Questions related to Conceptual Density Functional Theory
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
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"
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.
I want to build polymer for quantum espresso calculation. Can anyone suggest a suitable open source software to build it.
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?
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.
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?
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?
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.
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?
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
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?
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?
Please let me know what should I put as command in input file for running Opt+Freq calculations at different temperatures?
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.
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.
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?
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.
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
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.
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.
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?
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;
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.
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.
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?
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.
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?
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.
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?
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?
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?
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.
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
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?
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:
Ga 69.723 Ga.pbe-n-van.UPF
As 74.92160 As.pbe-n-van.UPF
Ga 0.0 0.0 0.0
As 0.25 0.25 0.25
12 12 12 0 0 0
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.
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.
I am looking for a method to calculate the planarity index of the compounds (By finding Dihydral angle or some Density Functional Theroies).
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?
"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?
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.
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.
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.
Can someone recommend me an article describing the Thomas-Fermi-Dirac-Almadi potentials for determining the ionic orbital characteristics?
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?
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
--- traceback not available
Can anyone give a suggestion on how to eradicate this error?
Thanks in advance.
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?!
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?
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 ?
I would like to do first principle studies(using DFT) for this technique to compare experimental and theoretical value.
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.
I found these two formulas in different articles, which one is better to use and reasonable?
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?
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?
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?
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.
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.
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.