First-principles Calculations

First-principles Calculations

  • 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
    ADDGRID = .TRUE.
    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)
    LHFCALC = .TRUE.
    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 · Jülich Supercomputing Centre
    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.
  • Christopher F Buurma added an answer:
    How to find mobility of a particular system using VASP?
    Can I find the mobility from the vasp calculations?
    Christopher F Buurma · Epir Technologies Inc.
    Mobility of each carrier species is normally computed through the dispersion (derivatives) of the associated band diagram (Energy vs k-points) from an ab-initio calculation. You can take the hole or electron bands and compute the mobility of each carrier species.
    Great care however must be exercised when interpreting band diagrams from density functional theory. The H-K theorem guarantees charge density and total energy will match (with a perfect functional) but makes no warranty on the band diagrams. You have been warned!
  • Marek Wojciech Gutowski added an answer:
    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?
    Marek Wojciech Gutowski · Institute of Physics of the Polish Academy of Sciences
    My favorite tool for such task is gnuplot - a free software designed primarily to produce various graphs. It is also able to make nonlinear fits, using Levenberg-Marquardt method. Not only the unknown parameters but also their uncertainties are computed and reported. gnuplot is available both for Windows and Linux.
  • 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
    G-Y-M-C-E-M1-A-X-G-Z-D......etc.
    In band structure calculations I have to give k points in this format..
    12
    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
    doi:10.1016/j.commatsci.2010.05.010
    (Images are in the Wikipedia: http://en.wikipedia.org/wiki/Brillouin_zone)

    Regards,

    Camps
  • 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 http://www.cryst.ehu.es/cryst/get_kvec.html
  • Kotagiri Gangaprasad asked a question:
    Does anyone know about DFT summer schools?
    I want to attend DFT summer schools. If anyone knows please let me know the details.
    Is there any website for DFT related schools?
  • 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 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?
    I have an organic structure. I want to predict and judge its transition properties. Could I judge about it based on its LUMO? How can I predict about its transition properties based on molecule's ground state?
    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.
  • Sanjiv K Jha 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.
    Sanjiv K Jha · New Mexico State University
    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.
  • Gyorgy Banhegyi added an answer:
    How to explain Raman (also IR) active or inactive modes?
    In point group table I observed the modes. Some are Raman active and some are IR active? How should we explain those modes? Let's we take one example: Point group D2h(mmm).
    Gyorgy Banhegyi · Bay Zoltán Nonprofit Ltd. for Applied Research
    Hugh, it was long time ago. Anyway: IR activity presupposes non-zero transition dipole moment, while Raman activity presupposes non-zero transition polarizability. Those modes which transform similarly to x, y or z (as shown by the character table) are IR active, while those, which transform similarly to xy, yz or xz are Raman active. See e.g. http://books.google.hu/books/about/Molecular_Vibrations.html?id=CPkvsDrPiv0C&redir_esc=y
  • George Fitzgerald added an answer:
    How the "smearing" will affect the geometry optimization and density of states (DOS) when calculated by the Density Functional Theory?
    During electronic structure calculations and geometry optimization using DFT, smearing is used which replaces smooth functions in place of actual functions of DOS. What is the drawback in using this smearing? Using large smearing values causes structural deformations. Why?
    George Fitzgerald · Universal Display Corporation
    smearing excites electrons into the virtual space. This has the effect of smoothing SCF convergence, but it also increases the anti-bonding character of the wavefunction. As you go to higher smearing you push more electrons into the virtual space and destabilize the system. Eventually, your smearing will make the system totally unphysical.

    The advantage of the method is that it improves SCF converge a LOT in many cases. I think the maximum value that you choose is a judgment call. When I need smearing, I start at 0.005 au. I will not go over 0.010 au. If I need larger smearing then there is usually something wrong, like bad geometry or wrong spin state. Most DFT programs will print both the total energy with smearing and extrapolated to zero smearing. If those values are getting too far apart then you know your smearing is too large
  • Kebbab Zoubir asked a question:
    Is there free software (like phonon code) which can help us for studying phonon dispersion in solid materials?
    Any free software which can be used with DFT calculation (like Win2k code)?
  • Andrii 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?
    Andrii Vasylenko · National Academy of Sciences of Ukraine
    It clarifies a lot =)
    Thank you for such a helpful answer, Deniel. References on software are really valuable.
    P.S. Why I thought of such a small amount of atoms for a surface case... it was a mistaken suggestion only, which goes out of a correct way of calculating the bulk Silicon with 2 atoms per unit cell though.
    0.0 0.0 0.0
    1/4 1/4 1/4

    That gave me a feeling that one might add an atom on top of it to get a "slab" unit cell in 111 direction
  • José R B Gomes 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.
    José R B Gomes · University of Aveiro
    Q: "Or maybe this pre-optimization step is done automatically within G2 method..."

    A: Yes, if you use G2 keyword the geometry will be optimized at the HF/6-31G(d) level of theory (first step). Then (2nd step), frequencies will be calculated at the same level of theory. In the 3rd step, the structure will be further optimized at the MP2(Full)/6-31G(d) level. The geometry optimized in the latter step will be used for single-point calculations at the QCISD(T,E4T)/6-311G(d,p), 4th step, MP4/6-311+G(d,p), 5th step, MP4/6-311G(2df,p), 6th step, and MP2/6-311+G(3df,2p), 7th step, levels of theory.

    Q: "there is no difference what functional/basis set was used to prepare initial structure?"

    A: G2 will optimize the structure provided in the input file (initial structure) to the closest minimum on the potential energy surface (i.e., it will be optimized at the HF/6-31G(d) level of theory and then, steps 2-7 above will follow in cascade).
  • Roshanak Teymoori added an answer:
    How do you identify the energy levels of a1, a2 and e states from Density of States Plot?
    We know that due to C3v symmetry, energy levels splits into a1, a2, and e states. How do you identify the approximate energy level of each state (a1, a2 and e1) from Density of states of a particular system?
    Roshanak Teymoori · University of Alberta
    hi this is the same question I have !!! I am doing gaussian calculation for VOF3 and would like to know how to assign each energy levels based on a1, a2, e?
  • Xianda Li added an answer:
    How to calculate the enthalpy of formation using the first principle calculation result?
    For example I have the total energy of the following:
    Mg2Ni (hcp): a eV,
    Mg (hcp): b eV,
    Ni (fcc): c eV.

    In the cell of Mg2Ni, Mg and Ni there are 36, 2, 14 atoms, but considering not all atoms contribute solely to one cell, the real numbers of atoms in a cell are Mg12Ni6, Mg2, Ni4, so:

    Enthalpy of formation of Mg2Ni: a/6-b-c/4

    However I found this doesn't agree with what I've found in other's articles.
    Xianda Li · Institut Franche-Comté Electronique Mécanique Thermique et Optique Sciences et Technologies
    Well I think I've found the problem. It's due to the wrong Ni numbers in a fcc nickel cell. When it was calculated, it has used the primitive cell which has only 1 nickel atom in the cell rather than the conventional cell. So the correct way should be:
    a/6-b-c
  • Mukesh Kumar added an answer:
    How to set up GW+BSE calculation in VASP?
    I am trying to set up GW/BSE calculation on VASP (new version 5.3), Does anyone have an idea about it ? Please share your view !
    Mukesh Kumar · National Institute for Materials Science
    Thank you for reply ! I will check Abinit...
  • Dinesh K. Dixit added an answer:
    What are good references for learning the necessary programming for first principles calculations of material properties?
    Also, what are good references for the approach of first principles calculations, i.e. how crystal structure affects properties, how nearest neighbor interactions affect the properties, etc.?
    Dinesh K. Dixit · Indian Institute of Technology Bombay
    @Jeffrey Sir......thank you so much.

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