sh Copy the VASP calculation related files (CONTCAR, INCAR, KPOINTS, OSZICAR, OUTCAR, POTCAR) from all the first-level subdirectories in the current directory to a temporary directory, then pack these files into a ZIP file, and finally delete the temporary directory. save+zip_all_OUTPUT.sh
save+zip_OUTPUT.sh Copy the CONTCAR files from all the first-level subdirectories in the current directory to a temporary directory, then pack these files into a ZIP file, and finally delete the temporary directory. save+zip_OUTPUT.sh
scpfiles2cfff.sh Use the scp command via SSH to copy files or directories from the local machine to a remote server, and handle any interactive prompts that may appear. scpfiles2cfff.sh -path
ta.sh Get energy and force from OUTCAR/OSZICAR ta.sh or ta.sh -g