First-principles Calculations

First-principles Calculations

  • Yin Li added an answer:
    How to define a crystal structure in quantum-espresso (pwscf)?

    In the tutorial of quantum-espresso (pwscf), the tutor demonstrated how to set up a unit cell using the parameters list below.




    Only 1 atom is enough to define this face-centered cubic. As far as I understand from this parameter, the software will know where to place 14 atoms in one cubic (8 corners and 6 face centers).

    However, I was confused by the second example. The tutor only used 2 atoms to define a diamond structure (Fig 1).





    Si 0.0 0.0 0.0

    Si 0.25 0.25 0.25

    If the first Si was considered as the atoms whom should be placed in the 8 corners and 6 face centers in one cubic, how does the software know where to place the second Si? How does the software distinguish the diamond structure from fluorite structure (Fig2)?

    Yin Li · University of Pécs

    Thanks, Vaibhav! I will try it.

  • Darshana Wickramaratne added an answer:
    Can anyone help with the following issues about hse06 hybrid functional calculations using vasp 5.3.5?

    I am not asking here how to set up the hybrid functional calculations (with hse06) in vasp, which has been outlined in many places for example the vasp wiki. I encountered the problem that exactly same set up working well in vasp 5.2.12 did not work for vasp 5.3.5.

    I started with a PBE functional calculation and saved the WAVECAR. Then I perform the HSE06 calculation reading the wavefunction and using Damped keyword to do the digonalization. While the vasp 5.2.12 and 5.3.5 presented the same energy in the PBE calculation, the same setup converged quickly in 5.2.12 within roughly 15 steps but diverged in 5.3.5 after three or four steps. Indeed, the first three steps in 5.3.5 did make sense with a negtive energy close to the converged one in 5.2.12. But for some reasion, the iteration just diverged and large positive energy was yielded afterwards. I read the mannual and did not find significant change in the INCAR for vasp 5.2.12 and 5.3.5.

    I have tried to google the similar topic and found no one mentioned the same problem as I had. Has anybody here noticed my problem and can you suggest some hints? Thanks in advance

    A portion of my INCAR for the HSE06 calculation.

    HFSCREEN = 0.2

    TIME = 0.4
    AEXX = 0.25
    AGGAX = 0.75
    AGGAC = 1.0
    ALDAC = 1.0
    ALGO = Damped
    PRECFOCK = Fast !--> used PRECFOCK = Normal for high quality calculations

    Darshana Wickramaratne · University of California, Riverside

    Dear Bin Jiang,

    I found frequent numerical instabilities using VASP 5.3.x and the Intel v13 compilers (EDWAV errors) - using v12 of the Intel compilers seemed to provide more stable results at the expense of being a slower calculation.  

  • V. V. Bannikov added an answer:
    What are the effects of high electron density at the fermi level regarding the oxygen reduction reaction?

    I recently synthesized a doped cobalt oxide and high electron density (dxy) is observed right at the fermi level through first principle calculations. Does anyone know what are the effects of high electron density at fermi level? 

    V. V. Bannikov · Russian Academy of Sciences

    It the first-principles calculations are ordinary DFT calculations they may highly overestimate the DOS at Fermi level for the compounds with open-shell transition metals.

  • Sayyed Faramarz Tayyari added an answer:
    How to properly apply Gaussian G2 method?
    I would like to ask what is the proper way to use this Gaussian composite method for high-accurate energy calculations? Do I need to pre-optimize my molecule using the same functional and basis set (in this case: MP2/6-31G*) as its required for starting geometry in G2 method? Or maybe this pre-optimization step is done automatically within G2 method and there is no difference what functional/basis set was used to prepare initial structure? Moreover, should I use OPT keyword or just G2 alone? I noticed that in case of correcting energies of transition state structures, the OPT(TS) keyword was needed, otherwise the molecule was optimized either to reactants or products.
    Sayyed Faramarz Tayyari · Ferdowsi University Of Mashhad

    Simply type G2 or G3 then everything goes automatically. However, you cal also apply 

    solvent effects by adding, for example, SCRF=(PCM,solvent=...).

  • Jian Hui Lan added an answer:
    How do you calculate the energy of a gas phase oxygen molecule in its triplet ground state?

    I would like to calculate the oxygen vacancy formation.

    Eform,vac = Edefective - Eperfect - 1/2 EO2

    I read that the energy of oxygen vacancy was referenced to the oxygen gas energy in its triplet ground state. I would like to know how to calculate the triplet ground state O2 energy?

    I heard that the O pseudopotential should be test by binding energy and bond length of O2 molecule? Would you please give me some suggestions or references?

    Jian Hui Lan · Chinese Academy of Sciences

    Dear Pro. Fiorentini,

    I have to say I learned much from your latest reply. Thanks!

  • Ahmad Bahmani added an answer:
    How can I find out the atomic position of a crystal with known space group(using website)?

    In the following link, the atomic position of different space groups has been shown.

    For a first principle calculation, I need to know the atomic position of a compound. I found the crystal space group (e.g. Immm (Pearson number:71)). But for adding atoms in materials studio, I don't know how I should find the atomic position.

    I really appreciate if you help me to find out how to use this website. What should be replaced by x, y, z?

    Best wishes,

    Ahmad Bahmani · Seoul National University

    Dear Sir, 

    Thank you so much, as you said the crystal of Mg7Zn3 is same as Mg51Zn20.

    For the case of Ca2Mg6Zn3 I found the following article. 

    DOI: 10.1017/S1431927602010413

    But the simulation is so lasting long. But the simulation takes so long. 

    Best regards

  • Andrij Vasylenko added an answer:
    How to find Cartesian atomic coordinates of Silicon in a unit cell on a surface?
    How can one find these or reciprocal coordinates for a couple of layers in a slab?
    Andrij Vasylenko · National Academy of Sciences of Ukraine

    I would build a unit cell according to ME Fleet (1981) Acta Crystallographica B, 37, 917 :

    Space Group Fd-3m (No. 227)
    a=8.3941 Å

    Atomic Positional Parameters
    Fe1 8a 0.1250 0.1250 0.1250
    Fe2 16d 0.5000 0.5000 0.5000
    O 32e 0.2549 0.2549 0.2549

    With a software like Avogadro it is possible to fill the unit cell, multiply it and to build a slab.

  • Giuseppe Pintaude added an answer:
    How could hardness of metals or alloys be quantified or measured theoretically?

    From the first-principles calculation or basics of dislocation movements, density or anything else aiding to introduce hardness of metals and alloys.

    Giuseppe Pintaude · Federal Technological University of Parana

    Very interesting paper Li! Congrats.

  • What is the good software for nonlinear curve fitting rather than Excel and Origin?
    What is the good software for nonlinear curve fitting rather than Excel and Origin?
    Larraga-Gutierrez Manuel Jose · Instituto Nacional de Neurología y Neurocirugía

    I recommend gnuplot, free software with a lot of features. Easy to use.

  • Zeyad Adnan Saleh added an answer:
    What type of analysis we can do to except band gap measurement using UV-visible spectroscopy?

    I would like to do first principle studies(using DFT) for this technique to compare experimental and theoretical value.

    Thank you.

    Zeyad Adnan Saleh ·

    yes , you can do that by taking the absorption spectra and the electrical properties of thin films for the materials which are under investigation. we do do that when we studied the effect of doping  in aromatic system.

  • Waheed Adeniyi Adeagbo added an answer:
    How can I calculate the defect formation energy by DFT?

    The paper "first principle calculations for point defects in solids, Rev. Mod. Phys. 86 (1)" gives the defect formation energy formula:

    Ef[D(i,q)] = Etotal[D(i,q)] – Etotal[defect_free] + Sum[n(i)*μ(i)] + q*E(Fermi) + ∆q

    μ(i) is the corresponding chemical potential of the ith point defect

    E(Fermi) is the charge potential

    ∆q is "a correction term that accounts for finite k-point sampling in the case of shallow impurities, or for elastic and/or electrostatic interactions between supercells."

    I know how to get the total energy of perfect and defect structures. but with respect to the latter three items μ(i), E(Fermi), ∆q how to calculate?

    Thanks in advance!

    Waheed Adeniyi Adeagbo · Martin Luther University of Halle-Wittenberg

    By following P hys. Status Solidi RRL, 1-5 (2014) / DOI 10.1002/pssr.201409032


    Modelling Simul. Mater. Sci. Eng. 17 (2009) 084002 (14pp)

    E_formation (D,q) = E (D,q) - E(host defect free) + Sum[n(i)*µ(i)] +

                                                q( Ev + delta E_F )

    E_formation (D,q) = formation energy of point defect D with supercell charge q

    E (D,q) = total energy of the point defect D with supercell charge q

    E(host defect free) = E(host defect free) = total energy of host supercell
    containing equivalent number of atoms as that of the
    defect supercell

    Sum[n(i)*µ(i)] = The growth conditions for the crystal are
    incorporated through the chemical potentials µ(i)
    of the elemental species with the number n(i) of atoms added
    ( n(i) negative) or removed ( n(i) positive) from the pure host

    Ev + delta E_F: The Fermi level E_F is referenced with respect
    to the valence band maximum Ev and is related to Ev as
    Ev+ delta E_F (from pure host caluculations)

    Ev            E_F          Ec

    0   (if EvBMmax)    Ec

    Ev = valence band maximum
    Ec = conduction band minimum
    Eg = band gap

    .i.e. Ev < E_F < Ec
    if we set Ev to zero, then E_F is between 0 and Eg (as varying parameter.)

    Now what is Ev?
    In principle, Ev can be obtained from total energy difference between neutral calculation E(n) and one charge calculation

    Ev = E(N) - E(N-1) for N---->large

    Or simply do a test neutral calculation with a unit cell.
    Then subtract one electron SLOWLY.
    i.e. from delta(q) = 0e to 1e removed in the interval delta(q) such as of 0.01.

    Then plot the total energy

    E(delta(q)=0)- E(delta(q)) vs log10(1/delta(q))

    A curve with saturation value will be obtained. This saturated value should gives Ev (It is equivalent to the energy needed
    to add or remove a charge to alter the Fermi energy in the charged calculations)

    In VASP e.g. if one plots the DOS, the Fermi Energy obtained from OUTCAR should be equal to Ev (IF the fermi level
    lies exactly at the VBM, OTHERWISE one needs to shift the Fermi level to the VBM. The amount of this shift is subtracted from Fermi energy obtained in OUTCAR file.

    One could compare all these numbers in the 3 methods described.

    e.g. Consider ZnO with 96 atoms total, remove One Oxygen atom and put charge q
    Then we have ZnO:Vo:q

    E_formation (ZnO:Vo:q) = E_tot_supercell(ZnO:Vo:q) - [ E_tot_supercell (ZnO) - 1µ(one O) ] +q ( Ev + delta E_F)

                      E(95 atoms) -  [E(96 atoms of  pure)  minus E(one oxygen atom) ]


    as explained

    µO approx. = 1/2E(O2) ( Put 2 oxygen atoms in a large supercell)
    Half of the total energy of O2 molecule gives the chemical potential of oxygen (µO).

  • David Foster added an answer:
    How to find mobility of a particular system using VASP?
    Can I find the mobility from the vasp calculations?
    David Foster · Oregon State University

    Note that the effective mass that is used in mobility calculations can be different than the effective mass associated with the density of states.  The former is given as m_c = 3/(1/m1 + 1/m2 + 1/m3) (see Sec 1.4.2 of Sze and Ng "Physics of Semiconductor Devices, 3rd ed.") instead of the usual geometric mean of m1,m2,m3.  Here m1 is the effective mass along principle axis 1.  The calculated effective mass using dense k-point lines and the second derivative is a low-temperature value.  It can vary from this (and becomes less well-defined) at room temperature when the CB/VB are not well approximated by a paraboloid all the way up to Delta E = kT.

    The effective mass is used in formulas for mobilities associated with phonon scattering and defect scattering, which assume that you know the elastic constant and defect concentration in the material respectively.  The elastic constant is easily looked up for known materials (or can be estimated using a VASP calculation).  Extrinsic defects densities come from doping defect densities, but intrinsic defect densities may be harder to look up (and they are a major project to calculate and the results can be off by more than an order of magnitude).  Calculate the mobility for phonons first, and if it is doped, calculated the mobility from extrinsic defects.  Then you can estimate the minimum intrinsic defect density at the intrinsic defect mobility becomes significant.  Hopefully, someone can tell you "the intrinsic defects in that material should be well below that room-temperature significance threshold".  I believe this is true in many cases. But for example, in CuInSe2, the intrinsic copper vacancies ~10^17 or 10^18 cm^{-3} (I believe) may be non-negligible at low temperatures, maybe even room temperature.  I have not looked at numbers enough to know at what temperature a 10^17 concentration would become important.

    In addition to the warning given by Buurma, there is the issue of the approximation of the functional you are using.  Band structure comparisons that I have seen between GGA and GGA+GW (more accurate, but very expensive to converge) look like the second derivatives agree well.  But I wouldn't expect a phonon-mediated mobility calculated this way to be more accurate than within a factor of, say, 5.

  • Kingsley Onyebuchi Obodo added an answer:
    How can I calculate the guarantee of accuracy from the plane wave basis kinetic energy cutoff, Monkhorst-Pack mesh and Supercells atoms number?

    How to calculate the guarantee of accuracy from the plane wave basis kinetic energy cutoff, Monkhorst-Pack mesh and Supercells atoms number?

    I read

    "... using a plane wave basis kinetic energy cutoff of 800 eV and a 4 X 4 X 4 M-P mesh for k-points of the 40-atom supecells. These ensured an accuracy in the total energy of ~ 5 meV/formula unit. ..."

    How to get the "5 meV/formula unit"?

    Kingsley Onyebuchi Obodo · Johnson Matthey

    In addition to previous statements on the k-point issue:

    To carry out a supercell calculation with same accuracy as your unit cell. The number of k-points should be scaled, otherwise one calculation will be more accurate than the other.

    Also, except you are introducing dopants or carrying out some modifications to your conventional unit cell, it is advisable to carry out your band structure calculation on your unit. You would have the benefits of faster calculation and more accurate band structure because you can increase the number of your k-points and other convergence criteria.

    Michael has provided a good answer on how to determine the kpoints for both unit cell and supercell calcations

  • Shuai Zhao added an answer:
    Is the K-points path the same as the primary cell for a superlattice?

    In the first principle calculation, to plot the bands structure we need to calculate the bands along a K-points path through high symmetric K-points.

    Then, my question is if calculate the superlattice (2 x 2 x 2) bands structure, is its K-points path the same as that of the primary cell? If not, then how to set the K-points path for the superlattice?

    Thanks in advance.

    Shuai Zhao · Kyushu Institute of Technology

    Dear Vaibhav, thank you very much for your answer.

  • Danny E. P. Vanpoucke added an answer:
    Can you help me with VASP calculation of elastic moduli for hybrid functional (HSE,PBE0)?
    I'm trying to calculate elastic moduli for a system using a hybrid functional. My INCAR for the system is

    ENCUT = 600 # Energy cutoff for planewave truncation (higher -> more accurate energy)

    ISTART = 0 # 0 - Start new calculation
    ISPIN = 1 # Non-spin-polarized calculation
    IBRION = 6 # Calculation of elestic constant matrix (symmetry on)
    ISMEAR = 0 # Gaussian smearing
    SIGMA = 0.01 # Smearing width (eV)

    ISIF = 3 # Full relaxation / calculate full stress tensor

    NELMIN = 8 # Minimum number of electronic steps

    PREC = Accurate
    LREAL = .FALSE. # Projection done in reciprocal space

    LWAVE = .FALSE. # Do not write WAVECAR
    LCHARG= .FALSE. # Do not write CHGCAR, CHG
    LVPOT = .FALSE. # Do not write LOCPOT
    LVHAR = .FALSE. # Do not write LOCPOT

    ## PBE0 (Hybrid functional)
    PRECFOCK = Fast
    ALGO = Damped
    TIME = 0.4

    This works for regular LDA/PBE functionals, but not for hybrid functionals as VASP changes the k-point set on-the-fly, which causes an error:

    "internal ERROR in RE_READ_KPOINTS: the total number of non zero k-points in the full Brillouine zone has changed"

    Does anyone have any experience with this particular problem and, if so, could you suggest a fix or an alternative? Any help is very much appreciated. My version of VASP is 5.2.12

    (PS already tried IBRION=7 or 8, which is not implemented for HF calculations)
    Danny E. P. Vanpoucke · Ghent University

    If the issue is the k-points changeing, just switch symmetry off, in that case you will get a non-reduced sampling of the brillouin zone (which is more expensive, but should not die due to this error)--> ISYM = 0

  • Viorel Chihaia added an answer:
    How to keep slab layers constant in Lammps?
    I have a 14 layers slab and want to perform optimization for the topmost half layers by keeping rest of them constant. How to achieve this?
    Viorel Chihaia · Institute of Physical Chemistry
    I understand that you are interested to do a minimization with some frozen atoms. You have to create a group with the particles that must be fixed and apply zero force to that group (with 'fix setforce' command). If you are interested in MD, then you may apply the solutions above.
    IMPORTANT NOTE: In case of layered systems (interfaces of solid-liquid, graphite) you have to remove the rotation and translation of each layer. Otherwise, the layers will fly in the simulation box. Because the weak interactions between layers, the rotation motion of the layers is hindered by the presence of the other layers and the rotation motion of each layer will be transformed during the simulations into translation motion. The result: the layers will start to fly in the simulation box.
  • Oleg Chizhko asked a question:
    What is the surface of a three component system for the transformation from liquid to solid state of matter?
    Gibbs triangle is a three dimensional surface, in which finite elements are oriented according to a chemical potential of formation for three neighboring phases.
  • Niyaz Safarov added an answer:
    What is the best program to make beautiful 3D atomic figures?
    For now I'm using CrystalMaker.
    Niyaz Safarov · Baku State University
    PyMol is the best
  • Ihosvany Camps added an answer:
    How can I find the k-points for band structure calculation?
    I would like to find the k-points for Monoclinic system.
    The path follows the trend like this
    In band structure calculations I have to give k points in this format..
    G 0 0 0 10 ( this we know)
    Y ? ? ? 10 (10 is the points b/w symmetry points )
    M ? ? ? 10
    C ? ? ? 10

    My doubt is how to find the Y, M and C points.
    Is there any software for all systems or website?
    Ihosvany Camps · Universidade Federal de Alfenas
    You can take a look at the paper:
    Comp. Mat. Sci. 49: 299–312. 2010
    High-throughput electronic band structure calculations: Challenges and tools
    Wahyu Setyawana, Stefano Curtarolo
    (Images are in the Wikipedia:


  • Tanmoy Chakraborty asked a question:
    Does anyone know how to calculate free energy using quasi-harmonic Debye model using PHONOPY?
    For some unstable states, one should expect negative phonon frequencies in the harmonic approximations. If you have negative phonon frequency then you can't get the free energy using that. For that, you have to use quasi-harmonic Debye model.
    Now, in my case, I want to calculate those using PHONOPY program package. Can anybody help me?
  • Danylo Zherebetskyy added an answer:
    How to find the Band structure of a material using VASP?
    I would like to find the band structure and I have to give the Brillouin Zone path, But How? Please suggest me any video lectures or PDF for this content.
    Danylo Zherebetskyy · Lawrence Berkeley National Laboratory
    Defenetly use vasp tutorials and very important find the correct Brillouin zone and high symmetry k-point paths for your crystals using
  • Peram sreenivasa Reddy asked a question:
    How do you install KKR-ASA code and how do you run the examples?
    I want to install the KKR-ASA code in my system. In the code folder I have subfolders named bgfm, blas, bstr, lmtolib, lsgf, and spcm. I went into the folder bgfm/source and put make option in my terminal. Finally it is showing that the file named lmtolib is not there. How can I prevent this from happening? Can someone show me an example?
  • Krisztián Palotás added an answer:
    What is CPA-EMTO code?
    I want to know about the CPA-EMTO code. Where can I get this code for a sample test?
    Krisztián Palotás · Budapest University of Technology and Economics
    Probably the best is to contact Prof. Levente Vitos directly, he could provide you details with the CPA-EMTO code. Good luck!
  • Dipayan Sen added an answer:
    Is UFF (Universal Force Field) potential a good choice for modelling metal clusters?
    I tried both UFF and EAM for such systems and EAM potentials seems to be producing better results.
    Dipayan Sen · Jadavpur University
    thanks for your reply. i tried up to 30 atom clusters for Pd with UFF and EAM. But UFF (with gulp, and i used a genetic algorithm to search for global minima) is not giving very much coherent results, whereas with EAM I am getting .regular shaped clusters.
  • Marcin Andrzejak added an answer:
    How to confirm that my band gap is correct in the absence of experimental results?
    I calculated band gap for my material and I want to confirm with experimental results but I seem to have encountered an absence of experimental results. What's another way?
    Marcin Andrzejak · Jagiellonian University
    Find a functional that is most commonly used in such problems and based on the published results for systems, for which experimental data exist, determine the errorm margin. This can give you some estimate where energetically your band-gap may lie. Otherwise, find a suitable research group and try to convince them to measure the band gap for your material. This is probably the safest way...
  • Dipayan Sen added an answer:
    How create a crystal structure in Material studio for AB0.5C0.5O3?
    A-0 0 0
    B 0.5 0.5 0.5
    C 0.5 0.5 0.5
    O 0.5 0.0 0.5
    O 0.5 0.5 0.0
    O 0.. 0.5 0.5
    Dipayan Sen · Jadavpur University
    to make a crystal structure, three parameters are needed: shape (space group), size (lattice parameter) and location of atoms (fractional coordinates). if you have all of these, then make a 3D atomistic document---->Build-crystals-Build Crystal--->input lattice parameters and space group to make the empty cell. Then you can insert atoms in the structure from Build-Add Atoms.
    (P.S. assuming the data you have mentioned above are fractional coordinates, there is one severe inconsistency - Both B and C are situated at the same location.
    From these I get the picture that 6 O atoms at the face centres, 1/8th of A as it is sitting in a corner and 1 each of B and C as they are sitting in middle of the cell!)
  • Zuheir Subhi El-bayyari asked a question:
    The Role of Pd-Re Alloys in Medical Devices and its applications? In what shape and structure?
    I want to understand and simulate such alloys to study their structural stability with increasing temperature. Any comments please?
  • Marcin Andrzejak added an answer:
    Is it possible to predict electronic transition properties of a molecule based on its molecular orbitas?


    Marcin Andrzejak · Jagiellonian University
    What do you mean by transition properties then? Would you clarify?
  • Roman Leitsmann added an answer:
    How to understand the reciprocal space (k-space). How will it work in PwScf calculation?
    I am very confusing about reciprocal space. It does not exist but why we are using and what is the role of k-points in PwScf calculations.
    Roman Leitsmann · AQcomputare Company
    In quantum mechanics the wave functions |psi> can be represented in different ways. One way the the real space representation of the wave function psi(r) = , another possibility is the k-space representation psi(k) = . Both representations are conneted via a Fourier-transfomation. In this sense both representations exist.
  • Closed account added an answer:
    What software to use for Raman and IR theoretical modes?
    Is there any free software to find Raman theoretical modes? I know Gaussian 3 package but it is a licensed version.
    PWSCF (Quantum Espresso) can be used to study the Raman (the system should not be a metallic one) and IR spectra of the system. Also, the software is free.

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