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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?
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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
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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.
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COMSOL multiphysics is the best in my opinion.
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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.
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Dear Syed Shaheen Shah the link of the Crystallography open database is given. If you cant find your CIF file in this link I can make a new CIF file for you in Full proof refinement. The CIF file of NiCO is also attached below.
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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.
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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.
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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.
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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.
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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?
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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
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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).
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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.
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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?
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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 ?
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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.
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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?
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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.
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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
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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.
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Hey,
Please share your work on UMAT and resources (except popular imechanica tutorial).
Thanks.
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ABAQUS UMAT Lectures for beginners are given here:
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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.
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Hello Sumit,
I agree that OC is a well meant software, but downright unusable to the mortal user.
Here is a link with a third party GUI (called CAE) for OpenCalphad, the link also includes an example book!
More links and examples here:
Greetings Rico
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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.
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Samar Fawzy
Send me the paper, please.
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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!
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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
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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?
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Safwan al-qawabah Thank you! Do you know where I can get SDB files though?
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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.
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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.
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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.
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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.
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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
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I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the said force field. So, how do I include an additional force field in GROMACS? Or, can I even use other force fields not included in the package?
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The easiest way to go is to actually prepare your system with Amber (as Glycam06 is in Amber format, as far as I know) and then use some converting tool to switch to gromacs, for example parmed
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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?
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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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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.
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Ty so much for the detailed information, Misha.
I will try these steps.
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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?
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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.
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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.
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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?
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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
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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!
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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.
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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.
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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?
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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.
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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.
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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.
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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?
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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.
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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.
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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.
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I am trying to install this software but it doesn't work
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How do I get this 'intel64", ? I see I don't have this directory and it's properties are required here,
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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
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Thank you Mohammed M. Obeid for your discussion about magnetic properties using CASTEP and the Figures you shared.
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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.
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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:
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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?
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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.
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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.
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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
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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.
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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.
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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)?
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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.
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I need someone who has knowledge in SRIM-TRIM code for irradiation damage assessment to assess my designed code for me.
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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
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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.
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I want to make structure of DBT (C12H8S) adsorbed TiO2 (100) surface. I have made TiO2 (100) surface from material studio, now I want to adsorb DBT molecule. How can make such type of structure in material studio ?
Shilendra
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You can move the molecule up, down, right or left by pressing alt+shift+up(down etc keys) but first you need to select your molecule with the Select Fragment option in the shortcut menu. Also you can rotate your selected molecule by pressing shift+up(down etc) keys of your keyboard.
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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.
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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.
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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?
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Go thorough this tutorial Unit Cells for Various Lattice Types:
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As title, just roughly calculation is OK.thanks anyway 
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I recommend you to read this paper:
Best regards
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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.
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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
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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.
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I want to make Al/SiC structure in material studio. how can i do it? there is pure Al structure and SiC structure in material studio software. I want to delete group atoms from bulk of Al and replace them with SiC particles .
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Have you explored packmol (http://m3g.iqm.unicamp.br/packmol/home.shtml). Although its tailored towards molecular systems, you may find it has some advantages over the Materials Studio builder.
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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
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The Populations analyses and their different corresponding bonds types.
best regards sincerely,
BENGHIA Ali
PhD in Physic and Chemistry of Materials,
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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?
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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.
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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.
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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:
But, use search engine and look for Harold S. Park of Boston University, that professor does a lots of good mechanical properties calculations on some exotic/complicated systems.
Good luck and best for you...
Manuel
ps. Look at my profile and please if you consider my work important and useful please cite it.
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I am a researcher of materials science and metallurgical engineering. I am interested to work with atomic level and electronic modeling of the structure and properties of materials,materials informatics and simulation in future. Currently i am learning Python. I have basics of C and MATLAB . What will be the useful programming languages to learn for me?
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It's hard for me to understand that C gets some recommandations whereas C++ gets ignored. Also Julia should be taken into account for structured and efficient simulations. The best thing is to get advice from within the community that you plan to join.
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Dear all,
I am trying to calculate  ΔG of adsorbed species by using VASP. For this I need to calculate Zero point energies and Entropy of absorbed species. But I am confused with that. What type of calculations do I need to get ZPE and Entropy. Please help me in this case.
Thanks in advance.
anjibabu
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Dear Experts, I believe that there is no "arbitrary" things in science. Everything must be selected precisely with knowledge. I am trying to study the ferromagnetism in MgO rocksalt by introducing some defects Vmg and Vo using CASTEP code implemented in materials studio package. So, How can I select the position of vacancy in the supercell? Should I select all the position one by one and by comparing the formation enthalpy of each position and then choose the lowest formation enthalpy of that position. Your comments will really help me to understand more about this issue. The figure bellow is 2x2x1 supercell of 32 atoms of Mg16O16 with two vacancy of Mg to give the formula Mg14O16. I got high magnetic moment based on Mulliken population analysis and oxygen high spin and low spin is responsible for this behavior. Thanks in advance.. Mohammed
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Hello,
If you want to calculate single defect then you want each defect to separate enough distance so that they won't mutually interact. You should know the density of defect of your experimental example, usually it is not that dense to have two defect in one cell.
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I want to use pp.x for calculation of work function for a semiconductor slab,
I have calculated the difference between the fermi energy and vacuum level using the plot_num=(1 and 11), for investigate the effect of including xc term.
Including xc term give rise to significant ( about 1 eV) decrease in total potential in vacuum region.
which one is physically meaningful?--considering xc potential or not?-
furthermore, the fermi energy in output is strongly sensitive to degauss value?
I think if we set occupation~fixed--without any smearing-- we should consider the VB edge as the Fermi energy at 0K.
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XC is zero for zero density so it should decay in the vacuum but since your vacuum is finite, you have nonzero density which results in non zero XC. Omitting this XC is, therefore, a better approximation for the true vacuum.
If XC contribution to the WF is large, the error due to slab-slab interaction should be large too, since it means you have significant density inbetween. Consider running an scf with a larger vacuum after your system has relaxed in the tight one.
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I'm interested in learning to model ta-C and other (carbon) thin films deposited on solid substrates with PVD (FCVA). The modeled films could be up to 100 microns in thickness. Deposited film structure, intrinsic stresses, substrate bonding, electric properties, surfce topology and whynot protein adhesion would be some interesting characteristics to study with the model.
Also the eruption of ions and macromolecules by arc from the cathode could be an interesting modelling topic.
I thought to ask here if someone would have any recommandations on what software and modelling approach would be fruitful for this kind of research.
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For simulation I recommend Matlab.
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These alloys cannot deform via common deformation mechanism.
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The range of ufg metals is wide, ranging from below 1 µm down to 100 nm.
And there is a good range of grain sizes where you can model the material behavior using rather conventional material models based on the early work of Conrad.
This can be easily extended to ultra fine grained fcc metals, and we even showed recently that ufg bcc metals can be well described. Not only in terms of strength, but also concerning rate-sensitivity and activation volume.
If you are interested, we showed this recently in an attached open access article in Acta Materialia (August 2017):
Best regards,
Daniel
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i am trying to use yambopy to my system. since i am a beginner at it, i can not really use it.
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In our experience, there was a considerable bug, so I think it is difficult for beginners to use.
The yambopy code seems to be in the early stage of development. Create automatic workflows for yambo using python. The yambopy project aims to provide a simple set of python scripts to read and edit yambo input files. Therefore, you should first become familiar with Python.
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Dear experts,
I think that CaSiO3 has direct and indirect band gap. I am trying to know the direct and indirect band gaps of wollastonite( location of BZ point). A band gab  of 5.022 eV at gamma (G) point  according to LDA (castep code) ( is that direct or indirect band ). There is another interesting minimum conduction band at B point ( is it related to indirect band gap) with valence band minimum at C point . I really need to interpret the results shown in the figure below accurately. any help will be appreciated.   
best regards
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Materials Studio software.
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How can we calculate quantum capacitance as a functional of local electrode potential and stored charge on 2D materials by DFT calculations? Please post your answers including the procedure of calculation of capacitance properties of super-capacitor from DFT outputs by utilizing capacitance equations.
Thank you.
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How to get values for the constants D0, E, α, β, Tb, K and effective plastic strain rate for flow stress model of Johnson and Cook in DEFORM software? Also brief that from where the values for other parameters i.e., A, B, C, m, n could be found?
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Dear all
Adding the tabular form of your data and try to convert them to those models you wanna use. hope found it useful.
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Hello everyone.  I was hoping if anyone had information on material models for 3D printed parts.  Specifically, it would be nice to have models for the plastics ABS and PLA.  Thanks in advance.
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fyi maybe useful : there are available right now simulation software for fabricated 3D print product, we can simulate the strength of the 3Dprinted model according to the set of printing parameter given 
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  • Do i compute it for a rectangular (parallelepiped) sample first and then make corrections for a cylindrical model?
  • Can i use FEA or Finite Difference approach?
  • Is it Ansys or Thermocalc which is best suitable?
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If you interest about the heat transfer from / to the rotating cylinder, please notice:
If you interest about the cylinder with/ without heat transfer and focus on the hydrostatic characters please notice:
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Hi,
I found the total partial density of states but I would like find the each atom partial phonon density of states with PWScf package.
Thanks in advance.
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Dear Sir, Aktürk Ethem.
Please can you send me input file for partial phonon density of states , thanks in advance at rizwan.mphil.cssp@pu.edu.pk
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Hello superiors,
I am looking for a method (which is compatible with VASP) to do Transport calculations on Surface Slab (say 111, 001 or 110 surface ).
I can do bulk transport calculation using BoltzTrap. BoltzTrap need space group for the calculation and I can easily provide space group for Bulk.
But when I am doing for an Surface what is the space group I need to give in BoltzTrap ??
My 2nd question is ----
how I can do Spin-Transport calculation on the surface of Topological Insulators ?
I will highly appreciate your anykind of comments.
Best Regards & Thanks,
Chanchal
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First you need to build a model of the phenomenon.
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While modeling amorphous materials computationally, I have seen papers using periodic boundary conditions. But glasses/amorphous materials doesn't have any periodic nature. Is it some kind of approximation? Or do we have some other way to model aperiodic materials?
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with my team we have modeled electrolyte and fluoride glass with the periodic boundary conditions, but these conditions are used just to reproduce the macroscopic system from an elementary simulation box, as in The MMC an the MD simulations for example. The periodic boundary conditions are not necessarily related to the structure. If you have any technical question on the use of the periodic boundary conditions do not hesitate.
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How can we calculate the impurity (dopant) carrier (electrons and holes) concentration in the host material at 0K by DFT calculations and at room temperature by using semi-classical theory or some alternative method?
Is there anyway to calculate the impurity carrier concentration with BoltzTraP code?
I am vasp user.
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Dear Muhammad,
welcome,
As for the calculation of the carrier concentration in doped crystalline semiconductors one uses the following rules:
The material is known in the sense, its effective density of states  in the conduction band Nc and valence band Nv,its energy gap , and the intrinsic  concentration ni.
The doping concentration and the energy level of the dopant in the energy gap, that is the ionization energies. Also the temperature is assumed.
- The mass action law is valid such that n0p0=ni^2. n0,p0 are electron and and hole concentration,
- The neutrality equation is valid such that Nd+ + p0=  Na- +n0, where Nd+ and N- are ionized impurities concentration,
- The final and third rule is that the fermi statistics is valid: f(E)= 1/( 1+ exp ( E-Ef)/kT,
These three rules are used to calculate n0, and p0.
There are many simplification assumptions to estimate n0 and p0..
The DFT may be used to determine the donor and acceptor levels as well as the density function of states. instead of  determining them on experimental basis.
Best wishes
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I have the data concerning a simulated polycrystalline grain structure (the set of crystallographic directions). Each grain consists of minimum 1000 cells. I would like to obtain pole figures to analyze my data. How can I do it?
I have already tried to construct pole figures for untextured polycrystal using a stereographic projection. However, the results are weird, and, according to the pole figure (001) obtained, I do obtain the texture near the 001 pole.
I would be grateful if you could give me any advice or maybe suggest some literature.
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If I remember correctly MTEX includes a code generating a non-textured orientation distribution. Even if you will develop an own code (as I've heard preferred are quaternions) you should compare it with MTEX. If you are not familiar with it don't hesitate to contact Ralf Hielscher.
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Can anyone suggest a good simulation software for fiber reinforced polypropylene composites study? Open software with available tutorial is preferred. Thanks!
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ANSYS Composite PrepPost
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Interested researcher may wish to send their email as well to future communications. We’ve some experimental results already & need DFT calculations to have a deeper insight into the system. Please only reply in case you are really interested and have some time to devote for our problem. We aim to finish this work soon & publish under this joint collaboration.
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Anirban, unfortunately, my area of competence in the experimental luminescence and optical spectroscopy. So while I can not help you in DFT calculations.
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Figure 1 (from Langmuir, 2013, 29 (7), pp 2175–2184) shows a typical sequence of approaching, colliding, and departing of a pair of nanospheres in a MD simulation. Initially, the two nanospheres move close to each other (Figure 1a) at an initial relative velocity of Vr,0 =300 m/s. Then, they continue moving toward each other and reach a position of close proximity (Figure 1b). After that, the overlapping of two nanospheres occurs (Figure 1c). Figures 1d, e, f demonstrate the following dynamic departing process. It is shown that the two nanoparticles can rebound out of the reach of each other after the overlap if a very large initial velocity is applied. Changing the initial relative velocity Vr,0 will produce different collision dynamics. I am trying to repeat this in Materials Studio 2016 for my research. Please help.
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The forces you are interested in are called mean forces in statistical mechanics, and they are the associated to the derivative of the relevant landau free energy. One way to compute them is to use constrained or restrained MD (give a look here for RMD
- you need to prune a lot from this paper, if you contact me privately I'll give you the relevant details). In practice, you compute what is the "thermodynamics" force to keep the sphere at a given distance between them, and if you do it as I proposed this includes the effect of solvent and any other element present in your simulation box. Hope this can help
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