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Conceptual Density Functional Theory - Science topic

The quest for the theoretical basis of the HSAB behavior has creadted CDFT
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Hi, I can not optimize a palladium (II) coordination complex in Gaussian 09W, the calculation ends with an error. Should I treat the wave function as an open shell or as a closed shell? Thank you
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I think your additional information code has some mistakes.
How about change your additional information as
Pd 0
lanl2dz
****
S C N H O 0
6-311g(d,p)
****
Pd 0
lanl2dz
maybe the element name problem.
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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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Hi VASP users,
I am doing Eu(4.16%. 8.32% etc.) doped calculation in 3*2*1 supercell after relaxing the structure I am visualizing the CONTCAR for 4.16% doping it is showing all atoms but for higher doping concentration CONTCAR is showing some atoms missing. I am using ISIF=4 for relaxing the structure. I have attached here POSCAR and CONTCAR files for 8.32 % doping concentration.
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  1. Hello all, In my case, 10 atoms are missing in CONTCAR file. See attached. what might be the reason behind this. Thnak in advance.
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What basis they can say Raman active or IR active in the phonon spectrum. How do I understand this.
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Firstly, each phonon has different frequency at different q points (q is the phonon wave vector). To be able to identify the frequencies at a specific q point, momentum should be conserved, so:
ki=ks+q (ki,ks, being the incident and scattered light wave vector, respectively)
So for example for the Gamma point (q=0), ki=ks , forward scattering should be performed.
At each q point, the system has #atoms*3 degrees of freedom and frequencies. The symmetry of the modes can be found from the character table. In the last column of the character table, the symmetries are given in terms of Cartesian system and rotations. What do they mean? It means that the incident and the scattered wave should have the same symmetry; for example if the function for A1 irreducible representation(irrep) in c3v point group is x^2, it means the polarization of the incident and scattered wave should both be parallel to x, while in the E irrep, function xy means that incident and scattered weaves should have x and y polarization or vice versa.
Given that, we can assign the modes to each irrep.
How do we know if the modes are TO or LO?
We know that the dipole moment vector is along the vibration direction of the atoms, that means if dipole moment is parallel to the propagation direction q, the mode is LO and it is TO if the two vectors are perpendicular.
I hope it helps.
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I want to build polymer for quantum espresso calculation. Can anyone suggest a suitable open source software to build it.
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Yosef Nikodimos thank you for your suggestion. Vesta is a good software
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Has anyone already performed DFT calculations for cellulose and functionalized cellulose monomers?
How can we do it to calculate the bond dissociation enthalpies and IR frequencies?
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I think I can help you. For the first querry, No I have not. For the second querry i have to ask a few things.
Which software do you use for it?
Number of atoms of your calculation.
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Hi. I am calculation adsorption Li ion on carbon surface. I find Li ion is adsorbed effectively on the surface forming LiC5. Also on modifying the carbon atom assembly by doping N and H, the adsorption is maximum at N. Now the query is, is it mandatory to have Lic6 (like in graphene) for the Li ion to be adsorbed to cathode?
PS: I am trying to design a stable material for cathode in battery applications.
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Hi Dr Samaras
The structure is similar to Graphene (not graphene)with slight modifications that the particular region is having hole created with nearest 5 carbon atoms. The temperature and pressure values are set to default. Room temperature and atmospheric pressure.
Thank you
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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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Hi everyone,
I am looking for reviews of works and recent findings about Metal-ion batteries materials. At the moment, Is there any commercially available anode material (other than graphite) in Metal-ion battery technology.? How come (Na/K)-ion batteries are still being researched while Li-ion batteries are common worldwide?. Are there any new rechargeable consumer battery technologies in theory or under development that improve on lithium that is presently used in most all modern-day electronics? How might it stack up in terms of capacity, size ratio vs. lithium?
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Dear Khossossi,
To my knowledge there is no commercially available material for Na anodes. The most used ones in labs are: hard carbon, alloys like antimony, tin .. and conversion materials like oxides.
The same graphite used in Li-ion can be used for K-ion (with less capacity).
Cheers
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Dear All
In a tetragonal unit cell of MAPbI3 (containing 4 units of MAPbI3), after making a 2*1*1 supercell, I have replaced one MA+ with smaller cation and did relaxation using ISIF =3 in VASP. I was expecting a decrease in the values of average Pb-I bond length and average Pb-I-Pb angle after doping with smaller cation (due to strain relief in the extended PbI6 octahedra) but the increased values of these bond lengths and bond angles was observed, which increased the unit cell volume. What might be the reason for that?
Thanks in advance.
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Hi Ankur,
It was to give you an idea. Cell and atoms optimization at 0K can also lead to little rotation of PbI6 octahedra.
The expansion of cell due to high inter-atomic distances, so reduction in number of H-bonds can be one of this reason.
Hilal.
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Hi,
I want to make an input file for using ONIOM method in Gaussian. System contains nanotube functionalized(by amino acid) interacting with a complex protein. when i want to build 3 layer for different(low, mwdium and high) levels, it's really hard to choose part of protein,... for high level. Is there any easier and reliable way to make correct input for this objective?
Regards
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Thank you so much dear shanon for your detailed answer. It was really helpful.
Best
Roja
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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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I want to get underground knowledge about this topic and more specifically DFT method.
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Hello,
There are plethora of books, notes & websites available to acquaint you with theoretical chemistry and Density functional theory.
As mentioned in the above answer "Introduction to Computational Chemistry" by Frank Jensen + "Essentials of Computational Chemistry: Theories and Models" Book by Christopher J. Cramer, are good start for beginners.
Now, I know going through book by book is most of the time a length process but fruitful, however, there are series of Lecture notes on Theoretical Chemistry & Electronic Structure Methods by Dr. Sherrill which you can access free of cost:
Also from MIT open Lecture series:
-
->Proceed in order you want.
--> Now, coming to your specific need to learn DFT, ok Density Functional Theory is a mathematical tool that is being used in chemistry for performing theoretical calculation. For you to understand DFT you first need to clear your basics and get a grip on Matrix Algebra, Dirac Notations, Calculus & Differential Equations because you gonna need a lot, from the sources mentioned above. When you reach this end there is a simple startup book for DFT for chemists its:
"A Chemist's Guide to Density Functional Theory" Book by Max C. Holthausen and Wolfram Koch.
Hope this helps,
Regards
Ajay Khanna
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I tried b3lyp/6-31g(d) which is approx. 100nm red shifted from experimental UV-vis absorption. cam-b3lyp/6-31g(d) is about 100nm blue shifted.wb97xd/6-31g(d) is further blue shifted to 150-200 nm. Can we guess some basis set based on these data or there is only hit and trial base method only?
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The main problem with DFT (and to an extent TD-DFT) is that there is no systematic way to calculate almost any property in different substrates. I mean, a functional which gives a nearly perfect fit with the experimental result for a given molecule could be a disaster for a different one. And (answering your question) the relation between the basis set and the result is not as critical as the relation between the functional and the result.
So yes, you have to do some benchmark to look for the best functional for your systems. I agree with Silvia in the method for the optimization (you can even optimize with no solvent model if your system is very large and the solvent is non polar), for the TD-DFT calculations use at least a triple-zeta basis set (I particularly like the aug-cc-pVTZ, but a split-valence set with polarization and diffuse functions may work well too) and test as many functionals as you can. Hybrid functionals (B3LYP, the M06 family...), some long-range corrected (like CAM-B3LYP or LC-wPBE)... look in the bibliography for others (in my case BP86 works flawlessly, but remember what I said in first paragraph!)
Hope you find it helpful
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I am interested in knowing what the physical interpretation of NBO analysis is. I have done NBO calculation for some molecules using GAMESS code. How can NBO explain the stability of molecules?
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@Radwan Alnajjar by a NBO calculation you can understanding the delocalization of the electron density from the occupied Lewis-type (donor) NBOs to properly unoccupied non-Lewis-type (acceptor) NBOs [43–47] within the molecule.
This analysis uses the second-order perturbation energies 𝐸(2) [donor (𝑖) → acceptor (𝑗)] that involve the most important delocalization instances, when you submit a nbo calculation in the .log output (in gaussian software for exemple) its given the second order pertubation energies, and by the transtions energies you can estimate the hyperconjugative interactions, intramolecular interactions and in the case of a dimer for exemple you can estimate the energy of the intermolecular interaction
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Please let me know what should I put as command in input file for running Opt+Freq calculations at different temperatures?
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Dear Sujan,
In window of additional keywords write order " Temperature = a suitable value " and check the updating and then run your calculation.
Regards,
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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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provide the necessity information regarding DFT
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thank you @christian Jensen
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The procedure of calculation.
Total energy vs  strain
The strain exist in the material, 
1.The strain by stretch. 
2.The strain by shear.
3.The strain by pressure.
We have to vary the parameters (stretch, shear and pressure) by 0.01 to find out the total energy and by fitting the parabola, we will ascertain the particular elastic constant (C11, C22, C33, C12 and etc.).
I am in little bit of confusion. Please clarify about it.
Thanks in advance ..Have a good day.
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Please Use the Elastic software interface to QE.
Please follow the steps:
1. Install elastic package and give the path as mentioned in the software.
2.Add all the executables to bashrc
3.Prepare one of your optimized input file (i.e, scf.in)
4. ElaStic_Setup_Espresso
please enter the values when it is requested.
5. I will create Dst01 and Dst 02 (i.e, stress and strain method)
6. Then run QE calculations for each distortion.
8.Just come main directory and run executable :> Elastic_Analyze
9. It will create Elastic.2nd.in 
10. enter eta_max and polynomial fit order and Run
11..Elastic_Result
12. Elastic_2nd_out file will be generated and it consists of all of your results.
All the best.
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I determined the value of U (the screened Coulomb interaction between electrons that are treated in DFT+Hubbard correction of the Fe bcc i found 4.46 ev with ABINITpackage),but when I try to activate the determination of J by marco-uj=3 , it doesn't work. Any help or advice?
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Prof. Syrotyuk, So if the d-orbital of an element is fully occupied (for example, incase of Zn), will the use of U value be effective on the band structure calculation ?? In such case can we neglect the use of U values??  I need your comments prof. please. Thank you.
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I am trying to calculate the interfacial energy between two crystalline phases. Any guidance in this matter will be very helpful.
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The most useful tool for developing interface is ASE-GUI (https://wiki.fysik.dtu.dk/ase/ase/gui/gui.html). You need to have basic understanding about python. I highly recommend this tool for developing crystal structures.
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I am trying to do fat band analysis for spin down only. Now using p4vasp, I can't plot the bands for spin up and spin down separately. Does anyone have any idea how to do this? or Is there any other tool which is able to plot band structure separately along with fat band? 
I would appreciate any help.
Ashis
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Hi Ashis Kundu
You can use p4vasp to plot the band structure  from vasprun.xml. When you need more control on which files and formats should be used, select Graph/Export. Graph can be exported into following format: 
XmGrace agr file - contains the graph layout. I recommend to save graph in this format and to use XmGrace. In the menu bar in xmgrace,  select plot/set appearance.  Then select data sets in the top window until number of bands-1 (for example if nbnd=32, you can select data set from zero to 31) so they are highlighted in black for spin up.   Select data sets from 32 to 64  so they are highlighted in blue for spin down 
Best wishes
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Please, give me an input containing the double hybride functional PBEP86 with D2 dispersion for Gaussian 09. Furthermore, I would like to know what kind of scaling factor I should use for the harmonic frequencies. (Perhaps should I apply the value 0.9973 as written in the Table 1 of the Martin's article /DOI: 10.1021/jp508422u/?) I attached a .txt file with a 3D structure. Thank you for your help! Roland
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See http://gershom2112.drupalgardens.com/content/how-run-dsd-pbep86-d3bj for the explanation on how to run DSD-PBEP86-D3. Use the command line provided over there but:
- replace def2QZVP with cc-pVTZ
- replace empiricaldispersion=gd3bj with empiricaldispersion=gd2
+ read about the D2 implementation for DSD-PBEP86 and, if some of the parameters (S6, S8 and so on) are different, change them using setenv command (linux only)
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I want to study phase segregation in Eu doped LaVO4 system. I am replacing La from Eu in certain percentage like 6.25, 12.5 and 18.5 etc. Since EuVO4 is also exit so there is a possibility of phase segregation. How will I confirm at what percentage of doping it will segregate phase ?
Any good literature on such type of study.
Thank You
Shilendra
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Mr./Mrs/Miss Sharma,
By a representative set of computations at different % of Eu studying the free Gibbs energy of the systems. The number computations should be representative from a chemometric point of view (about 20) 
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I would like to know that how to locate conical intersection using GAMESS. I have a potential energy surface plot for the variation in radius but I want to know how to make calculations for the excitation part.I hereby attached input file and a log file to interpret .
Please help me with the d5 keyword as well since I am being stuck in there.
Thank You.
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Thank you Anton , 
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How can we predict the magnetic state of the materials from density of states (DOS) that is either the material is ferromagnetic, antiferromagnetic, ferrimagnetic or paramagnetic? 
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There is a way to calculate the magnetic moment from a spin polarised DOS calculation. The equation for the magnetic moment, μ from such a calculation is μ = (Nup- Ndown)μB, where Nup and Ndown are the number of spin-up and spin-down valence electrons, respectively. The Nup/down are related to the spin-up or spin-down density of states, n±(E) ('+' for spin-up and '-' for spin-down) via the relation
Nup = ∫ n+(E) dE and a corresponding equation for Ndown, where the integral goes on the domain (-∞,0) for a DOS with its origin shifted on to the Fermi level. Hence the magnetic moment is
μ = μ[n+(E) - n-(E)] dE.
You can approximate the integral via the trapezium rule. To work this out for specific orbital contributions for specific atoms, you can calculate the partial/projected DOS (PDOS) and apply the same equation. If you are working out the average magnetic moment for a particular layer (assuming a surface), you can straightforwardly average the PDOS for each atom in a layer, and work out the integral in the same manner as above. The proof is simple, and you can find it attached.
If you need any further assistance in the matter, please do feel free to contact me.
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I want to change the uniform strain, the range is from 10% to 15% with an increment of 1%, namely, both compressive strain and tensile strain and want to see the variations of energy eigenvalues of the highest valence band (HVB) and highest valence band (LCB) at some specific k-points as functions of uniform strain. 
Please someone guide me about this that how to change the strain and where to see the variations of energy eigenvalues?
Thanks in advance;
Regard;
Zahir
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Dear Zahir,
I don't know VASP but it should be fairly straightforward. All you have to do is apply the strain (by reducing the lattice constants by a fixed percentage), perform a fixed-cell geometry optimisation (to relax the ionic positions), and compute the stress at the end. That gives you the stress-strain relationship for this particular strain, so all you do is repeat over the strain range you're interested in. A few things to watch out for:
a) Depending on the sign convention used by the code, your computed stress will probably be minus the stress you want -- you want the external stress that, when applied, would give this strain, but most codes will give you the internal stress that arises from the cell itself when you strain it;
b) If your system passes through a phase transition at these pressures/strains then you probably won't capture that correctly. As a first step, you can slightly perturb the atomic positions, so that the forces aren't zero by symmetry, and this will allow spontaneous symmetry-breaking. This would capture transitions like the ferroelectric distortions in SrTiO3 etc. In general, however, you would need to do a separate E-P or E-V plot  for each phase, to determine where the transitions are.
Hope that helps,
Phil Hasnip 
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DFT
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Amjad Sir,
You can look onto the link:
It a visual tutorial for both w2web & Command line interface of wien2k calculation
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Dmol3, DFT, Material studio, Theoretical calculations, geometry optimization
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I had same problem. finally I solved my problem by decreasing smearing value.
I mean in the first simulation you should choose larger smearing value like 0.05. when it finished you should do new simulation on optimized structure with smaller smearing value like 0.03. you should continue this method to your desired smearing value like 0.005. good luck 
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Hi all,
I have managed to obtain a UV-VIS spectra using Guassian 09 at the level of theory of TD-DFT/PBEPBE/6-31G(d) of a pre-optimised structure for a perylene derivative. However, the results show only two of the three expected absorption peaks.
Are there any general techniques/steps used when trying to obtain realistic absorption spectra that I have missed?
Any help regarding this will be greatly appreciated. 
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I suspect that adding excited states with Nstates is not good at all.
From what I've understood, the three expected peaks should be vibrationally resolved features of the first S1<-S0 transition, so adding other Sn<-S0 can only create more confusion.
In order to recover vibrationally resolved UV-Vis spectra I suggest the works of Vincenzo Barone and Julien Bloino.
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Hi,
Does anyone have idea about the empirical/EAM/model potential of Ti and Ta? How accurate these potentials and where from can I get it? I would be thankful if anyone can come up with this solution.
Thanks
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Tanmoy! Please write directly to john Moriarty either through RG or sent email to moriarty2@llnl.gov. Alex
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We have tried to study a hydrolysis mechanism using Gaussian 09 programme for a trans platinum complex both in gas as well as in solvent medium. In this study, we have used only one explicit water molecule. Since, in my case, it is a two step hydrolysis process and at each step only one water molecule at a time is taking part. If we considered more water molecules into the system than what will be the effect on the overall results. Is it necessary to consider more than one water molecule into the system to study the hydrolysis porcess?
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Dear Iftikar Hussain,
Generally in my DFT calculations,  I use one molecule of water; this molecule acts as a  a nucleophile. However, in some cases where the hydrolysis is catalyzed by an acid or base I use two water molecules:  the second water molecule can donate  H+ or OH- depending if the hydrolysis is acid or base-catalyzed reaction.
IF you reaction is not catalyzed by an acid or base you can use one water molecule, then take the optimized structure and run calculation with solvent dielectric effect, PCM model where the dielectric constant of water is 78.39.
Hoping this will be helpful,
Rafik
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Hello,
I have been working with DFT (LDA and GGA), and now I need to performance some DFT+U calculations.
But my problem is get U and J values.
I have read lot of paper, but still and can't understand how to get this values.
I know that there are some methods to get U and J value, like
  • Rotationally invariant (Liechtenstein et al)
  • Simplified (rotationally invariant) approach (Dudarev et al)
and the methods more cites to obtain U and/or J are:
  • Linear-response (Cococcioni et al.)
  • Constrained RPA or cRPA (Aryasetiawan et al.)
I believe I'm losing some detail to understand those methods.
How to calculate U and/or J values?
Should I use values reported before, how test it?
Also is mention that is accepted fit to some structural parameter (e.g. lattice constant, band structure, etc.), I tried to fit to lattice constant (with cell and shape relaxation) but the values are not consistent.
I open to other suggestions!
Sorry, if I do some questions, but I try give details necessaries.
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Dear Maximo,
In general, I would recommend the method of Cococcioni et al. but it requires your DFT program to apply their "Hubbard-alpha" potential. This is certainly possible in Quantum Espresso and there are on-line tutorials on how to do it, and I've recently implemented it in my own code (CASTEP) but I'm not sure about other DFT programs.
However you compute U and J (usually just U_eff = U-J) it is not a straightforward process because you have to converge your calculations very well with respect to cut-off energy, k-point sampling and supercell size. For Cococcioni's method you also have to perform very precise calculations because the U_eff (=U-J) is computed using numerical derivatives of your calculation result.
The value you get for U_eff will depend strongly on the implementation of DFT+U in the program; specifically, the basis set used to apply the Hubbard operator. Comparing results between different basis sets can easily give U_eff values which differ by a factor of 2 or more. For this reason you have to be careful when using values published in the scientific literature; ideally you would only use values computed with the same program you are using, but failing that you should at least use ones computed with the same U method and basis set.
The main aim of the Hubbard U is to correct for the effects of self-interaction, in particular that localised states (usually d- and f-states) are too close to the Fermi energy. With that in mind, it is usually sufficient to use a U_eff value which pushes them away from the Fermi level so that they do not hybridise incorrectly with the bonding states; the precisely "correct" value of U_eff is not necessary to capture this important effect. You should not fit to the band-gap of the material, as this will not be correct for the correct U_eff, and trying to get the right value will usually lead to an overly large U_eff and hence bands which are too flat. If you do want to fit something to get U_eff I expect the band-width would be a reasonable choice (though this does ignore the fictitious nature of the Kohn-Sham eigenvalues and associate them directly with electrons or quasiparticles).
Hope that helps.
Phil Hasnip
(CASTEP developer)
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I want to write my own program to find the energy of a system. I need some algorithm or some formulas to write the program. Can anyone tell step by step procedure to do it?
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Dear Jeremy
Thanks for your reply.
I'll go through the link and will be in touch with you in this regard.
Regards
Sriram.S
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I want to learn DFT (both simulation and theory). I am a beginners in this field. What is the best way to learn it?
Thank you everyone in advance for your valuable suggestions.
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Dear Abdul,
Regarding the DFT theory:
DFT, ab initio and semi-imperical such  as AM1 and PM3 are quantum mechanics (QM) methods. 
QM is the correct mathematical description of the behavior of electrons and thus of chemistry. In theory, QM can predict the property of an individual atom or molecule in an exact manner. In practice, the QM equations have only been solved exactly for one electron systems. A myriad collection of methods has been developed for approximating the solution for multiple electron systems.
The quantum mechanics includes: (1) ab-initio, (2)semi-empirical and (3) DFT methods.
 1-      Ab initio Methods:
The term ab initio is Latin for ``from the beginning''. This name is given to computations that are derived directly from theoretical principles with no inclusion of experimental data. This is an approximate quantum mechanical calculation. The approximations made are usually mathematical approximations. Ab initio methods typically are adequate only for small systems and are based entirely on theory from first principles. The ab initio molecular orbital methods (QM) such as HF, G1, G2, G2MP2, MP2 and MP3 are based on rigorous use of the Schrodinger equation with a number of approximations. Ab initio electronic structure methods have the advantage that they can be made to converge to the exact solution, when all approximations are sufficiently small in magnitude and when the finite set of basic functions tends toward the limit of a complete set. The convergence is usually not monotonic, and sometimes the smallest calculation gives the best result for some properties. The disadvantage of ab- initio methods is their enormous computational cost. They take a significant amount of computer time, memory, and disk space.
 2-      Semi-empirical Methods:
 Semi-empirical calculations are set up with the same general structure as a Hartree-Fock (HF) calculation in that they have a Hamiltonian and a wave function. Within this framework, certain pieces of information are approximated or completely omitted. Usually, the core electrons are not included in the calculation and only a minimal basis set is used. Also, some of the two-electron integrals are omitted. In order to correct for the errors introduced by omitting part of the calculation, the method is parameterized. Parameters to estimate the omitted values are obtained by setting the results to experimental data or ab initio calculations. Often, these parameters replace some of the integrals that are excluded.
The advantage of the semi empirical calculations is that they are much faster than ab initio calculations and their disadvantage is that the results can be erratic and fewer properties can be predicted reliably. If the molecule being computed is similar to molecules in the database used to parameterize the method, then the results may be very good. If the molecule being computed is significantly different from anything in the parameterization set, the answers (solutions) may be very poor[1].
The commonly used semi-empirical methods are MINDO, MNDO, MINDO/3, AM1, PM3 and SAM1. Calculations of molecules containing up to100 atoms (this number can be increased if super computers are utilized) can be handled using semi-empirical methods[9, 10].
 3-      Density functional theory (DFT):
             DFT has become very popular in recent years. This is justified based on the pragmatic observation that it is less computationally intensive than other methods with similar accuracy. This theory has been developed more recently than other ab initio methods to investigate the electronic structure (principally the ground state) of many-body systems, in particular atoms, molecules, and molecules in the condensed phases (solid phase).
With this method the energy of a molecule can be determined from the electron density using functions that is functions of another function. This theory originated with a theorem by Hoe burg and Kohn. The original theorem was applied for the ground-state electronic energy of a molecule. A practical application of this theory was developed by Kohn and Sham who formulated a method similar in structure to the Hartree-Fock method.
The DFT method is adequate for calculating structures and energies for medium-sized systems (30-60 atoms) of biological, pharmaceutical and medicinal interest and is not restricted to the second row of the periodic table.
Although the use of DFT method is significantly increasing some difficulties still encountered when describing intermolecular interactions, especially van deer Waals forces (dispersion); charge transfer excitations; transition states, global potential energy surfaces and some other strongly correlated systems. Incomplete treatment of dispersion can adversely affect the DFT degree of accuracy in the treatment of systems which are dominated by dispersion.
 Reference for DFT, you can read:
Parr, R.G. and W. Yang, Density-functional theory of atoms and molecules. Vol. 16. 1989: Oxford university press.
 Regarding the use of DFT:
You need to use the following programs:
The following programs were exploited in the design calculations:
 Arguslab: For drawing the chemical structures and initial optimization of the structures using UFF and AM1 methods. This program is download free.
Gausian 2009: For running all QM calculations (optimization, frequency, IR and Raman spectra, energies and etc.). This program is NOT free. You should purchase it. It can be uploaded on PC.
 Molden: For viewing Gaussian outputs such as DFT outputs. This program is free download.
There are alternatives for Molden such as Gaussian View and etc.
Regarding the keywords to be used in your DFT calculations:
you should access Gaussian 09 manual which is available on line. you use goog;e search "Gaussian 09 manual".
Hoping this will be helpful,
Rafik
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We run a DFT calculation with TURBOMOLE employing DFT/BP86/RI/def-TZVP, and we can get the simulated Raman spectrum from the “control” file. However, we do not know how to find out the Raman tensor results from our DFT calculation files ("control" file? or "raman.out" file?). And what we want is the Raman Tensors data.
Or we have to calculate Raman tensor with other programs?
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I'm not sure if you can extract the tensor from the TURBOMOLE output. As an alternative, I would suggest to use DALTON (http://www.daltonprogram.org/www/download.html) and then the dar2.f from:
Hope this helps...
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Suppose "A" 2D sheet  is placed on some substrate "B" (B=C+D like MoS2, etc)". How can the p-orbitals of "A" hybridize with d-orbitals of "B" however, B has unfilled p-orbitals as well?
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Thank you for adding your answer. Could you explain more with some reference for my understanding?
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What are the characteristics of shallow or defect states appear in the band gap? How can we explain the presence of these defect states in band gap? More specifically, the defect or shallow states mean those states which appear in the band gap of the material due to doping or vacancies in the actual material.
Secondly, how can we overcome such defect states in the band gap and what are the disadvantages of these states?   
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 I have modified my question, I am interested to distinguish the defect states appear in the band gap of the material due to doping or vacancy, so that real band gap may be defined accurately. 
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I have listed the k points used for bands and phonon dispersion of ZincBlende BN but it appear the dispersion is not curve (continuous) at the same axis on both plots. Check the dispersions are attached.
64
0.00000000 0.00000000 0.00000000
-0.25000000 0.25000000 -0.25000000
0.25000000 -0.25000000 0.25000000
0.25000000 -0.25000000 -0.25000000
-0.25000000 0.25000000 0.25000000
-0.25000000 -0.25000000 0.25000000
0.25000000 0.25000000 -0.25000000
0.25000000 0.25000000 0.25000000
-0.25000000 -0.25000000 -0.2500000
0.50000000 -0.50000000 0.50000000
-0.50000000 0.50000000 0.50000000
0.50000000 0.50000000 -0.50000000
-0.50000000 -0.50000000 -0.50000000
0.00000000 0.50000000 0.00000000
-0.50000000 0.00000000 0.00000000
0.00000000 -0.50000000 0.00000000
0.00000000 0.00000000 0.50000000
0.00000000 0.00000000 -0.50000000
0.50000000 0.00000000 0.00000000
0.75000000 -0.25000000 0.75000000
-0.75000000 0.25000000 -0.75000000
-0.75000000 -0.25000000 -0.75000000
0.75000000 0.25000000 0.75000000
0.25000000 -0.75000000 0.75000000
-0.25000000 0.75000000 -0.75000000
-0.75000000 0.25000000 0.75000000
0.75000000 -0.25000000 -0.75000000
0.75000000 0.25000000 -0.75000000
-0.75000000 -0.25000000 0.75000000
0.75000000 0.75000000 -0.25000000
-0.75000000 -0.75000000 0.25000000
-0.75000000 -0.75000000 -0.25000000
0.75000000 0.75000000 0.25000000
-0.75000000 0.75000000 0.25000000
0.75000000 -0.75000000 -0.25000000
-0.25000000 0.75000000 0.75000000
0.25000000 -0.75000000 -0.75000000
0.25000000 0.75000000 -0.75000000
-0.25000000 -0.75000000 0.75000000
-0.25000000 -0.75000000 -0.75000000
0.25000000 0.75000000 0.75000000
0.75000000 -0.75000000 0.25000000
-0.75000000 0.75000000 -0.25000000
0.50000000 0.00000000 0.50000000
-0.50000000 0.00000000 -0.50000000
0.00000000 -0.50000000 0.50000000
-0.50000000 0.00000000 0.50000000
0.50000000 0.00000000 -0.50000000
0.50000000 0.50000000 0.00000000
-0.50000000 -0.50000000 0.00000000
-0.50000000 0.50000000 0.00000000
0.00000000 0.50000000 0.50000000
0.00000000 0.50000000 -0.50000000
0.00000000 -0.50000000 -0.50000000
0.50000000 -0.50000000 0.00000000
0.00000000 -1.00000000 0.00000000
0.00000000 0.00000000 -1.00000000
-1.00000000 0.00000000 0.00000000
-0.50000000 -1.00000000 0.00000000
0.00000000 1.00000000 -0.50000000
0.00000000 1.00000000 0.50000000
0.50000000 1.00000000 0.00000000
0.00000000 -0.50000000 -1.00000000
0.00000000 0.50000000 -1.00000000
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Dear Mustapha,
try xcrysden visualizer to generate k point in special path in BZ
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I am interested in calculating excimer emission from exciton coupling between two monomers  using Gaussian.
Does it mean I just input two monomers with a defined intermolecular distance and then use Long range corrected TD-DFT to calculate the excimer emission?
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Hi Kai Lin Woon 
the all method for TD-DFT and emission is existing in gaussian user guide , but i say summary  the cycles.
1-opt ground state in solvent or gas phase
2-compute TD-DFT energy (absorptions) 
3-opt TD-DFT just singlet 
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Hello everyone,
Iam doing DFT calculations on GaAs and wanted to check the results for the Monolayer and bilayer. So please guide me how to setup Monolayer and Bilayer in quantum espresso.
This is the input file:
&control
calculation='scf',
restart_mode='from_scratch',
outdir='./tmp',
prefix='gaas',
pseudo_dir='/home/abhi/src/espresso-5.2.1/pseudo/',
/
&system
ibrav=2,
celldm(1)=10.6827,
nbnd=8,
nat=2,
ntyp=2,
ecutwfc=20,
occupations='fixed',
/
&electrons
mixing_beta=0.7,
diagonalization='david'
/
ATOMIC_SPECIES
Ga 69.723 Ga.pbe-n-van.UPF
As 74.92160 As.pbe-n-van.UPF
ATOMIC_POSITIONS alat
Ga 0.0 0.0 0.0
As 0.25 0.25 0.25
K_POINTS automatic
12 12 12 0 0 0
Thanks,
Abhinav
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 Hey Adraiana thanks for the answer.
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Is it possible to calculate electronic energy of a cation X+ without relaxation of its orbitals compared to those of netural X in DFT, HF, ...?! In other words, can one model a hypothetical atom with arbitrary orbital energies and then calculate its electronic enery?(keeping in mind the quantum mechanics doesn't allow the levels to have arbitrary energies!) I want to calculate vertical ionization potential (for atoms and molecules) using DFT or HF, and I need to reduce the effects of orbital relaxation, self interaction errors, derivative discontinuity and ... to obtain IP equal to negative value of HOMO (Koopman's theorem).  However, Koopman's theorem refers to cations that are neither electronically nor geometrically relaxed.
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I understand what you want to do: (1) Store the orbitals for X on file (2) Read them back in for a calculation on X+ (3) Evaluate the energy of X+ with the orbitals for X....no SCF iterations whatsoever.
The problem is how to tell the electronic structure program not to do ANY iterations and just evaluate the energy for the cation with the orbitals for the neutral. I tried to do that a number of years ago with Gaussian03 (or was it G98?) by playing with the IOPs etc.  Even specifying just 1 SCF evaluation and a ridiculously low SCF convergence criterion (so that the calc might 'think' it was converged right at the beginning) I was never quite sure whether the calculation had in fact iterated once --- or the energy of X+ had just been evaluated (using guess=read) as desired.
If you are currently using Gaussian, play with the IOP's and see wif you can set it up right. Otherwise, I would look at the manuals for GAMESS or ORCA to see if I could do  the calcs there.
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Using VASP I calculated the activation barrier of vacancy diffusion on the surface of ZnO for a 2x2 3 layered cell, where i had removed 1 oxygen atom out of 4 on the surface, and it came out to be 1.35eV and then I calculated the migration barrier for a 3x3 3 layered cell, where I had removed 1 out of the 9 oxygen atoms on the surface, the barrier came out to be 1.67 eV.
The thing which is bugging me is, why is the barrier higher at a lower vacancy concentration. Is there an explanation for this? I was wondering if i should use a similar sized cell for both the calculations ( a 6x6 cell)? The only thing that is different in the two calculations are the KPOINTS. For the 2x2 cell I have used a 2x3x1 mesh and for the 3x3 cell I have used a 1x2x1 mesh.
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Hi Salman, 
I will be calculating the same property in SiO2 using vasp. Since I am new in this field, can you please detail me how do you calculate vacancy migration barrier?
Thanks very much
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I am looking for a method to calculate the planarity index of the compounds (By finding Dihydral angle or some Density Functional Theroies).
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I am trying to find out the structure of a transition state
for a decomposition reaction (HXeXeF→HXeF+Xe) by using QST3 and I get the following error:
Inconsistency: ModMin= 2 Eigenvalue= 1.54137914D-03.
Error termination via Lnk1e in /usr/share/apps/g09/l103.exe
Does anyone have an idea of what this means and how to solve it?
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Hamiltonian seems to have difficulty in locating a transition state for your reaction.
What i suggest is, the guess TS structure what ever u have given in QST3 input, take it seperately and run it for TS using PM6. It may or may not give you exact TS, but it will guess some initial TS stucture. Take that guess as TS coordinates in QST3. Make sure that, in all the three structures (reactant, product and TS) the atom labels are same and take care of spin multiplicity.
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"If absolute quantum yield of compound say X is present in THF and can this absolute quantum yield be taken as standard for measurements of relative quantum yield of same compound in different solvents?"
If yes, then how? Is there any formula for it?
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This is a commonly encountered issue regarding QY calculation by secondary standard method and one of the reasons that refractive index correction becomes important in QY calculation. Thus, when the solvents of the standard and the sample are different, refractive index correction should be introduced. For e.g., see references:
Journal of Colloid and Interface Science 363 (2011) 529–539
J. Phys. Chem. B 2010, 114, 12528–12540
J. Phys. Chem. B 2011, 115, 10322–10334
J. Phys. Chem. B 2011, 115, 11938–11949
Photochem. Photobiol. Sci., 2010, 9, 57–67
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Hello,I need to identify aromaticity in some molecule and qualitatively compare between them. I've already performed NICS using gaussian but it seems to be highly dependent on basis set as well as on DFT functional and I'm not finding any fixed trend between them. So, is there any other methods to calculate aromaticity in any open-source software.By the way my molecules are three dimensional cage structure,so things are bit complicated.
Thanks in advance for reply.
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Dear Turbasu,
Did you try to make NBO analysis? It could help you to determine aromacity in your compounds.
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I am running my job on 4 nodes which contains 32 cores. My job is showing warning  and suggesting for optimal performance
NPAR = 4 - approx SQRT( number of cores)
I am not getting it !
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The dash in the expression 4 - approx SQRT( number of cores) is not a minus sign. It is meant to suggest the range, as in "4 to approx SQRT ...".  I usually make sure that the number of cores on a given node is a multiple of NPAR, and then jobs seem to run well.  So, on a 10-core node, I would set NPAR = 2 or 5 (but not 4 or 8).  On a 64-core node, I may set it to 8 or 16. VASP manual says one must experiment to see what works well.
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ADF-External code®, made by Michele Romeo in 2011, was used to produce all the angle-resolved DFT spectra of O2 on Ag(110) after a DFT pre-processing with the ADF® code.
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ADF-External code®, made by Michele Romeo in 2011, was used to produce all the angle-resolved DFT spectra of O2 on Ag(110) after a DFT pre-processing with the ADF® code.
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I would like to estimate ionicity of a liquids by estimating the molar conductivity with the Einstein Law and with the Nernst−Einstein approximation.
I have already a NVT trajectory. I can calculate the diffusion coefficient. What should I do next? 
I would like to know  if some script or software can do that from a trajectory?
Thanks for your help.
Maxime
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I've just spoken to colleagues who are used to use DL_POLY but I didn't got any positive response. So maybe you should do some scripting. Another way (people say that it might help) is to use the estimated D:
If your system is homogeneous and the diffusion coefficient don't suffer over or underestimation as it described here:
I think the results derived by tracing ions and direct implementation of Nernst-Einstein formula will be very similar.
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Can someone recommend me an article describing the Thomas-Fermi-Dirac-Almadi potentials for determining the ionic orbital characteristics?
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I suppose You mean Thomas-Fermi atomic model, Cristi. The best is original work of Fermi. Landau simply coppied it in his text book (volume 3, Quantum mechanics).
Regards,
Eugene.
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I have been working with FSI (Fluid-solid interaction) using COMSOL 4.4 to simulating transport of particles in a fluid through obstacle array. Doing so I must apply extra force per area acting on the surface of moving particle and perpendicular to the surface of the obstacle. Unfortunately I can’t add contact force on the boundary of obstacle and staked in the middle. Can any body suggest a means to do it?
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Dear Metages Gashaw
you can use another softwares, for instance ADINA. its very good in FSI problems
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I am doing DFT calculation on sugar lipid system. The command I used is
"#n opt freq=noraman b3lyp/6-311++g(d,p) geom=connectivity scf=qc".
I get error message as below:
LinEq1: Iter=992 NonCon= 1 RMS=2.17D-10 Max=3.09D-09 NDo= 1
LinEq1: Iter=993 NonCon= 1 RMS=2.14D-10 Max=3.02D-09 NDo= 1
LinEq1: Iter=994 NonCon= 1 RMS=2.23D-10 Max=2.91D-09 NDo= 1
LinEq1: Iter=995 NonCon= 1 RMS=2.05D-10 Max=2.41D-09 NDo= 1
LinEq1: Iter=996 NonCon= 1 RMS=2.03D-10 Max=2.61D-09 NDo= 1
LinEq1: Iter=997 NonCon= 1 RMS=2.10D-10 Max=2.61D-09 NDo= 1
LinEq1: Iter=998 NonCon= 1 RMS=2.24D-10 Max=2.65D-09 NDo= 1
LinEq1: Iter=999 NonCon= 1 RMS=2.08D-10 Max=2.47D-09 NDo= 1
LinEq1: Iter=*** NonCon= 1 RMS=2.07D-10 Max=2.51D-09 NDo= 1
CPHF failed to converge in LinEq1.
Error termination via Lnk1e in /pkg/chem/gaussian/g09d01/g09/l508.exe at Mon Jan 5 17:54:15 2015.
Job cpu time: 10 days 13 hours 0 minutes 32.4 seconds.
File lengths (MBytes): RWF= 6033 Int= 0 D2E= 0 Chk= 98 Scr= 1
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
rdx 000000000000abd9, rsp 00007fffac218c08, rbp 00007fffac2191f0
rsi 000000000000000b, rdi 000000000000abd9, r8 0000000000000000
r9 00002afe95f83e10, r10 ffffffffffffffff, r11 0000000000000202
r12 0000000000000000, r13 0000000000000000, r14 00007fffac219238
r15 00000000000003e6
--- traceback not available
Can anyone give a suggestion on how to eradicate this error?
Thanks in advance.
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In order to improve SCF/DFT convergence, especially when diffuse basis functions are used, I would recommend to use higher precision integrals:
  Integral(Grid=Ultrafine,Acc2e=12)
Also, make sure that the SCF covnergence is tight enough. As you use SCF=QC, I guess you had convergence problems in your SCF calculation: try to add SCF(QC,Conver=9) and see whether you can get to convergence.
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This the deal , when I try to run siesta, e.g.:
mpirun -np 4 /home/guilherme/siesta-3.2/Obj/siesta < AlFeO3.fdf | tee saida.out
appeared the mensage:
mpirun noticed that process rank 1 with PID 17811 on node guilherme-Inspiron-N5010 exited on signal 6 (Aborted).
And when I change -np 4 to -np 1 like:
mpirun -np 1 /home/guilherme/siesta-3.2/Obj/siesta < AlFeO3.fdf | tee saida.out
it's ok... but this way it's a normal way... without parallel mode!!
Anyone know what is going on?!
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I had a similar problem, the compilation went fine, but the code ran in serial mode. Probably editing by hand the arch.make was the problem. To fix this, here is what I did:
cd ~/Siesta/siesta-3.2-pl-5/Obj/
sh ../Src/obj_setup.sh
../Src/configure --enable-mpi MPIFC=/home/cgoehry/Siesta/openmpi/bin/mpif90 FC=/home/cgoehry/Siesta/openmpi/bin/mpif90 --with-blas=/usr/lib/atlas-base/libcblas.a --with-lapack=/usr/lib/atlas-base/liblapack_atlas.a --with-scalapack=/home/cgoehry/Siesta/scalapack/lib/libscalapack.a --with-blacs=/home/cgoehry/Siesta/scalapack/lib/libscalapack.a
make
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I have heard about 150% or higher relative (compared to 3 inch x 3 inch NaI(Tl) for 1332 keV photons) efficiency HPGe.
I want to know the largest volume or dimensions available for HPGe crystal used in detectors.
I also want to know the highest efficiency available for HPGe detector and its crystal dimensions.
Is the end-cap diameter of HPGe related to its diameter, or is there some standard in which smaller dimensions HPGe crystal are placed?
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HPGe detector efficiency (number in %) is usually compared the efficiency of 3 inch NaI(Tl) crystal @ Co-60 photopeak (1332.5 keV). So sometimes this value may be higher than 100%. 
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My doubt is about sites occupation. In my compound there are 4 different sites, they are: Fe1 and Fe2 (occupied more by Iron) and Al1 and Al2 (occupied more by Alluminio). To do the simulation considering 100% of the sites Fe1 and Fe2 occupied by Iron and the other two by Alluminio, it's ok. But it's not correct! In the real system the Fe1 its 75% occupied by Iron, and 25% by Aluminio... and the same for the other sites...
So ... how I can I do this?!
I don't know if are clear what I just say...
I put in attached my FDF ... but in that case I'm considering 100% of the sites Fe1 and Fe2 occupied by Iron and the other two by Alluminio.
So... How I can rewrite my .fdf ?
Really Thank!!
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Dear Guilherme,
 Our Site Occupancy Disorder (SOD) program:
can help you deal with these situations, by generating the symmetrically different configurations in a given supercell. It also helps to perform a statistical mechanics analysis of the spectrum of energies for the whole ensemble, so you can describe both ordered and disordered solids. Hope it helps. 
 Kind regards,
Ricardo.
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I would like to do first principle studies(using DFT) for this technique to compare experimental and theoretical value.
Thank you.
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GW or HSE are good for calculate the band gap and band structure
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Recently I was encountered with a problem where structure shown in figure is not able to get converted to any product. May be possibly due to its resonance effect or any other effect between the neighboring groups (cyano and amino). Neither cyano group is reactive nor amino group is reactive. Do I have any alternative option to prove this hypothesis via any computational software/webserver/informatics/molecular modeling, that the concern molecule is highly stable or inert for any reaction  Even I don't know which software is better for these calculations.
Any other relevant information regarding the query will be helpful.
Please suggest me a way to solve this problem.
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Mechanical stability can be checked by computing the force constants (or the Hessian matrix of the energy second derivatives). If it is positive definite then your molecule is stable, meaning it will not deform as it is at its energy minimum.
Chemical stability maybe checked by calculating the HOMO-LUMO gap. An open-shell system would be unstable and can chemically react very easily, while a large gap molecule would be inert (such is the case of rare gas atoms where the gap is large), because it will not easily hybridize with the atom or molecule that is approaching it.
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I found these two formulas in different articles, which one is better to use and reasonable?
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Dear Sarah,
 
You are focused on a key concept so-called Molecular Hardness or Chemical Hardness which belongs to the context of Conceptual Density Functional Theory. Formally, it is defined as the partial derivative of the total energy (E) with respect to the number of electrons (N). Since N is a discrete variable, the use of finite difference approximation (FDA) is mandatory.
At the beginning, the expression:
Eta = (1/2)(I-A)         (*)
was accepted as the FDA for the  Molecular Hardness because after a Taylor expansion, you obtain a second-order term involving the derivative aforementioned and the 1/2 factor.
However, the modern mathematical expression is the following:
Eta = I -A. (**)
It comes from a pure algebraic deduction by means of finite difference approximation because I = E(N-1) - E(N) and A = E(N)-E(N+1), so that:
Eta = E(N-1) - E(N)- E(N)+E(N+1) = E(N-1) - 2E(N) +E(N+1) = I-A
In practice, the 1/2  factor is irrelevant, but you have to specify what kind of mathematical expression has been used: the old notation (*) or the current notation (**), but qualitatively you will obtain the same information.
I agree with Carlo Tovar.
Best wishes,
Jorge
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I am attempting to model the reduction of oxygen at an electrode surface and need to find a way to alter the potential of the system. Does the "field" keyword allow for this?
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It is a non trivial pursuit. Why don't you used the experimental value. There is a group in PNL USA (Aaron Appel is the name of a young member of that group) that can estimated the formal O2 potential in different organic solvent. May be that will help.
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I have a 14 layers slab and want to perform optimization for the topmost half layers by keeping rest of them constant. How to achieve this?
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I understand that you are interested to do a minimization with some frozen atoms. You have to create a group with the particles that must be fixed and apply zero force to that group (with 'fix setforce' command). If you are interested in MD, then you may apply the solutions above.
IMPORTANT NOTE: In case of layered systems (interfaces of solid-liquid, graphite) you have to remove the rotation and translation of each layer. Otherwise, the layers will fly in the simulation box. Because the weak interactions between layers, the rotation motion of the layers is hindered by the presence of the other layers and the rotation motion of each layer will be transformed during the simulations into translation motion. The result: the layers will start to fly in the simulation box.
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If you are doing Bulk calculation with lattice parameter a=b=c then best way is to choose monkhorst pack scheme with kx = ky = kz.
For convergence, input different no. of k points in KPOINTS file, note down final energy you get in OUTCAR/OSZICAR. Use that no. of kpoints at which you get minimum energy.
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I am doing DFT calculations on defects (vacancies) in semiconductors. I need to calculate the formation energy for defects. I did some literature search, and found that most people use
the formula including atomic chemical potentials, but some others simply use E_defect=E_v-(N-n)/N*E_pc, with E_v the energy of the supercell containing vacancies, N the total number of atoms in a perfect supercell, n the number of vacancies, and E_pc the energy of the perfect supercell.
Could you explain what is the significance of these two, and the difference between them? Even in what kind of situation either of them should be applied?
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It depends on what you wish to use as 'basin' (and physicist or chemist inclination:) I guess). Let's assume a different type of defect : an oxygen vacancy in CeO2.
Then you can either take:
Ed=Ef - Ei + 0.5 EO2
(Ed= defect formation energy, Ef= total energy of cell with vacancy, Ei= Total energy of cell wo vacancy, EO2 binding energy of O2)
or
Ed=Ef - Ei + µO
(with µO the chemical potential of O)
In the latter case you need to find/choose this chemical potential, which is based on the assumption that the formation of an oxygen vacancy requires a different amount of energy depending on the chemical environment (is there O2 gas present) Then the O rich environment leads to µO=0.5EO2. For the O poor environment one looks at the heat of formation of Ce2O3, and distills a µO out of this, as a result your Ed now becomes a linear function of µO.
As you can see the first equation is merely one extreme case of the latter. The latter equation allows you to compare different systems that can be in competition, and may provide you with "environmental conditions"(=oxygen rich/poor) where one competing system will be better than the other and vice versa. This can be very usefull, however, if you are comparing systems where the chemical potential term is the same for all your systems, you will just end up with parallel lines (making the first equation the most efficient one)
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I am trying to run single point calculations on Gauss 09 for Mulliken population analysis on large graphene/graphite (940-1411 atoms).
I was having difficulty with memory issues (single CPU lic) running dftba for single point. I have stepped my convergence (beginning with conver=1, and increasing by reading in my previous checkpoint files). I found my results oscillating and failing.
I decided to try scf=(qc,conver=5,maxcycle=500). This worked, which concerned me.
It not only worked, but worked much faster than my failed sp calculations. I know Gauss's old default convergence for single point was N=4 for single point. As my calculation was done in less than two hours compared to the days it was taking for DIIS, I have become concerned at the accuracy of the QC using conver=5. I cannot find anything indicating my approach is bad, but also I cannot find anything syaing my approach should yield reasonable results.
Can anyone please tell me if this approach is reasonably accurate?
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The only issue I found with scf=qc conver=5, up to 5 there is an approximation that runs. The rigorous qc calculations don't start until after that level of convergence. If I can fin my old files to share with I will post them. I didn't get a chance to see if the approximation is accurate by comparing output files from systems that were better known. I remember being stunned that something so rigorous would complete quicker than its counterparts.
Would you mind posting the last two or three outputs (including the final) for your convergence failure? I should have asked for those first. When you said it crashed after 256 cycles, there is the possibility it is memory related (although I would be stunned with 8GB set aside), but just in case.....
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How can I implement pwscf and fermi energy to compute a ternary alloy of material?
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Dear Dr. Mustapha,
May I assume you have no previous working knowledge of quantum espresso?
Download and install the pwscf here:
Also you will need the xcrysden viewer from the same url.
Follow one or more Hands-on tutorials from:
Making sure you are able to perform elemental systems (common examples Si and Ge) as described in the tutorials, you may go on to prepare input for few other single elements. I am sure you will get help from the forum as mentioned by Yavar Taghipour at:
In addition, you can run the code using gui:
http://www-k3.ijs.si/kokalj/pwgui/ with this I also assume you are not using hpc clusters.
Best wishes.
adebayo
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I created a unit cell with using literature data.The crystal structure is Monoclinic with P2/m space group. I plan to double the unit cell along the C-axis which leads to the B atom taking the place of half of the unit cell and as usual about the C atom.The problem is that when I changed to along the c-axis the spacegroup has been changed P1/m.
What is the exact solution for it?
How do you solve these types of calculations?
Thanks in advance.
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Good luck with your calculations.
Be sure your approach and your results.
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For example, I performed calculations to evaluate binding energy for a complex (let us assume A-B) using TURBOMOLE and by taking same structures i tried to find out the bonding energy contributions using ADF. Both the values (binding energy and total bonding energy) differs quite a bit (by 40-100 kcal mol-1). I know that the level of calculations can contribute significantly to these parameters. Thus, I have used almost same computational level for both the software. For ADF, as it uses slater type basis set, TZ2P is used while for TURBOMOLE, TZVP is used. It would be a great help if anybody expalin the defination of the term and their differences.
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Thanks Dr. Goumans, I will post it to ADF mailing list then.
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I found in gaussian that gibbs free energy is sum of the total electronic energy and correction to the gibbs free energy but in some articles its sum of just gibbs free energy in the output of freq.
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[reactants]->[products]
For the equation above (AH+H2O -> A- + H3O+) you would have:
Greaction=[G(A-)+G(H3O+)]-[G(AH)+G(H2O)]
And the four Gs can be obtained from the four different opt freq calculations in Gaussian, just like I said before. Also, Hammett equation or not, please take into account that vacuum H3O+ or even H3O+ calculated with PCM solvation is not a realistic description for a hydrated proton.
Good luck in your endeavor.
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After adding hydrogen,the acid separated.
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You can calculate the proton affinity through chemical equation follows (molecule) + H+ ---> (moleculeH)+, the energy balance is the proton affinity.
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