• 👋 Hi, I’m @chenyubi14
• 👀 My expertise are VASP, shell, python. I mainly work on first-principles calculations, espectially phonon, thermal transport, defect calculations, etc.
• 🌱 Vasptools contains general functions like density of state calculations, wavefunction output, and also specific functions that is useful only if you have the same need as me.
• 📫 How to reach me: post an issue on github. I don't want to get emails.

I post every function I developed, but they are sometimes one-time used. I am tired of deleting them, so you may ignore the extra functions. I am also too lazy to write README for every function I wrote. I will do it at request by Wechat/email/Slack.

I recommend download the scripts in a single folder, so add export SCRIPT=/path/to/scripts in your ~/.bashrc or ~/.bash_profile files. pymatgen needs to be installed, along with many other python packages.

VASP inputs

I have a special INCAR format. You may look at INCAR_template for an example. The fixed INCAR format has several benefits:

(1) You can directly diff path1/INCAR path2/INCAR in terminal to see the difference of two jobs.

(2) You will have a way to edit INCAR easily, as provided by my code.

If you want to make your own template, it is very easy. Just edit INCAR_template, and run python incar_generate.py, so the file class0_incar.py storing INCAR comments will be updated with new formats following INCAR_template. Remember to not use = in INCAR_template randomly, because incar_generate.py uses = to identify a tag.

frequently used functions and commands

python $SCRIPT/op_bs_dos.py for submit a job to calculate density of states

python $SCRIPT/draw_dos1_element.py can plot the density of state plot

python $SCRIPT/update_edit_incar.py can update the INCAR file to the newest format

python $SCRIPT/update_edit_incar.py mode: please read the file update_edit_incar.py. It contains many modes to fit in different situations. For example, if you want to change one tag for many directories. Create a mode in the update_edit_incar.py file, and run this command.

python $SCRIPT/out_wavefunc1.py + arguments: will output a file storing the wave function of a band. The output file will be readable by VESTA

usage for specific functions

phonon calculations

You have to download phonopy (https://phonopy.github.io/phonopy/), third_order (https://bitbucket.org/sousaw/thirdorder/src/master/), ShengBTE (https://www.shengbte.org/)

sh $SCRIPT/pho_1_super.sh will generate supercell jobs for each finite displacement file for 2nd order phonon dispersion. It will also give you the manage.sh file to submit jobs at once.

sh $SCRIPT/pho_2_forceSets.sh will generate the phonopy output file FORCE_CONSTANTS for 2nd order

sh $SCRIPT/pho_3_dow_3rd.sh will generate finite displacement for 3rd order phonon. Use sh $SCRIPT/pho_3_dow_3rd.sh run to generate folders. I will also generate 'manage.sh' and 'check.sh' for submitting jobs and checking job outputs.

python $SCRIPT/pho_4_out_2ndforceconstant.py will plot force_trace as a function of atom distance, for a specific atom you selected.

python $SCRIPT/pho_5_1*.py or python $SCRIPT/pho_5_2*.py: generate the CONTROL file as the input for ShengBTE

python $SCRIPT/pho_7_write_bornall.py: write the BORN file which is used in pho_5_2_generate_control_NAC.py

electronic structure by Boltztrap

You have to download Boltztrap (https://gitlab.com/sousaw/BoltzTraP2).

python $SCRIPT/fermi_*: these files are just using the functions in the pymatgen (https://pymatgen.org/pymatgen.electronic_structure.boltztrap2.html)

defect

python $SCRIPT/draw_KS1_insideBG.py draws the Kohn-Sham(KS) states within band gap. It is ususally useful to plot defect KS states.

file types

##class*.py

files starting with class: module files to be imported/used in other files

class0_functions1,2,3.py: small functions

class1_read.py: a class to read VASP input and output

class2_update_input.py: a class of editting VASP input files

class3_smaller_folder.py: a class dealing with op_*.py files, it usually generate subdirectories for operations like density of state calculations

class95_energyf_fromTL.py: plot formation energy from transition levels, usualy from others' calculated transition levels

class96_formationenergy.py: plot formation energy diagram from own computed jobs

class99_last_drawmulinfo.py: a class stored information for drawing graphs

class0_incar.py: a function write INCAR file with detailed comments.

##op*.py

files starting with op: often used to create a subdirectory for some functions

op_bs_dos.py: density of states (dos) calculations. Assume the current directory has a self-consistent output WAVECAR and CHGCAR, create a subdirectory called "dos_non-self", edit the INCAR in "dos_non-self" for dos calculations.

##out*.py

files starting with out: generate useful information from VASP output file

out_draw.py: draw data. Rotate over many folders to read data, and then get the plot information.

out_formH.py: output the formation enthalpy for a single folder

out_table_band.py: generate a latex table with bandgap information

##draw*.py

files starting with draw: rigorously these files should belong to out*.py, but draw*.py are too many, so I decided to have a new starting string. draw*.py have to draw a diagram, and out*.py has some ouputs other than a diagram.

##energyf*.py

files starting with energyf: plot formation energy diagrams. Please refer to another repository (chenyubi14/easy_defect_formation_energy). It should be contained in draw_ files, but it may contain too many different materials -> a separate file format might be neater.