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Effective mass with (VASP?) calculation of bandstructure structure by matching ApproxFun to bands, WIP. The idea is to read in the structure of the team and calculate the effective mass associated with the extrema of the team, in an automagic way. Currently, it is at the EIGENVAL file level with VASP, which is once walked in the Brillouin space between high symmetry locations (such as Gamma and L, Gamma and R) to form a team structure. With these tabular band functions, the code then builds chebyshev/Fourier zooms to the function, solving the mounting problem with linear algebra via the Vandermonde array. The ApproxFun package then provides direct access to the analytical solutions of this approximate function by finding the extrema (where f'=0) and the associated effective mass (meff=f'') associated with these points. Plans [ ] Make the code pass through the mutual space [ ] Read directly in the full zone Brillouin (WAVECAR), locate the extrema and calculate the effective masses associated with the extreme (Fermi Pockets) thus discovered [ ] do it at WAVECAR or equivalent level, directly using plane waves as Fourier coefficients in approxFun'ctions Other codes Page 2 Effective mass of (VASP?) calculate the band structure by matching ApproxFun to bands, WIP. The idea is to read in the structure of the team and calculate the effective mass associated with the extrema of the team, in an automagic way. Currently, it is at the EIGENVAL file level with VASP, which is once walked in the Brillouin space between high symmetry locations (such as Gamma and L, Gamma and R) to form a team structure. With these tabular band functions, the code then builds chebyshev/Fourier zooms to the function, solving the mounting problem with linear algebra via the Vandermonde array. The ApproxFun package then provides direct access to the analytical solutions of this approximate function by finding the extrema (where f'=0) and the associated effective mass (meff=f'') associated with these points. Plans [ ] Make the code pass through the mutual space [ ] Read directly in the full zone Brillouin (WAVECAR), locate the extrema and calculate the effective masses associated with the extreme (Fermi Pockets) thus discovered [ ] do it at WAVECAR or equivalent level, directly using plane waves as Fourier coefficients in ApproxFun'ctions Other codes Effective mass is associated with the electronic curvature of the band along a specified direction throughout the momentum space. For semiconductors, in general, it's a good idea to know the effective mass around the high symmetry point of $\Gamma$ ($\Gamma \equiv \vec k=(0,0,0)$), both for the highest occupied team (valence syndrome) and for the lowest, unoccupied team (conducting team). As an effective mass of the curvature of the assembly, it is proportional to the second energy bands in relation to the k-wave vector. Another option is to match the electronic band to parabolic dispersion, as shown in question $E(k) = E_0 + \frac{\hbar^2 k^2} {2m^*}$, but be aware of the system in the simulation if it represents parabolic bands. I know that Virtual Nano Lab software performs calculations when the band structure is plotted. In addition to my own script (which is a very strict python program), I don't know about free alternatives. effmass is a Python 3 package for calculating different definitions of effective mass from the electronic bandura structure of semiconductor material. It consists of a base class that calculates the effective mass and other related properties of the selected segments of the band structure. The module also includes functions for locating estremi bandstructure and plotting approximations to dispersion. Examples can be found in jupyter notepad here. The API documentation is here. The source code is available as a git repository in . The paper catalog contains Vasp input (POSCAR), Vasp output (OUTCAR/PROCAR) and band structures generated for academic work using this software: The impact of non-paraabolilic electronic bandwidth structure on the optical and transport properties of Phys photovoltaic materials. Rev.B 99 (8), 085207 - also available on arXiv.. Features effmass can: Read in bandstructure: This requires output files VASP PROCAR and OUTCAR. It is assumed that you have passed through a piece of 1D brillouin zone, earning maxima and minima of interest. effmass uses the vasppy Python package to analyze vasp output. Find extrema: They correspond to the maxima of the Valencian team and the minima of the conduction band. You can also locate highs and minima within a specific energy range. Calculate curvature, transport and optical effective masses: Curvature (aka inertia) and transport masses are calculated using derived polynomised functions. The optical effective mass can also be calculated using Kane dispersion. Degree assessment not parabolicity: Kane's quasi-linear dispersion parameters are calculated to quantiture not parabolic in a given energy range. Calculate quasi-fermi level for a given media concentration: This requires a VASP DOSCAR output file. Using state density data and assuming no thermal smudging, effmass can calculate the energy to which states are occupied. This is a useful approximation to the quasi-Fermi level. Chart fits dispersion: You can visualize selected segments of the bandura structure and zoom to dispersion (assuming that kane, square or higher fit order) can be visualized. The effmass package is aimed at theoretical semiconductor physicists and chemists who have a basic knowledge of Python. Depending on the and zoom level for, it may be that one of the packages listed here will suit your needs better. Development Use github problem tracker for feature requests and error reports. If you want to contribute, do so through a pull request. All collaborators must read and comply with the code of conduct. In particular, we welcome the contribution that would extend effmass so that it can analyse the output from other electronic structure codes. Installing effmass is a Python 3 package and requires key packages from the SciPy ecosystem: SciPy, NumPy, and Matplotlib. If you haven't installed these packages before, it might be best to install them using your preferred package manager (e.g. Homebrew). Note that together they will use >100MB of disk space. effmass can then be built using pip pip python package manager: pip3 install --user effmass Or download the latest version from GitHub, and install the effmass python3 cd setup.py install or clone the latest version of git clone git@:lucydot/effmass.git development and install in the same way. cd effmass python3 setup.py install tests Automatic testing of the latest approval happens here. Manual tests can be run using python3 -m pytest This code has been tested in Python version 3.6. Documentation An overview of effmass and the sample code can be found in the Jupyter notebook, which is available in a paper directory. Api documentation is available here. Referring to effmass If you use this code in your research, please cite the following article: Whalley, Lucy D. (2018). effmass - an effective mass package. Journal of Open Source Software, 3(28) 797. Bibtex @misc{Whalley_JOSS2018, author = {Lucy D. Whalley}, title = {effmass: Effective Bulk Package}, Volume = {3}, Problem = {28}, Pages = {797}, Month = {Aug}, Year = {2018}, doi = {10.21105/joss.00797}, url = { } vaspkit There are five ways to run vaspkit under interactive UI or command-line mode on the tenant. We will use KPOINTS generation (task 102) as an example to illustrate the use of vaspkit. Simply type vaspkit in the terminal to start interactive UI mode; vaspkit -task 102 -kpr 0.04 to generate a KPOINTS file with mutual space resolution $2\pi \times 0.04$ $?^{-1}$. For more details, run vaspkit -help. Note that some of the functionality is still implemented!; echo -e 10220.04| vaspkit; (echo 102; echo 2; echo 0.04)|vaspkit; vi cmd.in (any file name, if you want), including the following content: then run vaspkit <cmd.in. if someone wants to run vaspkit in batch mode, for example, to generate a KPOINTS file in for and in 'ls' to echo ${i} cd ${i} vaspkit -task 102 -file POSCAR -kpr 0.04 cd .. ready Or use echo command -e to input for VASPKIT: echo -e 10220.04 | vaspkit means input 102, 2, 0.04 in vaspkit. In order to Perform VASP calculations, you usually need 4 files, INCAR, POSCAR, POTCAR and KPOINTS. INCAR contains all keywords and tells VASP what to calculate; POSCAR contains lattice parameters, atomic coordinate information and atomic speed information (for MD); POTCAR is a pseudo potential file that is a type of USPP or PAW; KPOINTS, which may be included in INCAR, but not recommended to be omission. Provides information about K-points in the reciprocal space where the wave function integrates to obtain load density. 101) Customize INCAR file 102) Generate KPOINTS file for SCF 103 calculation) Generate POTCAR file with default setting 104) Generate POTCAR file with user-specified potential 105) Generate POSCAR file from cif (without fractional professions) 106) Generate a POSCAR file from Material Studio xsd (keep fixes) 107) Format the POSCAR file in a specific order of elements 108) Another procedure for generating VASP files and check 109) Check all VASP files Run VASPKIT in the directory containing POSCAR. Wprowad 1, aby wybra funkcj GENERATOR PLIK?W WEJCIOWYCH VASP, a nastpnie wprowad 101, aby wybra dostosuj plik INCAR, otrzymasz nastpujce informacje wywietlane: 101 +-------------------------- cieple porady --------------------------+ Musisz wiedzie, co robisz Niekt?re parametry w pliku INCAR Neet do zestawu / skorygowania rcznie +---------------------------------------------------------------+ ==================================================================================================================================================================================================================================================================================================================================================================================================================================Obliczenia MD) Dynamika molekularna GW) Obliczenia GW0 BS) Obliczenia BSE DC) Stala elastyczna EL) Obliczenia ELF BD) Analiza baderowa OP) Wlaciwoci optyczne EC) Statyczna stala dielektryczna PC) Rozloona gsto ladowania FD) Phonon-Finite-Displacement DT) Phonon-DFPT NE) Trcona gumka (NEB) DM) Dimer Method FQ) Obliczenia czstotliwoci LR) Rozlunienie kraty 0) Quit 9) Powr?t ------------>> Parametr?w klawisza wejciowego (STH6D3 oznacza HSE06-D3 Static-Calcualtion) Wprowad slowa dla okrelonego zadania. The generated INCAR file will contain the appropriate keywords that are required for this task. For example, to perform single-point (ST) calculations with hybrid functional correction hse06 (H6) and DFT-D3 (D3) vdW, enter STH6D3. If you type LR, one will get INCAR for the grid relaxation task with detailed comments: Global ISTART parameters = 1 (Read existing wavefunction; if any) # ISPIN = 2 (Spin polarized DFT) # ICHARG = 11 (non-self-consistent: GGA/LDA band) LREAL = Auto (projection operators: automatic) # ENCUT = 400 (Power cut-off for wave plane set, in eV) PREC = Normal (precision level) LWAVE = . True. (Write WAVECAR or not) LCHARG = . True. (Write CHGCAR or not) ADDGRID= . True. (Increasing the grid; helps GGA convergence) # LVTOT = . True. True. total electrostatic potential to LOCPOT or not) # LVHAR = . True. (Write ion + Hartree electrostatic potential to LOCPOT or not) # NELECT = (Electron No.: charged cells; watch out) # LPLANE = . True. (Actual space distribution; supercells) # NPAR = 4 (Max is no. nodes; do not set for hybrids) # NWRITE = 2 (Medium level output) # KPAR = 2 (Divides k-grid into separate groups) # NGX = 500 (FFT grid density for nice load / potential parcels) # NGY = 500 (FFT grid density for nice cargo / potential parcels) #NGZ = 500 (FFT grid density for nice load/potential parcels) Nsw grid relaxation = 300 (number of ion steps) ISMEAR = 0 (gaussian smudging method) SIGMA = 0.05 (please check smear width) IBRION = 2 (Algorithm: 0-MD; 1-Quasi-New; 2-CG) ISIF = 3 (optimization of atomic coordinates and lattice parameters) EDIFFG = -1.5E-02 (ion convergence; eV/AA) PREC = Accurate (precision level) If you want cleaner INCAR without comments, set the file ~/.vaspkit with: Automatically generated INCAR for the lattice relaxation task will be : Global parameters ISTART = 1 LREAL = Auto PREC = Normal LWAVE = . True. LCHARG = . True. ADDGRID= . True. Relaxation Grid NSW = 300 ISMEAR = 0 SIGMA = 0.05 IBRION = 2 ISIF = 3 EDIFFG = -1.5E-02 PREC = Exact users can also modify some parameters as they wish with these INCAR files. If an INCAR file already exists, the original INCAR will be replaced as the default. Edit ~/.vaspkit to change the INCAR output settings. Just change the line SET_INCAR_WRITE_MODE. SET_INCAR_WRITE_MODE to replace #override, join, back-up-old, back-up-new; OVERRIDE New content added to the tail of the original INCAR APPEND New content added to the tail of the old INCAR BACK-UP-OLD backup of the new INCAR BACK-UP-NEW NEW INCAR to INCAR.new For self-consistency calculations, users must prepare a KPOINTS file to determine the density of K-points and the method of automatic k-mesh generation. VASPKIT can automatically generate a KPOINTS file using an existing POSCAR file. Run VASPKIT 1) VASP Input File Generator, and then enter option 102 to generate a KPOINTS file for SCF calculations. Nastpnie wprowad schemat K-mesh zgodnie z nastpujcymi informacjami wywietlanymi: 102 ========================================================================================================================================================================================== 1) Monkhorst-Pack Scheme 2) Schemat gamma 0) Zamknij 9) Z powrotem ------------->> Wprowad 1, aby wybra oryginalny schemat Monkhorst-Pack, Wprowad 2, aby wybra schemat Skoncentrowany Na Gamma Monkhorst-Pack. Vaspkit will then ask us to enter the KPT-Resolved Value between the K-points in the cell $2\pi \times 0.04 ?^{-1}$. 2 ->> (01) Reading structural parameters from POSCAR file... +-------------------------- warm hands --------------------------+ * Accuracy levels: Gamma only: 0; Low: 0.06~0.04; Average: 0.04~0.03; Fine: 0.02-0.01. * 0.03-0.04 is generally precise enough! Precise! Value resolved by input KPT (e.g. 0.04, unit 2*PI/Angstrom): ------------>> The number of K-points increases when the value resolved by KPT (kpr) decreases. The number of K points decreases when the value of kpr increases. For each direction, the number is determined by \[N=\max \left(1,\left|\vec{b}_{i}\right| / \mathrm{kpr}\right)\] where \ (\vec{b}_{and}\) are reciprocal lattice vectors. These values are rounded to the next integer greater than or equal to N. The recommended value of ~0.04 ($2\pi \times 0.04 ?^{-1}$) is sufficient for most of the system. This parameter is similar to the KSPACING parameter in INCAR. But the unit is different. Kspacing is $?^{-1}$ and VASPKIT is $2\pi \times 0.04 ?^{-1}$. The first line of the output KPOINTS file shows the user-defined value resolved by KPT. K-Mesh Generated with a value recognized by KP (...): 0.020 0 Gamma 14 14 14 0.0 0.0 0.0 When generating KPOINTS, POTCAR will also be generated automatically. Or run VASPKIT 103 to generate POTCAR. 103 -->> (01) Reading structural parameters from POSCAR file... -->> (02) Written POTCAR file with standard potential! Reads information about items from POSCAR and combines the corresponding POTCAR with pseudo potential folders that can be set in ~/.vaspkit. GGA_PATH '~/POTCAR/GGA' # GGA Potential Path. PBE_PATH '~/POTCAR/PBE' # PBE Potential Path. LDA_PATH '~/POTCAR/LDA' # LDA Potential Path. POTCAR_TYPE PBE # PBE, GGA, or LDA; RECOMMENDED_POTCAR . True. # . True. Or. FALSE; Set POTCAR_TYPE to PBE, GGA, orLDA as you like. RECOMMENDED_POTCAR whether to use the recommended potentials from the VASP manual (Page 195, 2018.10.29, . If RECOMMENDED_POTCAR is . FALSE., POTCAR without extensions will be used. If RECOMMENDED_POTCAR is . TRUE. the official recommended POTCAR will be used. POTCAR TYPES: No extensions _ _d. Extension d, think of d half-core states as a state of value. _pv or _sv. Extensions _pv and _sv indicate that the p and s semi-core states are treated as states of value. _h and _s. Extending _h or_s means that the potential is harder or softer than the standard potential and therefore requires a higher or lower energy cut-off. Pseudo hydrogen. example: H.5 _GW. Used to calculate GW. If you want to generate POTCAR for GW calculations, set GW_POTCAR to . True. in ~/.vaspkit. GW_POTCAR . True. # . True. Or. FALSE; VASPKIT also provides option 104 for manual potcar generation, choosing the type of potential for each element. 104 -->> (1) Reading structural parameters from POSCAR file... Auto detected POTCAR_TYPE is O, type the one you want! O_h Auto detected POTCAR_TYPE ti, type the one you want! Ti_sv (2) A written POTCAR file with user-specified Potential! In this example, enter the customized potential type O and i Ti_sv was selected for Ti and O_h was selected to O. If there is no user-defined potential type in the list of potentials, vaspkit will ask the user to re-enter. VASPKIT can convert .cif and .xsd (Format Materials Studio) files in POSCAR format according to options 105 and 106. 105 will call /vaspkit.1.00/utilities/cif2pos.py script. 105 Please enter the file name cif-> al2o3.cif Requests type the order of the item 'ENTER' for the default! Example: Al O including CIF -->> (01)

POSCAR was generated ... 106 will call /vaspkit.1.00/utilities/xsd2pos.py script automatically. Note that atom correction information in the .xsd file is stored during the transformation. 106 Build->Symmetry->Make P1, and then select the atoms to determine, Modify->Constraints->fi x fractional position-> Type file name xsd-> CONTCAR-n2-3.xsd -->> (01) POSCAR was generated... 107 can change the order of elements in a POSCAR file. 107 -->> (01) Reading structural parameters from POSCAR file... Type a new order of items to sort. (Tip: The initial order of items in the POSCAR file is: Al O) ------------->> O Al -->> (02) Written POSCAR_REV! VASPKIT can make a format correction and pseudo potential control by option 109. VASPKIT automatically corrects INCAR and POSCAR formats and verifies that POTCAR and POSCAR are consistent. VASPKIT is very powerful in calculating the vasp band structure before and after the process. To perform band structure calculations, you must prepare a primitive cell and the corresponding K-point path (K-path) yourself in the Irreducible Brillouin Zone. The Irreducible Brillouin Zone is the first Brillouin zone reduced by all symmetries in the grid point group (crystal point group). Recognize and select points of high symmetry and connect them along the edge of the inseparable brillouin zone. For example, a conventional metal FCC cell, an Irreducible Brillouin zone, and high symmetry points: a conventional metal BCC cell, an Irreducible Brillouin zone, and high symmetry points: Path K is not unique. It is usually not necessary to select all the lines between all points of high symmetry. A representative and important line is selected and saved as a line mode in the KPOINTS file. For large-scale and scope-wide calculations, there should be a rule that defines the path from structured information. pymatgen and seeK-path provide some solutions, but can only be used in 3D. VASPKIT is a tool for generating K-path for 1D materials (task 301), 2D (task 302) and 3D (task 303) based on a systematic rule: Here are brillouin zones for 2D materials (V. Wang, Y.-Y. Liang, Y. Kawazeo, W.-T. Geng, high-performance computational control of two-dimensional semiconductors, Other ways to automatically obtain the K path using pymatgen( Computational Materials Science 49 (2010) 299?312. seek-path( Computational computational materials 128 (2017) 140?184. For suggested paths k bulk materials, VASPKIT uses the same algorithm as the seek-path website (Y. Hinuma, G. Pizzi, Y. Kumagai, F. Oba, I. Tanaka, Team Structure Diagram Paths based on Crystallography, Comp. Mat. Sci. 128, 140 (2017). MoS2 single-layer band structure without spin polarization without spin-orbital coupling. Because the K path that vaspkit generated is based on a normalized primitive cell, poscar must first be normalized. For 2D material: Keep the center of coordinates from the 2D material in |c|/2. (i.e. fractional coordinate with = 0.5%). This can be achieved with VASPKIT 921 or 923. VASPKIT 923 standardizes the 2D crystalline cell,(i) place the vacuum layer in the direction of z,(ii) place the 2D material in the coordination center with: For 3D material use VASPKIT 602 to generate a standardized primitive PRIMCELL.vasp cell and replace the original POSCAR. Here standardized POSCAR MoS2 : MoS2 1.0 3.1659998894 0.00000000000000 0.0000000000 -1.582999994 47 2.7418363326 0.000000000000 0.00000000000 0.00000000000000 18.409999847 4 S Mo 2 1 Direct 0.0000000000 0.0000000000 0.413899988 0.0000000000 0.00000000000 0.0000000000000000.0.0.00000000 0.0000 586099982 0.666666687 0.333333343 0.50000000000 92 +-------------------------- Warm tips --------------------------+ Please use these features with caution! +---------------------------------------------------------------+ ======================================================================================================================================================================================================================================================================================6) Stale elastyczne dla material?w 2D 927) Krawdzie pasma walencji i przewodzenia, o kt?rych mowa w poziomie pr?ni 929) Podsumowanie dla relaxedowej struktury 2D 0) Quit 9) Powr?t ------------>> 923 -->> (1) Odczyt parametr?w strukturalnych z pliku POSCAR... -->> (2) Pisemny POSCAR_NEW pliku! Optimize the geometry, and then perform one-point self-markup calculations to get CHGCAR. In the new folder run VASPKIT 302, download 2D files K-path: (Note: please check space group) 302 +-------------------------- Warm Tips -------------------------- + See example in vaspkit / examples / seek_kpath / graphene_2D. This feature is still experimental & check out the PRIMCELL.vasp file. +---------------------------------------------------------------+ -->> (1) Reading of structural parameters from POSCAR file... +------------------------- Summary ----------------------------+ Vacuum plate to be along the C axis Prototype: AB2 Total atoms in the input cell: 3 lattice constants in input cell: 3.166 3.166 18.410 Lattice angles in the input cell: 90,000 90,000 120,000 Total atoms in Cell: 3 fixed lattices in primitive cell: 3.166 3.166 18.410 Lattice angles in primitive cell: 90.000 90.000 1 2.000 2D Bravais Grating: Hexagonal Space Group: 187 Point Group: 26 [ D3h ] International: P-6m2 Symmetry Operations: 12 Suggested Path K: (shown in next next [ GAMMA-M-K-GAMMA ] +---------------------------------------------------------------+ -->> (2) Written primcell.vasp. -->> (3) Saved file KPATH.in to calculate band structure. -->> (4) File HIGH_SYMMETRY_POINTS for informational purposes. KPATH.in file contains the K path in linear mode. Copy it to KPOINTS is OK. cp KPATH.in KPOINTS . The default intersection is 20. Path K Generated by VASPKIT 20 Linear Mode Reciprocal 0.00000000000 0.0000000000 0.00000000 GAMMA 0.5 billion000000000 0.0 0.000000000 0.000000000 M 0.5000000000 0.000000000 0.0000000000 M 0.33 33333333 0.33333333333 0.000000000 K 0.3333333333 0.33333333333333 0.0000 0000000 K 0.00000000000 0.00000000000 0.00000 HIGH_SYMMETRY_POINTS 000 000 000 000 000 000 000 000 000 000 00 00 00 00 00 00 00 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 00 VASPKIT DO NOT promise the K-path is right, please compare the results with the seeK-path page ( points of high symmetry (in fractional coordinates). You can check them in the seekpath database [ . 0.00000000000 0.00000000000 0.00000000 GAMMA 0.3333333333 0.33333333333 0.3 3333333 0000000000 K 0.5000000000000 0.000000000000 M If you are using this module, please cite the following work: [1] V. Wang, N. Xu, VASPKIT: Pre-processing and post-processing program for VASP code. . [2] v. Wang, Y.-Y. Liang, Y. Kawazeo, W.-T. Geng, a high-performance demonstration of two-dimensional semiconductors, arXiv:1806.04285. Read CHGCAR's one-point calculations and submit the VASP band structure task. EXAMPLE INCAR ##### Initial I/O ##### SYSTEM = MoS2 ICHARG = 11 LWAVE = . True. LCHARG = . True. LVTOT = . False. LVHAR = . False. LELF = . False. LORBIT = 11 NEDOS = 1000 ##### SCF ##### ENCUT = 500 ISMEAR = 0 SIGMA = 0.05 EDIFF = 1E-6 NELMIN = 5 NELM = 300 GGA = PE LREAL = . False. PREC = Accurate After calculating whether the band structure after the process by VASPKIT option 21 Use 211 to get the basic band structure. If there is a python environment with matplotlib. VASPKIT can automatically output a drawing .png. By default, Fermi energy will be shifted to 0 eV. 211 -->> (01) Reading input parameters from INCAR file... -->> (02) Reading Fermi-Energy from DOSCAR... ooooooooo The Fermi Energy will be set to zero eV ooooooooooooooooo -->> (03) Reading Energy-Levels From EIGENVAL File... -->> (04) Reading Structural Parameters from POSCAR File... -->> (05) Reading K-Paths From KPOINTS File... -->> (06) Written BAND.dat File! -->> (07) Written file BAND_REFORMATTED.dat! -->> (08) Wrote klines.dat file! -->> (09) Wrote klabels file! -->> (10) Written file BAND_GAP! If you want to use the default setting, type 0 if modality type 1 0 UserWarning: findfont: Font family [u'arial'] not found. Back to DejaVu Sans Sans self.defaultFamily[fontext])) -->> (11) Chart generated! Output BAND.dat,BAND_REFORMATTED.dat,KLINES.dat, KLABELS, BAND_GAP files, BAND.dat,BAND_REFORMATTED.dat files record band information that can be opened directly by ORIGIN. BAND_REFORMATTED.dat: The first column is the length of the K path in unit ?-1, and the subsequent columns are the energy energies of each band. #K-Path Energy-Level 0.000 -14.278 -13.063 -5.798 -2.813 -2.813 -1.962 -1.693 ... 0.060 -14.268 -13.058 -5.787 -2.836 -2.802 -2.055 -1.710 ... 0.120 -14.239 -13.044 -5.752 -2.906 -2.769 -2.226 -1.761 ... 0.180 -14.190 -13.021 -5.695 -3.015 -2.716 -2.416 -1.840 ... 0.240 -14.123 -12.989 -5.619 -3.157 -2.642 -2.614 -1.943 ... 0.300 -14.039 -12.948 -5.528 -3.321 -2.817 -2.551 -2.064 ... 0.360 -13.938 -12.900 -5.428 -3.496 -3.023 -2.443 -2.195 ... 0.420 -13.823 -12.846 -5.329 -3.671 -3.232 -2.333 -2.322 ... 0.480 -13.696 -12.786 -5.244 -3.830 -3.441 -2.471 -2.190 ... ... The KLABELS file records the positions of high symmetry points on the band structure figures: K-Label K-Coordinate in gamma band structure charts 0.000 M 1.140 K 1.798 GAMMA 3.114 * Provide a label for each point of high symmetry in the KPOINTS file (KPATH.in). Otherwise, they will be identified as undefined in the KLABELS file BAND_GAP save information about the bandwidth slot, VBM, CBM, and its locations on the mutual grid, +-------------------------- Summary ----------------------------+ Band Character: Direct Band Gap (eV): 1.6743 VBM Value (eV): -0.2257 Eigenvalue CBM (eV) Value): 1.4485 HOMO & LUMO Bands: 9 10 LocationVBM: 0.333333 0.333333 0.000000 CBM location: 0.333333 0.333333 0.000000 +---------------------------------------------------------------+ NOTE: VBM and CBM are delimiated by Fermi Energy. If users have a python environment with matplotlib, VASPKIT can output the assembly.png drawing automatically: 212,213,214 get the predicted bandwidth structure: Make sure that LORBIT = 10 or LORBIT = 11 parameter in INCAR for output projection information. (212) Predicted band structure for selected atoms. select predicted atoms: Input number of selected atoms:1-4 7 8 24 or elements:C Fe H For example, if you want to draw a projected band structure on atoms 1 and 2, input 1-2: 212 -->> (01) Reading input parameters from incar file... -->> (02) Reading Fermi-Energy from DOSCAR FILE... ooooooooo The Fermi Energy will be set to zero eV ooooooooooooooooo -->> (03) Reading Structural Parameters from POSCAR File... -->> (04) Reading Energy-Levels From EIGENVAL File... -->> (05) Reading Band-Weights From PROCAR File... -->> (06) Reading K-Paths From KPOINTS File... | ---------------------------------------------------------------| Enter element symbol and/or atom-index to SUM [Total-atom: 3] format jest OK, np., C Fe H 1-4 7 8 24) ------------>> 1-2 -->> (07) Zapisany SELECTED_ATOM_LIST plik! -->> (08) (08) PBAND_A1.dat file! -->> (09) Written file PBAND_A2.dat! -->> (10) Wrote klines.dat file! -->> (11) Wrote klabels file! VASPKIT will eject two files: PBAND_A1.dat and PBAND_A2.dat. Each file contains information about the projection on selected atoms, and there the weight on each angular shoot, s py pz px dxy dyz dz2 dxz x2-y2 tot. The first column is the length of the K path in unit ?-1. The second column is the energy of the band. After the column there are projections of lm-orbitals on this band. The last column is the total projection of the selected atom on this band. #K-Path Energy s py pz px dxy dyz dz2 dxz x2-y2 tot #Band-index 1 0.000 -14.278 0.275 0.000 0.005 0.000 0.000 0.000 0.000 0.000 0.000 0.281 0.060 -14.268 0.276 0.000 0.005 0.000 0.000 0.000 0.000 0.000 0.000 0.281 0.120 -14.239 0.276 0.000 0.005 0.000 0.000 0.000 0.000 0.000 0.000 0.281 0.180 -14.190 0.277 0.000 0.005 0.000 0.000 0.000 0.000 0.000 0.000 0.282 0.240 -14.123 0.278 0.000 0.005 0.000 0.000 0.000 0.000 0.000 0.000 0.284 0.300 -14.039 0.280 0.000 0.005 0.001 0.000 0.000 0.000 0.000 0.000 0.285 0.360 -13.938 0.281 0.000 0.005 0.001 0.000 0.000 0.000 0.000 0.000 0.288 0.420 -13.823 0.283 0.000 0.005 0.001 0.000 0.000 0.000 0.000 0.000 0.290 ... #Band-index 2 3.114 13.063 0.315 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.316 3.045 -13.056 0.315 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.316 ... #Band-index 3 0.000 -5.798 0.018 0.000 0.125 0.000 0.000 0.000 0.000 0.000 0.000 0.143 0.060 -5.787 0.018 0.000 0.125 0.000 0.000 0.000 0.000 0.000 0.000 0.143 ... 213) Predicted band structure for each element, projection for each element: 213 -->> (1) Reading input parameters from INCAR file... -->> (2) Reading fermi level from DOSCAR file... ooooooooo Fermi Energy will be set to zero eV ooooooooooooooooo -->> (3) Read structural parameters from POSCAR file... -->> (4) Read energy-levels from EIGENVAL file ... -->> (5) Reading Band-Scales from PROCAR file ... -->> (6) Reading K-Paths from KPOINTS file ... -->> (7) Written PBAND_S.dat file! -->> (8) Written file PBAND_Mo.dat! -->> (9) Wrote klines.dat file! -->> (*) Klabels file written! The PBAND_S.dat and PBAND_Mo.dat format is the same as PBAND_A1.dat. These files can be opened by origin: Select the first and second lines, first draw the original band structure: Then find the position of high symmetry points from KLABELS: GAMMA 0.000 M 1.139 K 1.797 GAMMA 3.113 Label of these points: Then adjust the energy range. The original band structure without projection information is displayed as follows. From the ORIGIN chart configuration tag, add atoms, elements, or orbital projections to the band. Select the Bubble marker and add a projection. click OK. 214) Sum of predicted bandwidth structure for selected atoms: 214 -->> (01) Reading input from the INCAR file... -->> (02) Reading Fermi-Energy from File... ooooooooo The Fermi Energy will be set to zero eV ooooooooooooooooo -->> (03) Reading Structural Parameters from POSCAR File... -->> (04) Reading Energy-Levels From EIGENVAL File... -->> (05) Reading Band-Weights From PROCAR File... -->> (06) Reading K-Paths From KPOINTS File... | ---------------------------------------------------------------| Enter the element symbol and/or atom-index to SUM [Total-atom: 3] (Free format is OK, e.g., C Fe H 1-4 7 8 24) ------------>> 1-2 -->> (07) Saved SELECTED_ATOM_LIST file! -->> (08) Written file PBAND_SUM.dat! -->> (09) Wrote KLINES.dat File! -->> (10) Wrote klabels file! The PBAND_SUM.dat contains a total view of the selected atoms or elements. This is useful for exploring the layered band and comparing the surface band and the inner band. In addition to the K-path in linear mode, VASPKIT can also generate a K-path with even spacing between K-points in units 2$\pi$*?-1, which can be used for hybrid functional band structure calculations. Such a KPOINTS file contains two parts. The first part is the same as self-constiving calculations with K-weighted symmetry in the Irreducilbe Brillouin zone. And the second part is the 0-weighted K-points of the same k-path. To generate this KPOINTS file: Same as purely functional calculations. Do geometry optimization. Run 302 (for 2D materials) or 303 (for 3D materials) to obtain: standardized primitive cell (PRIMCELL.vasp) linear mode k path for calculating purely functional band structure (KPATH.in) high symmetry points in fractional coordinates. (HIGH_SYMMETRY_POINTS) You can check them in the seekpath database [ . Run 251 to generate a KPOINTS file for hybrid functional band structure calculations. Enter KPT resolution values to determine k-mesh density for SCF calculations and k-paths for band structure calculations. VASPKIT then reads KPATH.in file and generates a KPOINTS file for hybrid functional bandwidth structure calculation. Optional. Perform PBE SCF calculations based on the new generated KPOINTS file and get wave functions that can be read to calculate the hybrid operation of the next step. Sometimes this step will reduce the SCF time of the next step in hybrid functional calculations. Perform calculations of the hybrid functional band structure. After optimization. Run 302 302 +-------------------------- Warm --------------------------+ See example in vaspkit/ examples/seek_kpath/graphene_2D. This feature is still experimental & check out the PRIMCELL.vasp file. +---------------------------------------------------------------+ -->> (1) Reading structural parameters from POSCAR file... Summary ----------------------------+ Vacuum plate to be along the C axis Prototype: AB2 Total atoms in the input cell: 3 fixed grilles in the input cell: 3.184 3.184 18.410 Grating angles in the input cell: 90.000 90.000 90.000 Total number of atoms in primitive cell: 3 fixed lattices in primitive cell: 3,184 3,184 18,410 Lattice angles in primitive cell: 90,000 90,000 120,000 2D Bravais Lattice Hexagonal Space Group: 187 Point Group: 26 [ D3h ] International: P-6m2 Symmetry Operations: 12 Suggested Path K: (shown in the next row) [ GAMMA-M-K-GAMMA ] +---------------------------------------------------------------+ -->> (2) Written file PRIMCELL.vasp. -->> (3) Saved file KPATH.in to calculate band structure. -->> (4) File HIGH_SYMMETRY_POINTS for informational purposes. Wymie stary POSCAR przez nowy wygenerowany PRIMCELL.vasp: cp PRIMCELL.vasp POSCAR Prymitywny cell 1.0000000 3.18401832481292 0.000000000000000000000000000 -1.592000916240646 2,75744075540316 0,0000000000000 0,0000000000000000 0,0000000000000000000000000000 18.409999984740000 s Mo 2 1 1 1 DIRECT 0.000000000000000 0.000000000000000 0.4151505217091287 S1 0.00000000000000000 0.000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000.5848494782908713 S2 0,666666666666666666 0,33333333333333 0.5000000000000000000000000 Mo1 KPATH.in jest line-mode KPOINTS plik: K-Path Generated by VASKIT. 20 Linear Mode Reciprocal 0.0000000000 0.0000000000 0.000000000 GAMMA 0.5 billion000000000 0.0000 0.00000000000 M 0.500000000000 0.00000000000 0.000000000 M 0.33333 333333 0.33333333333 0.00000000 K 0.3333333333 0.33333333333 0.000000 000 K 0.000000000000 0.0000000000 0.000000000 GAMMA Run 251 to generate a KPOINTS file for hybrid functional bandwidth structure calculations. Select (1) Monkhorst-Pack or (2) Gamma Scheme to generate k-mesh for SCF calculations. Then enter the value of the K-Mesh weighted normal resolution and the 0-weighted K-path, respectively. VASPKIT will write a new KPOINTS according to the input of users. 251 -->> (1) Odczyt parametr?w strukturalnych z pliku POSCAR... =============================================================================================================================================================================================== 1) Monkhorst-Pack Scheme 2) Schemat gamma 0) Quit 9) Powr?t ------------->> 2 +-------------------------- cieple koc?wki --------------------------+ Warto rozdzielczoci wejciowej w celu okrelenia K-Mesh dla oblicze SCF: (Typowa warto: 0.03-0.04 jest og?lnie wystarczajco precyzyjne) ------------>> 0,05 warto rozdzielczoci wejciowej wzdlu cieki K do obliczania pasma: (typowa warto: 0,02-0,04 dla DFT i 0,04-00.06 dla hybrydowego DFT) ------------>> 0,05 +---------------------------------------------------------------+ -->> (2) Odczyt cieek K z pliku KPATH.in... +-- ------------------------ ----------------------------+ K-Mesh for SCF calculations : 7 7 1 Number of K-points along path K 1: 22 Number of K-points along path K 2: 13 Number of K-points along path K 3: 26 +---------------------------------------------------------------+ -->> (3) Written KPOINTS file! Here, the value of the K-Mesh and 0-weighted K-path weighted normal resolutions is set to 0.05. K-mesh output for SCF calculations: 7 7 1. And the number of k-points along each path line k: $\Gamma$-> M : 22, M -> K : 13, K -> -> : 26. The KPOINTS file: Parameters to Generate KPOINTS (Don't Edit This Line): 0.050 0.050 8 61 3 22 13 26 69 Reciprocal lattice 0.00000000000000 0.00000000000000 0.00000000000000 1 0.14285714285714 0.00000000000000 0.00000000000000 6 0.28571428571429 0.00000000000000 0.00000000000000 6 0.42857142857143 0.00000000000000 0.00000000000000 6 0.14285714285714 0.14285714285714 0.00000000000000 6 0.28571428571429 0.14285714285714 0.00000000000000 12 0.42857142857143 0.14285714285714 0.00000000000000 6 0.28571428571429 0.28571428571429 0.00000000000000 6 0.00000000000000 0.00000000000000 0.00000000000000 0 0.02380952380952 0.00000000000000 0.00000000000000 0 ... ... ... 0.02666666666400 0.026666666400 0.000000000000000000 0.013333333200 0.0133333333333333333333333333333333333 0.000000000000 0.000000000000000000 0.000000000000000000000000000000 0.#### Initial I/O ##### SYSTEM = Hybird Functional ISTART = 1 ICHARG = 1 LWAVE = . True. LCHARG = . True. LVTOT = . False. LVHAR = . False. LELF = . False. LORBIT = 11 NEDOS = 1000 ##### SCF ##### ENCUT = 500 ISMEAR = 0 SIGMA = 0.05 EDIFF = 1E-6 NELMIN = 5 NELM = 300 GGA = PE LREAL = . False. # PREC = Exact # ISYM = 3 ##### Geo opt ##### EDIFFG = -0.01 IBRION = 2 POTIM = 0.2 NSW = 0 # no Geo_opt ISIF = 3 # 2 does not optimize cells #### HSE #### LHFCALC = . True. AEXX = 0.25 HFSCREEN = 0.2 ALGO = ALL # or Damped TIME = 0.4 Extract band structure information by 252. band data is stored in band.dat band-reformatted.dat. High symmetry point positions on bandwidth structure figures are recorded in KLABELS. (Note: error in version 0.73, please use new version) 252 -->> (01) Read input parameters from INCAR file ... -->> (02) Reading Fermi-Energy from DOSCAR file ... ooooooooo Fermi Energy will be set to zero eV ooooooooooooooo -->> (03) Reading energy-levels from eigenval file... -->> (04) Reading structural parameters from POSCAR File... -->> (05) Reading K-Paths With KPATH.in File... -->> (06) Written BAND.dat File! -->> (07) Written file BAND_REFORMATTED.dat! -->> (08) Wrote klines.dat file! -->> (09) Wrote klabels file! -->> (10) Written file BAND_GAP! If you want to use the default setting, type 0 if modality type 1 0 -->> (11) Chart is generated! if the python and matplotlib enviornment is set correctly. VASPKIT will automatically draw a band for the band figure.png. The following parameters should be set in ~/.vaspkit. PYTHON_BIN ~/anaconda3/bin/python3 PLOT_MATPLOTLIB . TURE. You can also draw a drawing from band.dat or BAND_REFORMATTED.dat according to ORIGIN, which is described in section 3.2. Compared to KPOINTS linear mode (option 302 and 303). The biggest advantage of the 25 is that the k-spacing along the K path is averaged, saving processing costs. Versions before 0.72 had the same the number of K-points for the power line, resulting in an uneven distribution of K on different paths, as shown in the elevator figure below. Latest Latest Latest VASPKIT supports automatic determination of the number of K-points on different energy band paths based on a given k-point interval, thus ensuring even splashing throughout the band calculation, as shown in the figure below on the right. The KPOINTS generated from vaspkit 251 maintains the spacing between each point k. Thus, you can use less 0-weighted k-points to get a similar skilled band structure and thus, take the time when performing bandwidth structure calculations. For a projected hybrid functional band structure, use 253,254,255: Make sure that LORBIT = 10 or LORBIT = 11 parameters in INCAR for output projection information. 253) Download the projected band structure for selected atoms 254) Get the designed bandwidth structure for each ELement 255) Get the sum of the predicted bandwidth structure for selected atoms For example: with 253 free format input is available. You can enter any atom by its index and any symbol of elements. The projected band structure is saved for each element one by one. -->> (01) Reading input parameters from incar file... -->> (02) Reading Fermi-Energy from DOSCAR file... ooooooooo The Fermi Energy will be set to zero eV ooooooooooooooooo -->> (03) Reading Structural Parameters from POSCAR File... -->> (04) Reading Energy-Levels From EIGENVAL File... -->> (05) Reading Band-Weights From PROCAR File... -->> (06) Reading K-Paths From KPATH.in File... | ---------------------------------------------------------------| Enter the element symbol and/or atom-index to SUM [Total-atom: 3] (Free format is OK, e.g., C Fe H 1-4 7 8 24) ------------>> 1-3 -->> (07) Saved file SELECTED_ATOM_LIST! -->> (08) Written file PBAND_A1.dat! -->> (09) Written file PBAND_A2.dat! -->> (10) Wrote PBAND_A3.dat File! -->> (11) Wrote klines.dat file! -->> (12) Wrote klabels file! Elements predicted bandwidth structure obtained using 254, 254 -->> (01) Reading input parameters from incar file ... -->> (02) Reading Fermi-Energy from DOSCAR file ... ooooooooo Fermi Energy will be set to zero eV ooooooooooooooooo -->> (03) Reading structural parameters from poscar file... -->> (04) Energy-level reading from EIGENVAL file ... -->> (05) Reading Band-Weights From PROCAR file ... -->> (06) Reading K-Paths from file KPATH.in ... -->> (07) Written PBAND_S.dat file! -->> (08) Written file PBAND_Mo.dat! -->> (09) Wrote KLINES.dat File! -->> (10) Wrote klabels file! All input atoms will be summarized and displayed in the band structure using 255: 255 -->> (01) Reading input parameters from incar file... -->> (02) Reading Fermi-Energy from DOSCAR file... Fermi Energy will be set to zero eV ooooooooooooooooo -->> (03) Read structural parameters from poscar file... -->> (04) Reading energy-levels from EIGENVAL File ... -->> (05) Reading Band-Scales with PROCAR File ... -->> (06) Reading K-Paths from KPATH.in file ... ... Enter the element symbol and/or atom-index to SUM [Total-atom: 3] (Free format is OK, e.g., C Fe H 1-4 7 8 24) ------------>> 1-2 -->> (07) Saved SELECTED_ATOM_LIST file! -->> (08) Written file PBAND_SUM.dat! -->> (09) Wrote KLINES.dat File! -->> (10) Wrote klabels file! Additional: band structure can also be down by pymatgen package: For electrons or holes in a solid, the effective mass (m*) is the amount that is used to simplify band structures by modeling the preservation of a free particle with that mass. With the highest energy of the valence band in semiconductors (Ge, Si, GaAs, ...) and the lowest conduction band energies in semiconductors (GaA, ...), the E(k) band structure can be locally approximated as: \[E(\mathbf{k})=E_{0}+\frac{\hbar^{2} \mathbf{k}^{2}}{2 m^{*}}\] where E(k) is the electron energy in wave k in this band, E0 is the constant energy edge of that band. Thus, m* can be calculated using the following equation: \[\frac{1}{m^{*}}=\frac{1}{\hbar^{2}} \frac{\partial ^{2} E}{\partial k_{i} \partial k_{j}}\] We are usually interested in m* from one point of high symmetry to another point of high symmetry. Thus, the direction $k_{i}$ and $k_{j}$ are the same as K -> M, K -> $\Gamma$. To obtain a partial derived second-order, the KPOINTS file should contain K-points very close to that symmetry point. VASPKIT can generate a KPOINTS file for VASP calculations and automatically get an effective mass. (Note: Now VASPKIT only supports efficient mass calculation for uncharged & non-magnetic semiconductor!) Find bandwidth edges by band structure calculation. VBM is in K, and CBM is also in K. Select a direction to make a derivative of the second row. Here we select K -> M, K -> $\Gamma$ to calculate their effective electron and hole mass. Prepare POSCAR and VPKIT.in: 1 #1 for pre-process (KPOINTS generation), 2 for post-process (calculate m*) 6 # number of points for matching square functions. 0.015 # k-cutoff, unit ?-1. 2 # number of jobs to efficiently calculate weight 0.33333333 0.33333333 0.000 0.000 0.000 K-> # Specified two K points and direction 0.333333 0.3 333333 0.000 0.500 0.000 0.000 K->M # Specified two K-points and direction Run VASPKIT 912 and enter the parameters of the K-Mesh schema, and VASPKIT will generate a KPOINTS file based on the VPKIT.in file with 0-scale K-points. +-------------------------- Warm Tips --------------------------+ Test ONLY for uncharged & unmagnetic semiconductor! +---------------------------------------------------------------+ -->> (01) Read file VPKIT.in... -->> (02) Read structural parameters from POSCAR file... 1) Monk scheme 2) Gamma scheme 0) Close 9) Return ------------->> 2 +-------------------------- warm tips --------------------------+ - Accuracy levels: accuracy: 0; Low: 0.06~0.04; Average: 0.04~0.03; Fine: 0.02-0.01. - 0.03-0.04 is generally precise enough! +---------------------------------------------------------------+ KPT input settled value (e.g. 0.04, unit 2 * PI / Angstrom): ------------>> 0.04 1 -->> (03) Written KPOINTS file! ->> (04) INCAR file written! -->> (05) Written POTCAR file with standard potential! The generate the KPOINTS is: Parameters to Generate KPOINTS (Don't Edit This Line): 0.0400 12 2 6 24 Reciprocal lattice 0.00000000000000 0.00000000000000 0.00000000000000 1 0.11111111111111 0.00000000000000 0.00000000000000 6 0.22222222222222 0.00000000000000 0.00000000000000 6 0.33333333333333 0.00000000000000 0.00000000000000 6 0.44444444444444 0.00000000000000 0.00000000000000 6 0.11111111111111 0.11111111111111 0.00000000000000 6 0.22222222222222 0.11111111111111 0.00000000000000 12 0.33333333333333 0.11111111111111 0.00000000000000 12 0.44444444444444 0.11111111111111 0.00000000000000 6 0.22222222222222 0.22222222222222 0.00000000000000 6 0.33333333333333 0.22222222222222 0.00000000000000 12 0.33333333333333 0.33333333333333 0.00000000000000 2 0.33333300000000 0.33333330000000 0.00000000000000 0 # K-> 0.32795808307727 0.33136593967371 0.00000000000000 0 0.32258316615454 0.32939857934742 0.00000000000000 0 0.31720824923180 0.32743121902113 0.00000000000000 0 0.31183333230907 0.32546385869484 0.00000000000000 0 0.30645841538634 0.32349649836855 0.00000000000000 0 0.33333300000000 0.33333330000000 0.00000000000000 0 # K->M 0.33673240318272 0.32574567174541 0.00000000000000 0 0.34013180636544 0.31815804349082 0.00000000000000 0 0.34353120954815 0.31057041523622 0.00000000000000 0 0.34693061273087 0.30298278698163 0.00000000000000 0 0.35033001591359 0.29539515872704 0.00000000000000 0 Submit VASP job. Replace the first line of VPKIT.in to 2. Then restart VASPKIT 913 to obtain an effective mass of electron and hole. 913 +-------------------------- Warm Tips --------------------------+ Test ONLY for uncharged & unmagnetic semiconductor! +---------------------------------------------------------------+ -->> (01) Read VPKIT.in... -->> (02) Reading of structural parameters from POSCAR file... -->> (03) Reading input parameters from INCAR file... -->> (04) Energy-levels reading from EIGENVAL file... +-------------------------- Summary ----------------------------+ Effective mass is achieved by matching third-order polynomial, which gives masses are less sensitive to employed kpoints. Band index: LUMO = 10 HOMO = 9 Effective mass (in m0) Electron (prec.) Hole (prec.) Path Index K 1: K-> 0.480 (0.2E-07) -0.577 (0.2E-07) Track Index K 2: K->M 0.527 (0.8E-07) -0.705 (0.2E-06) Korm?nyos et al. calculated the effective masses of electron carriers and holes for MoS2 monodis layers at 0.44 and 0.54, respectively Mater 2D. 2 (2015) 049501]. Note: If the valorization team and the conducting bottom of the team are degenerate, such as GaAs and GaN, it will be difficult to guarantee accuracy at the moment. The electronic structures of real materials are disturbed by various structural defects, impurities, fl?uctuations of chemical composition in complex alloys and so on. In DFT calcualtions, these defects and disproportionate structures are typically studied using supercell (SC) models. However, interpreting the band structures $E(\vec{k})$ compared to $\vec{k}$ is most effective in the original cell (PC). Popescu and Zunger [see PRL 104, 236403 (2010) and PRB 85, 085201 (2012)] have proposed an effective band structure (EBS) method that can develop supercellular band structures in the Brillouin zone (BZ) of the primitive cell. Such band development techniques greatly simplify the analysis of results and allow direct comparisons with experimental measurements, such as photocast spectroscopy (ARPES), often represented along the directions of high primitive symmetry of the BZ cell. Next, we will build a rectangular mos$_2$ supercell with a single sulphur vacancy and a band of perfoms developing calculation using VASP along with VASPKIT codes. First step: Prepare the following files; POSCAR for monolayer MoS$_2$ primitive cell MoS2-H.POSCAR 1.00000000000000000 3.1904063769892548 0.0000000000000000 0.0000000000000000 -1.5952031884946274 2.7629729709066906 0.0000000000000000 0.0000000000000000 0.0000000000000000 17.6585355706663840 Mo S 1 2 Direct 0.3333333429999996 0.6666666870000029 0.5000000000000000 0.6666666870000029 0.3333333429999996 0.4117002781430051 0.6666666870000029 0.3333333429999996 0.5882996918569924 KPATH.in file for MoS$_2$ primitive cell (not for supercell), you can genenate it by run vaspkit with task 302 for 2D or 303 for bulk, or edit it manually. We select K-Path M-K-$\Gamma$ for mos2 monolith. KPATH for MoS2 20 Linear Mode Rec 0.00000000000000 0.500000000000 0.0000000000 # M 0.333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 333333333 0.333333333333 0.00000000000 # K 0.00000000000000 0.0000000000000000000000.00.00.000.00 0.0000000.00.0000000 0.0000000.00.0.00000000000.00.0000000.00.000000000.000000000000.0000000000.0.000000000.00.0000000000.00.0000000000.00.00000000000.00.000000000.00. True.. To aviod error 'ERROR! Calculated NPLANE= **** != NPLANE input= ****', set PREC=N or average/lower power cut-off value. SYSTEM = MoS2 ISTART = 1 LREAL = F PREC = N LWAVE = . True. LCHARG = F ISMEAR = 0 SIGMA = 0.05 NELM = 60 NELMIN = 6 EDIFF = 1E-08 file TRANSMAT.in (optional). The content of this file is read transformation matrix from TRANSMAT.in file, if any. 2 0 0 # must be three integers 0 3 0 # must be three integers 0 0 3 # must be three integers, where the first row is a comment row, and integers from the second line to four rows are elements of 3$:raw-latex:times'$3 transmission matrix relacja wektor?w krat pomidzy superkom?rk $E(\vec{A})$ spelnia $E(\vec{a})$ \ [\begin{split}\left(\begin{array}{l}{\vec{A}_{1}} \\ {\vec{A}_{2}} \\ {\ve c{A}_{3}}\end{array}\right)= M \cdot\left(\begin{array}{l}{\vec{a}_{1}} \\ {\vec{a}_{2}} \\ {\vec{a}_{3}}\end{array}\right)=\left(\begin tablica}{lll}{m_{11}} & {m_{12}} & {m_{13}} \\ {m_{21}} & {m_{22}} & {m_{23}} \\ {m_{31}} & {m_{32}} & {m_{33}}\end{array}\right) \cdot\left(\begin{array}{l}{\vec{a}_{1}} \\ {\vec{a}_{2}} \\ {\vec{a}_{3}}\end{array}\right)\end{split}\] Jeli elementy o przektnej w $M$ s zerowe, wektory siatki superkom?rki bd r?wnolegle do tych z pierwotnej kom?rki. Second step: Run vapskit with task 400 to generate SUPERCELL.vasp and TRANSMAT (if TRANSMAT.in does not exist). We modify the SUPERCELL.vasp file by removing the sulfur atom to create a vacancy S signle (V:math:'_text{S}') of the point defect; The primitive cell of the MoS$_2$ monolithic layer belongs to the hexagonal crystal system. We can build a rectifier-supercell using vaspkit with task 400. If the TRANSMAT.in does not exist, vaspkit will read 9 $M$ items in the dialog menu (see following commands). Otherwise, the $M$ items will be read from the TRANSMAT.in. vaspkit -task 400 +---------------------------------------------------------------+ | VASPKIT version: 1.00.RC (17 Jun 2019) | | Pre- and post-processing program for VASP code | | Run VASPKIT in command-line mode | +---------------------------------------------------------------+ -->> (01) Reading structural parameters from POSCAR... Enter a new verse in the old categories: (THERE MUST BE THREE INTEGERS, e.g. 1 2 3) 4 0 0 Enter the new verctor b grille in terms of old: 2 4 0 Enter the new grille verctor c in terms of old: 0 0 1 +-------------------------- Summary ----------------------------+ Transformation Matrix P is: 4 0 0 2 4 0 0 0 1 Lattice constants in the new cell: 12 762 11.052 17.659 Lattice Angles in new cell: 90.00 90.00 90.00 Total number of atoms in the new cell: 48 New cell volume is 16 times old cell +---------------------------------------------------------------+ -->> 02) Written supercell.vasp file Third step: cp SUPERCELL.vasp POSCAR and cp TRANSMAT TRANSMAT.in (if TRANSMAT.in does not exist) and run vaspkit with task 281 to generate the KPOINTS file; ------------>> 28 +-------------------------- Warm Tips --------------------------+ See some examples in vaspkit/examples/band_unfolding. It only supports the KPOINTS file generated by VASPKIT. Please set LWAVE = . True. in the INCAR file. +---------------------------------------------------------------+ Generate KPOINTS file for band calculations 282) Calculate effective band structure 0) Close 9) Return ------------>> 281 -->> (01) Read structural parameters from POSCAR file... POSCAR... | Selective dynamics are activated! | +---------------------------------------------------------------+ =============================-------------------------- ------------>>============================================================================================================================================================================================================================================================--------------------------+ Warto rozdzielczoci wejciowej do okrelenia K-Mesh dla oblicze SCF: (typowa warto: 0,02-0,03 jest og?lnie wystarczajco precyzyjna) ------------>> 0,03 warto rozdzielczoci wejciowej wzdlu cieki K do obliczania pasma: (typowa warto: 0,02-0,04 dla DFT i 0,04-0,006 dla hybrydowego DFT) ------------>> 0,03 +---------------------------------------------------------------+ -->> (02) Readin Transformation Matrix z pliku TRANSMAT.in... -->> (03) Czytanie cieek K z pliku KPATH.in... +-------------------------- Podsumowanie ----------------------------+ K-Mesh do oblicze SCF: 3 3 1 # Na podstawie na SC wzajemnej dlugoci kraty Liczba K-Point wzdlu K-Path 1: 21 # Na podstawie pc wzajemnej dlugoci kraty Liczba K-Point wzdlu K-Path 2: 43 # W oparciu o PC wzajemnej dlugoci kraty +--------------------------------------------------------------- + Forth krok: Przelij zadanie vasp; Fifth step: Run vaspkit with task 282 to get EBS; ------------>> 282 +-------------------------- Warm Tips --------------------------+ The current version only supports the Stardard version of the VASP code. +---------------------------------------------------------------+ -->> (01) Read header information in WAVECAR file... +--------------------- WAVECAR Header --------------------------+ SPIN = 1 NKPTS = 68 NBANDS = 252 ENCUT = 280.00 Coefficients Precision: Complex*8 Maximum G-values: GX = 18, GY = 16, GZ = 25 Estimated maximum number of plane waves: 30159 +--------------------------------------------------------------+ -->> (02) Start reading wavecar file, let your time ^.^ Percentage completed: 25.0% Percentage completed: 50.0 0% Percentage completed: 75.0% Percentage completed : 100.0% -->> (03) Readin Transformation Matrix from file TRANSMAT.in... -->> (04) Reading Fermi-Energy from doscar file ... ooooooooo The Fermi Energy will be set to zero eV ooooooooooooooooo -->> (05) Reading KPOINTS_MAPPING_TABLE.in file... -->> (06) Reading K-Paths From KPATH.in File... -->> (07) Start to Calculate Effective Band Structure... Completion percentage: 25.0% Percentage completed: 50.0% Percentage completed: 75.0% Percentage completed: 100.0% -->> (08) Written EBS file.dat! -->> (09) Wrote klabels file! Last step: You can use vaspkit/examples/band_unfolding/eps_plot.py or other scripts to print. In semiconductor physics, the usual structure of the electronic band (or simply the structure of the 2D band) is the structure of the 2D band, which shows the change in energy along the path line K. VASPKIT can also perform a 3D band structure that selects the K-path on the surface of the Irreducilbe Brillouin zone. And calculate the K-dependent bandwidth energies on the Points K. This method is often applied to 2D materials such as graphene. Prepare the GRAPHENE POSCAR and INCAR files for SCF calculations as a description in section 3.1 Run VASPKIT and select 231 to generate a KPOINTS file to calculate the 3D band. The execution interface is as follows. The generated KPOINTS contains 1-weighted KPOINTS and 0-weight KPOINTS (Note that for a smooth 3D energy band, the resolution value used to generate the KPOINTS file should be set to approximately 0.01) 231 +-------------------------- Warm tips --------------------------+ * Accuracy levels: (1) Low: 0.04~0.03; (2) Average: 0.03~0.02; (3) Fine: 0.02~0.01. * 0.015 is generally precise enough! +---------------------------------------------------------------+ KP-Resolved Value Input (unit: 2 * PI / Ang): ------------>> 0.015 -->> (01) Read structural parameters from POSCAR file ... -->> (02) KPOINTS file written! Submit the VASP job. When vasp calculation is complete, run vaspkit again and enter 232 or 233. Command 233 can transfer the VBM band and the CBM band to the band. HOMO.grd and BAND. LUMO.grd. 232 can get computational data of any other band. Here we dial 233: ------------>> 233 +-------------------------- warm --------------------------+ ONLY reliable for band structure calculations! +---------------------------------------------------------------+ -->> (1) Reading input parameters from INCAR file... -->> (2) Reading structural parameters from POSCAR file... -->> (3) Reading fermi level from DOSCAR file... ooooooooo Fermi Energy will be set to zero eV ooooooooooooooooo -->> (4) Reading Energy-Levels From EIGENVAL File... -->> (5) Reading Kmesh From KPOINTS File... -->> (6) Written BAND. HOMO.grd. -->> (7) Written band. FILE LUMO.grd. -->> (8) Written files KX.grd and KY.grd. run python VASPKITdir/examples/3D_band/how_to_visual.py to obtain a 3D band structure. The shape of fermi's surface comes from the periodicity and symmetry of the crystalline grid and from the occupation of electronic energy bands. prepare optimized POSCAR FCC Cu. Keep in mind that it must be primitive cells. Run VASPKIT and enter 261 to generate KPOINTS and POTCAR files to calculate Fermi's surface. ------------>> 261 +-------------------------- Warm Tips --------------------------+ \* Accuracy Levels: (1) Average: 0.02~0.01; (2) Well: < 0.01; \* 0.01 is generally precise enough! +---------------------------------------------------------------+ KPT-Resolved Value Input 2 * PI / Angstrom): ------------>> 0.008 -->> (1) Read structural parameters from POSCAR file ... -->> (2) KPOINTS file written! Submit the VASP job. Once vasp calculation is complete, restart vaspkit, enter 262 262 fermisurface.bxsf file containing fermi surface data. ------------>> 262 -->> (1) Reading input parameters from an INCAR file... -->> (2) Reading structural parameters from a POSCAR file... -->> (3) Reading fermi level from a DOSCAR file... ooooooooo Fermi Energy will be set to zero eV ooooooooooooooooooo -->> (4) Reading Energy-Levels From EIGENVAL File... -->> (5) Written file FERMISURFACE.bxsf! Start the XcrySDen software and follow the steps below. The fifth band through the surface of Fermi, so we choose band No. 5, then click on The Selected option, and then get the surface of Fermi in Cu. The dipol transition moment (TDM) or transition moment, usually de-marked by the transition between the initial state and the final state b, is the electrical dipole moment associated with the transition between the two states. In general, TDM is a complex number of vectors that contains phase factors associated with two states. Its direction gives the polarity of the transition, which determines how the system will interact with the electromagnetic wave of a given polarity, while the size square gives the force of interaction due to the distribution of the charge in the system. The SI unit of the transition moment is the coulomb meter (Cm); debye (D). The probabilities of a transition between the value and the conduction band are revealed by the calculated sum of TDM squares (in the Debey unit$^2$). For example, we ask the perovskite phase of cubic CsPbI$_3$ and present the structures of the PBE calculation bands and the corresponding TDM in the following figure. This system has a total of 44 valencian electrons. Then calcualte squares the moment dipole transition from the highest valencia band (band index 22) to the lowest conduction band (band index 23). The results are well in line with the previous discovery (see ref. J. Phys. Chem. Lett. 2017, 8, 2999-3007). The calculation process is very similar to the calcuation band structure, except for the LWAVE = setting. True. in the INCAR file. More details about these calculations are given in vaspkit/examples/tdm. ------------>> 71 ==========================================================================================================================================================================================================12) Transition Dipole Moment at Single kpoint 713) Transition Dipole Moment for DFT Band-Structure 0) Quit 9) Back ------------>> 713 +-------------------------- Warm Tips --------------------------+ Zobacz przyklad w vaspkit/examples/tdm. KPOINTS support only created by VASPKIT for hybrid band structure. +---------------------------------------------------------------+ (e.g. 4 5 means obtaining a TDM of 4 to 5 bands in general ------------>> 22 23 +-------------------------- Warm Tips --------------------------+ The current version only supports the Stardard version of the VASP code. +---------------------------------------------------------------+ -->> (01) Read header information in WAVECAR... +--------------------- WAVECAR Header --------------------------+ SPIN = 1 NKPTS = 80 NBANDS = 36 ENCUT = 400.00 Coefficients Precision: Complex*8 Maximum G-values: GX = 11, GY = 11, GZ = 11 Estimated maximum number of plane waves: 5575 +---------------------------------------------------------------+ -->> (02) Start reading wavecar file, let your time ^.^ Percentage completed: 25.0% Percentage completed: 50.0 0% percentage completed: 75.0% Percentage completed 100.0% -->> (03) Reading K-Paths from KPOINTS file ... -->> (04) Start to calculate Dipole Moment transition ... Completion percentage: 25.0% Percentage completed: 50.0% Percentage completed: 75.0% Percentage completed: 100.0% -->> (05) Written TDM file.dat! If you want to calculate the TDM square between two states at one point k. Wystarczy uruchomi vaspkit z zadaniem 712, na przyklad, 71 ========================================================================================================================================================================================================) Transition Dipole Moment at Single kpoint 713) Transition Dipole Moment for DFT Band-Structure 0) Quit 9) Back ------------>> 712 +-------------------------- Warm Tips --------------------------+ Zobacz przyklad w vaspkit/examples/tdm. Please set LWAVE = . True. in the INCAR file. +---------------------------------------------------------------+ ONE kpoint input and TWO bands separated by spaces. (e.g. 1 4 5 means obtaining a TDM between 4 and 5 bands at 1 cap) ------------>> 1 22 23 +-------------------------- Warm Tips --------------------------+ The current version only supports the Stardard version of the VASP code. +---------------------------------------------------------------+ -->> (01) Read header information in WAVECAR... +--------------------- WAVECAR Header --------------------------+ SPIN = 1 NKPTS = 80 NBANDS = 36 ENCUT = 400.00 Coefficients Precision: Complex*8 Maximum G-values: GX = 11, GY = 11, GZ = 11 Estimated maximum number of plane waves: 5575 +---------------------------------------------------------------+ Square TDM (Debye^2): X Y Z Total 0,000 201,617 0.000 201.617 Cleary, calculate the total TDM square in $\text{X}$ for cubic CsPbI$_3$ is 201.62 Debey$^2$. VASPKIT is very powerful in DOS results after the process is complete. Set LORBIT = 10 or 11, VASP will bring out the DOS and spread out l or lm-distributed predicted DOS for each atom to DOSCAR and vasprun.xml. VASPKIT can extract this information as user input. Merits: No doscar or vasprun.xml. Directly extract useful DOS on the server. Choosing pdos is convenient. Elements, atoms, and orbital elements can be selected and summed to sum Automatic change of farm energy up to 0 eV. It can read outcar's E-fermi energy form and move DOS data through the E-fermi. If someone does not want to do a shift, just close it in ~/.vaspkit SET_FERMI_ENERGY_ZERO . False. # . True. Or. FALSE; The output file can be read by ORIGIN directly without modification. Option 11 is used for dos after the process. O p t and o n s Functions 1 1 1 Get total DOS input: None.Output: TDOS.dat the total number of DOS; ITDOS.dat contains an integral integer SUM of DOS. Spin up and down are saved in a single file. Example: Total dos $\Theta$-Al2O3 unit cell 1 1 2 Output projected DOS for selected atoms to separate files. Input: Enter the element symbol and/or atom-index to SUM [Total-atom: 80] (The free format is OK, e.g.C Fe H 1-4 7 8 24). Output: SEL ECTED_ATOM_LIST; PDOS_A_UP(_DW), pdos file for each selected atom; IPDOS_A_UP(_DW), an integral pdos file for each selected atom; Spin up and down are saved in different files. 1 1 3 Output predicted DOS for each item to separate files. Output: PDOS_Elements_UP (_DW).dat, pdos file for each item (sum of all atoms of each element). IPDOS_Elements_UP (_DW).datSpin up and down are saved in different files. 1 1 4 The output sum of the predicted DOS for the selected atoms into a single file. Input: Enter the element symbol and/or atom-index to SUM [Total-atom: 80] (The free format is OK, e.g.C Fe H 1-4 7 8 24). Output:TED_ATOM_LIST SELEC; PDOS_SUM_UP(_DW), pdos file for the sum of selected atoms; IPDOS_A_UP(_DW), integral pdos; Spin up and down are saved in different files. 1 1 5 Sum of the predicted DOS for selected atoms and orbitals into a single file. Input: Enter the element symbol and/or atom-index to SUM [Total-atom: 80] (The free format is OK, e.g.C Fe H 1-4 7 8 24). Enter the orbitals to the sum. Which orbital? s py pz px dxy dyz dz2 dxz dx2 f-3 ~f3, all for summation ALL. Output: PDOS_USER.dat Spin up and down are saved in a single file. Enter /vaspkit.0.73/examples/LDOS_PDOS/Partial_DOS_of_CO_on_Ni_111_surface, Run VASPKIT (113) The predicted state density for each element, VASPKIT will output PDOS_Ni.dat, PDOS_C.dat, and PDOS_O.dat, which contain PDOS information ni, C, and O: Run VASPKIT (114) The sum of the predicted state densities for the selected atoms, and then enter 6 7, VASPKIT will derive the sum of the PDOS CO molecule. Run VASPKIT (115) Sum of predicted DOS for selected atoms and orbitals. If we want s i p orbtial o, s i p orbtial C, d orbtial ni. Enter the symbol and/or the number of atoms in total [Total-atom: 7] (Free format is OK, e.C e.g.C Fe H 1-4 7 8 24), press Enter if you want to end e ntry! ------------>> About Orbitals Entrance to the Sum that Orbital? s py pz px dxy dyz dz2 dx2 f-3~f3, all for ALL summation. S...... Input O - s - O - p - C - s - C - Ni - d - Enter - 0, Then PDOS_USER.dat file will be generated in this folder, which contains: #Energy O_s O_p C_s C_p Ni_d -27.10266 -27.10266 0.00000 0.00000 0.00000 0.00000 -26.92966 0.00000 0.00000 0.00000 0.00000 0.00000 -26.75566 0.00000 0.00000 0.00000 0.00000 0.00000 -26.58266 0.00000 0.00000 0.00000 0.00000 0.00000 ... ... The Enter symbol and/or number of atoms command accepts free format input. You can enter 1-3 4 Ni to collect PDOS by selecting items 1, 2, 3, 4 and Ni. Input orbitals to sum supports only standard input. If you use LORBIT = 10, you can only select s p d f. If you use LORBIT = 11, s py pz px dxy nozzle dz2 dxz dx2 f-3 f-2 f-1 f0 f1 f2 are also supported. DOS rolled over to D-states that interact with adsorbate status may have a d-predicted DOS center. \[\varepsilon_{\mathrm{d}=\frac{\int_{-\infty}^{\infty} n_{{\mathrm{d}}(\varepsilon) \varepsilon d \varepsilon}{\int_ <3>{-\infty}^{\infty} n_{\mathrm{d}}(\varepsilon) d \varepsilon}\] VASPKIT 503 can calculate the d-band center for each atom directly from VASP DOS outputs. Users can set the energy range for calculations. Example: Pt metal cell, the energy window is set to Fermi energy. 503 +-------------------------- Warm tips -------------------------+ See example in vaspkit/examples/d_band_center. d-Band Center is sensitive to the number of uneasy bands. In any case, trends are more important than Absolute Energies. +---------------------------------------------------------------+ -->> (01) Reading input parameters from INCAR file... -->> (02) Reading Fermi-Energy from DOSCAR... ooooooooo Fermi Energy will be set to zero eV ooooooooooooooo -->> (03) Reading DOS data from doscar file... -->> (04) Reading structural parameters from POSCAR file... +------------------------ Your option --------------------------+ The default integration energy window is [-11.82 24.30] Do you want to change the change (Y/N)? y Please enter a new power window with blank (e.g. -10 10) -11.8 0 +---------------------------------------------------------------+ -->> (05) Written file D_BAND_CENTER! the d band center for each atom and the total center of band d is saved in the file D_BAND_CENTER as follows: # Atom ID d-Band-Center (eV) Pt1: -3.1184 Total: -3.1184 Note: The integration energy window is [-11.80 0.00]. The calculated d-band-center shown here are references to fermi level, i.e. E_F = 0 eV. Calculating the free energy change in catalysis is one of the most important things. But VASP does not have a module that can directly calculate molecular free energy. Therefore, the adjustment of free energy in some publications is inconsistent, inaccurate. (Note: Computational chemistry programs, such as Gaussian, have a complete module for calculating free energy.) The equations used to calculate thermochemical data for gas in VASPKIT are equivalent to gaussian. ( The partition function from any component can be to specify the entropy S contribution from this component: \[S=N k_{B}+N k_{B} \ln \left(\frac{q(V, T}{N}\right)+N k_{B} T\left(\frac{\partial \ln q}{partial T}\right)_{V}\] When molar values are given $n=N / N_{A}$ and based on close-up of the ideal gas, $N_{A} k_{B}=R$, We write S as: \[[/start{split}\begin{aligned} S &=R+R \ln (q(V, T))+R T\left(\frac{\partial \ln q}{\partial T}\right)_{V} \\ &=R \ln (q(V, T) e)+R T\left(\frac{\partial \ln q}{\partial T}\right)_{V} \\ &=R\left(\ln \left(q_{_mathrm{t }} q_{\mathrm{e}} q_{\mathrm{r}} q_{{\mathrm{v}} e\right)+T\left(\frac{\partial \ln q}{\partial T}\right)_{V}\right) \end{align{end{split}\] Internal thermal energy , which can also be obtained from partition functions : \[U=N k_{B} T^{2}\left(\frac{\partial \ln q}{\partial T}\right)_{V} =R T^{2}\left(\frac{\partial \ln q}{\partial T}\right)_{V}\] Translation partition functions, electronic, rotating, vibrating contributions are calculated as a list of equations in ( . Then entropy correction and internal thermal energy correction are calculated at a specific temperature and presure. \[U=E_{t}+E_{e}+E_{v}+E_{r}\] \[S=S_{t}+S_{e}+S_{v}+S_{r}\] For linear molecules, the degree of freedom of vibration is 3N - 5, VASPKIT neglects the smallest frequencies 5. For nonlinear molecules, the degree of freedom of vibration is 3N - 6, VASPKIT neglects the smallest 6 frequencies. VASPKIT also includes zero energy (ZPE) in the correction of thermoenergy energy from the OUTCAR frequency calculation. \[\varepsilon_{\mathrm{ZPE}}=\frac{h u}{2}\] Gibbs (G) and enthalpy (H) energy include PV = NRT based on ideal gas approximation. Gibbs free energy G can be obtained using total entropy S, Finally VASPKIT will output: Zero-point energy $\varepsilon_{\mathrm{ZPE}}$; Korekta termiczna do U(T), = $\varepsilon_{\mathrm{ZPE}}$ + $\Delta U_{0 \rightarrow T}$ Korekta termiczna do H(T), = $\varepsilon_{\mathrm{ZPE}}$ + \$\Delta U_{0 \rightarrow T}$ + PV = \ (\varepsilon_{\mathrm{ZPE}}\) + $\Delta H_{0 \rightarrow T}$ Korekta termiczna do G(T), = $\varepsilon_ <3>{\mathrm{ZPE}}$ + $\Delta U_{0 \rightarrow T}$ + PV + TS = $\varepsilon_{\mathrm{ZPE}}$ + $\Delta G_{0 \right RWW}$, gdzie $\Delta U_{0 \rightarrow T}$, $\Delta H_{0 \rightarrow T}$ i $\Delta G_{0 \rightarrow T}$ s energi midzyplonowymi, entalpi, i Gibbs wolna r?nica energii midzy 0 K i T K. Wykonaj obliczenie czstotliwoci. After calculation, check frequencies: 1 f = 46.979964 THz 295.183821 2PiTHz 1567.082879 cm-1 194.293584 meV 2 f = 1.95 2595 THz 12.268518 2PiTHz 65.131565 cm-1 8.075288 meV 3 f = 1.120777 THz 7.042052 2PiTHz 37.385108 cm-1 4.635164 meV 4 f/i= 0.006984 THz 0.043884 2PiTHz 0.232971 cm-1 0.0 28885 meV 5 f/i= 1...232971 cm-1 0.028885 meV 5 f/i= 1....232971 cm-1 0.028885 meV 5 f/i= cm-1 0.02885 meV 5 f/i= 1....232971 cm-1 0.02885 meV 5 f/i= 1...232971 cm-1 0.02885 meV 5 f/i= 1...23 0 46106 THz 6.572876 2PiTHz 34.894327 cm-1 4.326347 meV 6 f/i= 1.294104 THz 8.131095 2PiTHz 2PiTHz cm-1 5.351986 meV Due to O2 being a linear molecule, VASPKIT neglects the smallest five frequencies. In the same folder, run VASPKIT 502. Input temperature (K), pressure (Atm) and spin multiplicity in turn. 502 +-------------------------- Warm Tips --------------------------+ See example in vaspkit/examples/thermo_correction/ethanol. This feature was brought by Nan XU, Jincheng Liu and Sobereva. Included vibration, translation, rotation & electron input. Gas molecules should not be with any fix. -->> (01) Reading structural parameters from CONTCAR file... -->> (02) Analysis of molecular symmetry information... Molecular symmetry is: D(inf)h Linear molecule found! +---------------------------------------------------------------+ Please specify the temperature (K)! 298.15 Please input pressure (Atm)! 1 Please enter spin multiplicity!-- (Number of unpared electrons + 1) 3 ------------>> -->> (03) Frequency extraction from OUTCAR... -->> (04) Reading outcar file... -->> (05) Calculating thermal corrections ... U(T) = ZPE + Delta_U(0->T) H(T) = U(T) + PV = ZPE + Delta_U(0->T) + PV G(T) = H(T) - TS = ZPE + Delta_U Delta_U(0->T) + PV - TS Zero-point energy E_ZPE: 2,240 kcal/mol 0.097144 eV Thermal correction to U(T): 3.3 72 4 kcal/mol 0.161475 eV Thermal correction to H(T): 4,316 kcal/mol 0,187167 eV Thermal correction to G(T): -10,302 kcal /mol -0.446723 eV Entropy S: 205.141 J/(mol*K) 0.002126 eV Yes, ZPE is 0.097144 eV. The thermal correction on U(T, H(T) and G(T) is 0.161475, 0.187167 and -0.446723 eV, respectively. Entropy correction is \[S= -[G(T)-H(T)] / T=0.0021261 \mathrm{eV} / \mathrm{K}=205.13 \mathrm{J} \cdot \mathrm{K}^{-1 1} \cdot \mathrm{mol}^{-1}\] To obtain o2 free energy, add G(T) to electronic energy: G(O2) = -9,854 + -0.447 = -10,301 eV Unlike gas molecules, the distributed molecules form chemical bonds with the substrate, which limits the freedom of translation and rotation of adsorbed molecules. Thus, the contribution of translation and rotation to entropy and enthalpia is significantly reduced (so-called difficult translator / obstructed rotor model). This does not mean that there is no translational or rotational contribution. One common method is to assign a translational or rotational part of the cartridge to vibration, i.e. 3N vibrations of surface adsorbing molecules (except virtual frequency) are used to calculate thermoeneric energy correction. Low vibration frequencies have a large impact on entropy. It is very likely that a low frequency of vibrations will lead to abnormal entropy and free energy correction. This suggests that when the free energy of the surface adsorption molecule is corrected, the frequency share below 50 cm-1 is calculated as 50 cm-1, and VASPKIT also does. And VASPKIT neglects traffic due to its small contribution. And the term PV is also Finally, VASPKIT ejects zero-point energy $\varepsilon_{\mathrm{ZPE}}$; Thermal correction to U(T) = H(T) = $\varepsilon_{\mathrm{ZPE}}$ + $\Delta U_{0 \rightarrow T}$ Thermal correction to G(T) = $\varepsilon_{\mathrm{ZPE}}$ \) $\Delta U_{0 \rightarrow T}$ + TS = $\varepsilon_{\mathrm{ZPE}}$ + $\Delta G_{0 \rightarrow T}$ Repair all plate metal atoms, perform frequency calculations for adsorbed molecule. Check frequencies: $ grep cm OUTCAR 1 f = 10.904836 THz 68.517103 2PiTHz 363.746154 cm-1 45.098792 meV 2 f = 10.827330 THz 68.030119 2TPi Hz Hz 68.030119 2TPi Hz Hz 10.827330 361.160834 cm-1 44.778253 meV 3 f = 10.751668 THz 67.554721 2PiTHz 358.637024 cm-1 44.465340 meV In the same folder run VASPKIT 501. Input temperature (K). 501 +-------------------------- Warm --------------------------+ This feature was brought by Nan XU, Qiang LI and Jincheng LIU. See example in vaspkit/examples/thermo_correction/ORR. Just vibrations! No Translation & Rotation & Electron input. +---------------------------------------------------------------+ Please enter temperature (K): ------------>> 298.15 -->> (01) Reading outcar file ... +-------------------------- Summary ---------------------------- + Neglect of PV contribution to adsorbed molecule translation. To avoid incorrect entropy, frequencies less than 50 cm-1 are set to 50 cm-1. U(T) = H(T) = ZPE + Delat_U(0->T) G(T) = H(T) - TS = ZPE + Delat_U(0->T) - TS temperature (TS K): 298.1 E_ZPE energy consumption: 1,549 kcal/mol 0.067171 eV Thermal correction to U(T): 2,206 kcal/mol 0.. 095670 eV Thermal correction to H(T): 2,206 kcal/mol 0.095670 eV Thermal correction to G(T): 1,207 kcal/mol 0.052342 eV Entropy S: 14.021 J/(mol*K) 0.000145 eV So ZPE is 0.067171 eV. Thermal correction to U(T), H(T) and G(T) are 0.095670, 0.187167 and -0.446723 eV, respectively. In the linear spray area, stress $\boldsymbol{\sigma}$ solid response to external strain load $\boldsymbol{\varepsilon}$ meets the right of generalized Hooke and can be simplified in Voibit Notation \[\sigma_{i}=\sum_{j=1}^{6} c_{i j} \varepsilon_{j},\], where the strain or stress is represented as a vector with 6 independent components, i.e. a vector with 6 independent components. $1 \leq i, j \leq 6$. $C_{and j}$ is a second-order elastic tensor expressed by a symmetric matrix of 6 ? 6 in GPa units. You can specify the elastic stiffness tensor $C_{and j}$ based on derived stress and strain curves. An alternative approach to the calculation of theoretical elastic constants is based on energy variability by applying small strains to the balance grid configuration. Elastic energy $\Delta E\left(V,\left\{\varepsilon_{i}\right\}\right)$ of the solid under approximately harmonic load is given by \[\Delta 0\right)=\frac{V_{0}}{2} \sum_{i, j=1}^{6} C_{i j} \varepsilon_{j} \varepsilon_{i},\] where $E\left(V,\left\{\varepsilon_{i}\right\}\right)$ and $E\left(V_{0}, 0\right)$ are the total energies of distorted and un distorted lattice cells, respectively with volume $V$ and $V_0$. The energy deformation method corresponds to the fact that the elasticity stiffness tensor comes from a second-order derivative of total energy compared to the strain. In general, the stress and strain method requires higher computational precision to achieve the same accuracy as the energy deformation method. Nevertheless, the former requires a much smaller set of interference than the latter. Given that energy deformation has less stress sensitivity than stress, the first method is implemented in VASPKIT. We take diamond as an example and calculate its flexible contants (vaspkit/examples/elastic/diamond_3D). Thera is three independent elastic constants for the FCC crystal: $\mathrm{C}_{11}$, $\mathrm{C}_{12}$ and $\mathrm{C}_{44}$. Thus, the elastic energy is given by \[\begin{split}\Delta E\left(V,\left\{\varepsilon_{i}\right\}\right)=\frac{V_{0}}{2}\left[\begin{array}{cccccc} \varepsilon_{1} & \varepsilon_{2} & \varepsilon_{3} & \varepsilon_{4} & \varepsilon_{5} & \varepsilon_{6}\end{array}\right]\left[ \begin{array}{cccccc}{C_{11}} & {C_{12}} & {C_{12}} & {0} & {0} & {0} \\ {C_{12}} & {C_{11}} & {C_{12}} & {0} & {0} & {0} \\ {C_{12}} & {C_{12}} & {C_{11}} & {0} & {0} & {0} \\ {0} & {0} & {0} & {C_{44}} & {0} & {0} \\ {0} & {0} & {0} & {0} & {C_{44}} & {0} \\ {0} & {0} & {0} & {0} & {0} & {C_{44}}\end{array}\right] \left[ \begin{array}{l}{\varepsilon_{1}} \\ {\varepsilon_{2}} \\ {\varepsilon_{3}} \\ {\varepsilon_{4}} \\ {\varepsilon_{5}} \\ {\varepsilon_{6}}\end{array}\right]\end{split}\] To determine the elastic constants for the cubic phase , we apply the three-axis shear strain $\varepsilon=(0,0,0, \delta, \delta, \delta)$, to the crystal. Then $\Delta E=\frac{V_{0}}{2}\left(C_{44} \varepsilon_{4} \varepsilon_{4}+C_{44} \varepsilon_{5} \varepsilon_{5}+C_{44} \C_{44} \varepsilon_{6} C_{44} C_{44} \\varepsilon_{6}\right)$ $C_{44}$ can be calculated from ${frac{\Delta E}{V_0}=\frac{3}{2} C_{44} \delta^{2}$. Similarly, my appply $\varepsilon=(\delta, \delta, 0,0,0,0)$ and download $\Delta E=\frac{V}{2}\left(C_{11} \varepsilon_{1} \varepsilon_{1}+C_{11} \C_{11} \C_{11} varepsilon_{2} \varepsilon_{2}+C_{12} \varepsilon_{1} \varepsilon_{2}+C_{12} \varepsilon_{2} \varepsilon_{1}\right)$ Apply $\varepsilon=(\delta, \delta, \delta, 0.0.0)$ to get $\frac{\Delta E}{V_0}=\frac{3}{2}\left(C_{11}+2 C_{12}\right) \delta^{2}$. Na math::'mathrm{C}_{11}', math::'mathrm{C}_{12}' and math::'mathrm{C}_{44}' can be calculated by solving these equations. The relationship of lattice vectors between distorted and completely relaxed lattice cells is: \[\begin{split}\left( \[\begin{split}\left( \\ {\boldsymbol{b}^{\prime}} \\ {\boldsymbol{c}{\prime}}\end{array}\right)=\left( \begin{array}{l}{\boldsymbol{a}} \\ {\boldsymbol{b}} \\ {\boldsymbol{c}}\end{array}\right) \cdot(\boldsymbol{{I}+\boldsymbol{\varepsilon})\end{split}\] where math::'boldsymbol{I}' is an identity matrix, Strain Tensor $\boldsymbol{\varepsilon}$ is defined by \[\begin{split}\boldsymbol{\var epsilon}=\left( \begin{array}{ccc}{\varepsilon_{1}} & {\frac{\varepsilon_{6}}{2}} & {\frac{\varepsilon_{5}}{2}} \\ {\frac{\varepsilon_{6}}{2}} & {\varepsilon_{2}} & {\frac{\varepsilon_{4} {2}} \\ {\frac{\varepsilon_{5}}{2}} & {\frac{\varepsilon_{4}} {2}} & {\varepsilon_{3}}\end{array}\right)\end{split}\] Fisrt Step:Prepare the following files: Prepare a fully relaxed POSCAR file containing a standard conventional diamond cell. You can get a standard conventional cell by running vaspkit with task 603/604; Run vaspkit with task 102 to generate KPOINTS with fine k-mesh. Prepare INCAR as follows. Global parameters ISTART = 0 LREAL = F PREC = High LWAVE = F LCHARG = F ADDGRID= . True. Electronic relaxation ISMEAR = 0 SIGMA = 0.05 NELM = 40 NELMIN = 4 EDIFF = 1E-08 Ion relaxation NELMIN = 6 NSW = 10 0 IBRION = 2 ISIF = 2 (must be 2) EDIFFG = -1E-02 4,Prepare VPKIT.in file and set the firt line value to 1 (1 means preprocessing); 1 ! 1 for pre-processing; 2 for 3D processing! 2D for two dimentional, 3D for bulk 7! number of strain cases -0.015 -0.010 -0.005 0.000 0.005 0.010 0.015 ! Strain range and run vaspkit-201 ------------>> 201 -->> (01) Reading VPKIT.in File... +-------------------------- Warm Tips -------------------------- + See example in vaspkit/examples/flexible/diamond_3D, Require fully relaxed and standardized cell conversion. +---------------------------------------------------------------+ -->> (02) Read structural parameters from POSCAR file... -> Folder C44 was successfully created! -> strain_-0.015 folder created successfully! -> strain_-0.010 folder created successfully! -> strain_-0.005 folder created successfully! -> strain_0.000 folder created successfully! -> strain_+0.005 folder created successfully! -> strain_+0.010 folder created successfully! -> strain_+0.015 folder created successfully! -> C11_C12_I folder created successfully! -> strain_-0.015 folder created successfully! -> strain_-0.010 folder created successfully! -> strain_-0.005 folder created successfully! -> strain_0.000 folder created successfully! -> strain_+0.005 folder created successfully! -> strain_+0.010 folder created successfully! -> strain_+0.015 folder created successfully! -> C11_C12_II folder created successfully! -> strain_-0.015 folder created successfully! -> folder created successfully! -> strain_-0.005 folder created successfully! -> strain_0.000 folder created successfully! -> strain_+0.005 folder created successfully! -> -> folder was successfully created! -> strain_+0.015 folder created successfully! The second step is to batch perform DFT calculations using vasp code; Third step: Modify the value of the first line in VPKIT.in file to 2 (2 means final processing); and run vaspkit-201 again. You will get the following information, ------------>> 201 -->> (01) Reading VPKIT.in File... +-------------------------- Warm Tips --------------------------+ See example in vaspkit/examples/flexible/diamond_3D, Require fully relaxed and standardized convertional cells. +---------------------------------------------------------------+ -->> (02) Read structural parameters from POSCAR... -->> (03) Calculate energy vs. strain adjustment factors. -->> Current catalog: C44 adjustment accuracy: 0.817E09 C11_C12_I: 0.814E-08 C11_C12_II: 0.135E-07 +-------------------------- Summary ----------------------------+ Based on Strain and Energy method. Crystal Class: m-3m Space Group: Fd-3m Crystal System: Cubic system Including Point group classes: 23, 2/m-3, 432, -43m, 4/m-32/m There are 3 independent elastic constants C11 C12 C12 0 0 0 C12 C11 C12 0 0 0 C12 C12 C11 0 0 0 0 0 0 C44 0 0 0 0 0 0 C44 0 0 0 0 0 0 C44 Stiffness Tensor C_ij (in GPa): 1050.640 126.640 126.640 0.000 0.000 0.000 126.640 1050.640 126.640 0.000 0.000 0.000 126.640 126.640 1050.640 0.000 0.000 0.000 0.000 0.000 0.000 559.861 0.000 0.000 0.000 0.000 0.000 0.000 559.861 0.000 0.000 0.000 0.000 0.000 0.000 559.861 Compliance Tensor S_ij (in GPa^{-1}): 0.000977 -0.000105 -0.000105 0.000000 0.000000 0.000000 -0.000105 0.000977 -0.000105 0.000000 0.000000 0.000000 -0.000105 -0.000105 0.000977 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.001786 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.001786 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.001786 Elastic stability criteria as discussed in PRB 90 , 224104 (2014): Criteria (i) C11 - C12 > 0 met. Criteria (ii) C11 + 2C12 > 0 met. Criteria (iii) C44 > 0 met. Mean mechanical properties of polycrystyline: +---------------------------------------------------------------+ | Scheme | Voigt - Episode Reuss | Hill | +---------------------------------------------------------------+ | Module Bulk K (GPa) | 434,640 | 434,640 | 434,640 | | Shear Module G (GPa) | 520,716 | 516,130 | 518,423 | | Young E Module (GPa) | 1116.342 | 1109,298 | 1112,824 | | P-wave Module (GPa) | 1128,929 | 1122,814 | 1125,871 | | Poisson Ratio v | 0,072 | 0,075 | 0.073 | | Bulk/shear ratio | 0.835 | 0.842 | 0.838 | +---------------------------------------------------------------+ Pugh Ratio: 1,193 Cauchy Pressure (GPa): -433,220 Universal Flexible Anisotropy: 0.044 Ansotropia Chung-Buessem: 0.004 Ratio Poisson: 0.073 Longitudinal wave speed (in m/s): 17945,173 Transverse wave speed (in m/s): 12177,146 Mean wave speed (w (w 13280.911 Debye temperature (in K): 2212,889 References: [1] Voigt W, Lehrbuch der Kristallphysik (1928) [2] Reuss A, Z. Angew. Mathematics. Moss. 9 49?58 (1929) [3] Hill R, Phys. Soc. A 65 349?54 (1952) [4] Temperature of Debye J. Phys. Chem. Solids 24, 909-917 (1963) [5] Flexible wave speeds calculated using the Navier Calcualted elastic equation are well matched with the available experimental values, $C_{11}=1079$ GPa, $C_{12}=124$ GPa, and $C_{44}=578$ GPa. VASPKIT can also read elastic constants from outcar/ELASTIC_TENSOR.in file and specify various mechanical elements and elastic stability criterion. For more information, see vaspkit/examples/elastic. Linear optical properties can be obtained from the frequency-dependent complex dielectric function $\varepsilon(\omega)$ \[\varepsilon(\omega)=\varepsilon_{1}(\omega)+and \varepsilon_{2}((\\omega),\] where $\varepsilon_{1}(\omega)$ and $\varepsilon_{2} (\omega)$ are actual and delusional dielectric functions, and $\omega$ is the frequency of photons. The frequency-dependent linear optical spectra, e.g., refractive index $n(\omega)$, extinction coefficient $\kappa(\omega)$, absorption coefficient $\alpha(\omega)$, energy-loss function $L(\omega)$, reflectivity $R(\omega)$ can be calculated from the real $\varepsilon_{1}(\omega)$ and $\varepsilon_{2}(\omega)$ parts [See Ref. A.M. Fox, Optical Properties of Solids]: \[n(\omega)=\left[\frac{\sqrt{\varepsilon_{1}^{2}+\varepsilon_{2}^{2}}+\varepsilon_{1}}{2}\right]^{\frac{1}{2}}\] \ [k(\omega)=\left[\frac{\sqrt{\varepsilon_{1}^{2}+\varepsilon_{2}^{2}}-\varepsilon_{1}}{2}\right]^{\frac{1}{2}}\] \[\alpha(\omega)=\frac{\sqrt{2} \omega}{c}\left[\sqrt{\varepsilon_{1}^{2}+\varepsilon_{2}^{2}}-\varepsilon_{1}\right]^{\frac{1}{2}}\] \[L(\omega)=\operatorname{Im}\left(\frac{-1}{\varepsilon(\omega)}\right)=\frac{\varepsilon_{2}}{\varepsilon_{1}^{2}+\varepsilon_{2}^{2}}\] \[R(\omega)=\frac{(n-1)^{2}+k^{2}}{(n+1)^{2}+k^{2}}\] In VASPKIT Ver. 1.00 or later , it is not necessary to run optical.sh extract the image and the actual parts of the dielectric function from vasprun.xml in the first step (optional). You can run vaspkit -task 711 to get these linear optical spectrums in one shot. The program will read the dielectric function from vasprun.xml directely if both REAL.in and IMAG.in files do not exist. We take Si as an example and calculate its optical properties in GW0 + BSE leve, as shown in the figure below. ------------>> 71 ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== Transition Dipole Moment at Single kpoint 713) Transition Dipole Moment for DFT Band-Structure 0) Quit 9) Back ------------>> +-------------------------- Warm Tips --------------------------+ See example in vaspkit/examples/Si_bse_optical. This module is NOT suitable for low-dimensional materials. low-sized. =============================================================================================================================================================================================== 1) eV 2) nm 3) THz ------------>> 1 -->> (01) Czytanie funkcji dielektrycznej z pliku vasprun.xml... -->> (02) Czytanie plik?w IMAG.in i REAL.in... -->> (03) Pisemne pliki optyczne Pomylnie! +---------------------------------------------------------------+ | * DISCLAIMER * | | Check consistency of results if necessary | | Any suggestion of improvements is welcome | | (^.^) (^.^) GOOD LUCK | |---------------------------------------------------------------| | We would appreciate if you cite in your research with VASPKIT.| | Ref. V. Wang, N. Xu, J.C. LIU, VASPKIT: A Pre- and Post-Process| | program for the VASP code. | +---------------------------------------------------------------+ VASPKIT is powerful in structure editing. Read and modify construction files. The VASPKIT 400 option can build a supercell and rotate the lattice vector. Requires three coefficients for each new vector by the following equation: \[\begin{split}\left(\begin{array}{l}{A} \\ {B} \\ {C}\end{array}\right)=\left(\begin{array}{lll}{c_1} & {c_2} & {c_3} \\ {\ {\ {\ {\ {\ {c_4} & {c_5} & {c_6} \\ {c_7} & {c_8} & {c_9}\end{array}\right)\left(\begin{array}{l}{a} \\ {b} \\ {c}\end{array}\right)\end{split}\] A, B, and C are new lattice vectors, and a, b and c are old lattice vectors. Example: Build $\operatorname{Au} (111)-(\sqrt{3} \times \sqrt{3}) R 30^{\circ}$ a motherboard build a supercell with a new lattice vector length of $\sqrt{3}$a. 400 -->> (01) Reading structural parameters from POSCAR file... Enter a new verse in the old categories: (THERE MUST BE THREE INTEGERS, e.g. 1 2 3) 1 -1 0 Enter the new verctor b grille in the old categories: 2 1 0 Enter the new verctor c grille in the old categories: 0 0 1 +-------------------------- Summary ----------------------------+ Transformation Matrix P is: 1 -1 0 2 1 0 0 1 Fixed lattice angles in the new cell: 4,0 995 4,995 17,064 Lattice angles in a new cell: 90.00 90.00 60.00 Total number of atoms in the New Cell: The volume of the new cell is 3 times greater than the old cell VASPKIT 401 can build a supercell by three digits C1, C2, C3. c_{3} c_{2} c_{1}/pl{array}\right)\left(\begin{array}{l}{a} \\ {b} \\ {c}\end{array}\right)\end{split}\] Na przyklad budowanie superkom?rki o dlugoci jest 2 razy w kierunku a i b i zachowaj wektor c. 401 =======================================================================================================================================================================================================) Okrelona nazwa pliku 0) Zamknij 9) Powr?t ------------>> 1 -->> (01) Odczyt parametr?w konstrukcyjnych z pliku POSCAR ... +-------------------------- Cieple koc?wki --------------------------+ Wprowad powtarzan jednostk wzdlu kierunk?w a, b i c z przestrzeni! (THERE MUST be three integers, e.g. 1 2 3) 3) 2 2 1 -->> (02) Written sc221.vasp VASP file the default structural optimization allows all atoms to move freely in all directions (x, y, z). In some cases, structural optimization calculations require some atoms to be repaired. For example, surface calculations with a plate model must fix some lower atoms. To repair atoms, the seventh line of POSCAR should be switched to selective dynamics (only the first character is relevant and must be S or S). This mode allows you to provide additional flags for each atom to indicate whether the corresponding coordinates of that atom can change during ionic relaxation. F means fix, and T means no fix. VASPKIT provides 402 options to fix atoms by layer: Enter the file name you want to fix. 1 for POSCAR, 2 for CONTCAR, 3 for a specific name, but should also be a POSCAR format. Enter the threshold (unit: ?) into separate layers. Only atomic layers with difference coordinates are greater than the threshold, these layers can be recognized. Otherwise, it will be recognized as a single layer. VASPKIT shows the suggested threshold and the corresponding layer number. VASPKIT then prints the recognized layer number. Select the layers you want to fix. VASPKIT will automatically repair these lower layers and eject the POSCAR_FIX. Before vasp calculation, cp POSCAR_FIX POSCAR. 402 ===================================================================================================================================>> ------------>>============================================================================================================================================================================================ Pr?g: 0,3 warstwy: 4 Pr?g: 0,6 warstwy: 4 Pr?g: 0,9 warstwy: 4 Pr?g: 1,2 warstwy: 4 Pr?g: 1,5 warstwy: 4 Wybierz pr?g do oddzielenia warstw-> 1 Znaleziono 4 warstwy, wybierz, ile warstw ma by naprawiony = > 2 Stale atomy to: 1 4 -->> (02) Pisemny plik POSCAR_FIX! VASPKIT 403 can also repair atoms, but using a number of coordinates with. As with option 402, first select the structured file, and then enter two numbers to set the coordinate range from. Then select the Fractional or Cartesian output format. will output POSCAR_FIX file. If you select fractional coordinates (1), the input z_min z_max numbers should be fractional coordination with, and the POSCAR_FIX output file is also saved as a fractional style. If cartesian coordinates (2) are selected, the input z_min z_max numbers should be cartesian coordination, and the POSCAR_FIX output file is also saved as a Cartesian style. 403 2) CONTCAR 3) Specified file name 0) Quit 9) Return ------------>> 1 -->> (01) Reading structural parameters from POSCAR file... +---------------------------------------------------------------+ | Selective dynamics are activated! | +---------------------------------------------------------------+ Atoms between the selected section in the z direction will be repaired Type Type z_max, Note: z_min < z_max 0 5 Read and write atomic coordinates as: (1) Fractional coordinates (2) Cartesian coordinates 2 Fixed atoms are: 1 4 -->> (02) File saved POSCAR_FIX! VASPKIT 407 can replace two lattice vector axes. The planar average for mesh files is one of the basic functions of VASPKIT. Supports all VASP output grid files such as CHGCAR, PARCHG, LOCPOT, ELFCAR. All such mesh files are saved using the following commands in Fortran: WRITE(IU,FORM) (((C(NX,NY,NZ), NX=1,NGXC),NY=1,NGYZ),NZ=1,NGZC) For one selected direction, such as the z. VASPKIT direction, make an XY average on each NZ, \[\sum_{and j} \Delta x_{i} \Delta y_{j} \rho_{i, j} / \sum_{i j} \Delta x_{i} \Delta y_{j}\] POTPAVG output.dat contains two columns. The first column is the z coordinate (in ?), the second column is Planar Average-Potential (in eV) or Densitiy (in e). Let's take locpot as an example. Contains total local potential (in eV) when LVTOT = . True. in an INCAR file or contains electrostatic potential (in eV) during LVHAR = . True. exists in the INCAR file. Electrostatic potential is desirable to evaluate operating functions, as the electrostatic potential converges faster to the vacuum level than the total potential. To obtain a working function, in the plane of the plate, the potential must be averaged along the direction of z (i.e. the normal direction of the plate). Hamiltonian from Kohn-Sham is: \[\hat{H}=-\frac{1}{2} abla^{2}-\sum_{A} \frac{Z_{A}}{\left|\boldsymbol{r}-\boldsymbol{R}_{A}\right|} +\int_{\infty} \frac{\rho\left(\boldsymbol{r}{\prime}\right)}{\left|\boldsymbol{r}-\boldsymbol{r}^{\prime}\right|} d \boldsymbol{r}^{\prime}+v_{x c}[\rho(\boldsymbol{r})]]\] Electrostatic potential is the sum of the second (ionic) and third (hartree) parts of hamiltonian . Perform optimization and single-point calculations to get the LOCPOT file, single-point INCAR as follows: ##### initial I/O parameters ##### SYSTEM = Au NCORE = 5 ISTART = 1 ICHARG = 1 LWAVE = . True. LCHARG = . True. LVTOT = . False. LVHAR = . True. LELF = . False. #### Electronic relaxation #### ENCUT = 400 ISMEAR = 1 SIGMA = 0.2 EDIFF = 1E-6 NELMIN = 5 NELM = 300 GGA = PE LREAL = Auto IDIPOL = 3 Run VASPKIT 426 FUNCTION, and choose a normal surface direction: 426 +-------------------------- Warm tips -------------------------- + You need to know what you are doing Check the convergence of the planar average value on vacuum thickness! +---------------------------------------------------------------+ ============================================================ ========================================================================================================================================================================================================================================================================================================================================================================= 1) x Direction 2) y Direction 3) from Direction 0) Close 9) Return ------------>> 3 -->> (1) Reading structural parameters from LOCPOT... -->> (2) Reading potential from locpot file... -->> (3) Written POTPAVG file.dat! +-------------------------- warm tips --------------------------+ Check check vacuum level compared to roughly vacuum! +---------------------------------------------------------------+ +-------------------------- ----------------------------+ Vacuum Level (eV): 6.695 +---------------------------------------------------------------+So the vacuum level is 6,695, POTPAVG.dat as follows: # Planar Distance (in Angstrom), Planar Average-Potential (in eV), or -Densitiy (in e) 0.0000 0.27377302E+0 0 1 0.1025 0.94832051E+00 0.2049 -0.13842911E+01 0.3074 0.40872693E+01 0.4099 -0.69356914E+01 0.5123 -0.96882699E+01 0.6148 -0.12150765E+02 0.7172 -0.14164741E+02 ... grep E-fermi OUTCAR E-fermi : 1.5199 XC(G=0): -6.7056 alpha+bet : -6.4642 Draw an average plane form of electrostatic potential. Thus, the work function can be calculated as: \[\Phi=E_{\mathrm{vac}}-E_{\mathrm{F}}\] $\Phi$ = 6,695 - 1.5199 = 5.1751 eV In addition to the average planar potential, VASPKIT can also calculate the macroscopic potential that is obtained by converging the planar averaging potential with the moving average. Eg. If someone wants to make macroscopic average potential in z-dirction, use z = average(x, y, with ? $\Delta$z') for each of where 2$\Delta$z' is the layer distance for repetiting structures. For example: MoS2/WS2 heterogeneous intersection. Perform one-point calculations with LVHAR = . TRUE., Run VASPKIT 427 to get the average planar and macroscopic potential potential of LOCPOT. Choose the direction in which you want the planar average to be? Enter the length of the period to calculate the macroscopic average. (To speed up convergence, this value should be close and less than the layer distance) The number of the input iteration to get a smoother macroscopic curve. 427 +-------------------------- warm tips -------------------------- + You need to know what you are doing Check the convergence of the planar average value on the thickness vacuum! +---------------------------------------------------------------+ ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== 1) x Direction 2) y Direction 3) from Direction 0) Close 9) Return ------------>> 1 -->> (01) Reading structural parameters from locpot file... -->> (02) Reading local potential from LOCPOT file... Enter the length of the period to calculate the macroscopic mean: (Typical value: minimum length of repeating unit.) ------------>> 1.5 Please enter the iteration number to get a smoother macroscopic curve: (Must be an integer. Can be gradually increased from 1 to 3.) ------------>> 3 -->> (03) File PLANAR_AVERAGE.dat! +-------------------------- Summary ----------------------------+ Maximum macroscopic mean: 0.099 Minimum macroscopic mean: -0.101 -->> (04) File MACROSCOPIC_AVERAGE.dat! Step 3. Draw chart charts MACROSCOPIC_AVERAGE.dat output and PLANAR_AVERAGE.dat when using spin-polarized (SPIN = 2), the CHGCAR output will contain the loading density and spin density. VASPKIT can extract load density and rotation density by options 311 and 312 respectively. Outputs are saved in CHARGE.vasp and SPIN.vasp. VASPKIT can also calculate spin-up & spin-down density according to option 313. Outputs are saved in SPIN_UP.vasp & SPIN_DW.vasp files VASPKIT is powerful for post-processing grid file from VASP, such as CHGCAR, ELFCAR, LOCPOT, PARCHG. CHGCAR contains lattice vectors, atomic coordinates, total charging density multiplied by volume on a thin FFT grid (NG(X,Y,Z)F) and one-way peacock ogcupcupancies. By e-sizing off two or more CHGCAR, You can get the difference in charging density. Note: Electrostatic potential (LOCPOT), electron localization function (ELFCAR) and partial charge density difference (PARCHG) calculations can also be performed using the same VASPKIT method. The difference in charge density is one of the important ways to test the electronic structure. Intuitively, it can obtain electron flow from the interaction of two fragments. And examine the essence of chemical bonding. There are several forms of load density difference.: (1)System-wide load density subtracts the density of two or more segments that make it up: \[\Delta \rho=\rho_{A B}-\rho_{A}-\rho_{B}\] (2)Difference in load density before and after self-constitution calculations. Also known as deform load density: \[\Delta \rho=\rho\left(A B_{\text { self-consistent }}\right)-\rho\left(A B_{\text { atomic }}\right)\] (3)Density in one electronic state subdues density in another. For example, the charging density in the applied electric field lowers the charging density without an external electric field. Another example is the density of the awakened state minus the density of the state of the ground. \[Delta \rho=\rho\left(A B_{\text { state 1 }}\right)-\rho\left(A B_{\text { state 0 }}\right)\] Among the three payload density differences listed above, regardless of calculations, must ensure consistency between cell parameters and atom coordinates. Take CO adsorption on surface Ni(100) as an example: Optimize co/ni structure(100), Perform onepoint self-forming calculation of Ni(100) and CO, respectively. NOTE: The atomic position of the CO and Ni(100) fragments should come from optimized CO/Ni(100) CONTCAR, DO NOT optimize CO and Ni(100) fragments! Start VASPKIT 314. to enter the path of three CHGCAR, respectively: 314 ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== get AB-A-B, type: ~/AB/CHGCAR ./A/CHGCAR .. /B/CHGCAR) (e.g. to obtain A-B, type: ./B/CHGCAR) ------------>> ./CHGCAR ./co/CHGCAR ./slab/CHGCAR -->> -->> Read structural parameters from ./CHGCAR... -->> (02) Read load density from ./CHGCAR... -->> (03) Reading structural parameters from ./co/CHGCAR... -->> (04) Read load density from ./co/CH GCAR file... -->> (05) Reading structural parameters from ./slab/CHGCAR... -->> (06) Read loading density from ./slab/CHGCAR file... -->> (07) Written CHGDIFF.vasp File! The CHGDIFF.vasp output is also a mesh that can be opened by VESTA. Do self-consistent calculations for the CO molecule. Perform a new folder, perform non-calculation mentions to output the atomic payload density superposition. Run VASPKIT 314 Enter the path of the two CHGCAR respectively. 314 ================================================================================================================================================================================================================================================================================================================ /B/CHGCAR) (np. w celu uzyskania A-B, typ: ~/A/CHGCAR ./B/CHGCAR) ------------>> ./CHGCAR ./deform/CHGCAR -->> (01) Odczyt parametr?w strukturalnych z pliku ./CHGCAR... -->> (02) Gsto ladowania odczytu od ./CH Plik GCAR... -->> (03) Odczyt parametr?w strukturalnych z pliku ./deform/CHGCAR... -->> (04) Gsto ladowania odczytu od pliku ./deform/CHGCAR... -->> (05) Written CHGDIFF.vasp File! Remove the CHGDIFF.vasp file and open it via VESTA. \[[Delta \rho=\rho\left(A B_{\text { self-consistent }}\right)-\rho\left(A B_{\text { atomic }}\right)\] Optimized inse structure without external electric field. Do a self-consistent single-point calculation based on an optimized structure. EFIELD = 0.05 IDIPOL = 3 LDIPOL = . True. EFIELD controls the size of the applied electrical force field in units eV/?. (3):Run VASPKIT 314 for the difference in charging density. Remove the CHGDIFF.vasp file and open it via VESTA. VASPKIT can extract kohn-sham (KS) orbital plane wave coefficients from the WAVECAR file and output the actual wave function of space. Users must enter which K point to plot and which bands to plot. Note: Now VASPKIT can only output wavefunction for a specific one K point and one band at a time. To sum several K-points or set the energy range, this can be done in the partial charge density calculations in vasp. Check the band structure or IBZKPT file to see which K point you want to plot? There is only one Gamma point to calculate the CO molecule. So input 1 Which K-POINT do you want to plot? (1< = ikpt <= 1) ------------>> 1 Check the band structure or EIGENVAL file to see which band you want to plot? The EIGENVAL file is displayed as follows. Five colums 1, team number; 2, spin the energy of the band; 3, spin down the energy band; 4, spin the profession number; 5, spin down the occupation number. 1 -29.245473 -29.245473 1.000000 1.000000 2 -14.032873 -14.032873 1.000000 1.000000 3 -11.728864 -11.728864 1.000000 1.000000 4 -11.728864 -11.728864 1.000000 1.000000 5 -9.029100 -9.029099 1.000000 1.000000 6 -2.131725 -2.131723 -2.131723 0.000000 7 -2.131725 -2.131723 0.000000 0.000000 8 -0.00143054 -0.143371 0.0000000 0.000000 If you want to check HOMO and LUMO or VBM and CBM, select band 5, 6, 7 in turn. 511 +-------------------------- Warm --------------------------+ Open WaveFunction files in real space with VESTA/VMD package. +---------------------------------------------------------------+ Which K-POINT do you want to plot? (1<= ikpt <=1) ------------>> 1 Which team do you want to plot? (1<= iband <=36) ------------>> 5 +-------------------------- Warm Tips --------------------------+ The current version only supports the Stardard version of the VASP code. +---------------------------------------------------------------+ -->> (01) Read header information in WAVECAR file... +--------------------- WAVECAR Header --------------------------+ SPIN = 2 NKPTS = 1 NBANDS = 36 ENCUT = 400.00 Coefficients Precision: Complex*8 Maximum G-values: GX = 25, GY = 25, GZ = 25 Estimated maximum number of plane waves: 65450 +---------------------------------------------------------------+ -->> (02) Wave function after process... ->> (03) Reading structural parameters from POSCAR file... -->> (04) File RWAV_B0005_K0001_UP.vasp! -->> (05) Written IWAV_B0005_K0001_UP.vasp File! -->> (06) Written RWAV_B0005_K0001_DW.vasp File! -->> (07) Written IWAV_B0005_K0001_DW.vasp File! Note: Now VASPKIT can only output wavefunction for specific K points and one band at a time. To sum several K-points or set the power range, this can be done in vasp partial charging calculations. The output file format is a VASP mesh file that is the same as CHGCAR and can be opened by VESTA. RWAV is a real part of wavefunction and IWAV is an imaginary part of wavefunction. Usually it is enough to plot and analyze the actual part. B0005 is the band number, K0001 is the K point number in the IBZKPT file. Spin ups and spin downs are output separately. Show RWAV_B0005_K0001_UP.vasp, RWAV_B0006_K0001_UP.vasp, and RWAV_B0007_K0001_UP.vasp... vesta. Check the IBZKPT file and the EIGENVAL file. EIGENVAL shows VBM and CBM in Gamma is: ... 287 -2.799024 1.000000 288 -2.799005 1.000000 289 -0.201544 0.000000 290 -0.201541 0.000000 ... Extract 288 and 289 bands at gamma point. Start VASPKIT, input 511-1-288 and 511-1-289. Open RWAV files by VESTA. 721 calculate the mean square displacement (MSD) based on the RESULTS OF VASP MD. First, prepare the POSCAR.ref reference structure file. Then run vaspkit 721 to calculate msd. The output msd.dat contains displacement information |x|, |y|, |z|, and MSD, RMSD. # ion_step |dx| |dy| |dz| MSD sqrt(MSD) 1 0.0000016 0.0000011 0.0000019 0.000000000 0.0000001 2 2 0.1724941 0.2677518 0.2270937 0.0001325 0.0115120 3 0.3367914 0,4461284 0.0005124 0,0226364 4 0,4918222 0,7752755 0,6499894 0.0010922 0.0330486 5 50.6370632 1.0074569 0.8382370 0.0018188 0.0426475 6 0.7959320 1.2340219 1.2340219 0.0026613 0.0515876 7 0.9545851 1.4665808 1.163088 4 0.0036234 0.0601945 8 1.1064692 1.6957629 1.1.1 193186163 0.0047342 0.068057 9 1.2477962 1.9293770 1.4885940 0.0060285 0.0776432 ATOM_DISPLACEMENT.dat contains displacement and RMSD information for each atom. 722 calculate the radial distribution function (RDF) also based on vasp md results. From to VASPKIT Option XDATCAR PDB 405 POSCAR/CONTCAR POSCAR (with Cartesian coordinates) 4061 POSCAR (with fractional coordinates) 4062 CIF (POSCAR.cif) 4063 ATAT (lat.in ) (experimental) 4064 XCrySDen (POSCAR.xsf) 4065 Quantum-Espresso (pwscf.in) 4066 Moose (elk.in) 4067 Siesta (POSCAR.fdf) 4068 PDB format (PDB Format (POSCAR.pdb) 4069 CIF POSCAR 105 xsd POSCAR 106 Bader results pqr 508 CHGCAR/PARCHG XcrySDen (.xsf) format 318 Gaussian format (.cube ) 319 LOCPOT/ELFCAR XcrySDen (.xsf) format 428 XcrySDen (.xsf) format 429 ? Copyright 2020, VASPKIT Development Team Built from sphinx using theme provided by Read the Docs. Documents.

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