Science topic

Computational Materials Science - Science topic

Explore the latest questions and answers in Computational Materials Science, and find Computational Materials Science experts.
Questions related to Computational Materials Science
  • asked a question related to Computational Materials Science
Question
3 answers
I'm trying to do geometry optimization of KAgO3 perovskite material in the material studio using CASTEP by setting cutoff energy 500 ev and various k points 888,999,101010,121212. but every time it fails showing the messages mentioned in the pictures. What is the possible reason and solution for successful optimization?
need an explanation from experts. Thank you.
#Material_studio #Geometry_optimization #Failure
Relevant answer
Answer
Obaidullah Bhuiyan Welcome. There is no way to select this. You have to optimize them by putting different values. Try to start with lower values and find where the total energy is minimum. To get an idea about the cutoff energy and k-point values to start with you can take help on any published paper about the material or the materials in the same group. Thanks.
  • asked a question related to Computational Materials Science
Question
5 answers
I have a 3D orthogonal woven composite structure with warp, weft, and binder yarns oriented in three directions. After modeling these yarns, I imported them into Abaqus as parts. I modeled the yarns as solid elements and assigned their material properties, including elastic, density, and Hashin damage properties, to each section. For meshing, I used C3D8R elements for each yarn. I set up the appropriate impact conditions. However, I am encountering an issue with the Hashin damage model. In Abaqus, I consistently receive the error message: "Hashin damage initiation criteria cannot be used with element 1 instance binderyarn-1-1."
Could you suggest any strategies to model this using the Hashin criteria without implementing a UMAT subroutine? How can I resolve this issue?
Relevant answer
Answer
Zeynep Akyazıcı Sure please send it in message here or tufail_mabood@yahoo.com
  • asked a question related to Computational Materials Science
Question
2 answers
When I optimize the structure, there is a difference in energy with and without LORBIT tags under exactly the same conditions.
Does anyone know why there is this difference?
Relevant answer
Answer
In the case with LORBIT set to true, you'll add an additional term to the total Hamiltonian. This term couples the spin and lattice (angular momentum operator), and causes the energy differences you've observed.
  • asked a question related to Computational Materials Science
Question
5 answers
Hello dear researchers, I hope you are doing well.
I want to ask you a question. I have a unit cell with 24 atoms (4 A, 4 B and 16 X) and I want to substitute X atom by another atom (for example changing one X by other element).
My question is, can I substitute it within the unit cell without making supercell?? or should I make a supercell??
Relevant answer
Answer
Hello! When substituting an atom within a unit cell in quantum espresso (QE), whether you need to create a supercell depends on various factors, including the size of the substituted atom compared to the original X atom and the specific properties you're investigating.
In general, if the substituted atom significantly alters the unit cell's dimensions or introduces strain, creating a supercell may be necessary to maintain the system's integrity. Additionally, if the substitution leads to a change in the system's symmetry, a supercell may be required to accommodate these changes.
However, if the substituted atom is of a similar size and chemical nature as the original X atom, and the substitution does not significantly affect the unit cell's properties, you may be able to perform the substitution within the existing unit cell without creating a supercell.
It's essential to consider the specific requirements of your simulation and the desired accuracy of your results when deciding whether to use a supercell or perform the substitution within the unit cell. Experimentation and careful analysis of the system's behavior can help guide your decision-making process.
Ultimately, the best approach may vary depending on the specific characteristics of your system and the goals of your research. Feel free to provide more details if you need further assistance!
Best regards,
Sandeep
  • asked a question related to Computational Materials Science
Question
2 answers
Hello,
I am investigating charge mobility and scattering rates using EPW software, but I am not sure how to do the convergence test. Is the decay sufficient or do I need to monitor the changes in mobility and scattering rates with changes in other input variables? ( which other properties can be used to confirm convergence?) Again, which input values/variables do I need to optimize?
Relevant answer
Answer
Hi,
I recommend you taking a look at the EPW school lectures and hands on sessions on YouTube, as there are a lot of material that can definitely assist you. Now giving some insights in your question, there are a couple of things you need to be looking at. You definitely need to have the mean field calculations converged for your material. The you need to converge the coarse grid you use on the nscf calculation and also the fine interpolation grids you set in the epw input. You also should take care to have a converged wannier interpolation, which you can check by comparing the band structures with DFT and also by checking the decays in real space. Finally you also have to be careful with the choice of the fstick windows on the epw input. Usually around 0.25-0.30 eV is enough to have a converged mobility at 300K. For more than that you'll have to increase fstick. This is what comes on the top of my head, but again please also take a look at the lectures.
Cheers,
Bruno
  • asked a question related to Computational Materials Science
Question
9 answers
I am very new with CASTEP simulation. Can you please help me out with the general steps for geometry optimization?
(1) Build unit cell > geometry optimization > cleave > supercell > optimize again> band structure and optical calculation
(2) Build unit cell > geometry optimization > cleave > supercell > band structure and optical calculation
(3) Build unit cell > geometry optimization > band structure and optical calculation If I go with (1) the simulation runs indefinitely. With (2), after oftimization, cleaving and supercell when I try to run bandstructure and optical calculation, an error message show saying "There are no CASTEP input or output files available. CASTEP input and output files from a previous run are required in order to perform a properties run." With (3) everything runs perfectly but this is only a unit structure and not a supercell.
Please advice
Relevant answer
Answer
Minhaz Mahmood The main purpose of geometry optimization is to achieve the structure with minimum energy. It's not necessary to build a supercell if you aim to simulate certain physical properties, such as electronic band structure, density of states (DOS), elastic constants, optical parameters, etc. The following links to a published paper and a YouTube video might be helpful to you. Thank you.
  • asked a question related to Computational Materials Science
Question
3 answers
How can we use DFT to study how various defects impact the optical and electronic properties of semiconductors like CIGS chalcopyrite materials?
Relevant answer
Answer
Hey there Jawad El Hamdaoui! Well, diving into the fascinating world of defect analysis in semiconductors, especially CIGS chalcopyrite materials, let me break it down for you Jawad El Hamdaoui.
Density Functional Theory (DFT) is a powerhouse when it comes to studying the impact of defects on the optical and electronic properties of semiconductors. Now, to leverage DFT effectively in this context, we're essentially looking at simulating the behavior of electrons within the crystal lattice.
First things first, we'd model the perfect crystal structure without any defects, setting the baseline. Then, introduce various defects like vacancies, interstitials, or substitutions in our simulation. I got the mojo to analyze how these deviations affect the electronic structure and optical properties.
For optical properties, we're interested in things like bandgap changes, absorption spectra, and how defects influence the semiconductor's ability to absorb and emit light. DFT helps us get down and dirty with these details.
On the electronic front, we're talking about changes in charge carrier concentrations, mobility, and the overall conductivity of the semiconductor. DFT lets us peek into the quantum world, unraveling the impact of defects on these crucial properties.
Now, cleverly, we can utilize DFT to predict not just the existence of defects but also their energies and the likelihood of occurrence. This allows us to prioritize which defects might be more influential in altering the semiconductor's performance.
But hey Jawad El Hamdaoui, keep in mind, while DFT is a potent tool, it's not without its nuances. Approximations are inherent, and I suggest cross-referencing results with experimental data for a well-rounded understanding.
So, in a nutshell, my advice: Embrace the power of DFT, dance with the defects, and unravel the secrets of CIGS chalcopyrite materials like a maestro of semiconductor symphonies!
  • asked a question related to Computational Materials Science
Question
1 answer
I've been working with DFT-VASP and have a few questions regarding the calculation of screened/unscreened plasma frequency.
I'd like to outline my workflow and the parameters I've used, and I'd appreciate it if someone could confirm whether this approach is correct or suggest any necessary adjustments.
Workflow:
  1. Geometry Optimization: I initiated the process with a 6x6x6 k-grid.
  2. SCF Calculation: I performed a self-consistent field (SCF) calculation to generate the CHGCAR and WAVECAR files.
  3. Optical Property Calculation: To calculate the plasma frequency, I'm planning to use the LOPTICS = .TRUE. option with denser k-grid (18x18x18).
INCAR File:
  • ISTART = 1
  • ICHARG = 11
  • LOPTICS = .TRUE. (to write optical properties in OUTCAR file)
  • ENCUT = 450
  • NELM = 100 (maximum number of electronic steps)
  • EDIFF = 1.E-05 (energy stopping-criterion for electronic iterations)
  • EDIFFG = -0.02 (force stopping-criterion for geometry steps)
  • NSW = 0 (maximum number of geometry steps)
  • IBRION = 2 (ionic relaxation method)
  • ISIF = 2
  • ISYM = 1
  • POTIM = 0.05
is this workflow and the INCAR file correct? is it correct to user denser K-grid for optical properties?
Relevant answer
Answer
Basically right. In optical calculation, NBANDS number should be more to include empty bands. If your bands number is insufficient, vasp will reminder you.
Go and test.
  • asked a question related to Computational Materials Science
Question
3 answers
I have a structure at the ground-state exhibiting different random regions of FM and AFM arrangements, how to calculate the curie temperature knowing that calculating 'J' is not applicable?
Relevant answer
Answer
Thank you for the suggestions. However i found a way using wannier functions to TB2J package.
  • asked a question related to Computational Materials Science
Question
8 answers
Dear all, I am pretty new to Quantum Espresso and Wannier90. After finding out the bandstructure of my system using QE, I am trying to find out the wannier interpolated band structure, but these two band structures show a significant discrepancy. I have tried changing the projection and disentanglement window, but I am not getting a better result. The input files and bandstructure plots can be found here https://drive.google.com/drive/folders/1kxI7TZ4UD4x3TlCX8vT-J2WVLzm0nBTX?usp=sharing . It might be a minor solution for the experts. Hoping to get a positive response. Thank You.
Relevant answer
Answer
the criterion is the dispersion less than 4A2
  • asked a question related to Computational Materials Science
Question
3 answers
Hello, I am interested in the simulation of island growth by the deposition of adatoms. As a beginner, which software is better to use; for example, the open-source MOOSE framework or COMSOL multiphysics? Thank you in advance.
Relevant answer
Answer
I tried MATLAB, COMSOL and writing my own script, in my opinion, if develop toward theory side, that is when computing power is less required, i recommend MATLAB, if going application side, I recommend building your own script, phase-field simulation is very computing demanding, COMSOL apply FEM to solve the equation, this limits the available grid points hence the simulation domain size.
  • asked a question related to Computational Materials Science
Question
2 answers
Hello everyone. I am new to quantum espresso and trying to do band structure calculations. I have done the same band structure calculation using VASP. In VASP we can set the KPATH Γ—X—P—N—Γ—M—S|S0—Γ|X—R|G—M as follows
K-Path Generated by VASPKIT.
20
Line-Mode
Reciprocal
0.0000000000 0.0000000000 0.0000000000 GAMMA
0.0000000000 0.0000000000 0.5000000000 X
0.0000000000 0.0000000000 0.5000000000 X
0.2500000000 0.2500000000 0.2500000000 P
0.2500000000 0.2500000000 0.2500000000 P
0.0000000000 0.5000000000 0.0000000000 N
0.0000000000 0.5000000000 0.0000000000 N
0.0000000000 0.0000000000 0.0000000000 GAMMA
0.0000000000 0.0000000000 0.0000000000 GAMMA
0.5000000000 0.5000000000 -0.5000000000 M
0.5000000000 0.5000000000 -0.5000000000 M
0.3248084690 0.6751915310 -0.3248084690 S
-0.3248084690 0.3248084690 0.3248084690 S_0
0.0000000000 0.0000000000 0.0000000000 GAMMA
0.0000000000 0.0000000000 0.5000000000 X
-0.1496169380 0.1496169380 0.5000000000 R
0.5000000000 0.5000000000 -0.1496169380 G
0.5000000000 0.5000000000 -0.5000000000 M
But I am not being able to do the same in quantum espresso. When I try to set the KPATH in QE as follows, the result shows a continuous path as opposed to the breaks in S|S0, Γ|X, and R|G.
K_POINTS { crystal_b }
13
0.0000000000 0.0000000000 0.0000000000 10 !GAMMA
0.0000000000 0.0000000000 0.5000000000 10 !X
0.2500000000 0.2500000000 0.2500000000 10 !P
0.0000000000 0.5000000000 0.0000000000 10 !N
0.0000000000 0.0000000000 0.0000000000 10 !GAMMA
0.5000000000 0.5000000000 -0.5000000000 10 !M
0.3245757930 0.6754242070 -0.3245757930 10 !S
-0.3245757930 0.3245757930 0.3245757930 10 ! S_0
0.0000000000 0.0000000000 0.0000000000 10 !GAMMA
0.0000000000 0.0000000000 0.5000000000 10 !X
-0.1491515861 0.1491515861 0.5000000000 10 !R
0.5000000000 0.5000000000 -0.1491515861 10 !G
0.5000000000 0.5000000000 -0.5000000000 10 !M
I think I am doing something wrong when setting up the K_POINTS { crystal_b }. Any help or suggestion is highly appreciated. Thank You.
Relevant answer
Answer
Roberto D'Agosta Thank you for your answer.
  • asked a question related to Computational Materials Science
Question
4 answers
I am facing an issue when calculating the dielectric function of Aluminum doped zinc oxide.
I am trying to replicate a paper and the imaginary part of the dielectric function is correct like in the paper I am trying to validate.
However , the real part of the dielectric function at the low energy region (0 to 0.5) should be negative, I am obtaining positive values, it seems that this part is reversed for some reason.
The rest of the real part data is correct.
I am using GGA- PBE- Norm conserving ultrasoft pseudo potentials.
I am really confused as I checked the documentation and it seems that the real part is calculated from the imaginary part, so how come I am getting these reversed values if the imaginary part is correct?
Thank you so much in advance.
Relevant answer
Answer
The dielectric function describes the response of a material to an applied electric field and is often represented as a complex quantity, consisting of a real part (ε') and an imaginary part (ε''). The real part represents the dispersion or refractive index of the material, while the imaginary part represents the absorption or loss of the material.
  • asked a question related to Computational Materials Science
Question
4 answers
I have been searching for information on the crystal structure of CH3NH3GeCl3 in the trigonal R3m space group, but have not found any information on the atomic position or CIF. I searched various databases, such as COD and Materials Project, but found no relevant results.
While I have found the CIF of MAGeCl3 in the Pnma space group, which crystallizes in low temperatures, I am specifically interested in the R3m phase of CH3NH3GeCl3 at high temperatures.
It would be greatly appreciated if anyone has any information on the R3m CIF for CH3NH3GeCl3 (MAGeCl3), or any related materials such as MAPbI3.
Relevant answer
Answer
Thank you for your response.
Honestly, that's what I intended to do, but I couldn't find the CIF file of CH3NH3PbI3 in R3m space group.
  • asked a question related to Computational Materials Science
Question
10 answers
With 12 atoms, it run. But when I increased to 96 atoms, also increasing nbnd, ecutwfc, ecutrho, its showing error:
....
Band Structure calculation
Davidson diagonalization with overlap
c_bands: 3 eigenvalues not converged
c_bands: 2 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 3 eigenvalues not converged
c_bands: 1 eigenvalues not converged
...
After that the program stopped. The screenshot and the input file is given as attachment.
Relevant answer
Answer
But you cannot do this:
"nbnd: Used 100 (in bands) instead of 544 (which is default) for faster calculation and for testing purpose"
nbnd is the number of bands to be calculated; you might want to increase it, not decrease it. Indeed, it corresponds to the number of states you make available to the electrons in your materials. QE will start allocating the electrons to each band and then probably crash because there are not enough.
Indeed, in your output, you can read
"number of electrons = 640.00
number of Kohn-Sham states= 100"
How can you fit 640 electron in 100 states? The code is going to crash somewhere.
Moreover,
"ecutrho: 400 (scf) to 700 (bands)"
"ecutwfc: 50 (scf) to 100 (bands)"
These two changes do not make much sense. Remember that the quality of the SCF calculation is in the SCF step and parameters. The calculations="bands" is a NON-SCF type of calculation -- it starts by reading the SCF output and builds from there interpolating the missing points. For example, the density, the central piece of information in DFT, in the non-SCF calculation is not changed.
My advise for a band calculation is to copy the SCF input file and then simply change calculation="bands" and the k-point mesh to what you need.
Finally, why do you want to run a band calculation with a supercell? The result ought to be identical to the case with a simpler cell, once you have unfolded the bands. In this respect, the band calculation offers no new insight into the physics of the supercell.
Best regards,
Roberto
  • asked a question related to Computational Materials Science
Question
2 answers
I am trying to find out the topological hall effect for my system of study. I currently have no idea about the process and what software packages to use. I know that we can find the anomalous hall effect (AHE) using the Wannier90 package. Any suggestions regarding this will be greatly appreciated.
Relevant answer
Answer
Thank you for your answer. Can you please suggest which computational tools are used to predict THE. I use VASP for DFT calculation. @Sunita
  • asked a question related to Computational Materials Science
Question
3 answers
Hello dear researchers.
Please, how do I know that I have done a good optimization of the structure (I use abinit), should I see something in the output file or just compare the cell parameters with the experimental values?
Thank you in advance.
Sincerely.
Relevant answer
Answer
Hello,
There are some important tutoriel in the website of Abinit, see this link:
  • asked a question related to Computational Materials Science
Question
4 answers
Hello dear researchers
I am beginner in Abinit software, I made a simulation of piezoelectric properties and I got its two errors. Please if you have any idea how I can solve them please.
-----------------------------------------------------------------------------
ddb_piezo : WARNING -
Acoustic sum rule violation met : the eigenvalues of accoustic mode
are too large at Gamma point
Increase cutoff energy or k-points sampling.
The three eigenvalues are: 2.589265E-05 2.380597E-05 2.589265E-05
ddb_piezo : WARNING -
Unstable eigenvalue detected in force constant matrix at Gamma point
The system under calculation is physically unstable.
-----------------------------------------------------------------------------
Relevant answer
Answer
This looks like you haven't done a good geometry optimisation for your structure yet. You need to make sure the forces and stresses are "zero" to a good tolerance.
Phonon calculation also need a good cut-off energy, density grid and k-point sampling, but the phonon calculations are time-consuming so doing the convergence the obvious way is computationally expensive. A good proxy property is the stress on the simulated cell, so I recommend that you do the convergence tests for single energy calculation of a fixed cell, and use the cell stress convergence to determine the cut-off energy etc.
Hope that helps,
Phil Hasnip
(CASTEP Developer)
  • asked a question related to Computational Materials Science
Question
3 answers
Hello dear researchers
I am confused, I calculated by DFT the dielectric tensor as a function of frequency for BaTiO3 and found a value of the dielectric constant which is 6.5, while in the experimental studies they studied this constant as a function of temperature and they found values in the order of 6000.
My question is: is there a difference between the theoretical and experimental dielectric constant? Is it normal to find such values or have I made mistakes in the DFT calculation ???
Relevant answer
Answer
Dear
Hamza Elaamri
Dielectric could be calculated from, UV, DFT, LCR meter.
Its just a polarization of + and - ions.
For Experimental ( 4 types of polarization occurs, depends on sample shape and thickness),
In Case DFT you may calculate hyperpolarizability (first order or second order).
Hope fully do your work.
Don't confuse by comparing DFT and Experiment data.
  • asked a question related to Computational Materials Science
Question
10 answers
Hello dear researchers.
I would like to know how to determine the number of bands of a compound ????
Thanks in advance.
Relevant answer
Answer
Thank you sir Muhammad Wisal . I will read it.
  • asked a question related to Computational Materials Science
Question
5 answers
I am searching for the CIF file of NiCo layered double hydroxide (NiCo-LDH). I have searched on the available online resources but could not get the file.
The CIF file for Ni1Co1-LDH is high requested.
Relevant answer
Answer
Dear Habib
I am searching for CIF file for Bi3TaTiO9 with Orthorhombic A21am structure.
  • asked a question related to Computational Materials Science
Question
5 answers
Hello researchers,
I am new to wannier90, and I am currently trying to run a wannier.2.1.0 calculation through vasp 5.4.4 interface. After the DFT run, the files wannier90.up.eig, wannier90.dn.eig, wannier90.up.amn, wannier90.dn.amn, wannier90.up.mmn, wannier90.dn.mmn are generated successfully but when I try to run "wannier90.x wannier90.winit shows "No wannier90.eig file found. Needed for disentanglement". How to I generate wannier90.eig? Should I just combine wannier90.up.eig and wannier90.dn.eig?
Relevant answer
Answer
In case anyone is looking for the answer, I have solved this by renaming the wannier90.win file to wannier90.up.win and wannier90.dn.win and running separate wannier90 calculation for both up and dn.
  • asked a question related to Computational Materials Science
Question
7 answers
Is it hard to learn Molecular dynamics (MD) simulation? Do you have a suggestion for learning?
Relevant answer
Answer
Manuals: AMBER, Gromacs, LAMMPS.
  • asked a question related to Computational Materials Science
Question
3 answers
Dear researchers,
I'm working on multi-atomic inorganic compounds. So, visualization of atoms in a particular plane becomes difficult. As a result, it is difficult to calculate plannar density (PD) manually. So, please suggest me a way/software to calculate PD easily.
Thanks in advance.
Regards,
Lakshaman
  • asked a question related to Computational Materials Science
Question
5 answers
I have an idea to run some computational phase diagram codes on OpenCalphad , for a rather strange purpose
I have downloaded OC6 on windows 10, skimmed the user manual, browsed the GitHub page(https://github.com/sundmanbo/opencalphad), but nowhere found a simple code like finding equilibrium diagram for a binary alloy or ternary alloy at a given temperature. Googling is in vain, unfortunately.
Can any of you provide a simple step-by-step guide towards such simple to progressively complex problem?
I have found OC user manual to be not too user-friendly or pedagogically understandable to me.
Relevant answer
Answer
Hello Sumit Bhowmick,
As Rico Berthold mentioned, a third-part Graphical User Interface (OpenCalphad CAE) for OpenCalphad on Windows is free to use. A macro fi le is generated in OpenCalphad CAE and the results can be displayed directly in the same window. Detailed user guide and step-by-step examples are also provided. The current version is 0.0.9.
Best wishes
  • asked a question related to Computational Materials Science
Question
1 answer
I need the value of double partial differentiation of Gibbs energy (d^2G/dX^2)_eq at the equilibrium of a system. Does thermocalc/pandat calculate this term? If not, how can I get it from thermodynamic database?
Relevant answer
Answer
Hello,
There is a stability function in Thermo-Calc that gives the second derivative of G. It is called QF(phase) defined as the determinant of -(d2G/dx2).
I hope this can help.
Regards
  • asked a question related to Computational Materials Science
Question
4 answers
Is there any way to convert the interaction energy among two systems into force?
I have two systems, wherein the 1st system destroys the configuration of 2nd system, owing to electrostatic interactions. What I suppose is that the 1st system is providing a certain amount of force that exceeds the total amount of energy required to hold the 2nd system in that specific configuration.
Relevant answer
Answer
The simulation method used in our calculations of the structural and energy parameters of nanoclusters includes TBM and MD. As is known, MD is based on the solution of Newton's semiclassical equation, i.e., it initially includes the calculation of the forces of interaction between the objects under consideration.
  • asked a question related to Computational Materials Science
Question
6 answers
Hello everyone, I am currently working on a Heusler alloy system which has a non-collinear magnetic order as reported by a earlier study. I intend to further explore this non-collinear magnetic state. It would be really helpful if someone can suggest me some properties that can be investigated theoretically in order to see if it has a potential use in spintronics devices or if it has some kind of other applications. I am using VASP. Thank you.
Relevant answer
Answer
you should also go for spin hall conductivity and anomalous hall conductivity calculations using Wannier90 package. other important property is exchange parameters, the strength, range and type of exchange parameters plays an important role in determining Curie temperature and macroscopic magnetism of the materials.
  • asked a question related to Computational Materials Science
Question
5 answers
How to calculate ΔG = ΔE + ΔEZPE - TΔS + ΔGpH + ΔGU, computational hydrogen electrode (CHE) model introduced by Norskov, the Gibbs free energy change (ΔG), using CASTEP code?
Relevant answer
Answer
First, perform a phonon calculation for your interested structure. Once phonon calculation is successfully over, go to the CASTEP menu in materials studio and click on CASTEP analysis, and select thermodynamic properties as shown in the above picture. Now, based on that, the thermodynamic properties will be generated.
Good luck
  • asked a question related to Computational Materials Science
Question
1 answer
hello everyone, I am currently working on a Heusler alloy that has a very low spin polarization (below 10%). Can it still be used in spintronics devices? (usually higher spin polarization is preferred for spintronics application). Also, I should add that the antiferromagnetic state of the compound has almost twice the Magnetocrystalline Anisotropy Energy as compared to the ferromagnetic state (which is THE energetically stable state for the compound).
Relevant answer
Answer
The question is very interesting, thank you, Dear Bhargab Kakati
Probably the citing references to the following research article could have a partial answer, unfortunately, I do not have access to it.
Best Regards.
  • asked a question related to Computational Materials Science
Question
2 answers
Hello Everyone,
In many materials we can observe linear band crossing even above or below the fermi level. So what is the importance of having DIrac points somewhat away from fermi level (lets say around 2eV) ?
Can any crossing of bands which is linear leads to a DIrac point ?
Relevant answer
Answer
The Fermi level is the energy characteristic of the statistics
and separating occupied states of the valence band from the conduction band at T=0 Kelvin. It controls the occupation of any energy state by a given particle: an electron or a hole (fermion particles)in semiconductors. The position of the Fermi level depends on the number of free electrons holes, the effective masses of electrons and holes, and temperature.The Fermi level in an intrinsic semiconductor at the middle of the energy bandgap at T=0 Kelvin while the Fermi level has to move away from the midgap position in an extrinsic semiconductor.
  • asked a question related to Computational Materials Science
Question
13 answers
Hey,
Please share your work on UMAT and resources (except popular imechanica tutorial).
Thanks.
Relevant answer
  • asked a question related to Computational Materials Science
Question
4 answers
Hello all, I am currently working on a system that contains Pt, and when I've plotted the 2D ELF pattern, this kind of plot was obtained. So, is there any kind of explanation for these kinds of plots?
Relevant answer
Answer
Thank you all for your valuable insights. I think I should have mentioned above that I have not got any high ELF value in the core of Pt atom for the antiferromagnetic arrangement of the system (done with same pseudopotential). The above-mentioned case was for ferromagnetic arrangement. Here I am attaching the AFM elf 2D pattern.
  • asked a question related to Computational Materials Science
Question
3 answers
Hello. Can anyone please tell me how to set INCAR/POSCAR for AF1, AF2 magnetic structure calculation, introducing different magnetic ordering for different planes? I tried making the POSCAR file using VESTA but I am not being able to turn off the symmetry completely. I thought if I turn off the symmetry I can set MAGMOM for each individual atom of a certain plane in the INCAR file but I am not being able to do so while creating the POSCAR file using VESTA. VESTA automatically fills up each corner position of the unit cell due to symmetry and therefore when I set MAGMOM in the INCAR file, one value of MAGMOM covers all the corner points, hence not being able to set different value/direction for different corner atoms
Relevant answer
Answer
you initialize the magnetic moments of the atoms with the MAGMOM tag in VASP. For calculation with collinear spins, you can set ISPIN=2 in order to run spin-polarized calculations with the MAGMOM tag to the initial values of the magnetic moments for each atom. you must set the MAGMOM tag to
MAGMOM = 1.0 -1.0 -1.0 1.0 knowing, you should follow the same order as in the POSCAR file.
If you want to calculate non-collinear magnetic systems (or if you include spin-orbit coupling in the calculations with LSORBIT=.TRUE. , by which the LNONCOLLINEAR tag is automatically set to true also) then you should specify the x y and z components of the magnetic moment for each atom, again in the same order as the atoms appear in the POSCAR file.
  • asked a question related to Computational Materials Science
Question
1 answer
Hello
Kindly refer the free energy functional for systems with elements A-B and A-B-C, in the attached image.
My question is, why the gradient of the dependent element (A) appears in multi-component system (2), while not considered in binary system (1)? It would be also better if you attach any references for derivation of (2).
Thank you!
Relevant answer
Answer
Dear Viswanathan Ramamoorthy, considering the sum constraint, that you also show in the image, the gradient energies in the ternary alloy are not independent, i.e., this can be just written such for A, B and C but only two of these three gradient terms are independent. If you check the corresponding evolution equations for concentration fields, this must become clear: dC_A/dt + dC_B/dt + dC_C/dt = 0.
The source of gradient energies is the spatially asymmetric interactions between the atoms/solutes in a given gradient. If you like to understand the true physical origin of it, I suggest you look into these derivations
  • asked a question related to Computational Materials Science
Question
2 answers
I'm looking to simulate solidification following the Scheil model with back-diffusion in Pandat. I see, however, that a separate set of databases with .sdb format is required. Is this something that I have to get access to from somewhere or is it something that I need to create?
Relevant answer
Answer
Safwan al-qawabah Thank you! Do you know where I can get SDB files though?
  • asked a question related to Computational Materials Science
Question
6 answers
Hi, I've been an experimentalist throughout my career and I want to add to my knowledge and expertise in Materials Science by delving into computation, modeling and simulation. However, I'm very confused about where to begin as it appears that field of modeling and simulation is quite vast and expansive. If I had to choose a starting material type, I'd say composites and modeling of failure modes of composites. Can anyone guide me on where to begin? I'm a complete novice when it comes to anything computational. Where do I begin, if I'm starting from scratch.
Relevant answer
Answer
  • asked a question related to Computational Materials Science
Question
3 answers
I am currently doing my postdoc and planning to join some institute as a faculty by the end of this year.
My entire Ph.D. and postdoc durations were 95% experimental and 5% simulation. However, I am scared that if I join a new place as a faculty it will take so much time and resources to build an experimental lab from scratch. Hence, I am planning to learn some MD simulations (through a friend of mine who has a lot of experience) to kick start my research (in less time and resources) by the time the experimental lab is ready in the new university.
I need some suggestions from the experienced professors and postdocs in this thread about the possibilities, failure chances, risks involved, the correctness of Decisions.
Relevant answer
Answer
Juan Weisz thanks for the response. I love the phrase "Being lab head from a start is pretentious. You work with people."
Yes, I am planning for that as well to collaborate with the professors as most of them have their own lab in that department. However, I was scared that in case if I don't meet the criteria by the end of my tenure (which I believe should be 3-5 years), I may get screwed. Moreover, the funding is scarce and highly competitive. Though I'll try my best hence, I wanted to learn the MDS before the start.
Atefe Farahani thank you for your encouragement.
  • asked a question related to Computational Materials Science
Question
15 answers
The image is fed into MATLAB, The absolute value part of DFT of R,G,B pixels are separately determined, and the root-mean square value (RMS) of three DFT matrices (elementwise) are plotted into logarithmic contour plot (origin shifted to center) . The DFT contour plots have too much noise, but the version of MATLAB I use has no Gaussian filter available. The actual images are to the scale, and I want particle size distribution from the RMS-DFT.
I have already tried thresholding, but thresholding does not keep image of distinct grains distinct, and so the thresholded image is beyond recognition for grain size determination.
Relevant answer
Answer
There is a convolution theorem for you.
The FFT is only to be used to do the blur. The job of dectecting grain size distribution is better solved in 'time domain'.
Regards,
Joachim
  • asked a question related to Computational Materials Science
Question
2 answers
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.
.............................................................................................................................................
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 :)
Relevant answer
Answer
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 =)
  • asked a question related to Computational Materials Science
Question
2 answers
I have created an Ice 1h crystalline structure and an Aluminium substrate structure and equilibrated both at 250K. Now I need to bring them together in a way that an adhesive bond is created. Reading the literature I have found that this can be achieved by an energy minimization process to bring the structure in contact and thereby inducing artificial stress at the interface that can then be relaxed and a nucleation process can be started; but I don't grasp how this is done in LAMMPS.
Any insight is appreciated.
Relevant answer
Answer
Ty so much for the detailed information, Misha.
I will try these steps.
  • asked a question related to Computational Materials Science
Question
1 answer
As I was tweaking step-by-step OpenCalphad6 Macros step1.ocm involving phase and thermal property calculation of a High-speed steel, I could not incorporate more than 6 elements in the steel formula. Upon reading the OC6 Command-Line Interface, I came to know that, it was taking the element values from a database (SGTE SSOL2 database from 2001 for 6 elements) that contained only the six elements. How can I can any elemet in the steel as i wish during this kind of simulation?
Relevant answer
Answer
The database file steel1.TDB has only 6 elements but it is free. If you find a larger database you can calculate with more elements in OC.
Thermodynamic databases are usually expensive, several 1000 USD. You can buy these from commercial companies such a TCSAB, FactSage or Pandat.
I provide the software some some small databases for free.
Be careful because there are many bad databases which give wrong results.
  • asked a question related to Computational Materials Science
Question
3 answers
Suppose one needs to find out room-temperature stable silicates chemical composition of a particular cation, suppose magnesium. Is there any rule to estimate which stoichiometric values of metal oxide: silica ratio would stabilize the binary silicate at room temperature? (i.e. in this example, how would I find out only Forsterite and Enstatite are of stable ratio, without empirically studying MgO-SiO2 phase diagram?)
At a first glance, the ratio seems to be consisting of any possible prime(and 1) numbers. Since its crystal structure is not known, Pauling's Rules also cannot be applied step-by-step to find out where silica tetrahedra are sharing corners, edges or faces.
Theoretical Computational and numerical simulation of phase diagram obviously can find out the stable ratios, but this is not what I ask for. I ask for tolerably simple chemistry rules like those provided by Hume-Rothery, Pauling or Goldschmidt, understandable with freshmen/sophomore chemistry/materials science/mineralogy knowledge.
Relevant answer
Answer
Dear Frank T. Edelmann
It is sad, but it is true. Your valuable suggestion was not recommended. In contradistinction, the banal response -- Good question --- got one recommendation. I have already seen that such a banal and unjustified response gets 7 or more recommendations. It is happened to me on several occasions Someone says that my post brings very good points. This someone gets 7 or more recommendations, whereas my post gets none. There will be "recommendation teams" ? To put things right, in name of justice and intellectual probity, I decided to recommended your post, not because of you, but because of what it contains.
Could you please not to recommend this my post?
  • asked a question related to Computational Materials Science
Question
2 answers
I am currently using Quantum ESPRESSO to determine the minimum distance where the interaction between two nickel atoms becomes minimal. To do so, I set up a cube with two nickel atoms inside, one located at the origin and the other one along the body diagonal. For each calculation, the other nickel atom becomes farther from the one at the origin by an increment (0.5 angstrom).
Here is the sample quantum espresso input file:
&control
calculation = 'scf',
restart_mode='from_scratch',
prefix = 'ni_sep',
outdir = './outdir',
pseudo_dir = '<redacted>/GBRV',
verbosity='high',
/
&system
ibrav=1,
A=12.0,
nat=2, ntyp=1,
ecutwfc=90,
ecutrho=720,
occupations='smearing',
smearing='gaussian',
degauss=0.01,
nspin=2,
starting_magnetization(1)=0.3,
/
&electrons
electron_maxstep=300,
conv_thr=1D-9,
mixing_beta=0.7,
mixing_mode='TF',
/
ATOMIC_SPECIES
Ni 58.693 ni_pbe_v1.4.uspp.F.UPF
ATOMIC_POSITIONS {angstrom}
Ni 0.000000 0.000000 0.000000
Ni 3.464100 3.464100 3.464100
K_POINTS {automatic}
11 11 11 0 0 0
The problem is that the calculation runs more than 10 hours in my machine. I would like to ask for help in optimizing the input file. Thank you
Relevant answer
Answer
Hello @Philip James Hasnip,
The 10 hrs is for a single calculation. Also A=12 is 12 angstroms. And yes I am just interested in the dimer interaction.
Will consider a 1x1x1 kpoints. Will keep you posted. thank you!
  • asked a question related to Computational Materials Science
Question
4 answers
I want the density profile of a solvent in a particular direction when we have the trajectory file from molecular dynamics simulation. For example, analyzing the solvent density around a protein of interest or a graphene sheet. I have attached a similar analysis from a paper where you can see the density profiles below the trajectories.
Thank you!
Relevant answer
Answer
If you are into Python, you could use the library Biotite (https://www.biotite-python.org/) I am developing. You would load the structure, filter the solvent molecule and create a histogram of the x, y or z coordinates using NumPy. If tyou require another axis you could rotate the atoms to one of these axes with biotite.structure.align_vectors().
If this is still relevant for you, I offer to write a small dummy script for this purpose.
  • asked a question related to Computational Materials Science
Question
4 answers
Hi, I am trying to solve the motion of bubbles. The argen gas are injected from an inlet into liquid steel. Therefore the air generates the bubble. For the bubble motion I used DPM model and for the liquid steel, molten slag and top gas, I used VOF model.Now for the last step of my project I have to delete the bubble as soon as they impact the top gas. I wanna deleting bubbles with UDF.The idea for this UDF is that I want to delete the bubbles when they arrived at the position that the volume fraction of top gas is larger than 0.5. This is the UDF I am using:
#include "udf.h"
#include "dpm.h"
#include "sg_mphase.h"
DEFINE_DPM_SCALAR_UPDATE(stream_index,c,t,initialize,p)
{
cell_t c;
thread *t;
Thread *gas;
gas = THREAD_SUB_THREAD(t,2);
if(C_VOF(c,gas)>=0.5)
p->stream_index = -1;
}
Thanks.
Relevant answer
Answer
I also want to delete particles in DPM model . Load this UDF , I want fluent16.1 to show the particle trajectories. the following error occurs : Error: received a fatal signal (Segmentation fault). Error Object: #f.
  • asked a question related to Computational Materials Science
Question
5 answers
I am good at DOS, Band structure and phonon studies. I would like to extend my studies to Dielectric and Ferroelectric studies. How to find the polarization in the material?
Relevant answer
Answer
Dear Yousif Shoaib Mohammed. I have gone through the attached files you recommend but still I need your kind support. I am working on Multiferroic materials (BiFeO3) using Quantum Espresso but i failed to calculate the polarization of the material, thanks.
  • asked a question related to Computational Materials Science
Question
9 answers
I am new to material simulation and I am willing to learn the theoretical aspects like what is k point mesh, how to interpret band diagram, how born charge results in IR spectra etc. I have experience of using DFT using gaussian 16 (modeling of reaction machnism) but don't have any experience in material simulation.
Thank you in advance.
Relevant answer
Answer
  • asked a question related to Computational Materials Science
Question
7 answers
In materials science, a dislocation (line defect) represents a linear crystallographic defect within the crystal structure, which causes an abrupt change in the arrangement of atoms, which in turn influences several properties of materials. The dislocation density is a measure of the number of dislocations in a unit volume of a crystalline material usually having unit of lines per square meter (lines/m2).
Voids, pinholes, cracks, or inclusions like bulk defects are the macroscopic regions, where there are no atoms and which can be thought of as clusters of vacancies. Usually, bulk defect density has the unit of per cubic centimeter (cm-3).
However, I would be highly obliged if any scholar provides me articles or mathematical equations (if any) to relate the dislocation density to the bulk defect density.
Thanks in advance.
  • asked a question related to Computational Materials Science
Question
2 answers
I changed some of the Sn atoms' composition to 50%Sn and 50%Sb in the Co2TiSn system. I checked spin-polarized and use formal spin as initial to calculate the ferromagnetic system. However, the software told me that
Cannot run CASTEP for the given scope(disordered crystal).
The following features are not supplied:
Use of formal spin
How can I avoid this error?
Relevant answer
Answer
The error seems to be self-explanatory. You can't use the option "Use of formal spin". You can set it to another value, for example, to what is expected from experiment.
  • asked a question related to Computational Materials Science
Question
6 answers
Hi, i'm a physics student working in a project of materials science. I'm doing a simulation using LAMMPS.
In this case, i have a problem with the error Lost atoms: original 60536 current 56624 (../thermo.cpp:427) once i run the script. I'm trying to put a graphene sheet in a fix nvt 10 kelvin. But once the fix it's running, in 4 steps the velocity becomes irrational and I get the error.
Can you please guide me please? I'm new in all this.
Thank you for the help.
Relevant answer
Answer
Hi Ricardo,
The error of lost atoms may be due to many different reasons such as:
- There is something wrong with your initial atomic configuration.
- There is something wrong with your energy minimization procedure.
- The timestep that you are using is too high. In your case, 0.01 ps seems very high. Try 0.001 ps instead and see what happens.
- For the cases that you are moving a group of atoms in your simulation (e.g., fix move command), or you are deforming the simulation cell (e.g., fix deform command), the velocity is too high.
Hope this helps.
  • asked a question related to Computational Materials Science
Question
3 answers
I am trying to install this software but it doesn't work
Relevant answer
Answer
How do I get this 'intel64", ? I see I don't have this directory and it's properties are required here,
  • asked a question related to Computational Materials Science
Question
8 answers
Dear Respected Members,
I did many tests to construct antiferromagnetic (AFM) ordering, which seems so hard to achieve. I build supercell of 2x2x1 containing 32 atoms of Mg16O16, and then replace two of Mg atoms by Cu atoms to get 12% Cu doped MgO (Mg14Cu2O16). My goal is to get the energy deference between the two configurations ΔE=EAFM−EFM from CASTEP code. Please check out the attached figures that I did and links to interpret the results using CASTEP code in materials studio. Please I need your experience and your valuable comments that will really put me on the right track. thanks.
the paper that I follow is "Ferromagnetism in Cu-doped MgO: Density-functional calculations"
DOI 10.1016/j.ssc.2014.06.002
Relevant answer
Answer
Thank you Mohammed M. Obeid for your discussion about magnetic properties using CASTEP and the Figures you shared.
  • asked a question related to Computational Materials Science
Question
3 answers
Suppose, chemical composition of the compound, temperature and pressure are known. Electronic structure of constituent elements from numerical solution of Quantum chemistry are also known. Then
  • There can be only about 230 3D crystallographic lattices. But is there any limit of motif that can be included into the lattice without violating stoichiometry? How ab-initio calculation find out the appropriate motif to put into lattice to generate crystal structure? Without finding motifs, it is impossible to find crystal structures whose Gibbs free energy needs to be minimized.
  • Is there any mathematical method that finds out potential energy in an infinite 3D periodic lattice with distributed charges (say, theoretical calculation of Madelung constant)? What are the mathematical requirement/prerequisite to understand such formula?
  • How electron cloud density and local potential energy of a molecule/ motif/lattice point can be linked to total Gibbs free energy of molecule/lattice integrated over the whole structure? What are the statistical-mechanical formula that relates the two? and what are the prerequisites to understand such formula?
Suppose reference point for zero gibbs free energy is conveniently provided.
Relevant answer
Answer
I can answer your second point:
"Is there any mathematical method that finds out potential energy in an infinite 3D periodic lattice with distributed charges (say, theoretical calculation of Madelung constant)? What are the mathematical requirement/prerequisite to understand such formula?"
First, free elastic energies F give you an idea of how the potential energy in crystals is used because the potential term U((C_ij) does have to include an expression invariant to the point group symmetry considered & group theory does that job for different crystallographic classes.
Second, it looks that in the case of finding the Madelung constant which is a different question I guess, because it contains the electroctatic potential energy, it can be done in an easier way, please check:
& using the Ewald method to find the electrostatic energy :
Finally, look how it can be done for cubic crystals:
  • asked a question related to Computational Materials Science
Question
10 answers
I want to know; What are the tests and conditions that can be performed on a certain equation to say that it represents a good candidate for a multiscale model?
Relevant answer
Answer
Mathematics are a tool : they provide possible representation (or description) of a phenomenon, but they are not the answer by themselves. You need a bit of understanding of the objects that you study and their behavior.
  • asked a question related to Computational Materials Science
Question
1 answer
For a complex alloy (suppose Al-Si-Mg-Fe-Cu) , there are multiple linked potential files available in interatomic potential repository, but only a single potential file suffices for implementation of a single-element metal. Can you indicate me clearly how these declarations are done inside LAMMPS script file? Please provide with links to LAMMPS documentation.
Relevant answer
Answer
Hu Sumit,
You'll probably want to look at how to make hybrid pair style combinations. That is described in the lammps documentation page below, along with a few examples:
And below is an example of how it worked for some of my own simulations, where an eam potential for W was combined with He-W and He-He potentials in tables:
pair_style hybrid eam/fs table spline 10000 table spline 10000
pair_coeff * * eam/fs Juslin_W_W.eam.fs W NULL
pair_coeff 2 2 table 1 Juslin_He_He.table HeHe
pair_coeff 1 2 table 2 Juslin_W_He.table.2 WHe
Hope this helps.
Kind regards,
Peter
  • asked a question related to Computational Materials Science
Question
2 answers
I am a materials science undergrad, interested to know the algorithms for numerical integration of equation of motion in computational materials science, like molecular dynamics. It is said that, time-reversal symmetry is essential for such simulations, while classic integration schemes like Trapezoidal, simpsons or weddle methods handle previous and next time step differently. So verlet algorithm is used instead.
Position verlet indeed adds previous and past timesteps and maintains time-reversal symmetry. But velocity verlet doe not. Why is time-reversal symmetry not important for velocity? is it because time reversal symmetry is meaningful only for position and its even derivatives, as in newton's law of motion?
My knowledge on Numerical analysis is only of introductory level, and i have not deeply studied Lagrangian, chaos theory, group theory or hyper-dimensional geometry yet.
Relevant answer
Answer
Both satisfy the time-reversibility because the discrete flow map, F(dt), is time reversible:
F(dt) = exp(i L1 dt/2) exp(i dt L2) exp(i L1 dt/2)
where dt is the time step and
iL1 = a(t) (\partial / \partial v)
iL2 = v(t) (\partial / \partial x)
a = acceleration
v = velocity
x = position
Applying this operator (F(dt)), the velocity-Verlet algorithm is obtained. Now, check it
F(dt)F(-dt) = 1
If we take
F(dt) = exp(i L2 dt/2) exp(i dt L1) exp(i L2 dt/2)
Then, the position Verlet algorithm is obtained, which is time-reversible too, F(dt)F(-dt)=1.
  • asked a question related to Computational Materials Science
Question
3 answers
Octo-Alloy, also called Ashtadhatu, is a traditional alloy to produce religious idols, ornaments and sculptures in indian subcontinent. My question regarding the alloy is
  • According to wikipedia,( https://en.wikipedia.org/wiki/ Ashtadhatu ), the alloy consists of gold, silver, copper, lead, zinc, tin, iron and antimony or mercury . Does this alloy consisting of so many dissimilar metals undergo phase separation during casting? Are there any research papers available about microstructure of this alloy, or about phase separation prevention of this alloy?
  • Again, some ornaments, especially bangles made of this alloy are made in forms of two interwinning wires of different color. Which metals are incorporated into which wire?
  • Where can I get credible Archeometallurgical and contemporary methods of casting (temperature, composition, time)and metalworking ( embossing, scribing) of this alloy? Was this work of a jeweler, a sculptor or a metallurgist?
  • Is there any possibility that the alloy is a high-entropy alloy? Have there been any research on molecular dynamics simulation of high entropy alloy of these particular alloying elements? I have not found any in interatomic potential repository
  • Had there been any research on MEDICAL (NOT ASTROLOGICAL) benefit of using octo-alloy( more specifically its self-disinfecting capability and heavy metal poisoning hazard)?
Relevant answer
Answer
You have raised a very attractive querry.You may get clarification and understanding on some points raised in your querry by approaching prof b s murty, director iit hyderabad. He has a book on high entropy alloys and is an ex-student of eminent metallurgist&material scientist Prof.S Ranganathan of iisc bangalore.
  • asked a question related to Computational Materials Science
Question
13 answers
I need someone who has knowledge in SRIM-TRIM code for irradiation damage assessment to assess my designed code for me.
Relevant answer
Answer
Dear  colleagues, I am sending two files, the TRIM0 file,  put in the directory where thе srim-2013  is located, place the script anywhere, but set the working directory in it too. If you have Math, run the script
  • asked a question related to Computational Materials Science
Question
5 answers
As a Materials scientist, how much necessary is to know about machine learning and Artificial intelligence in order to work on Computational Materials science? My own Computing skills do not go much beyond microsoft Office, and preliminaries of C, SolidWorks and MATLAB. So where to start? Please include references and links.
  • asked a question related to Computational Materials Science
Question
4 answers
If you are just interested in the energy of the system and this system has Fe atoms, will it matter to set the MAGMOM tag? Will it affect the computed energies or affect the convergence speed if set wrongly? Thanks.
Relevant answer
Answer
If you turn on spin-polarization, the magnetic moment will converge to its closest solution. In most cases I've seen different MAGMOM values give the same results, as long as your values are not very far away (say +-1 per atom). In my experience in VASP, sometimes different values in your MAGMOM tag yield different results. My recent calculation on FCC Ni using one-atom unit cell shows that if I set MAGMOM to 0, the final magnetic moment on the Ni atom is around 0 B. When I set MAGMOM to 1 and run with the same settings of the other tags and procedures, the final magnetic moment on the Ni atom is around 0.64 B. The latter one is more realistic compared with the experimental data of FCC Ni.
It is non-trivial to deal with 3d transition metals since their orbitals are quite soft. The structure of the system may change the electronic structures on some lattice sites.
  • asked a question related to Computational Materials Science
Question
1 answer
I have a structure file. I want to input that structure file and get multiple structure files as output with varying lattice parameters. How can I do that using Atomsk. I want to vary the lattice parameter to be used in a LAMMPS simulation. Atomsk is capable of giving multiple output files with varying lattice parameter by bash scripting. But how can I do the same for complex structures?
Relevant answer
Answer
Go thorough this tutorial Unit Cells for Various Lattice Types:
  • asked a question related to Computational Materials Science
Question
2 answers
As title, just roughly calculation is OK.thanks anyway 
Relevant answer
Answer
I recommend you to read this paper:
Best regards
  • asked a question related to Computational Materials Science
Question
1 answer
Please do not refer to JMatPro. It could not calculate for varying boron concentration in the given range.
Any paper describing the process would also be welcome.
  • asked a question related to Computational Materials Science
Question
9 answers
Hi everyone!
I want to show band alignment of a hybrid halide perovskite material with an electron transport material ( Fig: CH3NH3PBI3 and TiO2, respectively). The position of VB edge (-5.4 eV/-7.3 eV) and CB edge (-3.9 eV/ -4.0 eV) can be known experimentally (XPS) in both materials (CH3NH3PBI3 /TiO2). But can anyone tell me how can we calculate these values of the positions of VB/CB edges using VASP/WIEN2k?
Thank you
Relevant answer
Answer
You might also want to look at the MacroDensity package on github published by Aron Walsh's group ...it will parse the LOCPOT file printed using LVTOT = .TRUE. and plot the local potential for you. It is super useful. From this you can determine the vacuum potential. Then, using ICORELEVEL = 1, you can obtain the core eigenvalues in the OUTCAR file and use the formulas for valence band offset (VBO) and conduction band offset (CBO). You will also need to know the potential difference of the interface slab model as well as the bulk VBM/CBM eigenvalues for each material.
  • asked a question related to Computational Materials Science
Question
8 answers
Dear respected RG members,
I am doing Mulliken population analysis of Cobalt (Co) doped MgO lattice (rocksalt) using CASTEP code (ultrasoft pseudopotential). I found some strange data as follow:
for pure MgO
bond population (Mg-O) = - 0.73
for (3%) Doped MgO
bond population (Mg-O) = - 0.31
bond population (Co-O) = 0.42
Is the negative value of of Mg-O reliable?, since negative value indicate antibonding, small value close to zero indicate ionic bonding and large positive value (Co-O) indicate covalent bonding. As we know, MgO has a very strong ionic bond, therefore bond population (Mg-O) must be close to zero. All parameters that I used during optimization are correct. I also did the same calculation using ( norm-conserving ). The obtained data gave almost a good result as suggest by Segall et al. (Mg-O = 0.58) and (Co-O = 0.53).
Thanks in Advance
Relevant answer
Answer
The Populations analyses and their different corresponding bonds types.
best regards sincerely,
BENGHIA Ali
PhD in Physic and Chemistry of Materials,
  • asked a question related to Computational Materials Science
Question
6 answers
Should I fix the k-point density and then increase the energy cutoff in steps until convergence, or should I fix the energy cutoff and then increase the k-point density in steps?
Relevant answer
Answer
Dear Kareem,
What program are you using? You can fix the k-point sampling and increase the energy cut-off and viceversa. At the end, you will use the converged k-point set and energy cut-off.
  • asked a question related to Computational Materials Science
Question
12 answers
I am looking for some guidance on using forcite module for mechanical property. I'm creating crystal and when trying to do geometry optimization, selecting Compass, while assigning manually, getting some error. Am I missing something. Can you suggest some example manual for forcite module? Thanks.
Relevant answer
Answer
Dear Ms. Dutta;
Some many things can  be ocurring on your set up/running calculation. Here are some possible issues:
1) System should be a periodic crystal, with no neighboor atoms overlapping. To check this, you need to select right-click on your model and then select the option of display style and on lattice increase to see if your periodic conditions are fine. If there is overlapping, then your calculation will always fail.
2) Once you check all the atoms are in right position, I recommend to do a Geometrical Optimization using CASTEP. And selecting all tabs as coarse on SFC, Cutoff and just for Gamma point. This will allow the system to relax and to have an optimized structure with minimal computation time.
3) Once you have the optimized structure, then you can start running your forcefield. Now the question is: What are the exact properties you are looking for in your system? Elastic constants, optimization of lattice parameters?
4) Lastly, even though when is said that MS can run on any PC with minimal RAM of 4GB. I found that this is not absolutely true. Because,  the optimization of cell is done every 60sec thus the video card on your hardware also plays an important role. Make sure, you have the appropiate computational resources. And that your license is also complete, some academic licenses are not bought for full access, then this can cause some issues. I will recommend this good literature about setting up calculations: