Ab Initio Calculations - Science topic

Dear Ms. Manal, you may use Multiwfn program:

If you decide to try on it, in the manual section 4.18 you'll find ground-to-excited state analysis.

Best, Pablo

Dear Doctor

Go To

[In order to develop and verify a dielectric breakdown model for bulk insulators thicker than 100 μm, the knowledge of the dominating conduction mechanism at high electric fields, or respectively voltages, is necessary. The dielectric breakdown is the electrical failure of an insulator. In some existing breakdown models, ohmic conduction is assumed as dominating conduction mechanism. For verification, the dominating dc conduction mechanism of bulk insulators at room temperature was investigated by applying high voltages up to 70 kV to the insulator until dielectric breakdown occurs. Four conduction models, namely, ohmic, space charge limited, Schottky, and Poole-Frenkel conduction, were employed to identify the dominating conduction mechanism. Comparing the calculated permittivities from the Schottky and Poole-Frenkel coefficients with experimentally measured permittivity, Schottky and Poole-Frenkel conduction can be excluded as dominating conduction mechanism. Based on the current density voltage characteristics (J-V-curve) and the thickness-dependence of the current density, space charge limited conduction (SCLC) was identified to be the dominating conduction mechanism at high voltages leading to dielectric breakdown. As a consequence, breakdown models based on ohmic conduction are not appropriate to explain the breakdown of the investigated bulk insulators. Furthermore, the electrical failure of the examined bulk insulators can only be described correctly by a breakdown model which includes SCLC as conduction mechanism.]

Hello Keshav Kumar Singh . I am facing the same error, is your problem solved. How did you identify the fragments?

Colored cotton as a base for Biofunctional textile

Thanks Martin Breza

The labeling is s p_y p_z p_x d_{xy} d_{yz} d_{z2-r2} d_{xz} d_{x2-y2}, with eventually more columns if the spin and/or the spin-orbit effects are taken into account. These kind of questions can be easily answered by taking a look at the VASP wiki: https://www.vasp.at/wiki/index.php/DOSCAR

Note that the orbital populations are not rotational invariants, i.e., the population of a particular orbital will depend on the orientation of the system within the unit cell defined in the POSCAR, so be careful about the interpretation of these values.

But why do you expect this to be wrong?

The heterostructure might have a different symmetry with respect to the parents.

Maybe if you look at the projection of the bands on the different atoms, you might discover how forming the heterostructure the atomic contribution changes and how the band moved to the Gamma point.

I hope this helps,

Roberto

Hello, Kindly refer to the provided video for a detailed, step-by-step guide on how to do surface energy calculation: https://youtu.be/yWLRM-83I8g?si=JreNXVu2uJ2uUDBz

Thank you

The program will write the data in CONTCAR file after each ionic step if SCF cycle is converged. Maybe you would check whether SCF procedure can converge during the first ionic step?

If it is ok, I would suggest to give some time for that the program can write all necessary files after calculation is done (maybe with the keyword "sleep" in your slurm script). Sometimes, my calculations is finished successfully, but I couldn't have WAVECAR file. But I have never happened it with CONTCAR file.

Regards.

The VASP WAVEDER file is an output file generated by the Vienna Ab initio Simulation Package (VASP), a computer program for simulating solid-state quantum mechanical properties. The WAVEDER file contains information about the electronic structure of a system being simulated, including the wave functions of the electrons in the system. This information can be used to calculate various properties of the system, such as its band structure and density of states.

The WAVEDER file is created during the calculation of electronic wave functions in VASP, and it contains a grid of points in space where the wave function is calculated. Each point on the grid corresponds to a specific atomic position in the crystal structure being simulated. The file also contains information about the energy levels of the electrons in the system, as well as their occupation numbers.

The WAVEDER file can be visualized using various software tools, such as VMD (Visual Molecular Dynamics) or XCrySDen, to explore the electronic structure of the simulated system. It is an important output file in electronic structure calculations and is often used in conjunction with other VASP output files to analyze the results of simulations.

Hello Chanchal K Barman,

Can you use this code familiarly? Now, I meet same questions like you. Can you provide any helps? Thanks a lot !

In my experience, don't trust anything before the 1980s when it comes to experimental phase diagrams; the error in their measurements was sufficiently large that a lot of things got mis-ascribed as cubic!

That said, if you are *certain* it is cubic, try ISIF = 7, which according to the vasp wiki allows the cell volume and ionic positions to relax, but not the shape of the cell.

Julio Cesar Gonzalez To obtain all potential configurations for a crystal structure containing interstitial atoms, utilize Python's pymatgen package. Pymatgen is a Python materials analysis toolkit that includes tools for creating and editing crystal structures. Here's how pymatgen may be used to produce all potential tetrahedral interstitial sites in a bcc structure:

from pymatgen import Structure

from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer

from pymatgen.analysis.local_env import CrystalNN

bcc = Structure.from_spacegroup("Im-3m", Lattice.cubic(2.8), ["Fe"],

[[0, 0, 0]])

# Get the tetrahedral interstitial sites

nn = CrystalNN(inter_cutoff=2.0)

tetrahedral_sites = nn.get_nn_sites(bcc, target_site_type="Tetrahedral")

# Get all possible interstitial configurations

for site in tetrahedral_sites:

bcc.make_supercell(3)

for i, frac_coords in enumerate(site.frac_coords):

bcc.append("Fe", frac_coords, coords_are_cartesian=False)

# Perform any other analysis on the new configuration

...

This programme creates the bcc structure, then discovers all of the tetrahedral interstitial sites and generates all conceivable configurations by adding an interstitial atom at each site. The generated structures can then be subjected to any further analysis or computation.

Thank you sir Muhammad Wisal . I will read it.

No idea

Assuming you mean ABINIT specifically, I recommend the online tutorials here:

You can do the scan using ORCA itself. If you are trying to create the input file, I would suggest using Gabedit.

Probably you can use Gaussian where many chemistry based reaction calculation are possible.

Dear Dong,

Absolute energy per se has no physical meaning if not as a convergence test. Energy differences are however important. You should check if QE and VASP give you the same energy differences, for example as the gap between occupied and empty states.

On the other hand, absolute energies might depend upon many parameters, for example, the pseudo potentials.

I hope this helps,

Roberto

I have done BSE calculation for Si , but can't extract vasprun.xml using p4vasp.

I tried several times, and each time shows.dat file show 0 data.

Can anyone please give me any suggestions?

Dear Jyri and Zhaoxi,

Thanks a lot for your responses. That was helpful.

Best,

Raghav

thank you . I will try that

From your &inputph file, the value for nq1, nq2 and nq3 are for cubic and not for orthorhombic structure.

Thank you, Jaafar Jalilian , for your quick reply!

Yes, the parent compound was optimized using VASP, but not the doped structures. I am unsure whether any relaxation (ionic positions or volume) procedure is available in the SPRKKR package. Please let me know if it is available, and I am very new to the package.

The package uses CPA approximations for the doping calculations, so it doesn't provide any supercell that could be optimized using VASP. I am interested in calculating exchange interaction with the Lichtenstein approach using the SPRKKR package.

Varying acidity of the system may also effect

Since you are relaxing the unit cell (ISIF=3), it changes and the related K-path also changes accordingly. Other papers might have not relaxed the unit cell. Doing only volume relaxation (ISIF=7) can also lead to the same K-path. However, maintaining the same K-path for doped samples may not necessarily be the best approach.

Thank you, Hadi Jabbar Alagealy I have already read through that resource but did not present a clear answer as to why the error message that I shared

The spin-orbit coupling terms in the Hamiltonian don't have anything to do with density functional theory as such; they're logically distinct issues.

How their presence is taken into account within density functional theory is the same as for any other term in the Hamiltonian.

For the technical details it suffices to use the keywords spin orbit coupling density functional theory in one's favorite search engine.

One example found is: https://orbi.uliege.be/bitstream/2268/25694/1/prb_78_045119_verstraete_Pb_phonons_PREPRINT.pdf

Of course there are many more.

I think when calculating the transport properties, the band structure is assumed to be temperature-independent. This should be a good assumption in most cases. The temperature dependence of the transport properties is then from the Fermi-Dirac statistical distribution and the temperature dependence of the scattering rate (relaxation time).

XPS can also be used to measure the band gap of wide band gap materials, as demonstrated in our publication:

This method is also independent of charging.

Nice to share the outstanding summary about "How to solve the error message in Gaussian" as follow:

Have a good day!!!

Mohamed Khedawy Thank you for your comment, however, the order of the atoms is the same because the job is done smoothly when I used a different computer.

Dear Dr. Abhinav Nag

In addition to the previous interesting answers, I guess that spin-polarized calculations are self-consistent and convergency depends strongly on initial values given as initial inputs to upgrade TM.

Please check:

Best Regards.

Somia Benchikh

1. follow the procedure at https://vaspkit.com/installation.html

2. for p4vasp see the link below, Sajjad has given a file. use it. though its not correctly identifying file location for me. If it works for you let me also know.

regards

Dear Dr. Anthony Nash,

As my best knowledge, it seems that you have been going the wrong way to look for a new reaction mechanism. Some TS structures, which you think and expect to see, often do not exist. To me, you should check again the possible reaction mechanisms, if everything is good; and then you guess and calculate the desired TS structures accordingly using Berny or QSTn algorithm. Finally, you check carefully the found TS structures using the IRC analysis and the negative frequency analysis.

Best regards.

This is due thevery few discretization points you have chosen in the k-spce

Thank you very much, Saurabh Singh. Your inputs are invaluable to me. I am trying to obtain elastic constants using DFT calculation. Yes, definitely ....I want to learn and implement those codes on my system. Can we calculate elastic constants of materials using those codes?

Regards

Subha Sanket Panda

thank to all of you for giving me the support.

Zhaoxi Sun , I mostly agree with the hierarchy of methods you suggested. However, before going down from QZ to TZ level or even further, you should definitely consider using a DFT-based composite method. These are slightly cheaper than (m)GGA/TZ but more accurate and robust (see attached figure). The perhaps best one is r2SCAN-3c (which is better for non-covalent interactions better than most hybrid/QZ approaches but 1000 times faster) but not yet widely available. B97-3c is also very good in many situations.

and figures

Chemical shifts observed in high-resolution X-ray photoelectron spectroscopy (XPS) spectra are normally used to determine the chemical state of the elements of interest. Often, these shifts are small, or an element is present in several oxidation states in the same sample, so that interpretation of the spectra is difficult without good reference data on binding energies of the likely constituents. In many cases, reference spectra taken from pure reference samples of the chemical components can aid the peak fitting procedure. However, reference materials are not always available, so that it becomes necessary to estimate the binding energies of likely components through quantum chemical calculations. In principle, such calculations have become much easier than in the past, due to the availability of powerful personal computers and excellent software. In practice, though, care needs to be taken in the approximations, assumptions, and settings used in applying such software to calculate binding energies. In this work, we present a general summary of the methods for the calculation of the core electron binding energies and compare the use of 2 of these methods using the popular “GAUSSIAN” software package. Furthermore, a series of results for molecules, containing elements of the second and the third row of the periodic table, are presented and compared with experimental results, in order to establish the quality and fitness-for-purpose of the quantum chemical-based predictions.

Hello Keshav Kumar Singh You have not written the shrinking factor part correctely. That is why you have got an error in line number 357 of your output file like this ERROR **** INPUT3 **** n-D SYSTEM - SHRINKING NOT DEFINED. You have to write it something like this

SHRINK

0 16

8 8 8

or accordingly whatever you want for your system.

Dear Tahereh,

With the scan keyword you will carry out what is called a rigid scan, this means that the program performs single-point calculations for different structures that vary ONLY the geometrical parameter you selected. This yields a very rough estimation of the potential energy surface, given that you are neglecting all possible relaxations that can take place upon modifying that coordinate. It is usually better (and, four your system, it is perfectly feasible) to perform a relaxed scan, in which the rest of the molecule is optimized at each step of the scan. This can be achieved with the opt=modredundant keyword.

To use this keyword, it is easier to work with Cartesian coordinates instead of z-matrix, just to simplify the input, which will look like this:

-----------------------------------------------

# opt=modredundant wb97xd/aug-cc-pVTZ

\blank line

title

\blank line

2 1

C coord_x coord_y coord_Z

H coord_x coord_y coord_Z

H coord_x coord_y coord_Z

H coord_x coord_y coord_Z

Cl coord_x coord_y coord_Z

\blank line

B 1 5 S 20 0.10

\blank line

-----------------------------------------------

If you take a look to the end of the input, the last written line says that for the bond (B) between atoms 1 and 5 (which correspond to C and Cl according to the Cartesian coordinates) you want to perform a scan (S) of 20 steps, with a step size of +0.10 angstrom (yes, you can do scans that reduce a distance/angle/dihedral just changing the sign of the last number).

Now, you can see that I have removed the td keyword. Given that TD-DFT excited states do not interact with the ground state (this is not CASSCF or any multireference method), the ground state PES will not be modified by them. And forcing the program to calculate the excited states at each step of the intermediate optimizations will increase the computational cost a lot. I think it is better to perform the scan just in the S0 PES, and once it is finished, carry out TD-DFT single-points at each point of the scan. While it involves submitting more calculations, the computational cost will be reduced.

You could have performed the relaxed scan optimizing the geometry not in the S0 surface, but on an excited state, of course. In that case, you need the td keyword, specifying the excited state you are interested. For instance, if you want to do the scan in the S1, the keyword should read td=(nstates=1,root=1). Again, you do not need the upper excited states, unless there are degeneracies.

Hope you find it helpful

Keshav Kumar Singh open the file in VESTA and export data in VASP format, it ask the option of coordinate system, select fractional coordinates.

VMD is a freely available software to calculate RDF and many more properties.

In bulk system, VASP assigns an arbitrary zero energy reference level, so the absolute values of VBM and CBM do not carry any meaning. This means that for different systems, you cannot compare their VBM/CBM position directly. In case of curiosity, VASP set the zero energy reference level in a way that the average potential from all atoms in the unit cell is zero, i.e., the Fourier component for G=0 is zero. If you understand, then you may realize that different systems have different average potential so that different systems have different zero energy reference level, and that's the reason why I say "VASP assigns an arbitrary zero energy reference level".

Thank you A.O. Boev and Bojidarka Ivanova for the response. Your answers is very helpful.

Dear Mark Ryan Tripole

I agree with Diship Srivastava 8 core Ryzen 7 3700X and 32GB is too much for the ab-initio calculations. But it all depends upon that which code you are using and how many number of atoms you have taken for your study.

So i am suggesting you that use SIESTA code which is pseudopotential based and free and open source based code.

Raman intensities depend on the derivative of the polarizability with respect to the normal modes. Apparently, Crystal17 can calculate polarizabilities. So, in principle you "just" would have to write a script that displaces your molecular geometry along all the normal coordinates, performs single point calculations of energy and polarizability for all these cases, calculates polarizability derivatives from that and squares the latter. Then you have the relative Raman intensities for all vibrations by "brute force" calculation.

It's pretty obvious that this is a lot of work. There are packages like SNF (https://reiher.ethz.ch/software/snf.html) that do that for you but I'm not aware of such a software for Crystal17.

@ Hanieh Moradi I misread your post, but I am glad it helps :)

You can calculate it by using Matdyn.x of the recent version of QE. Note it works well for cubic system but may be too complicated for others.

Best Regards,

Thank you Manoj Kumar Banjare sir for the publication. I am reading it now

In addition to the very interesting answers provided before, Prof. Abhinav Nag, I would like to point out that in the optical phonon brach occur an interesting macroscopic relationship for some insulators (ionic crystals), the Lyddane–Sachs–Teller relation (LST) which determines the ratio of the natural frequency of longitudinal optic lattice phonons of an ionic crystal to the natural frequency of the transverse optical lattice vibrations for long wavelengths (or zero) wavevectors.

The ratio is that of the static permittivity to the permittivity for frequencies in the visible range

Wikipedia commons source:

Hi Nelson David Arias Olivares and thank you so much for your answer! The Facio website has a Wineskin but it only works up to macOS Sierra. I ended up downloading the Windows ISO and setting it up with Bootcamp. Facio finally worked on there!

Theoretically that is correct, however, we are interested in bulk material. For that one has to take periodic boundary condition in consideration. However, in that case the result should be independent of the SC size. But the question remains as to how the equation should be written. Alireza Asiaee

please refer to the link below for more details

https://www.amazon.in/Materials-Modelling-Density-Functional-Theory/dp/0199662444

Dear Chiranjit Mondal, in addition to the useful and interesting answers given previously, you might want to check the following external post:

https://www.quora.com/In-simple-terms-if-possible-what-are-the-time-reversal-invariant-momenta-TRIM

Atom projected (site projected) DOS calculations almost always produce output for sites indexed based on the order you defined your coordinates in the input file.

So, if you know which atom is which in your input, it should be no problem working out which ofns to sum.

If your heterostructure is large, it may be convenient to use the ASE interface for QE to work out which atom indexes belong to which layer.

I hope this helps.

Comparisons are made with the experimental results @ Mohanned Alanber . I request you to go through the full manuscript.

A novel Excited state tuning approach has been proposed by us which predicts accurate vertical emissions/Fluorescence wavelengths. The following article gives a detailed description of the method and discusses the accuracy and reliability of proposed methodology.

QE has a utility program, ld1.x, that allows you to generate PPs. A full description of input parameters used to run this program can be found here:

Also, you can find some example input files for both relativistic and non-relativistic PPs in directory (/atomic/pseudo_library/PBE/). With some changes, you can generalize them so that they can be for the other elements not included there

Finally, you could also try the norm conserving Vanderbilt PPs, optimized for QE : https://github.com/pipidog/ONCVPSP

Hope this information helps and good luck!

@yuvam bhateja, Sir, the effect of shape of the nano materials on sensitivity can be understood in terms of conduction path confinement, surface effect, etc. But there is no trivial answer for the effect of shapes on selectivity. Influence of crystal symmetry may have influence on selectivity( 10.3389/fchem.2019.00839). Selectivity towards a particular target gas increases if the specific adsorption towards that species is high. The indirect answer lies in understanding whether just by manipulating the shapes, can we change these specific adsorption towards a particular species. Shall keep you updated if I get an answer for you're question.

I think it may be the problem with the VASP compilation or your memory allocation for that particular job. Try to decrease the number of cores and increase the memory per CPU in your script.

Hi,

Step by step process of accurate (both total and projected) DOS and band structure calculations using VASP and some ways of plotting the band structure and DOS of our system is explained in a Youtube video.

The link is:

I'm not a VASP user, I develop a different plane-wave DFT program (CASTEP; www.castep.org) but in general there are two ways you can achieve this:

a) A constrained variable-cell geometry optimisation

Here you would follow the method you set out in the original question and strain your system along one axis, e.g. the c-axis, then perform a variable-cell geometry optimisation but fix the axis you strained. You'll need to be careful to ensure your calculated stress is corrected for the finite basis set (i.e. that you've removed the Pulay Stress terms), for example using the method of Francis & Payne[1]. If you don't do that you'll have to make the cut-off energy extremely high to get reasonable results.

You'll have to look up how to do the constraints in VASP, but in CASTEP you'd do this with a standard variable-cell geometry optimisation but add:

%block cell_constraints

1 2 0 ! constraints on cell lengths a, b and c

3 4 5 ! constraints on cell angles alpha, beta and gamma

%endblock cell_constraints

to the CELL input file. The values are: "0" meaning fix, positive integer meaning "vary" and if any integers are the same it means "vary, but keep the ration of these constant". So for example you could fix the b/a ratio as well as fixing c by using

%block cell_constraints

1 1 0

3 4 5

%endblock cell_constraints

b) An applied uniaxial stress

The other way to investigate what you're interested in is to apply a stress, and see what the resultant strain is. In some ways this is easier, since you don't have to worry about constraints. Simply apply the external stress tensor you want, and do a standard variable-cell geometry optimisation. Again, I'm afraid you'll have to look up how you specify the stress in VASP, but for reference in CASTEP you'd add:

%block external_pressure

GPa ! Set the unit for the pressure

0.0 0.0 0.0 ! no stress in the a-direction

0.0 0.0 ! no stress in the b-direction

4.0 ! 4 GPa stress in the c-direction

%endblock external_pressure

to the CELL file to apply a 4 GPa uniaxial stress along the c-axis. You only supply the upper triangle of the 3x3 stress tensor -- since the tensor must be symmetric, CASTEP fills in the lower half for you. Then you just run a normal variable-cell geometry optimisation, and read off the final lattice constant to find the corresponding strain.

Hope that helps,

Phil Hasnip

(CASTEP Developer)

[1]

(the typo in the title is from Research Gate, sorry about that!)

I'm not a QE user, but I develop a similar program (CASTEP) and I don't think there should be any significant differences in how you approach this situation.

When simulating a molecule in the gas-phase, you need to ensure your lattice unit cell is large enough that the molecules do not interact strongly with each other. (You would usually only put a single molecule in the unit cell, but it will still interact with its periodic images in neighbouring cells.)

In general, you need to try a range of different unit cell sizes to investigate the effects of the spurious inter-molecular interaction. It is difficult to know beforehand exactly how large your unit cell should be, since it depends on the molecule, but as long as it doesn't have a large (macroscopic) dipole moment then I would expect somewhere between 10 and 16 A to be enough separation -- so your unit cell would be the width of the molecule plus 10 to 16 A. I usually start investigating at 8 A to get a baseline, and converge from there -- look at energies and forces, and any properties of especial interest (e.g. DOS features).

When you do your geometry optimisation, make sure that you do *not* optimise the lattice vectors, just optimise the atomic positions. This will probably be faster too, since it won't need to compute the stress on the cell (and that's quite computationally demanding).

As a side-note, if you sample the Brillouin zone at the gamma-point you will need a larger separation compared to sampling at the (1/4,1/4,1/4) point, though the gamma-point calculation may be faster. This is because (a) the gamma-point maximises the constructive interference between the wavefunctions of neighbouring cells (they are all in phase), and you want to minimise the interference, but (b) at the gamma-point the wavefunctions are real (not complex) in real-space, so there is less work to do.

By the way, a simple cubic cell is the simplest to set up, but you may find something more isotropic (e.g. a hexagonal phase) is actually more computationally efficient.

Note that none of these considerations are specific to your molecule, so you can quickly see what kind of behaviour you get with something small and simple. I would suggest you try something like methane, and then again with methanol (to see the effect of electrostatics). These will be really quick, so you can do a very good job very quickly and get all your mistakes out of the way!

Hope that helps,

Phil Hasnip

Hey Julian! I was solving a similar problem by adding more memory in my com-file, i.e. %mem=50GB and so on (depending on how much you need). Then it is good to empty the space where you store those files produced by Gaussian, or if you run on a super-computer to use the memory on the node itself rather than in your submission directory. Finally, one more solution is to use less processors but reserve the whole node. If you node has 20 cores you shall use, let's say 4 out of them. It worked for me as well.

My question is what is Band Gap Centre Approximation and since it says " the band gap center (i.e., Fermi level) " how will one tell they both are same when fermi level is either in conduction band minima or valence band maxima ? Is the value of fermi given in scf.out/.dos file not correct ?

Dear Abhinav

As far as I know, you can not calculate the thermal conductivity using Phonopy. You need to use another package (Phono3py) for this purpose. However, the projector augmented wave (PAW) Pseudopotentials are the best for performing the self-consistent field (SCF) calculation with Quantum Espresso. This approach is more close to the experimental results while it's computationally rather expensive.

If you have another question, just let me know.

- First, let's review some basic equation:

+ From VASP source code:

CDER(k, m, n, j) = <u_m|- i d/dk_j | u_n> = - <u_m| r_j |u_n> (j = x, y, z)