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A satellite peak does not affect the electronic structure.
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I am currently working on obtaining the transition state for the deprotonation of a carbocation by histidine. Initially, I froze the bond lengths between the histidine nitrogen and the proton, as well as between the proton and the methyl group being deprotonated. This approach resulted in a single imaginary frequency of over -1000 cm⁻¹ (please see the attached files: 1_input and 1_output).
I then attempted to release these constraints and recalculate the transition state. I have tried various keyword combinations, including calcfc, calcall, scf=qc, and IOP(1/8=1) in conjunction with the level of theory # opt=(ts,noeigen) freq mpw1pw91/6-31+g(d,p). However, the structure did not converge. The energy oscillates uniformly without reaching a minimum (attached is a graph showing this behavior).
Could you provide any suggestions on how to address this issue ?
Thank you for your time and assistance.
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The method you use to calculate a TS is correct, Opt=(TS,calcfc,noeigen). However, it is important to have a good approximation to the TS. You should first perform a scanning of how energy changes when methyl is deprotonated (see attached). To do that, do a scan job:
# opt=modredundant plus other keywords
.../...
.../...
B 1 2 S 10 0.10
This is only an example, replace 1 and 2 with the atom label of your molecule, S means scan type job, 10 -0.10 means ten steps with an increase of 0.10 angstroms. You need to adjust these parameters to your problem.
After the scan finishes, select the highest point and run TS optimization.
Hope this is helpful.
Best, Pablo
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E = ∆Vi ∆L/L0, where E is the deformation energy, and ∆Vi is the energy change of the ith band with lattice dilation ∆L/L0.
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Hello Sadhana Matth
This deformation energy is the difference between the energy of the equilibrium structure and a distorted structure. Calculate this is very easy, the difficult part is to set the correct distortion. Eg:
You have a cubic structure, with lattice parameter optimized a=b=c = 3.56, and then you calculate the energy of this structure, let's say it's -12.4 eV. If you change your lattice parameter to 3.7, and calculate the energy again, it would not be -12.4 eV. So you can calculate this energy difference, but the difficult part is to know what exactly is the "name" of this distortion. Also, this is not the only possible distortion.
Do you want only to calculate this deformation, or do you want to achieve the calculation of elastic constants, or something else?
Best regards,
Ricardo Tadeu
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Long story short, the VASP manual delineates that the metal-GGA could be utilized for hybrid functional with appropriate Fock operator using AEXX tag.
However, there are no explicit notifications regarding “screened hybrid functional for meta-GGA” such as HSE using HFSCREEN.
Is there any who have a experience for doing screened hybrid functional using meta-GGA (specifically, HFSCREEN)?
Important thing is it works and the result electronic structure is reasonable.
Thanks
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Eui-Cheol Shin ,why unfortunately? have you read carefully the parameters of range-separated part? Just chose meta gga instead of gga to use meta gga with range-separated part.
The accuracy of electronics structure depends on your system. Just do some comparson.
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I am writing a project on electronic structure with a molecular approach and a surface approach (plane waves). I have knowledge of the molecular part, but I am having difficulties describing the project for plane waves. I intend to use Gaussian for molecular structure and Quantum Espresso for plane waves.
I have the methodology for the molecular part and would like to know how to describe the same items for plane waves. Could someone please help me?
Below, I am placing the methodology for the molecular part:
Construction of systems and structural studies Reactivity index calculations (for the molecular part, Condensed Fukui Indices to Atoms are used) Reactivity index calculations (plane waves ???)
Opto-electronic properties (for the molecular area TD-DFT)
In particular, the aim is to evaluate data associated with the energy and spatial distribution of frontier orbitals, local and global density of states, reactivity indices, optical properties of the materials composing the chemical species, in order to establish simple rules for the preparation of materials with optimized properties.
Adsorption study
It is intended to evaluate adsorption processes of chemical species and reactions with the systems of interest through two different approaches: i) calculations of molecular electronic structure and ii) calculations of surface electronic structure.
Calculations of electronic structure Optimization of geometry of adsorbed systems will be performed in a DFT (and/or Hartree-Fock) approach with Grimme corrections to better describe interactions between unbound systems.
And how does the calculation of electronic structure for the surface work?
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Like the previous responder I can only give a partial answer or rather only a comment. Although many attempts have been made in the past, there are no genuine methods to treat surfaces. In a molecular package you treat atoms on an individual basis and you enter their coordinates. In a bulk package, a bandstructure program, you can do so only within the bulk unit cell. The rest of the geometry is controlled by the lattice, representing a 3-dimensional infinite periodicity. For the surface this periodicity needs to be broken in the direction perpendicular to the surface. Plane waves are just mathematics and the powertool there is the Fourier transform. In its integral representation it can handle any problem, also a cluster of atoms and mathematically this is even an easy process. It is a matter of numerical efficiency that this s not done in practice. The problem is the contribution of the nuclear cores to the potential. Since this contribution is singular at the core site, it requires an excessive amount of plane waves to require enough
accuracy. A technical way out is to replace the potentials by pseudopotentials, free from singularities, but still yielding good enough results. In the family of bandstructure methods, CLOPW is a good alternative, bu it has never been developed to a complete package, If you manage to use/develope the plane wave representation into a proper instrument to handle true surfaces that would be a good thing, but as far as I know that has not been done.
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TiF4 and HfF4 are interesting materials due to their low melting temprature, and they maybe used in electronic devices. But the study about their electronic prpperties is very rare.
Do you know the electronic structure of these materials, including their bandgap structure, the energy positions of conduction and valence band edge, Fermi level, etc.? Thank you!
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Will the Ti and F exist as ionic or molecules in the vapor phase when it heated in vacum?
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I'm trying to solve the integral shown in the picture.
I'm using python libraries to plot the integrand (numpy and matplotlib.pyplot), as well as scipy.integrate library to solve the integral.
However, I'd like to see other suggestions or tips to solve this problem.
Any comment will be well appreciated.
Thanks, Pablo
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In a degenerate system, for calculating the DOS effective mass, how can we find the degeneracy and also how can we determine the three directions (one longitudinal and one transverse) at the VBM. For DOS effective mass only one band is enough or do we need to consider the average of the degenerate bands. I have attatched a file of bandstructure which shows VBM at X (Source: Y. O. Ciftci, S. D. Mahanti, ‘Electronic structure and thermoelectric properties of half-Heusler compounds with eight electron valence count KScX (X = C and Ge)’ J. Appl. Phys. 119, 145703 (2016) What will be the three directions and degeneracy for this particular bandstructure.
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Mohamed Ali Lahmer Thankyou Sir for your reply. Along X-W how can we take the K- points from the data file because in the X-W direction if we consider the heavy hole band (band 1), then we get same value of effective mass if we take the same number of K -points for non-linear fitting.
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I heard that the electronic structure of the precursor is changed and the valence state difference occurs due to metal ion doping, so I wonder how this improves structural stability.
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Dear Hyowon Jang.
I think it is a principal of least action known from mechanics.
If we assume that space is discrete on fundamental level and consists of action quanta h (recall the formula for the photon energy ε=hν), and the outer electrons in an atom distort the surrounding space the most, then there will be nothing surprising in the fact that the valence electrons of neighboring atoms combine to distort the surrounding space together in a minimal way. This enhances the interaction of atoms with each other, makes the crystalline structure of the substance more ordered and strong.
You can better understand what was said if you get acquainted with my last year's report on how the thermal expansion of the elements of the periodic table in the solid state occurs and depends on:
Yours sincerely, Dulin Mikhail.
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It is commonly believed that the concept of electron spin was first introduced by A.H. Compton (1920) when he studied magnetism. "May I then conclude that the electron itself, spinning like a tiny gyroscope, is probably the ultimate magnetic particle?"[1][2]; Uhlenbeck and Goudsmit (1926) thought so too [4], but did not know it at the time of their first paper (1925) [3]. However, Thomas (1927) considered Abraham (1903) as the first to propose the concept of spinning electron [5]. Compton did not mention Abraham in his paper "The magnetic electron" [2], probably because Abraham did not talk about the relationship between spin and magnetism [0]. In fact, it is Abraham's spin calculations that Uhlenbeck cites in his paper [4].
Gerlach, W. and O. Stern (1921-1922) did the famous experiment* on the existence of spin magnetic moments of electrons (even though this was not realized at the time [6]) and published several articles on it [7].
Pauli (1925) proposed the existence of a possible " two-valuedness " property of the electron [8], implying the spin property; Kronig (1925) proposed the concept of the spin of the electron to explain the magnetic moment before Uhlenbeck, G. E. and S. Goudsmit, which was strongly rejected by Pauli [9]. Uhlenbeck, G. E. and S. Goudsmit (1925) formally proposed the concept of spin[3], and after the English version was published[4], Kronig (1926), under the same title and in the same journals, questioned whether the speed of rotation of an electron with internal structure is superluminal**[10]. Later came the Thomas paper giving a beautiful explanation of the factor of 2 for spin-orbit coupling[11]. Since then, physics has considered spin as an intrinsic property that can be used to explain the anomalous Seeman effect.
The current state of physics is in many ways the situation: "When we do something in physics, after a while, there is a tendency to forget the overall meaning of what we are working on. The long range perspective fades into the background, and we may become blind to important a priori questions."[11]. With this in mind, C. N. Yang briefly reviewed how spin became a part of physics. For spin, he summarized several important issues: The concept of spin is both an intriguing and extremely difficult one. Fundamentally it is related to three aspects of physics. The first is the classical concept of rotation; the second is the quantization of angular momentum; the third is special relativity. All of these played essential roles in the early understanding of the concept of spin, but that was not so clearly appreciated at the time [11].
Speaking about the understanding of spin, Thomas said [5]: "I think we must look towards the general relativity theory for an adequate solution of the problem of the "structure of the electron" ; if indeed this phrase has any meaning at all and if it can be possible to do more than to say how an electron behaves in an external field. Yang said too: "And most important, we do not yet have a general relativistic theory of the spinning electron. I for one suspect that the spin and general relativity are deeply entangled in a subtle way that we do not now understand [11]. I believe that all unified theories must take this into account.
What exactly is spin, F. J. Belinfante argued that it is a circular energy flow [12][15] and that spin is related to the structure of the internal wave field of the electron. A comparison between calculations of angular momentum in the Dirac and electromagnetic fields shows that the spin of the electron is entirely analogous to the angular momentum carried by a classical circularly polarized wave [13]. The electron is a photon with toroidal topology [16]. At the earliest, A. Lorentz also used to think so based on experimental analysis. etc.
Our questions are:
1) Is the spin of an electron really spin? If spin has classical meaning, what should be rotating and obeying the Special Relativity?
2) What should be the structure of the electron that can cause spin quantization and can be not proportional to charge and mass?
3) If spin must be associated with General Relativity, must we consider the relationship between the energy flow of the spin and the gravitational field energy?
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* It is an unexpectedly interesting story about how their experimental results were found. See the literature [17].
** Such a situation occurs many times in the history of physics, where the questioned and doubted papers are published in the same journal under the same title. For example, the debate between Einstein and Bohr, the EPR papers [18] and [19], the debate between Wilson and Saha on magnetic monopoles [20] and [21], etc.
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Reference:
[0] Abraham, M. (1902). "Principles of the Dynamics of the Electron (Translated by D. H. Delphenich)." Physikalische Zeitschrift 4(1b): 57-62.
[1] Compton, A. H. and O. Rognley (1920). "Is the Atom the Ultimate Magnetic Particle?" Physical Review 16(5): 464-476.
[2] Compton, A. H. (1921). "The magnetic electron." Journal of the Franklin Institute 192(2): 145-155.
[3] Uhlenbeck, G. E., and Samuel Goudsmit. (1925). "Ersetzung der Hypothese vom unmechanischen Zwang durch eine Forderung bezüglich des inneren Verhaltens jedes einzelnen Elektrons." Die Naturwissenschaften 13.47 (1925): 953-954.
[4] Uhlenbeck, G. E. and S. Goudsmit (1926). "Spinning Electrons and the Structure of Spectra." Nature 117(2938): 264-265.
[5] Thomas, L. H. (1927). "The kinematics of an electron with an axis." The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science 3(13): 1-22.
[6] Schmidt-Böcking, H., L. Schmidt, H. J. Lüdde, W. Trageser, A. Templeton and T. Sauer (2016). "The Stern-Gerlach experiment revisited." The European Physical Journal H 41(4): 327-364.
[7] Gerlach, W. and O. Stern. (1922). "Der experimentelle Nachweis der Richtungsquantelung im Magnetfeld. " Zeitschrift f¨ur Physik 9: 349-352.
[8] Pauli, W. (1925). "Über den Einfluß der Geschwindigkeitsabhängigkeit der Elektronenmasse auf den Zeemaneffekt." Zeitschrift für Physik 31(1): 373-385.
[9] Stöhr, J. and H. C. Siegmann (2006). "Magnetism"(磁学), 高等教育出版社.
[10] Kronig, R. D. L. (1926). "Spinning Electrons and the Structure of Spectra." Nature 117(2946): 550-550.
[11] Yang, C. N. (1983). "The spin". AIP Conference Proceedings, American Institute of Physics.
[12] Belinfante, F. J. (1940). "On the current and the density of the electric charge, the energy, the linear momentum and the angular momentum of arbitrary fields." Physica 7(5): 449-474.
[13] Ohanian, H. C. (1986). "What is spin?" American Journal of Physics 54(6): 500-505. 电子的自旋与内部波场结构有关。
[14] Parson, A. L. (1915). Smithsonian Misc. Collections.
[15] Pavšič, M., E. Recami, W. A. Rodrigues, G. D. Maccarrone, F. Raciti and G. Salesi (1993). "Spin and electron structure." Physics Letters B 318(3): 481-488.
[16] Williamson, J. and M. Van der Mark (1997). Is the electron a photon with toroidal topology. Annales de la Fondation Louis de Broglie, Fondation Louis de Broglie.
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[17] Friedrich, B. and D. Herschbach (2003). "Stern and Gerlach: How a bad cigar helped reorient atomic physics." Physics Today 56(12): 53-59.
[18] Bohr, N. (1935). "Can quantum-mechanical description of physical reality be considered complete?" Physical review 48(8): 696.
[19] Einstein, A., B. Podolsky and N. Rosen (1935). "Can quantum-mechanical description of physical reality be considered complete?" Physical review 47(10): 777.
[20] Wilson, H. (1949). "Note on Dirac's theory of magnetic poles." Physical Review 75(2): 309.
[21] Saha, M. (1949). "Note on Dirac's theory of magnetic poles." Physical Review 75(12): 1968.
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You are most welcome, Prof. Chian Fan
In Theoretical Solid State Physics are the so called noncentrosymmetric crystals, for them spin is not anymore a good quantum number, and a new term is introduce: Helicity.
Therefore your question is relevant.
Kind Regards.
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Density functional theory (DFT) gives the ground state electronic structure of a system (material). There are packages like QUANTUM ESPRESSO, VASP, etc., that calculates the electronic structure based on the DFT. I am wondering if it is possible to calculate the electronic band structure at a particular temperature in these codes so that the evolution of the band structure with temperature can be seen?
Any kind of help is highly appreciated.
Thank you !
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To calculate and compare the electronic band structure at different temperatures in the QUANTUM ESPRESSO code, you can follow these steps:
  1. Generate the input file for your system using the appropriate program, such as pw.x or bands.x.
  2. Modify the input file to include the temperature you wish to calculate the band structure for. This can be done by adding a 'occupations' keyword in the &SYSTEM namelist, followed by 'smearing' and 'degauss' keywords to specify the smearing method and broadening parameter.
  3. Run the calculation at the desired temperature using the appropriate command, such as mpirun -np [number of processors] pw.x < input_file > output_file.
  4. Repeat steps 2-3 for other temperatures you wish to compare.
  5. Once all calculations are completed, use a visualization tool such as XCrySDen or VESTA to visualize and compare the band structures.
It is important to note that the band structure can be affected by various factors such as the choice of exchange-correlation functional, pseudopotentials, and k-point mesh. Therefore, it is recommended to perform convergence tests to ensure the accuracy and reliability of the results.
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Can someone provide or give me an example how the VASP WAVEDER file looks like?
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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.
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Quantum Espresso is a popular open-source software package for quantum simulations of materials. It is widely used by researchers in material science to study the electronic, structural, and thermodynamic properties of materials. In this review, we will discuss some recent research works that have successfully utilized Quantum Espresso to solve complex material science problems. We will also discuss the limitations of the software package and potential avenues for future research in this field.
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in terms of electron structure and orbital hybridization
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This is essentially due to the difference between the 2p orbital energies in the Boron and Nitrogen atoms. A detailed discussion, with a comparison with the case o graphite is given in the beautiful book by F. Bassani and
G. Pastori Parravicini, "Electronic states and optical transitions in solids", published by Pergamon press.
A pdf copy of the book can be found under:
the science of the solid state - general editor: br pamplin
📷
ResearchGate
https://www.researchgate.net › post › download
📷
PDF
OPTICAL TRANSITIONS. IN SOLIDS by. F. BASSANI. Professor of Solid State Physics, University of Rome ... Electronic states and optical transitions in solids.
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In the Moller-Plesset Perturbation Theory, the second order correction to the ground state energy can be divided into a same-spin and an opposite-spin terms by integrating the spin out. This allows to get integrals using only space orbitals, just as specified on the psi4 website here: https://psicode.org/psi4manual/master/dfmp2.html
I was able to get the expresion for opposite spins. However, when trying to perform the integration for same spins, I haven't been able to get rid of one of the terms and get the expresion I want. This happens because all four orbitals have the same spin function, so every term should mantain after the integration.
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Something’s obviously missing here. The terms that describe the contribution of ``opposite spins" can come from, either the sector of total spin-1, or the sector of total spin-0. The terms that describe the contribution of ``same spins" can only come from the sector of total spin-1. So the statement that the second order correction can be divided in the way described is incomplete, because it doesn’t take into account the total spin. Two spin-1/2 combine to a spin-1 sector and a spin-0 sector.
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What specifications of laptop arerequired to run long electronic structure and optical properties calculations i.e., hybrid functional methods. Kindly share experience.
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Hello Aritra,
As Philip has said, you need plenty of RAM...I mean plenty. I have 32 GB DDR5 and corei7 12th gen CPU but it is still not enough. I am planning to increase the RAM size once the prices go down. However, when doing optimization, you can set the strategy to 'memory' as this will minimize the RAM requirements during the calculations (this is slower, but it gets the job done).
All the best.
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I am quite new to quantum chemistry calculations and I am trying to calculate the electronic structure of a single 102 atom organic molecule using ORCA software dft functionality. For other codes such as VASP and quantum espresso there is a k points directive that specifies the bloch vectors for band structure calculations of periodic structures. If I just put the geometry optimized single molecule structure to ORCA with B3LYP hybrid GGA, I get the required data, but I don't know if I am doing something wrong. Do I need to specify somewhere in the input file that my molecule is not periodic?
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Unlike periodic code such as CP2K, Quantum ESPRESSO, etc., ORCA can only calculate isolated systems, so you do not need to specify k-point at all. Despite ORCA can also study bulk or surface systems based on properly constructed cluster model, it is still essentially isolated problem.
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Hello all, I'm attempting to analyze the effect of defects on the electronic structure by adding them into a 4x4x4 supercell and looking at the band diagrams. I've only done band calculations for unit cells before and so wanted to clarify a couple of things. I know introducing the defects will break my symmetry (cubic) but I thought that it will still be 'near cubic' symmetry and that I could still treat it as cubic and get meaningful information by looking at those lines of symmetry (gamma to X, X to M, M to Gamma, Gamma to R, R to X and R to M). I expected to see 4x repeats along each line of symmetry due to using the supercell instead of the unit cell, but that's not what I got. Also I'm realizing that since I have an even number of super cells 0.5 0.5 0.5 is not the same point as it would be for a unit cell. Does anyone have a source for how to address this or do I just need to go through all of the geometry shifting in K Space manually? I found a couple of old links but they're all broken.
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I know that at nanoscale conductance is quantized and is determined by transmission probability and number of transmission channels (G value). I know that using uncertainty principle we can derive how I/V becomes 2e^2/h. However, I am a little confused by the zero bias and finite bias conductance. Does zero bias conductance mean that even if we do not apply any voltage, current would still flow?
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I can help as per my limited knowledge. You can post your question here, or start a new thread.
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Dear all, I am studying electronic structure of quantum dots using castep. And I would like to passivate the dangling bonds with hydrogen atoms, but as mentioned in the attached papers,there are two kinds of hydrogen atoms,real one and pseudo one.I think the usual way in castep is using real hydrogen atoms. And I would like to know whether we can use pseudo one in castep?
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The usual method is to use the hydrogen pseudopotential, and then to provide a fractional "mixture weight" for the pseudohydrogen atoms, e.g. in the cell file you might have
%block positions_frac
H 0.0 0.0 0.0 MIXTURE=(1 0.75)
%endblock positions_frac
To place 3/4 of a hydrogen at the origin. I'm not sure that we allow the mixture to go above 1 though, so you might not be able to have 1.25, as is used in parts of the paper you attached.
The alternative would be to create a pseudohydrogen pseudopotential, which you could just use like any other potential in CASTEP. I'm not sure whether the safety checks in CASTEP would let you have a fractional nuclear charge, but it might be worth investigating.
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Could someone help me, I have a cif file and I want to perform electronic structure calculations in abinit or qe, however, when viewing the cif file, it presents several identical structures spliced together, and with many hydrogen atoms (I'm not sure if it's hydrogen), Could someone help me or guide me on how to clearly see that structure. Thanks in advance
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Many software can visualize cif file. I think the VESTA (https://jp-minerals.org/vesta/en/) is suitable for visualizing the cif file.
Then, you can check if there are some atoms having less than lower than 1.0 of occupancy (in case of the structure has low crystallinity). In VESTA, we can detect them by non-full colored atoms (half or quarter or others depending on the occupancy). For electronic structure calculation, you need to fix the low occupancy atoms. If you can provide the cif file, I can help to fix the structure using VESTA.
I am not sure that hydrogen can be detected in XRD. Thus, I don't have any suggestions about it.
Best regards,
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Hello everyone.
I was wondering if there is litterature that study the influence of the hydrostatic pressure on the electronic band structure from a theoretical point of view. I've found many papers that shows the evolution of the band gap and the electronic structure with the pressure but not one with a theoretical study of that.
Best wishes.
Benjamin Martin.
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Dear Benjamin Martin in addition to the previous interesting post, I can add a few words just in case the model refers to the electrons-free model for a 3D Fermi surface, under external pressure P, the so-called electronic 2-1/2 electronic phase transition (Lifzhits transition -LT)
LT can happen and is due to the change of the topology of the 3D Fermi surface in normal metals or graphene. There are other ones, but this LT is investigated now mostly in the normal state of some heavy fermions.
Please read the following reference, it is an open-access article for the case of graphene, it is very instructive, theoretically consist in the calculation of an additional term to the Gibbs free energy (Omega free potential):
Best Regards.
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Hello everybody. I want to simulate the effect of Ag on the structure and electronic properties of CdTe. For this, I chose the cubic structure of CdTe and calculated the electronic properties in the Wien2k package. The band gap obtained is 1.51 eV (mBJ), which is in agreement with experiment. Then I replaced one Ag atom with Cd in the CdTe supercell with a size of 2 * 2 * 2. After optimization, I repeated the calculations, but at the same time I got a band gap of 0 eV. I thought that the problem was in optimization through Wien2k and decided to ask a friend from Russia for help to optimize the system on VASP, but after optimization on VASP nothing changed.
Please help me to properly optimize the structure and simulate the effect of Ag on the electronic structure of CdTe.
Thank you in advance
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Hi Nematov,
It is probably not a problem. The addition of Ag may introduce states at the Fermi level, and as such, the Ag-doped CeTe supercell system is metallic. You can use DOS and PDOS plots to verify.
Hope this helps.
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I am trying to learn Gaussian using the book Exploring Chemistry with Electronic Structure Methods. The book suggests using APFD model but every time I use it, an error appears (see below)
Server Error #2070
The processing of the last link ended abnormally.
All processing has been aborted.
I am still new to this, so troubleshooting is very difficult. Please help!
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First, you can find if the method is reliable for the sttudy of properties of your molecule (or related) in the literature. In addition, test computations in some molecular properties such as vibrational frequencies, UV-absorption, can help you with the selection of the m,ethod, expecting a low deviation with respect to empirical parameters if available.
APFD is not a popular functional, and it doesn't exhibit good performance (see e.g. Phys. Chem. Chem. Phys., 19, 32184 (2017)). B3LYP-D3(BJ)/6-311G** is not only popular but also robust. Many papers showed that if frequency correction factor is employed, B3LYP is still one of the best functionals for evaluating vibrational frequencies, at least for organic systems (see e.g. J. Chem. Theory Comput. 2010, 6, 2872–2887).
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I am currently running some QTAIM topology analyses of main group compounds to elucidate their electronic structures. In particular I would like to use delocalisation indices (DI) to quantify the amount of single- or double bond character in these species. The situation is complicated by the presence of non-nuclear attractors at the centre some of the bonds, preventing a direct interpretation of DI values. It seems possible to calculate an "effective" delocalisation index for the two atoms that are bonded but have a NNA located between them.
I read a footnote in a paper (Chesnut, Heteroatom Chemistry 2002, 13, 53) that mentions
"A non-nuclear attractor (NNA) is found in the Si Si bond midpoint in this molecule. An effective Si Si delocalization index is determined by presuming that half of the NNA belongs to each silicon atom. This removes the NNA from the picture while preserving the sum of the Fii and Fij terms."
I am a bit stuck at the moment, trying to reproduce the numbers for some of the compounds from the referenced paper. Has anyone experience with such situations and would be able to provide some more detail or a protocol on how to exactly obtain these effective DIs?
I'd appreciate any input. Thanks in advance.
Kind regards,
Tobias
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Dear Tobias Krämer sorry to see that your interesting technical question has received only a copy-and-paste answer which has not much to do with your original question. We are synthetic inorganic chemists, so I'm absolutely no expert in this area of theoretical chemistry. However, in my experience it often pays off to search the "Publications" and "Questions" section of RG for relevant literature references and closely related technical questions. This way I found for example the following potentially useful article:
On the presence of non-nuclear attractors in the charge distributions of Li and Na clusters
This paper is freely accessible as public full text on RG. I'm not even sure how relevant this is to your question, but I think you should give it a try. Many relevant references have been posted by RG members, some of them even as public full texts.
Good luck with your work and best wishes, Frank Edelmann
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Dear Colleagues,
I want to calculate the Electronic structure distribution and the structure of Simple molecules like H2 , H2O and NH3.
I want to calculate by first principle approach.
Please suggest me which process should I use for this.
Thanks and Regards
N Das
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Dear Prof. Dr. Nityananda Das,
As my experience in computational chemistry. You should use GaussView software to model and Gaussian software to calculate through some keywords. Density Functional Theory (DFT) is suitable in your case.
Reference:
Best regards.
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i am using quantum espeesso and need to understand what is k-space and how to set it.
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Almost all materials have crystalline structure. Many of them are polycrystals (they are made from many small crystals) but there are also monocrystals.
A monocrystal repeats at infinity the unit cell (BCC, FCC, HC, etc). This is named the direct lattice. There are not many unit cells in nature.
The crystalline structure can be viewed using X ray diffraction (XRD). At XRD you view the reciprocal lattice. The BCC direct lattice appears as FCC, the FCC direct latttice appears as BCC, etc
Therefore the reciprocal lattice is the lattice that you view using X ray diffraction.
given a1, a2, a3 the vectors of the unit cell (say cubic) in direct space the vectors of the reciprocal cell are
b1 = (a2 x a3) / [a1(a2 x a3)]
b2 = (a3 x a1) / [a1(a2 x a3)]
b3 = ...
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We know that the density functional theory (DFT) is nicely applicable for finding the material's electronic structure and related properties.
Is it possible to find the optical properties as well? If possible then please help me by sharing some well-written examples.
Thanks in advance.
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To complete excellent answers from Andrey Degtyarev and Ivan I Yakovkin , Density Functional Theory is well-defined for giving you optical properties at relative low-cost. There are some publications on the subject (mainly on materials and optoelectronics) such as these latter recently published I have in my personal bibliography:
Concerning the software, ORCA is really good (just my point of view) and tomorrow (July, 1st 2021) will be released ORCA 5.0 with many improvements and new possibilities (let's check it out !). By my side I know CASTEP is also a good software commonly used for this purpose.
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It is know that XPS (X-ray Photoelectron Spectroscopy) gives elemental composition (what elements are present) and the chemical state/s (what other elements they are bonded to). I wish to know how XPS helps in knowing overall ''electronic structure'' and ''density of electronic states'' in the material being characterized.
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Aman Arora XPS characterizes the surface of a material rather than the bulk. The surface and the bulk of a material must be different in a mixture or in the presence of air or moisture.
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Hello,
I am a newbie in theoretical solid-state physics. I am now trying to calculate
electronic energy-band structures using Quantum ESPRESSO solver.
The relevant cell (lattice) has following conditions;
1. This unit cell is described by three lattice vectors
1. They are, v1=(-0.5,0.5,0.0), v2=(0,1,-1), v3=(-0.5,0.5,1.0)
1. vectors are normalized with a-lattice length
1. This unit cell has eight-atoms
1. four cations (C) and four anions (A)
1. The system has effective cubic symmetry
Based on these conditions, I wrote a part of input file as below. C and A respectively
stand for cation and anion. I thought that the atoms should be just allotted
on apexes (vertices) of a cube. I wonder this Is correct?
Thanks for any advices. Answers using cif or VASP Poscar formats are also
very welcome so that they can be converted with cif2cell or Vesta.
CELL_PARAMETERS -0.5 0.5 0.0 0.0 1.0 -1.0 0.5 0.5 1.0 ATOMIC_POSITIONS C 0 0 0 C 1 1 0 C 0 1 1 C 1 0 1 A 1 0 0 A 1 1 1 A 0 0 1 A 0 1 0
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Use VESTA software to create your lattice. There is an option of exporting the .cif file as output. This is the output for the QE. If you are looking for new structures this will help.
(or)
If you are looking for old structures/ combinations use materials project website for the same.
Hope this helps.
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Dear all,
We came across an organic compound that shows possibly a very large Stokes shift and wonder what is the largest number in eV ever reported. Any suggestion from the experts?
Thanks for your help!
Keisuke
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Dear Keisuke Kajima,
an overview on a number of dyes with larges Stokes' shift can be found in Sednew et al. "Fluorescent dyes with large Stokes shifts for super-resolution optical microscopy of biological objects: a review"
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We all know that when solving the wave function of an electron, both the initial and boundary conditions can influence the energy state structure of the electron. We also know that the boundary condition is somehow determined by the particle size and its surface. So, how does the atomic structure of surface finally affect the electronic structure of a nanoparticle? Are there some specific examples to explain it?
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Dear Zeyu Zhuang for nanophysics, I don't know references about SES developments.
But, in general, the physics of the surface electronic states (SES) for 3D crystal semiconductors was developed a long time ago by the USSR physicist I. Tamm (1932) & the US physicist W. Shockley (1939).
The Wikipedia commons article points correctly to these 2 physicists, pioneers in SES.
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Without consulting the phase diagram (of still unexplored alloy systems) , how one can predict which alloying addition in an element would produce intermetallics with some given compositions? For example, how would one say that C is (one of the ) most crucial alloying element of Fe and Si of Al, with just consulting the periodic table and electronic structure? Of course, there is no objective definition of "most useful" alloy- the same alloying element raising strength would not be the one that raises ductility.
Some special properties can be reasoned as
  • Strength and ductility- estimable by formulae for Solid solution, precipitation, dispersion and grain boundary strengthening- but how to physically link solid solution strengthening or Pierres-Nabarro stress of an alloy from electronic structures? Can ductility in these cases also be estimated from first principles?
  • As for thermal and electrical properties, the phonon/electron scattering data may be generalizable for a bigger group of alloys to find out thermal and electrical conductivities- but how? The conductivity drop can be compared between solid solutions and intermetallic formers, but how to be sure that the alloy formed would be of any calculated phase distribution and of this certain electrical conductivity from first principles?
  • Corrosion resistance- The Pilling-Bedworth ratio is related to adherence of oxide or other protective films of metal- but how alloy composition can be related to strength, adherence and composition, and ultimately, reactivity of the protective film? Relative position of EMF series can be, of course, estimated from total lattice energy, ionization energy and hydration energy.
I have just mentioned the two extremes of intermetallic formation and complete immiscibility- (complete miscibilities are well explained by hume-rothery rules, and ultimately also depends on how one objectively measures electronegativity), because there is, to my knowledge, no concrete rules to predict nature of phase diagram (isomorphous or eutectic or peritectic or monotectic or...) between two elements, let alone two compounds.
While electronic band structures of an element are available to be computed by standard methods, there is no systematic way to predict crystal structure or computed thermodynamic properties from composition alone (that are vastly generalizable).
I think there are scientific factors like cosmic and geological abundance, position in EMF series (and hence ease of extraction) as well as socioeconomic factors like market demand as choice for an alloying element. But is it possible to locate useful alloying elements for any of the elements with same unified rationale? (say of Mo, Ru, Rh, Pm, Tl)
And again, is there seemingly any way to tell which pair of metals or elements would be completely immiscible in solid states?
In theory, it is all about minimizing gibbs free energy, and from specific heat data of a solid, one can extract both values of enthalpy and entropy term. If this technique is generalizable for any solid, then why it is not used pervasively? is it because we just cannot predict the specific heat without crystal structure, and from chemistry alone, there is no way to predict crystal structure? Is it not possible to obtain Gibbs free energy of overlapping electron orbitals solely from schrodinger's equation, just like total energy is extracted from eigenvalues of Hamiltonian?
Hume-Rothery rules or Darken-Gurry maps are good starting points, but not good enough. Machine-learning based prediction can make things more systematic but without potentially answering the "why"s in a language familiar to humans . Interatomic potentials are scarce and very rarely generailizable for any group of elements (like Lennard-Jones for gases). My question finally boils down to- prediction of effect of alloying of any two elements, and ultimately composition to crystal structure and phase diagram calculation from first principle- is it even partially possible, if yes, how?
....................................................................................................................................
P.S: Honorable Researchers, Please provide related research papers related to these questions, along with your valuable feedbacks. I am unashamedly open to admit my severe incompleteness of knowledge, and I am far from being master of these field of science. SO feel free to point out where I have mistaken, and also show me approach to synthesize such vast scientific knowledge into a coherent framework.
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See some of my related questions
  1. https://www.researchgate.net/post/What_can_be_theoretical_reason_for_these_patterns_of_Crystal_structures_in_periodic_table?_ec=topicPostOverviewAuthoredQuestions&_sg=qQHz-0jUZMihIai8gwUp1voPk-Tw5-YCl59uQgT88757TE3f6VQz9s6UGLULozUurbHcPQ3VJnXpw-YC
  2. https://www.researchgate.net/post/Is_there_any_special_rule_to_find_out_possible_room-temperature_stable_silicates_chemical_composition_if_not_crystal_structure_itself?_ec=topicPostOverviewAuthoredQuestions&_sg=qQHz-0jUZMihIai8gwUp1voPk-Tw5-YCl59uQgT88757TE3f6VQz9s6UGLULozUurbHcPQ3VJnXpw-YC
  3. https://www.researchgate.net/post/How-etchant-for-a-particular-alloy-system-is-developed-Can-it-be-estimated-from-first-principle-physics-chemistry-and-metallurgy?_ec=topicPostOverviewAuthoredQuestions&_sg=qQHz-0jUZMihIai8gwUp1voPk-Tw5-YCl59uQgT88757TE3f6VQz9s6UGLULozUurbHcPQ3VJnXpw-YC
  4. https://www.researchgate.net/post/What_are_the_factors_molecular_crystalline_structure_related_that_affect_refractive_index_of_ceramics_glasses_and_polymers_How?_ec=topicPostOverviewAuthoredQuestions&_sg=qQHz-0jUZMihIai8gwUp1voPk-Tw5-YCl59uQgT88757TE3f6VQz9s6UGLULozUurbHcPQ3VJnXpw-YC
  5. https://www.researchgate.net/post/How-computational-phase-diagram-techniques-can-find-Gibbs-free-energy-of-a-crystalline-phase?_ec=topicPostOverviewAuthoredQuestions&_sg=qQHz-0jUZMihIai8gwUp1voPk-Tw5-YCl59uQgT88757TE3f6VQz9s6UGLULozUurbHcPQ3VJnXpw-YC
  6. https://www.researchgate.net/post/How_can_symmetry_of_a_crystal_can_be_found_out_from_solely_electronic_structure_of_constituent_atoms?_ec=topicPostOverviewAuthoredQuestions&_sg=qQHz-0jUZMihIai8gwUp1voPk-Tw5-YCl59uQgT88757TE3f6VQz9s6UGLULozUurbHcPQ3VJnXpw-YC
  7. https://www.researchgate.net/post/How_binary_solution_models_were_derived_from_first-principle_thermodynamics?_ec=topicPostOverviewAuthoredQuestions&_sg=qQHz-0jUZMihIai8gwUp1voPk-Tw5-YCl59uQgT88757TE3f6VQz9s6UGLULozUurbHcPQ3VJnXpw-YC
  8. https://www.researchgate.net/post/How_crystal_structure_of_a_one-element_metallic_molecular_crystal_under_a_given_T_P_can_be_estimated?_ec=topicPostOverviewAuthoredQuestions&_sg=qQHz-0jUZMihIai8gwUp1voPk-Tw5-YCl59uQgT88757TE3f6VQz9s6UGLULozUurbHcPQ3VJnXpw-YC
  9. https://www.researchgate.net/post/What-decides-lowest-free-energy-crystal-structure-of-a-solid-at-a-given-temperature-and-pressure?_ec=topicPostOverviewAuthoredQuestions&_sg=qQHz-0jUZMihIai8gwUp1voPk-Tw5-YCl59uQgT88757TE3f6VQz9s6UGLULozUurbHcPQ3VJnXpw-YC
  10. https://www.researchgate.net/post/Why-metal-valency-affects-mutual-solubility?_ec=topicPostOverviewAuthoredQuestions&_sg=qQHz-0jUZMihIai8gwUp1voPk-Tw5-YCl59uQgT88757TE3f6VQz9s6UGLULozUurbHcPQ3VJnXpw-YC
Thank you very very much to hold your patience to read the whole post :)
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You asked a very broad question, but I hope my answer will undercover the understanding of some of the subquestions =)
Due to DFT is a tool, which operates with small atomic systems up to a couple of hundreds of atoms (you can consider and larger cell up to 400-500 atoms, but you lose in CPU time or accuracy of calculations), you can consider either single-phase atomic structures (solid solution or stoichiometric phase) or supercells with an interface between two different phases.
As for mechanical properties, you can estimate them using special equations, which have bulk moduli of considered phase as input parameters.
Bulk moduli can be easily calculated using DFT.
For example, you can read how I recently did that for Mo-Ni-B-C cermet.
From experimental data and mechanical properties measurements, we obtained that precipitation of κ-phase Mo10Ni3C3B decreases a hardness with increasing of stress intensity factor.
Then we calculated elastic constants of precipitated Mo10Ni3C3B and existed Mo2NiB2 and Mo2C phases and estimated bulk properties and hardness using special equations (See Supplementary https://lettersonmaterials.com/Upload/Journals/32862/boev_et_al_supplementary_material.pdf).
The bulk modulus, shear modulus, Young’s modulus, and Poisson’s ratio were estimated according to Hooke’s law and the Voigt-Reuss-Hill (VRH) model. For hexagonal polycrystalline crystal:
B=[2(C11+C12)+4C13+C33]/9,
G=(C11+C12+2C33−4C13+12C44+12C66)/30,
E=9BG/(3B+G),
ν=(3B−2G)/2(3B+G),
The Vickers hardness (HV) was calculated according to the empirical formula: HV= 2(K^2 G)0.585−3,
K=G/B
So, we obtained that the new Mo10Ni3C3B phase has a lower hardness and is able to decrease the hardness of the whole material.
Ratio B/G is an indicator for ductility properties.
Bond analysis using electron localization functions (provided in VASP) allowed us to define the nature of the bonding in considered phases.
Covalent bonding means stronger hardness and metallic bonding - more ductility/plasticity.
Also, it is important to analyze the anisotropy factors. That will be able to undercover different useful things.
If you have any questions, do not hesitate to ask me =)
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and I claim no originality of creating the image)
The reason of the following structures are given in wikipedia, with some exceptions, at room temperature.
  • usually BCC structure of alkali metal, group 5 (VB) and 6 (VIB) plus Mn and Fe
  • usually FCC structure of Noble Gases (not helium), and near right end of transitional elements?
  • usually HCP structure of group 3 (IIIB), 4 (IVB) and 12 (IIB) and also group 7(VIIB) and 8 (VIIIB, left group) except for first two (Fe, Mn)
  • HCP and DHCP of lantahnides and actinides?
If all of these can be explained in terms of electronic configuration , then a significant electronic-to-crystal structure interrelation in simpler terms can be obtained.
(and possibly, ratio of metallic bandgap or Fermi energy etc. like energy parameters and average electron K.E at room temperature, then I think the correlation would be stronger. Perhaps, if one replaces spherical model of a metallic atom with its feasible 3D dirctional variation of outermost electron shell geometry, the the correlation is likely to be even stronger)
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The trends are well known, but it is difficult to say in a single sentence, why this trends exist. The following can, however, be stated:
-Mn, Fe, Co deviate from the trend because of the magnetic contribution to the thermodynamic functions.
-the total cohesive energy is much larger than the differences between the energies of the crystal structures. So there are non-obvious subtle effects which are responsible for the energy differences and which determine the observed crystal structures. Some quantitative thoughts can be found in
(quick find by google scholar)
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It is hypothesized that the nature/energies/electron distribution of the frontier orbitals of a molecule changes under external field condition. Under applied bias, the molecule can be oxidised/reduced and this changes its electronic distribution and eventually the molecules ability to conduct current. Can we model such an hypothesis using DFT in Turbomole? Some information in this regard is very welcome.
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Almost all quantum chemistry codes support applying external electric field in calculations. My recent work about ultrastrong regulation effect of electric field on various properties of cyclo[18]carbon is a typical example: https://doi.org/10.1002/cphc.202000903.
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Dear Respected Colleagues,
We know Ground state Hydrogen Atom has it's Electronic structure as a spherically symmetric distribution and radially varies as given by 1S wave function.
I want to find the change of electronic structure distribution when two Hydrogen Atoms are taken closer and closer and form a stable Hydrogen Molecule.
Please suggest any method of solving this problem.
Thanks and Regards
N Das
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Dear R Monnier and Tian Lu,
Thanks a lot for helping me with Excellent answers .
Dear Tian Lu,
I am trying to follow your suggestions.
Excellent .
Thanks once again.
Best Wishes
N Das
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Hi everybody, I am a new user wien2k 14. I am trying to optimize the electronic structure of ternary alloy (with 8 atom in the unit cell) but I am not sure about the good k points number.
Thank you.
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It depends on the electronic structure of your system. If there is no partially occupied states (i.e. your system is insulating) then you can use a fairly small number of k-points. On the other hand, if some of the bands are partially occupied (i.e. the system is metallic), then you usually need a larger number of k-points. 'How many more' depends on the size of the system and complexity of the band structure at the Fermi level. In such cases, you may need to do a few test calculations with different sets of k-points to find the optimal k-number. Note that in some cases (mainly cubic systems), shifting the origin of k-mesh can dramatically reduce the number of k-points.
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In most electronic structures the fermi level is always shifted to zero , why ?
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Regarding electronic structure is there any relation to reduction of lattice constants and GGA approach?
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Hi Dr M.A. Hadi,
This fact is directly related to the improper account of electron-electron correlations (hartree and Hartree Fock electron-electron correlations) in the GGA approximation.
GGA under-estimates these correlation and therefore over-estimates lattice parameters and under-estimates energy bandgaps.
LDA approximation gives the reverse results (underestimates lattices parameters and overestimates energy bandgaps) but LDA is often closer to experimental values than GGA.
In fact there several other approximations within DFT-FP as well as DFT-PP approaches, see following references for better insight:
- DFT approximations: Which one to use ? by P. Blaha and F. Tran
- Accurate Band Gaps for Semiconductors from Density Functional Theory Hai Xiao, Jamil Tahir-Kheli, and William A. Goddard, The journal of Physical Chemistry Letters,https://core.ac.uk/download/pdf/4888374.pdf
Good luck and keep safe,
Best regards,
Professor A. Kadri
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I have prepared CeO2 based nano-particles. due to some technical issues some of the properties like electronic structure and magnetic properties are pending. the samples were prepared approximately 6-7 months before. Since nanoparticles have a tendency to agglomerate then for further characterization, may I have to anneal them again?
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thank you, sir. Actually, the sample is prepared before a year. it found in the literature that it gets agglomerate. they are nanoparticles. now I want to study electronic structure. I have doubt may I have to annealed or grind again after a year.
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Dear All
As I am new to research (study of Heusler alloys using DFT) ,I am trying to reproduce the results of the problems already published in research papers. I am currently working on the Heusler Alloy Co2MnSi and trying to find its electronic structure and magnetic properties etc.using Quantum espresso. I have been using different paseudopotentials (Ultasoft as well as Norm conserving) but not getting the lattice parameter correct. Although the magnetic moment is coming out to be accurate. So my question is how one decide which pseudopotential is to be used in a particular problem? And suppose we do not know the experimental values as say it is some novel material which has not been under the experimental lens; then how one go about in choosing a pseudopotential in such a case?
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Thanks a lot Sir for your help.
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To describe optical properties how can we make relation with electronic structure? Can any one provide a good reference?
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Dear Prof. M. A. Hadi, in addition to all the interesting answer of this thread, I will add some worlds for the case of normal metals, the high-frequency properties (called also optical properties) are separate from the low-frequency properties of the light-metal interaction. In the end, I will refer to the relation to the electronic structure.
I elaborate further, for frequencies below the plasma frequency, the refractive index - n is complex, so the wave is attenuated and does not propagate far into the metal.
For high frequencies above the plasma frequency, the refractive index n is real, hereby, the metal becomes transparent and behaves like a non-absorbing dielectric medium.
In addition, I guess, that the optical properties of a normal metal are two (mainly) the reflectivity and the skin depth.
The skin depth in normal metals also can be separated into two regimes, the normal and the anomalous skin effect. The experimental and theoretical work on the study of the Fermi surface of pure metals by the aid of high-frequency size effects relates their electronic structure and the optical properties.
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I know we can edit the layers (and make different cifs) and do the calculation for each layer separately to find their HOMO-LUMO. But I was wondering if there's a way to calculate HOMO-LUMO of each layer, while the layers are stacked in the heterostructure in a single cif. Thanks!
*I'm using Quantum Espresso. But I guess the problem is same the regardless of the code one is using.
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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.
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I'm new to electronic structure calculations. I have been doing some band structure calculations. I am seeing some crossing in the band structure, a pair of crossing actually. I plotted the S{z} component resolved bands also. The points seem to be of same sign of S{z}. So, how do I make sure that a crossing is Weyl point or something else?
P.S. I have done the SOC calculations. Attaching the picture. Look around -0.05meV.
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For reasons I explained above, no I don't think It can be a Weyl node, as long as the bands are of the same spin character. By the way, your energy scale is a bit large, so it is probably better to make sure this is a real crossing and not a tiny gap.
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Do we have a number for DOS (Nv, Nc) for 3D or 2D perovskites? Although I see few papers reporting DOS, I do not find a number. Or maybe I do not find a way to calculate DOS from the plots.
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Dear Prof. Azhar Fakharuddin ,
Last decade, it was common to use tight binding to calculate the DOS of strontium ruthenate, the first perovskite reported as been a superconductor.
Please you can look at the references within the following publication:
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I've tried to find proper answers for it but cannot find one.
1. So the question is that is it possible or reliable to apply external electric field on 3D system in VASP?
There are some works on 2D system with external electric field like graphene, but it seems like there's nothing regarding 3D system.
I found that EFIELD, LDIPOL, IDIPOL, EFIELD_PEAD are key tags to apply external electric field.
However, in the web ( https://www.vasp.at/wiki/index.php/EFIELD ) it states only about slab or molecule model.
Also, EFIELD_PEAD looks like it has no effect on geometry
( https://www.vasp.at/forum/viewtopic.php?t=17390&p=18296 ), only affects to electronic structure.
2. The second question here is that do the other three tags(EFIELD, LDIPOL, IDIPOL) also give changes to electronic structure only or geometrical change also?
Thank you
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It is physically meaningless to apply electric field in a 3D bulk system. Electric filed is by definition a gradient of potential, meaning that It starts from a particular point and ends at another point. In programs like VASP or QE, to model this behavior a saw-tooth like potential is created with two opposite slopes. In the first region the slope of potential is positive starting from the point you define and reaching its maximum at the end point that you again define. From the latter point a new potential with opposite slope is created that linearly reaches zero again at the starting point. This allows to maintain the translational symmetry of the whole Bloch space. Now within the positive slope range you can assume a dielectric slab, thin film or monolayer is placed and vacuum will fill the negative-slope one. Since vacuum contains no charge, then the negative slope potential will have no impact on your calculations. So everything will work just fine.
For a truly 3D system however, you can't separate the positive-slope region from the negative one, as they separately affect parts of your system. Using Poisson equation, it is easy to show the total effect of such an electric field will be Zero! Thus, it makes no sense to do such a thing for bulk systems. Hope this information helps!
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In general the low loss electron energy loss peak contain the information about the electronic structure of materials. From free electron model (Drude Model) the plasmon energy is given by a relation
Ep = sqrt. (ne2h2/ π m)
where,
n = conduction/valence electron density
e= electron (hole) charge
m= electron (hole) effective mass
h= Plank's constant
Once we have "n" values we can calculate Fermi wave vector and followed by Fermi energy. My concern is that, is it applicable for compound like Ni3Al, Ni3Nb and Fe3C, so on, or it is only applicable for solid solution alloys.
Thanks
PS M Jena
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The accuracy of determined Fermi energy level of depends on the energy resolution of the instrument.generally it is 0.5-1eV.
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I am doing research on modifying the bandgap of materials. I would like to know computationally the changes in the electronic structures of the host material with any modification like doping. I want to learn the computational methods available like DFT to calculate the electronic structures. Please suggest some reliable sources from where I can start learning this type of calculations.
Thanks
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refer free resources ...and published papers for symmetry ....
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I want to know where to find the details of calculating electronic structure of a solid state material using DFT in Quantum Espresso. Any reference or site where I can learn this?
I want a detailed lesson on it.
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Hi Vivek,
Please go to the following site: https://github.com/QEF/q-e/releases
After you download, unpack the tar folder. Then most of the folders inside it contain the 'examples' subfolder. You can find examples of every calculation which can be done using QE.
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Hi, I can not optimize a palladium (II) coordination complex in Gaussian 09W, the calculation ends with an error. Should I treat the wave function as an open shell or as a closed shell? Thank you
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I think your additional information code has some mistakes.
How about change your additional information as
Pd 0
lanl2dz
****
S C N H O 0
6-311g(d,p)
****
Pd 0
lanl2dz
maybe the element name problem.
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Hi all.
Although very trendy nowadays, Can DOS for a single molecule provide us any useful information about the electronic structure of that species in bulk.? If yes, can you give some references?
I am doing this calculation using Gaussian 09 on a planar sheet.
Thank you
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DOS map is usually divided into three types: total DOS (TDOS), partial DOS (PDOS) and overlap DOS (OPDOS). All of them can be easily calculated via Multiwfn code (http://sobereva.com/multiwfn) based on .fch file of Gaussian. See Section 3.12 of Multiwfn manual for systematical introduction and Section 4.10 for calculation and analysis examples.
TDOS map of single molecule is useful in intuitively revealing density of distribution of molecular orbitals in different energy regions, and gap is directly visible from this map. In addition, TDOS is very closely related to the photoelectron spectrum (PES) simulated with Koopmans' approximation, see Section 3.12.4 of Multiwfn manual for more detail.
PDOS map is able to vividly exhibit composition of MOs in different energy regions, this is useful in representing and discussing character of various MOs of a molecule.
OPDOS essentially corresponds to Mulliken overlap population between two specific fragments in various MOs, from this map you can graphically understand bonding and anti-bonding effect played by different orbitals in various energy range.
Some papers using various forms of DOS to discuss molecular systems are provided below:
J. Comput. Chem., 33, 580 (2012)
J. Comput. Chem., 38, 1574 (2017)
RSC Adv., 5, 78192 (2015)
J. Mol., Model., 23, 132 (2017)
J. Mol. Struct., 1108, 92 (2016)
RSC Adv., 7, 36038 (2017)
Phys. Chem. Chem. Phys., 19, 23373 (2017)
J. Phys. Chem. A, 121, 4009 (2017)
Struct. Chem., 28, 1935 (2017)
Nat. Comm., 8, 14551 (2017)
J. Phys. Chem. C, 119, 8349 (2015)
J. Inorg. Organomet. Polym., 25, 1502 (2015)
J. Mater. Sci., 52, 9739 (2017)
Synthetic Metals, 226, 129 (2017)
J. Mol. Model., 23, 316 (2017)
AIP Adv., 6, 125123 (2016)
Int. J. Quant. Chem., 117, e25449(2017)
Comput. Theor. Chem., 1115, 335 (2017)
Comput. Theor. Chem., 1117, 1 (2017)
Eur. J. Chem., 24, 17046 (2018)
In addition, there is a less noticeable form of DOS named local DOS, which is also known as spatial DOS. It can graphically reveal contribution of a point in 3D space to various MOs, and it has close relationship with scanning tunneling microscope (STM), see Section 4.10.2 of Multiwfn manual as well as DOI: 10.1039/c5cp07092a and DOI: 10.1016/j.cplett.2017.04.037 for practical examples.
PS: Recently I proposed a special form of PDOS named MO-PDOS, which is mainly used to distinguish different kinds of MOs in TDOS map and has been employed in my work DOI: 10.26434/chemrxiv.11320130
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My system has inversion symmetry. Therefore, I'm calculating the optical transition for a material which is allowed when parities of conduction band (CB) and valence band (VB) are different (there is some finite probability for it), otherwise it is zero. I have obtained the WAVEDERF file that contains some band number (occupied and unoccupied) with specific energy, and real and imaginary part of dipole transition matrix elements. I want to plot (K-path/K-points vs. optical transition probability), but do not know how to obtain this from WAVEDERF file.
Any help would be appreciated.
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- 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)
(k=wave vector; m, n are band indices, u is periodic part of the wave function; for now, I ignored spin index of CDER)
CDER can be obtained from WAVEDER or WAVEDERF using this function: https://github.com/hungpham2017/mcu/blob/master/mcu/vasp/utils.py#L82
+ The square of CDER is defined as the dipole transition matrix:
dipole transition matrix (k) = CDER(k, conduction_index, valence_index)^2
+ Finally the transition probability R per unit cell is given by:
R = pre-factor * sum_k (dipole transition matrix (k) )
or R(k) ~ CDER(k, conduction_index, valence_index)^2
To know the value of pre-factor, please see the section 6.2.2 of this book:https://www.springer.com/gp/book/9783642007095
If you are not interested in the absolute value of R(k) with the correct unit, then you just need to plot the R(k) ~ CDER(k, conduction_index, valence_index)^2 as a function of k.
- In practice, the function I wrote will read the WAVEDERF file and give you:
CDER(spin, k, m, n, j). Simply, do the math:
R(k) ~ CDER[spin, k, m, n, 0]**2 + CDER[spin, k, m, n, 1]**2 + CDER[spin, k, m, n,2]**2 with m, n are indices of conduction and valence band.
I will include this R(k) calculations (with correct unit) in my code soon.
Hope this is helpful
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  • Consider a simple ionic compound or metal. What would be symmetry of its crystal structure under a given temperature and pressure?
  • How and why free energy of crystal lattice with different symmetry vary differently with temperature and pressure? Why temperature and pressure selectively prefer some symmetry over other while P and T have themselves no spatial symmetry? (note, higher pressure do not universally prefer highest packing density phase, does it?)
  • how would an atom's/ion's coordination number dependent on shape of its electronic orbital?
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There is no simple answer to this question. If one assumes that the ions forming a lattice are rigid spheres, interacting with Coulomb potentials only, it is possible to state at which cation/anion size ratio the bcc lattice will become more stable than the fcc lattice.
But ions are not rigid. Furthermore, they also interact with dispersion (van der Waals) forces, and sometimes there are even stronger chemical interactions (for instance because of partially occupied d or f electron shells).
Increasing the pressure will always favour the denser phase (Le Châtelier's principle).
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How entering of triiodide ion into starch coils change electronic structure of iodine? iodine is post-transitional element, so , can ligand field theory be applied here? How the electronic transition of outermost p orbital produce visible color?
Please explain in simple terms, since my knowledge on electronic structure of complex ions , macromolecular ligands, ligand field theory and quantum chemistry are rather limited.
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I agree with Bartosz Trzaskowski about the charge transfer complex between amylose and (poly)iodides anions. Research has been made to characterize completely this structure : doi : 10.1002/anie.201601585
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I have a electronic structure (band-structure calculated using VASP), which contains \Gamma_{8}, \Gamma_{7}, \Gamma_{6} bands theoretically. Now, my question is, how can I identify and find out exact position of these bands with respect to band energy ?
Thanks,
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Dear All,
How does know number of bands corresponding to different element in compound for example LaVO4 (4 La, 4 V and 16 O atoms in unit cell) then how can I know number of bands corresponding to La, V, and O elements.
After running simulation number of bands are 112 . So how many bands corresponding to which elements.
Thank You
Shilendra
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I have done anharmonic frequency calculations in Gaussian09.(for acetone). At the end of the output file I can see the anharmonic frequencies. I do not see anharmonicity constant value(for different vibrational modes) though. Can we get anharmonicity constant value?
Also, I want to know how are anharmonic frequencies calculated? What theory is encoded within Gaussian software to calculate these values? How reliable are those?
Any reference paper will help.
Thank you.
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The reference papers are supposed to be in the links [Califano76, Miller80, Papousek82, Clabo88, Page88, Miller90, Page90, Barone04, Barone05]. Did you go through all of them? At first glance at least Barone05 is definitely about anharmonicity.
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hello dear researchers
i want to calculate electron affinity in quantum espresso code but i dont know how to do it. i red in a link that electron affinity calculation, related to delta scf calculation in DFT method but i dont know it. can you guide me about this?
thanks a lot
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dear mr Selvam
thanks for your helpful answer
cab you introduce the reference of this formula to me?
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Hello
I am a graduate student studying the electronic structure of penta-silicene bilayer. I want to know how to calculate the formation energy of penta-silicene bilayer. Can somebody give me some infomation about it?
thank you for taking time reading and answering my question
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Formation from elements - calculate energy of silicon in ground state, most likely that is one atom triplet. And compare it with energy of your penta-silicene bilayer after dividing to corresponding number of atoms.
Or you are looking for binding energy per atom, than you have to compare energy of single layer *2 and energy of double layer, result divide to number of atoms.
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I can see a lot of information for one specific space group on the 'international table of crystallography'. Say I know the space group of a crystal from XRD analysis, and I want to calculate electronic structure using first principle; but, I would need the positions of the atoms as well which I don't find what and how the authors put in their papers. So, I would be very grateful if someone who is much familiar with the 'international table of crystallography' or the Wyckoff things can help me. Thanks in advance!
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By principle you CAN NOT get the structure of a crystal by only knowing the space group, but SrTIO3 is a known compound, It has even an article in wikipedia. Please, see this site:
For cartesian coordinates, as the structure is cubic, the conversion is straightforward. The coordinates 0 remain 0 and 0,5 is replaced by 0.5*3.495=1.17475 angstroms. Is this you need?
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I'm studying about 2D material-penta silicene to accomplishment of graduate thesis. After a few steps of calculation, i realized it was wrong about position of atom in unit cell so can somebody give me some advise to do better ?
Thank all of you.
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First you need to create 2D structure properly. You can do it by VNL, then import it to CASTEP as a cif file.
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Is there a way, to get the same electronic structure of the Bilayer graphene and isolated monolayer graphene?
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I agree. Further I encountered that this phenomenon of getting the same electronic structure is called "superlubricity", If the twist angle is so small such that the two layers get decoupled and behave as the monoatomic layer.
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I performed relax calculations for MgO supercell with an Fe interstitial atom. The CONTCAR file which contains the final atomic positions indicate that only Mg and O atoms have moved with Fe being in the same initial position as given in the POSCAR file. It is quite strange that a single Fe atom in a big Mg32O32 supercell is able to distort the other atoms with itself not moving. PFA all the related files.
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With ISMEAR =-5, bloch method was used, this method is very suitable for the scf calculation, the gained dos curve is rather smooh and clear. of course you can use this during relaxation in insulator system, the premise is the system is still a isulator with the addition of fe, sure in your system this is ok, since the concentrition of fe is rather low. keep the isym to 0, no matter what kind of calculation was performed. IT is suggsted to keep parameters constant as possible. hope good.
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I found some guys publish their papers in high impact journals for photocatalysis and catalysis.
For example, a guy presented a calculation of the barrier of a catalytic activity on 1T MoS2 surface by considering only its monolayer. This is entirely incorrect. There are two reasons.
(1) 1T is much less stable than 1T' phase. (2) 1T' phase is only stable when some kinds of chemical species are intercalated to make significant charge transfer to MoS2. The charge transfer introduces significant effect on the electronic structure of MoS2. Their calculation should be redone from the beginning.
Chemical society should be more careful in undertstanding basic physics underlying the catalytic activity. Chemistry should not exclude physics.
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When I am concerned with a "wrong" (in my opinion) conclusion or observation, I write to the authors. When you receive an answer, you can judge how the authors master their subject. The response may be positive, with more exchange, even starting a collaboration ... When you see a significant problem not resolved properly by the author (answer like "the paper was written by my PhD, don't be cruel...") you can (you should) write a comment and submit to the journal in which the wrong things were published.
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I need to conduct some research on TiO2! I could use some help!
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Hope the attached article helps you.
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I am studying electronic structural features of 2D materials which contain almost more than 30-40 atoms in the unit cell. I think it is more tedious writing direct python scripts like for a 2 atom unit cell material. Can anyone please suggest me to succeed in this case?
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Hi Naga,
Have you tried p4vasp to treat the vasprun.xml output file. I think that code can help you to plot the bands.
Another option is to look into the vasptools from the UTexas they have openscripts which can serve you as a base.
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I am working on the organic-inorganic complex of Sn2+. I am trying to stabilize sn2+ by compelexing it with some organic molecules. How can I explain this stability is related to changing of electronic structure of Sn2+ by XPS and UPS. Is it possible to talk about electron affinity of Sn2+ by these two method?
Thank you in advance
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Dear Cheistian
The reason that the CuO and Cu2O 2p XPS binding energies are almost identical is that the strongest peak of CuO Cu 2p3/2 is due to the well-screened state, i.e. the dynamical charge transfer state (3d10) of CuO due to the creation of core hoe. Cu2O ground state is 3d10. The chemical shift between CuO and Cu2O is the energy difference between 2p3/2 so-called shake-up satellite (but this peak is in fact 3d9 poorly screened state) and Cu2O 2p3/2 (3d10) peaks. This is the case of transition metal compounds. Please check my old paper, Phys. Rev. Lett., 65, 2193-2196 (1990) and references therein (this is not an XPS but Ni X-ray emission spectra).
But for typical elements such as Sn, I do not know such rationalization. I hope someone will answer.
Yours sincerely
Jun
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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?
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Kindly visit the site. It is simplest way to find high-symmetry paths. you can see the path also. You just have to upload your POSCAR/xcrysden/quantum espresso input.
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First principle simulation of Semiconducting nanomaterials with VASP.
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Yes
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Dear all,
I want to calculate the band diagram of perovskite, for example: tetragonal crystal structure with some organic molecule on the edges or in center.
To do that I need to choose k-point path. It's quite difficult to choose them wisely for casual crystal cases, without molecules inside. What with the crystal cells containing molecules. If I obtain the the way of making Wigner-Seitz cell ( pl.wikipedia.org/wiki/Kom%C3%B3rka_Wignera-Seitza#/media/File:Bcc-animated.gif ) I can see that the edges of this cell in reciprocal space set the Brillouin zone (I think it's a definition), everything is okay with that for me untill I add a molecules on the unit cell edges or in the center. I belive it's gonna change the shape of the Wigner-Seitz cell of the same e.g. tetragonal structure without molecules.
Is it approximation when people in papers said that their perovskite is e.g. tetragonal and they set k-point path through the high symmetry lines and points like for simple tetragonal phase ( like for example here: en.wikipedia.org/wiki/Brillouin_zone#/media/File:Simple_Orthorhombic_Lattice_(Brillouin_zone).png )? If it is approximation what is the cost, limits etc.
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X Ray diffraction of tetragonal perovskite can be used full in extracting the K values before and after adding molecules